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.net.URL;
 110 import java.net.URLEncoder;
 111 import java.util.Arrays;
 112 import java.util.Deque;
 113 import java.util.HashMap;
 114 import java.util.List;
 115 import java.util.Map;
 116 import java.util.StringTokenizer;
 117 import java.util.Vector;
 118
 119 import org.jmol.viewer.Viewer;
 120
 121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 122         ItemListener, KeyListener, AlignViewControllerGuiI
 123 {
 124   public AlignViewControllerI avc;
 125
 126   public AlignmentPanel alignPanel;
 127
 128   public AlignViewport viewport;
 129
 130   // width and height may be overridden by applet parameters
 131   int frameWidth = 700;
 132
 133   int frameHeight = 500;
 134
 135   String jalviewServletURL;
 136
 137   /*
 138    * Flag for showing autocalculated consensus above or below other consensus
 139    * rows
 140    */
 141   private boolean showAutoCalculatedAbove;
 142
 143   private SequenceAnnotationOrder annotationSortOrder;
 144
 145   /**
 146    * Constructor that creates the frame and adds it to the display.
 147    *
 148    * @param al
 149    * @param applet
 150    * @param title
 151    * @param embedded
 152    */
 153   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 154           boolean embedded)
 155   {
 156     this(al, applet, title, embedded, true);
 157   }
 158
 159   /**
 160    * Constructor that optionally allows the frame to be displayed or only
 161    * created.
 162    *
 163    * @param al
 164    * @param applet
 165    * @param title
 166    * @param embedded
 167    * @param addToDisplay
 168    */
 169   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 170           boolean embedded, boolean addToDisplay)
 171   {
 172     this(al, null, null, applet, title, embedded, addToDisplay);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           HiddenColumns hidden, JalviewLite applet, String title,
 177           boolean embedded)
 178   {
 179     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 180   }
 181
 182   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 183           HiddenColumns hidden, JalviewLite applet, String title,
 184           boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237     viewport.initInformationWorker(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               getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
1452               true);
1453     }
1454     else
1455     {
1456       features = formatter.printGffFormat(viewport.getAlignment()
1457               .getSequencesArray(), getDisplayedFeatureCols(),
1458               getDisplayedFeatureGroups(), true);
1459     }
1460
1461     if (displayTextbox)
1462     {
1463       boolean frimport = false;
1464       if (features == null || features.equals("No Features Visible"))
1465       {
1466         features = "# No features visible - paste some and import them here.";
1467         frimport = true;
1468       }
1469
1470       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1471       if (frimport)
1472       {
1473         cap.setAnnotationImport();
1474       }
1475       Frame frame = new Frame();
1476       frame.add(cap);
1477       jalview.bin.JalviewLite.addFrame(frame,
1478               MessageManager.getString("label.features"), 600, 500);
1479       cap.setText(features);
1480     }
1481     else
1482     {
1483       if (features == null)
1484       {
1485         features = "";
1486       }
1487     }
1488
1489     return features;
1490   }
1491
1492   void launchFullApplication()
1493   {
1494     StringBuffer url = new StringBuffer(jalviewServletURL);
1495
1496     // allow servlet parameters to be passed in applet parameter
1497     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1498             : "?";
1499     url.append(firstSep);
1500
1501     url.append(
1502             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1503
1504     if (viewport.applet.getParameter("features") != null)
1505     {
1506       url.append("&features=");
1507       url.append(appendProtocol(viewport.applet.getParameter("features")));
1508     }
1509
1510     if (viewport.applet.getParameter("annotations") != null)
1511     {
1512       url.append("&annotations=");
1513       url.append(
1514               appendProtocol(viewport.applet.getParameter("annotations")));
1515     }
1516
1517     if (viewport.applet.getParameter("jnetfile") != null
1518             || viewport.applet.getParameter("jpredfile") != null)
1519     {
1520       url.append("&annotations=");
1521       url.append(appendProtocol(
1522               viewport.applet.getParameter("jnetfile") != null
1523                       ? viewport.applet.getParameter("jnetfile")
1524                       : viewport.applet.getParameter("jpredfile")));
1525     }
1526
1527     if (viewport.applet.getParameter("defaultColour") != null)
1528     {
1529       url.append("&colour=" + removeWhiteSpace(
1530               viewport.applet.getParameter("defaultColour")));
1531     }
1532
1533     if (viewport.applet.getParameter("userDefinedColour") != null)
1534     {
1535       url.append("&colour=" + removeWhiteSpace(
1536               viewport.applet.getParameter("userDefinedColour")));
1537     }
1538     if (viewport.applet.getParameter("tree") != null)
1539     {
1540       url.append("&tree="
1541               + appendProtocol(viewport.applet.getParameter("tree")));
1542     }
1543     if (viewport.applet.getParameter("treeFile") != null)
1544     {
1545       url.append("&tree="
1546               + appendProtocol(viewport.applet.getParameter("treeFile")));
1547     }
1548
1549     showURL(url.toString(), "FULL_APP");
1550   }
1551
1552   String removeWhiteSpace(String colour)
1553   {
1554     StringBuffer sb = new StringBuffer();
1555     for (int i = 0; i < colour.length(); i++)
1556     {
1557       if (Character.isWhitespace(colour.charAt(i)))
1558       {
1559         sb.append("%20");
1560       }
1561       else
1562       {
1563         sb.append(colour.charAt(i));
1564       }
1565     }
1566
1567     return sb.toString();
1568   }
1569
1570   String appendProtocol(String url)
1571   {
1572     try
1573     {
1574       new URL(url);
1575       url = URLEncoder.encode(url);
1576     }
1577     /*
1578      * When we finally deprecate 1.1 compatibility, we can start to use
1579      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1580      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1581      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1582      * ex.printStackTrace(); }
1583      */
1584     catch (java.net.MalformedURLException ex)
1585     {
1586       url = viewport.applet.getCodeBase() + url;
1587     }
1588     return url;
1589   }
1590
1591   public void closeMenuItem_actionPerformed()
1592   {
1593     PaintRefresher.RemoveComponent(alignPanel);
1594     if (alignPanel.seqPanel != null
1595             && alignPanel.seqPanel.seqCanvas != null)
1596     {
1597       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1598     }
1599     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1600     {
1601       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1602     }
1603
1604     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1605     {
1606       System.exit(0);
1607     }
1608
1609     viewport = null;
1610     if (alignPanel != null && alignPanel.overviewPanel != null)
1611     {
1612       alignPanel.overviewPanel.dispose();
1613     }
1614     alignPanel = null;
1615     this.dispose();
1616   }
1617
1618   /**
1619    * TODO: JAL-1104
1620    */
1621   void updateEditMenuBar()
1622   {
1623
1624     if (viewport.getHistoryList().size() > 0)
1625     {
1626       undoMenuItem.setEnabled(true);
1627       CommandI command = viewport.getHistoryList().peek();
1628       undoMenuItem.setLabel(MessageManager
1629               .formatMessage("label.undo_command", new Object[]
1630               { command.getDescription() }));
1631     }
1632     else
1633     {
1634       undoMenuItem.setEnabled(false);
1635       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1636     }
1637
1638     if (viewport.getRedoList().size() > 0)
1639     {
1640       redoMenuItem.setEnabled(true);
1641
1642       CommandI command = viewport.getRedoList().peek();
1643       redoMenuItem.setLabel(MessageManager
1644               .formatMessage("label.redo_command", new Object[]
1645               { command.getDescription() }));
1646     }
1647     else
1648     {
1649       redoMenuItem.setEnabled(false);
1650       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1651     }
1652   }
1653
1654   /**
1655    * TODO: JAL-1104
1656    */
1657   @Override
1658   public void addHistoryItem(CommandI command)
1659   {
1660     if (command.getSize() > 0)
1661     {
1662       viewport.addToHistoryList(command);
1663       viewport.clearRedoList();
1664       updateEditMenuBar();
1665       viewport.updateHiddenColumns();
1666     }
1667   }
1668
1669   /**
1670    * TODO: JAL-1104 DOCUMENT ME!
1671    *
1672    * @param e
1673    *          DOCUMENT ME!
1674    */
1675   protected void undoMenuItem_actionPerformed()
1676   {
1677     if (viewport.getHistoryList().isEmpty())
1678     {
1679       return;
1680     }
1681
1682     CommandI command = viewport.getHistoryList().pop();
1683     viewport.addToRedoList(command);
1684     command.undoCommand(null);
1685
1686     AlignmentViewport originalSource = getOriginatingSource(command);
1687     // JBPNote Test
1688     if (originalSource != viewport)
1689     {
1690       System.err
1691               .println("Warning: Viewport object mismatch whilst undoing");
1692     }
1693     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1694                                           // viewport.getColumnSelection().getHiddenColumns()
1695                                           // != null;
1696     updateEditMenuBar();
1697     originalSource.firePropertyChange("alignment", null,
1698             originalSource.getAlignment().getSequences());
1699   }
1700
1701   /**
1702    * TODO: JAL-1104 DOCUMENT ME!
1703    *
1704    * @param e
1705    *          DOCUMENT ME!
1706    */
1707   protected void redoMenuItem_actionPerformed()
1708   {
1709     if (viewport.getRedoList().isEmpty())
1710     {
1711       return;
1712     }
1713
1714     CommandI command = viewport.getRedoList().pop();
1715     viewport.addToHistoryList(command);
1716     command.doCommand(null);
1717
1718     AlignmentViewport originalSource = getOriginatingSource(command);
1719     // JBPNote Test
1720     if (originalSource != viewport)
1721     {
1722       System.err
1723               .println("Warning: Viewport object mismatch whilst re-doing");
1724     }
1725     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1726                                           // viewport.getColumnSelection().getHiddenColumns()
1727                                           // != null;
1728
1729     updateEditMenuBar();
1730     originalSource.firePropertyChange("alignment", null,
1731             originalSource.getAlignment().getSequences());
1732   }
1733
1734   AlignmentViewport getOriginatingSource(CommandI command)
1735   {
1736     AlignmentViewport originalSource = null;
1737     // For sequence removal and addition, we need to fire
1738     // the property change event FROM the viewport where the
1739     // original alignment was altered
1740     AlignmentI al = null;
1741     if (command instanceof EditCommand)
1742     {
1743       EditCommand editCommand = (EditCommand) command;
1744       al = editCommand.getAlignment();
1745       Vector comps = PaintRefresher.components
1746               .get(viewport.getSequenceSetId());
1747       for (int i = 0; i < comps.size(); i++)
1748       {
1749         if (comps.elementAt(i) instanceof AlignmentPanel)
1750         {
1751           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1752           {
1753             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1754             break;
1755           }
1756         }
1757       }
1758     }
1759
1760     if (originalSource == null)
1761     {
1762       // The original view is closed, we must validate
1763       // the current view against the closed view first
1764       if (al != null)
1765       {
1766         PaintRefresher.validateSequences(al, viewport.getAlignment());
1767       }
1768
1769       originalSource = viewport;
1770     }
1771
1772     return originalSource;
1773   }
1774
1775   /**
1776    * Move the currently selected sequences up or down one position in the
1777    * alignment
1778    *
1779    * @param up
1780    */
1781   public void moveSelectedSequences(boolean up)
1782   {
1783     SequenceGroup sg = viewport.getSelectionGroup();
1784     if (sg == null)
1785     {
1786       return;
1787     }
1788     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1789             up ? null : viewport.getHiddenRepSequences(), up);
1790     alignPanel.paintAlignment(true, false);
1791
1792     /*
1793      * Also move cDNA/protein complement sequences
1794      */
1795     AlignViewportI complement = viewport.getCodingComplement();
1796     if (complement != null)
1797     {
1798       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1799               viewport, complement);
1800       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1801               up ? null : complement.getHiddenRepSequences(), up);
1802       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1803               false);
1804     }
1805   }
1806
1807   synchronized void slideSequences(boolean right, int size)
1808   {
1809     List<SequenceI> sg = new Vector<>();
1810     if (viewport.cursorMode)
1811     {
1812       sg.add(viewport.getAlignment()
1813               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1814     }
1815     else if (viewport.getSelectionGroup() != null
1816             && viewport.getSelectionGroup().getSize() != viewport
1817                     .getAlignment().getHeight())
1818     {
1819       sg = viewport.getSelectionGroup()
1820               .getSequences(viewport.getHiddenRepSequences());
1821     }
1822
1823     if (sg.size() < 1)
1824     {
1825       return;
1826     }
1827
1828     Vector<SequenceI> invertGroup = new Vector();
1829
1830     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1831     {
1832       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1833       {
1834         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1835       }
1836     }
1837
1838     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1839
1840     SequenceI[] seqs2 = invertGroup
1841             .toArray(new SequenceI[invertGroup.size()]);
1842     for (int i = 0; i < invertGroup.size(); i++)
1843     {
1844       seqs2[i] = invertGroup.elementAt(i);
1845     }
1846
1847     SlideSequencesCommand ssc;
1848     if (right)
1849     {
1850       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1851               viewport.getGapCharacter());
1852     }
1853     else
1854     {
1855       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1856               viewport.getGapCharacter());
1857     }
1858
1859     int groupAdjustment = 0;
1860     if (ssc.getGapsInsertedBegin() && right)
1861     {
1862       if (viewport.cursorMode)
1863       {
1864         alignPanel.seqPanel.moveCursor(size, 0);
1865       }
1866       else
1867       {
1868         groupAdjustment = size;
1869       }
1870     }
1871     else if (!ssc.getGapsInsertedBegin() && !right)
1872     {
1873       if (viewport.cursorMode)
1874       {
1875         alignPanel.seqPanel.moveCursor(-size, 0);
1876       }
1877       else
1878       {
1879         groupAdjustment = -size;
1880       }
1881     }
1882
1883     if (groupAdjustment != 0)
1884     {
1885       viewport.getSelectionGroup().setStartRes(
1886               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1887       viewport.getSelectionGroup().setEndRes(
1888               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1889     }
1890
1891     boolean appendHistoryItem = false;
1892     Deque<CommandI> historyList = viewport.getHistoryList();
1893     if (historyList != null && historyList.size() > 0
1894             && historyList.peek() instanceof SlideSequencesCommand)
1895     {
1896       appendHistoryItem = ssc.appendSlideCommand(
1897               (SlideSequencesCommand) historyList.peek());
1898     }
1899
1900     if (!appendHistoryItem)
1901     {
1902       addHistoryItem(ssc);
1903     }
1904
1905     repaint();
1906   }
1907
1908   static StringBuffer copiedSequences;
1909
1910   static HiddenColumns copiedHiddenColumns;
1911
1912   protected void copy_actionPerformed()
1913   {
1914     if (viewport.getSelectionGroup() == null)
1915     {
1916       return;
1917     }
1918
1919     SequenceGroup sg = viewport.getSelectionGroup();
1920     copiedSequences = new StringBuffer();
1921     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1922     for (int i = 0; i < sg.getSize(); i++)
1923     {
1924       SequenceI seq = sg.getSequenceAt(i);
1925       int index = viewport.getAlignment().findIndex(seq);
1926       orderedSeqs.put(index, seq);
1927     }
1928
1929     int index = 0, startRes, endRes;
1930     char ch;
1931
1932     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1933     {
1934       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1935       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1936
1937       // create new HiddenColumns object with copy of hidden regions
1938       // between startRes and endRes, offset by startRes
1939       copiedHiddenColumns = new HiddenColumns(
1940               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1941               hiddenCutoff, hiddenOffset);
1942     }
1943     else
1944     {
1945       copiedHiddenColumns = null;
1946     }
1947
1948     for (int i = 0; i < sg.getSize(); i++)
1949     {
1950       SequenceI seq = null;
1951
1952       while (seq == null)
1953       {
1954         if (orderedSeqs.containsKey(index))
1955         {
1956           seq = orderedSeqs.get(index);
1957           index++;
1958           break;
1959         }
1960         else
1961         {
1962           index++;
1963         }
1964       }
1965
1966       // FIND START RES
1967       // Returns residue following index if gap
1968       startRes = seq.findPosition(sg.getStartRes());
1969
1970       // FIND END RES
1971       // Need to find the residue preceeding index if gap
1972       endRes = 0;
1973
1974       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1975       {
1976         ch = seq.getCharAt(j);
1977         if (!jalview.util.Comparison.isGap((ch)))
1978         {
1979           endRes++;
1980         }
1981       }
1982
1983       if (endRes > 0)
1984       {
1985         endRes += seq.getStart() - 1;
1986       }
1987
1988       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1989               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1990                       sg.getEndRes() + 1)
1991               + "\n");
1992     }
1993
1994   }
1995
1996   protected void pasteNew_actionPerformed()
1997   {
1998     paste(true);
1999   }
2000
2001   protected void pasteThis_actionPerformed()
2002   {
2003     paste(false);
2004   }
2005
2006   void paste(boolean newAlignment)
2007   {
2008     try
2009     {
2010       if (copiedSequences == null)
2011       {
2012         return;
2013       }
2014
2015       StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2016               "\t");
2017       Vector seqs = new Vector();
2018       while (st.hasMoreElements())
2019       {
2020         String name = st.nextToken();
2021         int start = Integer.parseInt(st.nextToken());
2022         int end = Integer.parseInt(st.nextToken());
2023         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2024       }
2025       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2026       for (int i = 0; i < seqs.size(); i++)
2027       {
2028         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2029       }
2030
2031       if (newAlignment)
2032       {
2033         String newtitle = MessageManager
2034                 .getString("label.copied_sequences");
2035         if (getTitle().startsWith(
2036                 MessageManager.getString("label.copied_sequences")))
2037         {
2038           newtitle = getTitle();
2039         }
2040         else
2041         {
2042           newtitle = newtitle.concat(MessageManager
2043                   .formatMessage("label.from_msname", new String[]
2044                   { getTitle() }));
2045         }
2046         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2047                 viewport.applet, newtitle, false);
2048         af.viewport.setHiddenColumns(copiedHiddenColumns);
2049
2050         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2051                 frameHeight);
2052       }
2053       else
2054       {
2055         addSequences(newSeqs);
2056       }
2057
2058     } catch (Exception ex)
2059     {
2060     } // could be anything being pasted in here
2061
2062   }
2063
2064   void addSequences(SequenceI[] seqs)
2065   {
2066     for (int i = 0; i < seqs.length; i++)
2067     {
2068       viewport.getAlignment().addSequence(seqs[i]);
2069     }
2070
2071     // !newAlignment
2072     addHistoryItem(new EditCommand(
2073             MessageManager.getString("label.add_sequences"), Action.PASTE,
2074             seqs, 0, viewport.getAlignment().getWidth(),
2075             viewport.getAlignment()));
2076
2077     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2078     viewport.getAlignment().getWidth();
2079     viewport.firePropertyChange("alignment", null,
2080             viewport.getAlignment().getSequences());
2081
2082   }
2083
2084   protected void cut_actionPerformed()
2085   {
2086     copy_actionPerformed();
2087     delete_actionPerformed();
2088   }
2089
2090   protected void delete_actionPerformed()
2091   {
2092
2093     SequenceGroup sg = viewport.getSelectionGroup();
2094     if (sg == null)
2095     {
2096       return;
2097     }
2098
2099     Vector seqs = new Vector();
2100     SequenceI seq;
2101     for (int i = 0; i < sg.getSize(); i++)
2102     {
2103       seq = sg.getSequenceAt(i);
2104       seqs.addElement(seq);
2105     }
2106
2107     /*
2108      * If the cut affects all sequences, warn, remove highlighted columns
2109      */
2110     if (sg.getSize() == viewport.getAlignment().getHeight())
2111     {
2112       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2113               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2114       if (isEntireAlignWidth)
2115       {
2116         String title = MessageManager.getString("label.delete_all");
2117         Panel infoPanel = new Panel();
2118         infoPanel.setLayout(new FlowLayout());
2119         infoPanel.add(
2120                 new Label(MessageManager.getString("warn.delete_all")));
2121
2122         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2123         dialog.setMainPanel(infoPanel);
2124         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2125         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2126         dialog.setVisible(true);
2127
2128         if (!dialog.accept)
2129         {
2130           return;
2131         }
2132       }
2133       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2134               sg.getEndRes() + 1);
2135     }
2136
2137     SequenceI[] cut = new SequenceI[seqs.size()];
2138     for (int i = 0; i < seqs.size(); i++)
2139     {
2140       cut[i] = (SequenceI) seqs.elementAt(i);
2141     }
2142
2143     /*
2144      * //ADD HISTORY ITEM
2145      */
2146     addHistoryItem(new EditCommand(
2147             MessageManager.getString("label.cut_sequences"), Action.CUT,
2148             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2149             viewport.getAlignment()));
2150
2151     viewport.setSelectionGroup(null);
2152     viewport.getAlignment().deleteGroup(sg);
2153
2154     viewport.firePropertyChange("alignment", null,
2155             viewport.getAlignment().getSequences());
2156
2157     if (viewport.getAlignment().getHeight() < 1)
2158     {
2159       this.setVisible(false);
2160     }
2161     viewport.sendSelection();
2162   }
2163
2164   /**
2165    * group consensus toggled
2166    *
2167    */
2168   protected void showGroupConsensus_actionPerformed()
2169   {
2170     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2171     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2172
2173   }
2174
2175   /**
2176    * group conservation toggled.
2177    */
2178   protected void showGroupConservation_actionPerformed()
2179   {
2180     viewport.setShowGroupConservation(showGroupConservation.getState());
2181     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2182   }
2183
2184   /*
2185    * (non-Javadoc)
2186    *
2187    * @see
2188    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2189    * .event.ActionEvent)
2190    */
2191   protected void showConsensusHistogram_actionPerformed()
2192   {
2193     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195   }
2196
2197   /*
2198    * (non-Javadoc)
2199    *
2200    * @see
2201    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2202    * .event.ActionEvent)
2203    */
2204   protected void showSequenceLogo_actionPerformed()
2205   {
2206     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2207     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2208   }
2209
2210   protected void normSequenceLogo_actionPerformed()
2211   {
2212     showSequenceLogo.setState(true);
2213     viewport.setShowSequenceLogo(true);
2214     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2215     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2216   }
2217
2218   protected void applyAutoAnnotationSettings_actionPerformed()
2219   {
2220     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2221   }
2222
2223   protected void makeGrpsFromSelection_actionPerformed()
2224   {
2225     if (avc.makeGroupsFromSelection())
2226     {
2227       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2228       alignPanel.updateAnnotation();
2229       alignPanel.paintAlignment(true, true);
2230     }
2231   }
2232
2233   protected void createGroup_actionPerformed()
2234   {
2235     avc.createGroup();
2236   }
2237
2238   protected void unGroup_actionPerformed()
2239   {
2240     if (avc.unGroup())
2241     {
2242       alignPanel.alignmentChanged();
2243     }
2244   }
2245
2246   protected void deleteGroups_actionPerformed()
2247   {
2248     if (avc.deleteGroups())
2249     {
2250       alignPanel.alignmentChanged();
2251     }
2252   }
2253
2254   public void selectAllSequenceMenuItem_actionPerformed()
2255   {
2256     SequenceGroup sg = new SequenceGroup();
2257     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2258     {
2259       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2260     }
2261     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2262     viewport.setSelectionGroup(sg);
2263     // JAL-2034 - should delegate to
2264     // alignPanel to decide if overview needs
2265     // updating.
2266     alignPanel.paintAlignment(false, false);
2267     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2268     viewport.sendSelection();
2269   }
2270
2271   public void deselectAllSequenceMenuItem_actionPerformed()
2272   {
2273     if (viewport.cursorMode)
2274     {
2275       alignPanel.seqPanel.keyboardNo1 = null;
2276       alignPanel.seqPanel.keyboardNo2 = null;
2277     }
2278     viewport.setSelectionGroup(null);
2279     viewport.getColumnSelection().clear();
2280     viewport.setSelectionGroup(null);
2281     alignPanel.idPanel.idCanvas.searchResults = null;
2282     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2283     // JAL-2034 - should delegate to
2284     // alignPanel to decide if overview needs
2285     // updating.
2286     alignPanel.paintAlignment(false, false);
2287     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2288     viewport.sendSelection();
2289   }
2290
2291   public void invertSequenceMenuItem_actionPerformed()
2292   {
2293     SequenceGroup sg = viewport.getSelectionGroup();
2294     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2295     {
2296       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2297     }
2298
2299     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2300     viewport.sendSelection();
2301   }
2302
2303   public void invertColSel_actionPerformed()
2304   {
2305     viewport.invertColumnSelection();
2306     alignPanel.paintAlignment(true, false);
2307     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2308     viewport.sendSelection();
2309   }
2310
2311   void trimAlignment(boolean trimLeft)
2312   {
2313     AlignmentI al = viewport.getAlignment();
2314     ViewportRanges ranges = viewport.getRanges();
2315     ColumnSelection colSel = viewport.getColumnSelection();
2316     int column;
2317
2318     if (!colSel.isEmpty())
2319     {
2320       if (trimLeft)
2321       {
2322         column = colSel.getMin();
2323       }
2324       else
2325       {
2326         column = colSel.getMax();
2327       }
2328
2329       SequenceI[] seqs;
2330       if (viewport.getSelectionGroup() != null)
2331       {
2332         seqs = viewport.getSelectionGroup()
2333                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2334       }
2335       else
2336       {
2337         seqs = al.getSequencesArray();
2338       }
2339
2340       TrimRegionCommand trimRegion;
2341       if (trimLeft)
2342       {
2343         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2344                 column, al);
2345         ranges.setStartRes(0);
2346       }
2347       else
2348       {
2349         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2350                 column, al);
2351       }
2352
2353       statusBar.setText(MessageManager
2354               .formatMessage("label.removed_columns", new String[]
2355               { Integer.valueOf(trimRegion.getSize()).toString() }));
2356       addHistoryItem(trimRegion);
2357
2358       for (SequenceGroup sg : al.getGroups())
2359       {
2360         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2361                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2362         {
2363           al.deleteGroup(sg);
2364         }
2365       }
2366
2367       viewport.firePropertyChange("alignment", null, al.getSequences());
2368     }
2369   }
2370
2371   public void removeGappedColumnMenuItem_actionPerformed()
2372   {
2373     AlignmentI al = viewport.getAlignment();
2374     ViewportRanges ranges = viewport.getRanges();
2375     int start = 0;
2376     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2377
2378     SequenceI[] seqs;
2379     if (viewport.getSelectionGroup() != null)
2380     {
2381       seqs = viewport.getSelectionGroup()
2382               .getSequencesAsArray(viewport.getHiddenRepSequences());
2383       start = viewport.getSelectionGroup().getStartRes();
2384       end = viewport.getSelectionGroup().getEndRes();
2385     }
2386     else
2387     {
2388       seqs = viewport.getAlignment().getSequencesArray();
2389     }
2390
2391     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2392             "Remove Gapped Columns", seqs, start, end,
2393             viewport.getAlignment());
2394
2395     addHistoryItem(removeGapCols);
2396
2397     statusBar.setText(MessageManager
2398             .formatMessage("label.removed_empty_columns", new String[]
2399             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2400
2401     // This is to maintain viewport position on first residue
2402     // of first sequence
2403     SequenceI seq = al.getSequenceAt(0);
2404     int startRes = seq.findPosition(ranges.getStartRes());
2405     // ShiftList shifts;
2406     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2407     // edit.alColumnChanges=shifts.getInverse();
2408     // if (viewport.hasHiddenColumns)
2409     // viewport.getColumnSelection().compensateForEdits(shifts);
2410     ranges.setStartRes(seq.findIndex(startRes) - 1);
2411     viewport.firePropertyChange("alignment", null, al.getSequences());
2412
2413   }
2414
2415   public void removeAllGapsMenuItem_actionPerformed()
2416   {
2417     AlignmentI al = viewport.getAlignment();
2418     ViewportRanges ranges = viewport.getRanges();
2419     int start = 0;
2420     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2421
2422     SequenceI[] seqs;
2423     if (viewport.getSelectionGroup() != null)
2424     {
2425       seqs = viewport.getSelectionGroup()
2426               .getSequencesAsArray(viewport.getHiddenRepSequences());
2427       start = viewport.getSelectionGroup().getStartRes();
2428       end = viewport.getSelectionGroup().getEndRes();
2429     }
2430     else
2431     {
2432       seqs = viewport.getAlignment().getSequencesArray();
2433     }
2434
2435     // This is to maintain viewport position on first residue
2436     // of first sequence
2437     SequenceI seq = al.getSequenceAt(0);
2438     int startRes = seq.findPosition(ranges.getStartRes());
2439
2440     addHistoryItem(
2441             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2442
2443     ranges.setStartRes(seq.findIndex(startRes) - 1);
2444
2445     viewport.firePropertyChange("alignment", null, al.getSequences());
2446
2447   }
2448
2449   public void findMenuItem_actionPerformed()
2450   {
2451     new Finder(alignPanel);
2452   }
2453
2454   /**
2455    * create a new view derived from the current view
2456    *
2457    * @param viewtitle
2458    * @return frame for the new view
2459    */
2460   public AlignFrame newView(String viewtitle)
2461   {
2462     AlignmentI newal;
2463     if (viewport.hasHiddenRows())
2464     {
2465       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2466               .getFullAlignment().getSequencesArray());
2467     }
2468     else
2469     {
2470       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2471     }
2472
2473     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2474     {
2475       for (int i = 0; i < viewport.getAlignment()
2476               .getAlignmentAnnotation().length; i++)
2477       {
2478         if (!viewport.getAlignment()
2479                 .getAlignmentAnnotation()[i].autoCalculated)
2480         {
2481           newal.addAnnotation(
2482                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2483         }
2484       }
2485     }
2486
2487     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2488
2489     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2490     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2491     PaintRefresher.Register(newaf.alignPanel,
2492             newaf.alignPanel.av.getSequenceSetId());
2493
2494     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2495             newaf.alignPanel.av.getSequenceSetId());
2496     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2497             newaf.alignPanel.av.getSequenceSetId());
2498
2499     Vector comps = PaintRefresher.components
2500             .get(viewport.getSequenceSetId());
2501     int viewSize = -1;
2502     for (int i = 0; i < comps.size(); i++)
2503     {
2504       if (comps.elementAt(i) instanceof AlignmentPanel)
2505       {
2506         viewSize++;
2507       }
2508     }
2509
2510     String title = new String(this.getTitle());
2511     if (viewtitle != null)
2512     {
2513       title = viewtitle + " ( " + title + ")";
2514     }
2515     else
2516     {
2517       if (title.indexOf("(View") > -1)
2518       {
2519         title = title.substring(0, title.indexOf("(View"));
2520       }
2521       title += "(View " + viewSize + ")";
2522     }
2523
2524     newaf.setTitle(title.toString());
2525
2526     newaf.viewport.setHistoryList(viewport.getHistoryList());
2527     newaf.viewport.setRedoList(viewport.getRedoList());
2528     return newaf;
2529   }
2530
2531   /**
2532    *
2533    * @return list of feature groups on the view
2534    */
2535   public String[] getFeatureGroups()
2536   {
2537     FeatureRenderer fr = null;
2538     if (alignPanel != null
2539             && (fr = alignPanel.getFeatureRenderer()) != null)
2540     {
2541       List<String> gps = fr.getFeatureGroups();
2542       String[] _gps = gps.toArray(new String[gps.size()]);
2543       return _gps;
2544     }
2545     return null;
2546   }
2547
2548   /**
2549    * get sequence feature groups that are hidden or shown
2550    *
2551    * @param visible
2552    *          true is visible
2553    * @return list
2554    */
2555   public String[] getFeatureGroupsOfState(boolean visible)
2556   {
2557     FeatureRenderer fr = null;
2558     if (alignPanel != null
2559             && (fr = alignPanel.getFeatureRenderer()) != null)
2560     {
2561       List<String> gps = fr.getGroups(visible);
2562       String[] _gps = gps.toArray(new String[gps.size()]);
2563       return _gps;
2564     }
2565     return null;
2566   }
2567
2568   /**
2569    * Change the display state for the given feature groups
2570    *
2571    * @param groups
2572    *          list of group strings
2573    * @param state
2574    *          visible or invisible
2575    */
2576   public void setFeatureGroupState(String[] groups, boolean state)
2577   {
2578     FeatureRenderer fr = null;
2579     this.sequenceFeatures.setState(true);
2580     viewport.setShowSequenceFeatures(true);
2581     if (alignPanel != null
2582             && (fr = alignPanel.getFeatureRenderer()) != null)
2583     {
2584
2585       fr.setGroupVisibility(Arrays.asList(groups), state);
2586       alignPanel.seqPanel.seqCanvas.repaint();
2587       if (alignPanel.overviewPanel != null)
2588       {
2589         alignPanel.overviewPanel.updateOverviewImage();
2590       }
2591     }
2592   }
2593
2594   public void seqLimits_itemStateChanged()
2595   {
2596     viewport.setShowJVSuffix(seqLimits.getState());
2597     alignPanel.fontChanged();
2598     alignPanel.paintAlignment(true, false);
2599   }
2600
2601   protected void colourTextMenuItem_actionPerformed()
2602   {
2603     viewport.setColourText(colourTextMenuItem.getState());
2604     alignPanel.paintAlignment(false, false);
2605   }
2606
2607   protected void displayNonconservedMenuItem_actionPerformed()
2608   {
2609     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2610     alignPanel.paintAlignment(false, false);
2611   }
2612
2613   protected void wrapMenuItem_actionPerformed()
2614   {
2615     viewport.setWrapAlignment(wrapMenuItem.getState());
2616     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2617     scaleAbove.setEnabled(wrapMenuItem.getState());
2618     scaleLeft.setEnabled(wrapMenuItem.getState());
2619     scaleRight.setEnabled(wrapMenuItem.getState());
2620     alignPanel.paintAlignment(true, false);
2621   }
2622
2623   public void overviewMenuItem_actionPerformed()
2624   {
2625     if (alignPanel.overviewPanel != null)
2626     {
2627       return;
2628     }
2629
2630     Frame frame = new Frame();
2631     final OverviewPanel overview = new OverviewPanel(alignPanel);
2632     frame.add(overview);
2633     // +50 must allow for applet frame window
2634     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2635             .formatMessage("label.overview_params", new String[]
2636             { this.getTitle() }), overview.getPreferredSize().width,
2637             overview.getPreferredSize().height + 50);
2638
2639     frame.pack();
2640     final AlignmentPanel ap = alignPanel;
2641     frame.addWindowListener(new WindowAdapter()
2642     {
2643       @Override
2644       public void windowClosing(WindowEvent e)
2645       {
2646         overview.dispose();
2647         if (ap != null)
2648         {
2649           ap.setOverviewPanel(null);
2650         }
2651       };
2652     });
2653
2654     alignPanel.setOverviewPanel(overview);
2655
2656   }
2657
2658   @Override
2659   public void changeColour(ColourSchemeI cs)
2660   {
2661     viewport.setGlobalColourScheme(cs);
2662
2663     alignPanel.paintAlignment(true, true);
2664   }
2665
2666   protected void modifyPID_actionPerformed()
2667   {
2668     if (viewport.getAbovePIDThreshold()
2669             && viewport.getGlobalColourScheme() != null)
2670     {
2671       SliderPanel.setPIDSliderSource(alignPanel,
2672               viewport.getResidueShading(), alignPanel.getViewName());
2673       SliderPanel.showPIDSlider();
2674     }
2675   }
2676
2677   protected void modifyConservation_actionPerformed()
2678   {
2679     if (viewport.getConservationSelected()
2680             && viewport.getGlobalColourScheme() != null)
2681     {
2682       SliderPanel.setConservationSlider(alignPanel,
2683               viewport.getResidueShading(), alignPanel.getViewName());
2684       SliderPanel.showConservationSlider();
2685     }
2686   }
2687
2688   protected void conservationMenuItem_actionPerformed()
2689   {
2690     boolean selected = conservationMenuItem.getState();
2691     modifyConservation.setEnabled(selected);
2692     viewport.setConservationSelected(selected);
2693     viewport.getResidueShading().setConservationApplied(selected);
2694
2695     changeColour(viewport.getGlobalColourScheme());
2696
2697     if (selected)
2698     {
2699       modifyConservation_actionPerformed();
2700     }
2701     else
2702     {
2703       SliderPanel.hideConservationSlider();
2704     }
2705   }
2706
2707   public void abovePIDThreshold_actionPerformed()
2708   {
2709     boolean selected = abovePIDThreshold.getState();
2710     modifyPID.setEnabled(selected);
2711     viewport.setAbovePIDThreshold(selected);
2712     if (!selected)
2713     {
2714       viewport.getResidueShading().setThreshold(0,
2715               viewport.isIgnoreGapsConsensus());
2716     }
2717
2718     changeColour(viewport.getGlobalColourScheme());
2719
2720     if (selected)
2721     {
2722       modifyPID_actionPerformed();
2723     }
2724     else
2725     {
2726       SliderPanel.hidePIDSlider();
2727     }
2728   }
2729
2730   public void sortPairwiseMenuItem_actionPerformed()
2731   {
2732     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2733     AlignmentSorter.sortByPID(viewport.getAlignment(),
2734             viewport.getAlignment().getSequenceAt(0));
2735
2736     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2737             viewport.getAlignment()));
2738     alignPanel.paintAlignment(true, false);
2739   }
2740
2741   public void sortIDMenuItem_actionPerformed()
2742   {
2743     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2744     AlignmentSorter.sortByID(viewport.getAlignment());
2745     addHistoryItem(
2746             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2747     alignPanel.paintAlignment(true, false);
2748   }
2749
2750   public void sortLengthMenuItem_actionPerformed()
2751   {
2752     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2753     AlignmentSorter.sortByLength(viewport.getAlignment());
2754     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2755             viewport.getAlignment()));
2756     alignPanel.paintAlignment(true, false);
2757   }
2758
2759   public void sortGroupMenuItem_actionPerformed()
2760   {
2761     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2762     AlignmentSorter.sortByGroup(viewport.getAlignment());
2763     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2764             viewport.getAlignment()));
2765     alignPanel.paintAlignment(true, false);
2766
2767   }
2768
2769   public void removeRedundancyMenuItem_actionPerformed()
2770   {
2771     new RedundancyPanel(alignPanel);
2772   }
2773
2774   public void pairwiseAlignmentMenuItem_actionPerformed()
2775   {
2776     if (viewport.getSelectionGroup() != null
2777             && viewport.getSelectionGroup().getSize() > 1)
2778     {
2779       Frame frame = new Frame();
2780       frame.add(new PairwiseAlignPanel(alignPanel));
2781       jalview.bin.JalviewLite.addFrame(frame,
2782               MessageManager.getString("action.pairwise_alignment"), 600,
2783               500);
2784     }
2785   }
2786
2787   public void PCAMenuItem_actionPerformed()
2788   {
2789     // are the sequences aligned?
2790     if (!viewport.getAlignment().isAligned(false))
2791     {
2792       SequenceI current;
2793       int Width = viewport.getAlignment().getWidth();
2794
2795       for (int i = 0; i < viewport.getAlignment().getSequences()
2796               .size(); i++)
2797       {
2798         current = viewport.getAlignment().getSequenceAt(i);
2799
2800         if (current.getLength() < Width)
2801         {
2802           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2803         }
2804       }
2805       alignPanel.paintAlignment(false, false);
2806     }
2807
2808     if ((viewport.getSelectionGroup() != null
2809             && viewport.getSelectionGroup().getSize() < 4
2810             && viewport.getSelectionGroup().getSize() > 0)
2811             || viewport.getAlignment().getHeight() < 4)
2812     {
2813       return;
2814     }
2815
2816     try
2817     {
2818       new PCAPanel(viewport);
2819     } catch (java.lang.OutOfMemoryError ex)
2820     {
2821     }
2822
2823   }
2824
2825   public void averageDistanceTreeMenuItem_actionPerformed()
2826   {
2827     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2828             "Average distance tree using PID");
2829   }
2830
2831   public void neighbourTreeMenuItem_actionPerformed()
2832   {
2833     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2834             "Neighbour joining tree using PID");
2835   }
2836
2837   protected void njTreeBlosumMenuItem_actionPerformed()
2838   {
2839     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2840             ScoreModels.getInstance().getBlosum62().getName(),
2841             "Neighbour joining tree using BLOSUM62");
2842   }
2843
2844   protected void avTreeBlosumMenuItem_actionPerformed()
2845   {
2846     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2847             ScoreModels.getInstance().getBlosum62().getName(),
2848             "Average distance tree using BLOSUM62");
2849   }
2850
2851   void newTreePanel(String type, String pwType, String title)
2852   {
2853     // are the sequences aligned?
2854     if (!viewport.getAlignment().isAligned(false))
2855     {
2856       SequenceI current;
2857       int Width = viewport.getAlignment().getWidth();
2858
2859       for (int i = 0; i < viewport.getAlignment().getSequences()
2860               .size(); i++)
2861       {
2862         current = viewport.getAlignment().getSequenceAt(i);
2863
2864         if (current.getLength() < Width)
2865         {
2866           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2867         }
2868       }
2869       alignPanel.paintAlignment(false, false);
2870
2871     }
2872
2873     if ((viewport.getSelectionGroup() != null
2874             && viewport.getSelectionGroup().getSize() > 1)
2875             || (viewport.getAlignment().getHeight() > 1))
2876     {
2877       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2878
2879       addTreeMenuItem(tp, title);
2880
2881       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2882     }
2883   }
2884
2885   void loadTree_actionPerformed()
2886   {
2887     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2888     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2889     cap.setTreeImport();
2890     Frame frame = new Frame();
2891     frame.add(cap);
2892     jalview.bin.JalviewLite.addFrame(frame,
2893             MessageManager.getString("label.paste_newick_file"), 400, 300);
2894   }
2895
2896   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2897   {
2898     TreePanel tp = new TreePanel(alignPanel, treeFile,
2899             MessageManager.getString("label.load_tree_from_file"), tree);
2900     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2901     addTreeMenuItem(tp, treeFile);
2902   }
2903
2904   /**
2905    * sort the alignment using the given treePanel
2906    *
2907    * @param treePanel
2908    *          tree used to sort view
2909    * @param title
2910    *          string used for undo event name
2911    */
2912   public void sortByTree(TreePanel treePanel, String title)
2913   {
2914     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2915     AlignmentSorter.sortByTree(viewport.getAlignment(),
2916             treePanel.getTree());
2917     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2918     // HistoryItem.SORT));
2919     addHistoryItem(new OrderCommand(MessageManager
2920             .formatMessage("label.order_by_params", new String[]
2921             { title }), oldOrder, viewport.getAlignment()));
2922     alignPanel.paintAlignment(true, false);
2923   }
2924
2925   /**
2926    * Do any automatic reordering of the alignment and add the necessary bits to
2927    * the menu structure for the new tree
2928    *
2929    * @param treePanel
2930    * @param title
2931    */
2932   protected void addTreeMenuItem(final TreePanel treePanel,
2933           final String title)
2934   {
2935     final MenuItem item = new MenuItem(title);
2936     sortByTreeMenu.add(item);
2937     item.addActionListener(new java.awt.event.ActionListener()
2938     {
2939       @Override
2940       public void actionPerformed(ActionEvent evt)
2941       {
2942         sortByTree(treePanel, title); // treePanel.getTitle());
2943       }
2944     });
2945
2946     treePanel.addWindowListener(new WindowAdapter()
2947     {
2948       @Override
2949       public void windowOpened(WindowEvent e)
2950       {
2951         if (viewport.sortByTree)
2952         {
2953           sortByTree(treePanel, title);
2954         }
2955         super.windowOpened(e);
2956       }
2957
2958       @Override
2959       public void windowClosing(WindowEvent e)
2960       {
2961         sortByTreeMenu.remove(item);
2962       };
2963     });
2964   }
2965
2966   public boolean sortBy(AlignmentOrder alorder, String undoname)
2967   {
2968     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2969     if (viewport.applet.debug)
2970     {
2971       System.err.println("Sorting " + alorder.getOrder().size()
2972               + " in alignment '" + getTitle() + "'");
2973     }
2974     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2975     if (undoname != null)
2976     {
2977       addHistoryItem(new OrderCommand(undoname, oldOrder,
2978               viewport.getAlignment()));
2979     }
2980     alignPanel.paintAlignment(true, false);
2981     return true;
2982   }
2983
2984   protected void documentation_actionPerformed()
2985   {
2986     alignPanel.av.applet.openJalviewHelpUrl();
2987   }
2988
2989   protected void about_actionPerformed()
2990   {
2991
2992     class AboutPanel extends Canvas
2993     {
2994       String version;
2995
2996       String builddate;
2997
2998       public AboutPanel(String version, String builddate)
2999       {
3000         this.version = version;
3001         this.builddate = builddate;
3002       }
3003
3004       @Override
3005       public void paint(Graphics g)
3006       {
3007         g.setColor(Color.white);
3008         g.fillRect(0, 0, getSize().width, getSize().height);
3009         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3010         FontMetrics fm = g.getFontMetrics();
3011         int fh = fm.getHeight();
3012         int y = 5, x = 7;
3013         g.setColor(Color.black);
3014         // TODO: update this text for each release or centrally store it for
3015         // lite and application
3016         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3017         g.drawString(MessageManager
3018                 .formatMessage("label.jalviewLite_release", new String[]
3019                 { version }), x, y += fh);
3020         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3021         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3022                 new String[]
3023                 { builddate }), x, y += fh);
3024         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3025         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3026                 y += fh * 1.5);
3027         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3028                 x + 50, y += fh + 8);
3029         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3030                 x, y += fh);
3031         g.drawString(MessageManager
3032                 .getString("label.jalview_distribution_lists"), x, y += fh);
3033         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3034                 x, y += fh + 8);
3035         g.drawString(
3036                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3037                 y += fh);
3038         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3039                 x, y += fh);
3040         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3041                 x, y += fh);
3042       }
3043     }
3044
3045     Frame frame = new Frame();
3046     frame.add(new AboutPanel(JalviewLite.getVersion(),
3047             JalviewLite.getBuildDate()));
3048     jalview.bin.JalviewLite.addFrame(frame,
3049             MessageManager.getString("label.jalview"), 580, 220);
3050
3051   }
3052
3053   public void showURL(String url, String target)
3054   {
3055     if (viewport.applet == null)
3056     {
3057       System.out.println("Not running as applet - no browser available.");
3058     }
3059     else
3060     {
3061       viewport.applet.showURL(url, target);
3062     }
3063   }
3064
3065   // ////////////////////////////////////////////////////////////////////////////////
3066   // JBuilder Graphics here
3067
3068   MenuBar alignFrameMenuBar = new MenuBar();
3069
3070   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3071
3072   MenuItem loadApplication = new MenuItem(
3073           MessageManager.getString("label.view_full_application"));
3074
3075   MenuItem loadTree = new MenuItem(
3076           MessageManager.getString("label.load_associated_tree"));
3077
3078   MenuItem loadAnnotations = new MenuItem(
3079           MessageManager.getString("label.load_features_annotations"));
3080
3081   MenuItem outputFeatures = new MenuItem(
3082           MessageManager.getString("label.export_features"));
3083
3084   MenuItem outputAnnotations = new MenuItem(
3085           MessageManager.getString("label.export_annotations"));
3086
3087   MenuItem closeMenuItem = new MenuItem(
3088           MessageManager.getString("action.close"));
3089
3090   MenuItem selectAllSequenceMenuItem = new MenuItem(
3091           MessageManager.getString("action.select_all"));
3092
3093   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3094           MessageManager.getString("action.deselect_all"));
3095
3096   MenuItem invertSequenceMenuItem = new MenuItem(
3097           MessageManager.getString("action.invert_selection"));
3098
3099   MenuItem remove2LeftMenuItem = new MenuItem();
3100
3101   MenuItem remove2RightMenuItem = new MenuItem();
3102
3103   MenuItem removeGappedColumnMenuItem = new MenuItem();
3104
3105   MenuItem removeAllGapsMenuItem = new MenuItem();
3106
3107   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3108
3109   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3110
3111   MenuItem sortPairwiseMenuItem = new MenuItem();
3112
3113   MenuItem sortIDMenuItem = new MenuItem();
3114
3115   MenuItem sortLengthMenuItem = new MenuItem();
3116
3117   MenuItem sortGroupMenuItem = new MenuItem();
3118
3119   MenuItem removeRedundancyMenuItem = new MenuItem();
3120
3121   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3122
3123   MenuItem PCAMenuItem = new MenuItem();
3124
3125   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3126
3127   MenuItem neighbourTreeMenuItem = new MenuItem();
3128
3129   BorderLayout borderLayout1 = new BorderLayout();
3130
3131   public Label statusBar = new Label();
3132
3133   MenuItem clustalColour = new MenuItem();
3134
3135   MenuItem zappoColour = new MenuItem();
3136
3137   MenuItem taylorColour = new MenuItem();
3138
3139   MenuItem hydrophobicityColour = new MenuItem();
3140
3141   MenuItem helixColour = new MenuItem();
3142
3143   MenuItem strandColour = new MenuItem();
3144
3145   MenuItem turnColour = new MenuItem();
3146
3147   MenuItem buriedColour = new MenuItem();
3148
3149   MenuItem purinePyrimidineColour = new MenuItem();
3150
3151   // MenuItem RNAInteractionColour = new MenuItem();
3152
3153   MenuItem RNAHelixColour = new MenuItem();
3154
3155   MenuItem userDefinedColour = new MenuItem();
3156
3157   MenuItem PIDColour = new MenuItem();
3158
3159   MenuItem BLOSUM62Colour = new MenuItem();
3160
3161   MenuItem tcoffeeColour = new MenuItem();
3162
3163   MenuItem njTreeBlosumMenuItem = new MenuItem();
3164
3165   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3166
3167   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3168
3169   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3170
3171   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3172
3173   MenuItem alProperties = new MenuItem(
3174           MessageManager.getString("label.alignment_props"));
3175
3176   MenuItem overviewMenuItem = new MenuItem();
3177
3178   MenuItem undoMenuItem = new MenuItem();
3179
3180   MenuItem redoMenuItem = new MenuItem();
3181
3182   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3183
3184   MenuItem noColourmenuItem = new MenuItem();
3185
3186   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3187
3188   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3189
3190   MenuItem findMenuItem = new MenuItem();
3191
3192   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3193
3194   MenuItem nucleotideColour = new MenuItem();
3195
3196   MenuItem deleteGroups = new MenuItem();
3197
3198   MenuItem grpsFromSelection = new MenuItem();
3199
3200   MenuItem createGroup = new MenuItem();
3201
3202   MenuItem unGroup = new MenuItem();
3203
3204   MenuItem delete = new MenuItem();
3205
3206   MenuItem copy = new MenuItem();
3207
3208   MenuItem cut = new MenuItem();
3209
3210   Menu pasteMenu = new Menu();
3211
3212   MenuItem pasteNew = new MenuItem();
3213
3214   MenuItem pasteThis = new MenuItem();
3215
3216   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3217
3218   MenuItem font = new MenuItem();
3219
3220   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3221
3222   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3223
3224   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3225
3226   MenuItem modifyPID = new MenuItem();
3227
3228   MenuItem modifyConservation = new MenuItem();
3229
3230   CheckboxMenuItem autoCalculate = null;
3231
3232   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3233           "Sort Alignment With New Tree", true);
3234
3235   Menu sortByTreeMenu = new Menu();
3236
3237   MenuItem inputText = new MenuItem();
3238
3239   MenuItem documentation = new MenuItem();
3240
3241   MenuItem about = new MenuItem();
3242
3243   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3244
3245   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3246
3247   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3248
3249   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3250
3251   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3252
3253   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3254
3255   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3256
3257   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3258
3259   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3260
3261   /**
3262    * Initialise menus and other items
3263    *
3264    * @throws Exception
3265    */
3266   private void jbInit() throws Exception
3267   {
3268     setMenuBar(alignFrameMenuBar);
3269
3270     /*
3271      * Configure File menu items and actions
3272      */
3273     inputText
3274             .setLabel(MessageManager.getString("label.input_from_textbox"));
3275     inputText.addActionListener(this);
3276     Menu outputTextboxMenu = new Menu(
3277             MessageManager.getString("label.out_to_textbox"));
3278     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3279     {
3280       MenuItem item = new MenuItem(ff);
3281
3282       item.addActionListener(new java.awt.event.ActionListener()
3283       {
3284         @Override
3285         public void actionPerformed(ActionEvent e)
3286         {
3287           outputText_actionPerformed(e);
3288         }
3289       });
3290
3291       outputTextboxMenu.add(item);
3292     }
3293     closeMenuItem.addActionListener(this);
3294     loadApplication.addActionListener(this);
3295     loadTree.addActionListener(this);
3296     loadAnnotations.addActionListener(this);
3297     outputFeatures.addActionListener(this);
3298     outputAnnotations.addActionListener(this);
3299
3300     /*
3301      * Configure Edit menu items and actions
3302      */
3303     undoMenuItem.setEnabled(false);
3304     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3305     undoMenuItem.addActionListener(this);
3306     redoMenuItem.setEnabled(false);
3307     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3308     redoMenuItem.addActionListener(this);
3309     copy.setLabel(MessageManager.getString("action.copy"));
3310     copy.addActionListener(this);
3311     cut.setLabel(MessageManager.getString("action.cut"));
3312     cut.addActionListener(this);
3313     delete.setLabel(MessageManager.getString("action.delete"));
3314     delete.addActionListener(this);
3315     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3316     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3317     pasteNew.addActionListener(this);
3318     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3319     pasteThis.addActionListener(this);
3320     remove2LeftMenuItem
3321             .setLabel(MessageManager.getString("action.remove_left"));
3322     remove2LeftMenuItem.addActionListener(this);
3323     remove2RightMenuItem
3324             .setLabel(MessageManager.getString("action.remove_right"));
3325     remove2RightMenuItem.addActionListener(this);
3326     removeGappedColumnMenuItem.setLabel(
3327             MessageManager.getString("action.remove_empty_columns"));
3328     removeGappedColumnMenuItem.addActionListener(this);
3329     removeAllGapsMenuItem
3330             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3331     removeAllGapsMenuItem.addActionListener(this);
3332     removeRedundancyMenuItem
3333             .setLabel(MessageManager.getString("action.remove_redundancy"));
3334     removeRedundancyMenuItem.addActionListener(this);
3335
3336     /*
3337      * Configure Select menu items and actions
3338      */
3339     findMenuItem.setLabel(MessageManager.getString("action.find"));
3340     findMenuItem.addActionListener(this);
3341     selectAllSequenceMenuItem.addActionListener(this);
3342     deselectAllSequenceMenuItem.addActionListener(this);
3343     invertSequenceMenuItem.setLabel(
3344             MessageManager.getString("action.invert_sequence_selection"));
3345     invertSequenceMenuItem.addActionListener(this);
3346     invertColSel.setLabel(
3347             MessageManager.getString("action.invert_column_selection"));
3348     invertColSel.addActionListener(this);
3349     deleteGroups
3350             .setLabel(MessageManager.getString("action.undefine_groups"));
3351     deleteGroups.addActionListener(this);
3352     grpsFromSelection.setLabel(
3353             MessageManager.getString("action.make_groups_selection"));
3354     grpsFromSelection.addActionListener(this);
3355     createGroup.setLabel(MessageManager.getString("action.create_group"));
3356     createGroup.addActionListener(this);
3357     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3358     unGroup.addActionListener(this);
3359
3360     annotationColumnSelection.setLabel(
3361             MessageManager.getString("action.select_by_annotation"));
3362     annotationColumnSelection.addActionListener(this);
3363
3364     /*
3365      * Configure View menu items and actions
3366      */
3367     newView.setLabel(MessageManager.getString("action.new_view"));
3368     newView.addActionListener(this);
3369     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3370     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3371     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3372     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3373     hideColumns
3374             .setLabel(MessageManager.getString("label.selected_columns"));
3375     hideSequences
3376             .setLabel(MessageManager.getString("label.selected_sequences"));
3377     hideAllButSelection.setLabel(
3378             MessageManager.getString("label.all_but_selected_region"));
3379     hideAllSelection
3380             .setLabel(MessageManager.getString("label.selected_region"));
3381     showAllHidden.setLabel(
3382             MessageManager.getString("label.all_sequences_columns"));
3383     showColumns.addActionListener(this);
3384     showSeqs.addActionListener(this);
3385     hideColumns.addActionListener(this);
3386     hideSequences.addActionListener(this);
3387     hideAllButSelection.addActionListener(this);
3388     hideAllSelection.addActionListener(this);
3389     showAllHidden.addActionListener(this);
3390     featureSettings
3391             .setLabel(MessageManager.getString("action.feature_settings"));
3392     featureSettings.addActionListener(this);
3393     sequenceFeatures.setLabel(
3394             MessageManager.getString("label.show_sequence_features"));
3395     sequenceFeatures.addItemListener(this);
3396     sequenceFeatures.setState(false);
3397     followMouseOverFlag.setLabel(
3398             MessageManager.getString("label.automatic_scrolling"));
3399     followMouseOverFlag.addItemListener(this);
3400     alProperties.addActionListener(this);
3401     overviewMenuItem
3402             .setLabel(MessageManager.getString("label.overview_window"));
3403     overviewMenuItem.addActionListener(this);
3404
3405     /*
3406      * Configure Annotations menu items and actions
3407      */
3408     annotationPanelMenuItem
3409             .setLabel(MessageManager.getString("label.show_annotations"));
3410     annotationPanelMenuItem.addItemListener(this);
3411     showGroupConsensus
3412             .setLabel(MessageManager.getString("label.group_consensus"));
3413     showGroupConservation
3414             .setLabel(MessageManager.getString("label.group_conservation"));
3415     showConsensusHistogram.setLabel(
3416             MessageManager.getString("label.show_consensus_histogram"));
3417     showSequenceLogo.setLabel(
3418             MessageManager.getString("label.show_consensus_logo"));
3419     normSequenceLogo.setLabel(
3420             MessageManager.getString("label.norm_consensus_logo"));
3421     applyAutoAnnotationSettings
3422             .setLabel(MessageManager.getString("label.apply_all_groups"));
3423     applyAutoAnnotationSettings.setState(true);
3424     Menu autoAnnMenu = new Menu(
3425             MessageManager.getString("label.autocalculated_annotation"));
3426     showGroupConsensus.addItemListener(this);
3427     showGroupConservation.addItemListener(this);
3428     showConsensusHistogram.addItemListener(this);
3429     showSequenceLogo.addItemListener(this);
3430     normSequenceLogo.addItemListener(this);
3431     applyAutoAnnotationSettings.addItemListener(this);
3432     showAlignmentAnnotations = new CheckboxMenuItem(
3433             MessageManager.getString("label.show_all_al_annotations"));
3434     showSequenceAnnotations = new CheckboxMenuItem(
3435             MessageManager.getString("label.show_all_seq_annotations"));
3436     sortAnnBySequence = new CheckboxMenuItem(
3437             MessageManager.getString("label.sort_annotations_by_sequence"));
3438     sortAnnByLabel = new CheckboxMenuItem(
3439             MessageManager.getString("label.sort_annotations_by_label"));
3440     showAutoFirst = new CheckboxMenuItem(
3441             MessageManager.getString("label.show_first"));
3442     showAutoFirst.setState(false); // pending applet parameter
3443     setShowAutoCalculatedAbove(showAutoFirst.getState());
3444     showAutoLast = new CheckboxMenuItem(
3445             MessageManager.getString("label.show_last"));
3446     showAutoLast.setState(!showAutoFirst.getState());
3447     showAlignmentAnnotations.addItemListener(this);
3448     showSequenceAnnotations.addItemListener(this);
3449     sortAnnBySequence.addItemListener(this);
3450     sortAnnByLabel.addItemListener(this);
3451     showAutoFirst.addItemListener(this);
3452     showAutoLast.addItemListener(this);
3453
3454     /*
3455      * Configure Format menu items and actions
3456      */
3457     font.setLabel(MessageManager.getString("action.font"));
3458     font.addActionListener(this);
3459     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3460     scaleAbove.setState(true);
3461     scaleAbove.setEnabled(false);
3462     scaleAbove.addItemListener(this);
3463     scaleLeft.setEnabled(false);
3464     scaleLeft.setState(true);
3465     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3466     scaleLeft.addItemListener(this);
3467     scaleRight.setEnabled(false);
3468     scaleRight.setState(true);
3469     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3470     scaleRight.addItemListener(this);
3471     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3472     viewBoxesMenuItem.setState(true);
3473     viewBoxesMenuItem.addItemListener(this);
3474     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3475     viewTextMenuItem.setState(true);
3476     viewTextMenuItem.addItemListener(this);
3477     colourTextMenuItem
3478             .setLabel(MessageManager.getString("label.colour_text"));
3479     colourTextMenuItem.addItemListener(this);
3480     displayNonconservedMenuItem
3481             .setLabel(MessageManager.getString("label.show_non_conserved"));
3482     displayNonconservedMenuItem.addItemListener(this);
3483     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3484     wrapMenuItem.addItemListener(this);
3485     renderGapsMenuItem
3486             .setLabel(MessageManager.getString("action.show_gaps"));
3487     renderGapsMenuItem.setState(true);
3488     renderGapsMenuItem.addItemListener(this);
3489     centreColumnLabelFlag.setLabel(
3490             MessageManager.getString("label.centre_column_labels"));
3491     centreColumnLabelFlag.addItemListener(this);
3492     seqLimits.setState(true);
3493     seqLimits.setLabel(
3494             MessageManager.getString("label.show_sequence_limits"));
3495     seqLimits.addItemListener(this);
3496
3497     /*
3498      * Configure Colour menu items and actions
3499      */
3500     applyToAllGroups.setLabel(
3501             MessageManager.getString("label.apply_colour_to_all_groups"));
3502     applyToAllGroups.setState(true);
3503     applyToAllGroups.addItemListener(this);
3504     clustalColour.setLabel(
3505             MessageManager.getString("label.colourScheme_clustal"));
3506     clustalColour.addActionListener(this);
3507     zappoColour
3508             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3509     zappoColour.addActionListener(this);
3510     taylorColour.setLabel(
3511             MessageManager.getString("label.colourScheme_taylor"));
3512     taylorColour.addActionListener(this);
3513     hydrophobicityColour.setLabel(
3514             MessageManager.getString("label.colourScheme_hydrophobic"));
3515     hydrophobicityColour.addActionListener(this);
3516     helixColour.setLabel(MessageManager
3517             .getString("label.colourScheme_helix_propensity"));
3518     helixColour.addActionListener(this);
3519     strandColour.setLabel(MessageManager
3520             .getString("label.colourScheme_strand_propensity"));
3521     strandColour.addActionListener(this);
3522     turnColour.setLabel(
3523             MessageManager.getString("label.colourScheme_turn_propensity"));
3524     turnColour.addActionListener(this);
3525     buriedColour.setLabel(
3526             MessageManager.getString("label.colourScheme_buried_index"));
3527     buriedColour.addActionListener(this);
3528     purinePyrimidineColour.setLabel(MessageManager
3529             .getString("label.colourScheme_purine/pyrimidine"));
3530     purinePyrimidineColour.addActionListener(this);
3531     // RNAInteractionColour.setLabel(MessageManager
3532     // .getString("label.rna_interaction"));
3533     // RNAInteractionColour.addActionListener(this);
3534     RNAHelixColour.setLabel(
3535             MessageManager.getString("label.colourScheme_rna_helices"));
3536     RNAHelixColour.addActionListener(this);
3537     userDefinedColour
3538             .setLabel(MessageManager.getString("action.user_defined"));
3539     userDefinedColour.addActionListener(this);
3540     PIDColour.setLabel(
3541             MessageManager.getString("label.colourScheme_%_identity"));
3542     PIDColour.addActionListener(this);
3543     BLOSUM62Colour.setLabel(
3544             MessageManager.getString("label.colourScheme_blosum62"));
3545     BLOSUM62Colour.addActionListener(this);
3546     tcoffeeColour.setLabel(
3547             MessageManager.getString("label.colourScheme_t-coffee_scores"));
3548     // it will be enabled only if a score file is provided
3549     tcoffeeColour.setEnabled(false);
3550     tcoffeeColour.addActionListener(this);
3551     conservationMenuItem
3552             .setLabel(MessageManager.getString("action.by_conservation"));
3553     conservationMenuItem.addItemListener(this);
3554     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3555     noColourmenuItem.addActionListener(this);
3556     abovePIDThreshold.setLabel(
3557             MessageManager.getString("label.above_identity_threshold"));
3558     abovePIDThreshold.addItemListener(this);
3559     nucleotideColour.setLabel(
3560             MessageManager.getString("label.colourScheme_nucleotide"));
3561     nucleotideColour.addActionListener(this);
3562     modifyPID.setLabel(
3563             MessageManager.getString("label.modify_identity_threshold"));
3564     modifyPID.setEnabled(abovePIDThreshold.getState());
3565     modifyPID.addActionListener(this);
3566     modifyConservation.setLabel(MessageManager
3567             .getString("label.modify_conservation_threshold"));
3568     modifyConservation.setEnabled(conservationMenuItem.getState());
3569     modifyConservation.addActionListener(this);
3570     annotationColour
3571             .setLabel(MessageManager.getString("action.by_annotation"));
3572     annotationColour.addActionListener(this);
3573
3574     /*
3575      * Configure Calculate menu items and actions
3576      */
3577     sortPairwiseMenuItem
3578             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3579     sortPairwiseMenuItem.addActionListener(this);
3580     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3581     sortIDMenuItem.addActionListener(this);
3582     sortLengthMenuItem
3583             .setLabel(MessageManager.getString("action.by_length"));
3584     sortLengthMenuItem.addActionListener(this);
3585     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3586     sortGroupMenuItem.addActionListener(this);
3587     pairwiseAlignmentMenuItem.setLabel(
3588             MessageManager.getString("action.pairwise_alignment"));
3589     pairwiseAlignmentMenuItem.addActionListener(this);
3590     PCAMenuItem.setLabel(
3591             MessageManager.getString("label.principal_component_analysis"));
3592     PCAMenuItem.addActionListener(this);
3593     autoCalculate = new CheckboxMenuItem(
3594             MessageManager.getString("label.autocalculate_consensus"),
3595             true);
3596     averageDistanceTreeMenuItem.setLabel(
3597             MessageManager.getString("label.average_distance_identity"));
3598     averageDistanceTreeMenuItem.addActionListener(this);
3599     neighbourTreeMenuItem.setLabel(
3600             MessageManager.getString("label.neighbour_joining_identity"));
3601     neighbourTreeMenuItem.addActionListener(this);
3602     avDistanceTreeBlosumMenuItem.setLabel(
3603             MessageManager.getString("label.average_distance_blosum62"));
3604     avDistanceTreeBlosumMenuItem.addActionListener(this);
3605     njTreeBlosumMenuItem
3606             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3607     njTreeBlosumMenuItem.addActionListener(this);
3608     sortByTreeMenu
3609             .setLabel(MessageManager.getString("action.by_tree_order"));
3610     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3611     Menu calculateTreeMenu = new Menu(
3612             MessageManager.getString("action.calculate_tree"));
3613     autoCalculate.addItemListener(this);
3614     sortByTree.addItemListener(this);
3615
3616     /*
3617      * Configure Help menu items and actions
3618      */
3619     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3620     documentation.setLabel(MessageManager.getString("label.documentation"));
3621     documentation.addActionListener(this);
3622     about.setLabel(MessageManager.getString("label.about"));
3623     about.addActionListener(this);
3624
3625     /*
3626      * Add top level menus to frame
3627      */
3628     alignFrameMenuBar.add(fileMenu);
3629     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3630     alignFrameMenuBar.add(editMenu);
3631     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3632     alignFrameMenuBar.add(selectMenu);
3633     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3634     alignFrameMenuBar.add(viewMenu);
3635     Menu annotationsMenu = new Menu(
3636             MessageManager.getString("action.annotations"));
3637     alignFrameMenuBar.add(annotationsMenu);
3638     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3639     alignFrameMenuBar.add(formatMenu);
3640     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3641     alignFrameMenuBar.add(colourMenu);
3642     Menu calculateMenu = new Menu(
3643             MessageManager.getString("action.calculate"));
3644     alignFrameMenuBar.add(calculateMenu);
3645     alignFrameMenuBar.add(helpMenu);
3646
3647     /*
3648      * File menu
3649      */
3650     fileMenu.add(inputText);
3651     fileMenu.add(loadTree);
3652     fileMenu.add(loadAnnotations);
3653     fileMenu.addSeparator();
3654     fileMenu.add(outputTextboxMenu);
3655     fileMenu.add(outputFeatures);
3656     fileMenu.add(outputAnnotations);
3657     if (jalviewServletURL != null)
3658     {
3659       fileMenu.add(loadApplication);
3660     }
3661     fileMenu.addSeparator();
3662     fileMenu.add(closeMenuItem);
3663
3664     /*
3665      * Edit menu
3666      */
3667     editMenu.add(undoMenuItem);
3668     editMenu.add(redoMenuItem);
3669     editMenu.add(cut);
3670     editMenu.add(copy);
3671     pasteMenu.add(pasteNew);
3672     pasteMenu.add(pasteThis);
3673     editMenu.add(pasteMenu);
3674     editMenu.add(delete);
3675     editMenu.addSeparator();
3676     editMenu.add(remove2LeftMenuItem);
3677     editMenu.add(remove2RightMenuItem);
3678     editMenu.add(removeGappedColumnMenuItem);
3679     editMenu.add(removeAllGapsMenuItem);
3680     editMenu.add(removeRedundancyMenuItem);
3681
3682     /*
3683      * Select menu
3684      */
3685     selectMenu.add(findMenuItem);
3686     selectMenu.addSeparator();
3687     selectMenu.add(selectAllSequenceMenuItem);
3688     selectMenu.add(deselectAllSequenceMenuItem);
3689     selectMenu.add(invertSequenceMenuItem);
3690     selectMenu.add(invertColSel);
3691     selectMenu.add(createGroup);
3692     selectMenu.add(unGroup);
3693     selectMenu.add(grpsFromSelection);
3694     selectMenu.add(deleteGroups);
3695     selectMenu.add(annotationColumnSelection);
3696
3697     /*
3698      * View menu
3699      */
3700     viewMenu.add(newView);
3701     viewMenu.addSeparator();
3702     showMenu.add(showColumns);
3703     showMenu.add(showSeqs);
3704     showMenu.add(showAllHidden);
3705     viewMenu.add(showMenu);
3706     hideMenu.add(hideColumns);
3707     hideMenu.add(hideSequences);
3708     hideMenu.add(hideAllSelection);
3709     hideMenu.add(hideAllButSelection);
3710     viewMenu.add(hideMenu);
3711     viewMenu.addSeparator();
3712     viewMenu.add(followMouseOverFlag);
3713     viewMenu.addSeparator();
3714     viewMenu.add(sequenceFeatures);
3715     viewMenu.add(featureSettings);
3716     viewMenu.addSeparator();
3717     viewMenu.add(alProperties);
3718     viewMenu.addSeparator();
3719     viewMenu.add(overviewMenuItem);
3720
3721     /*
3722      * Annotations menu
3723      */
3724     annotationsMenu.add(annotationPanelMenuItem);
3725     annotationsMenu.addSeparator();
3726     annotationsMenu.add(showAlignmentAnnotations);
3727     annotationsMenu.add(showSequenceAnnotations);
3728     annotationsMenu.add(sortAnnBySequence);
3729     annotationsMenu.add(sortAnnByLabel);
3730     annotationsMenu.addSeparator();
3731     autoAnnMenu.add(showAutoFirst);
3732     autoAnnMenu.add(showAutoLast);
3733     autoAnnMenu.addSeparator();
3734     autoAnnMenu.add(applyAutoAnnotationSettings);
3735     autoAnnMenu.add(showConsensusHistogram);
3736     autoAnnMenu.add(showSequenceLogo);
3737     autoAnnMenu.add(normSequenceLogo);
3738     autoAnnMenu.addSeparator();
3739     autoAnnMenu.add(showGroupConservation);
3740     autoAnnMenu.add(showGroupConsensus);
3741     annotationsMenu.add(autoAnnMenu);
3742
3743     /*
3744      * Format menu
3745      */
3746     formatMenu.add(font);
3747     formatMenu.add(seqLimits);
3748     formatMenu.add(wrapMenuItem);
3749     formatMenu.add(scaleAbove);
3750     formatMenu.add(scaleLeft);
3751     formatMenu.add(scaleRight);
3752     formatMenu.add(viewBoxesMenuItem);
3753     formatMenu.add(viewTextMenuItem);
3754     formatMenu.add(colourTextMenuItem);
3755     formatMenu.add(displayNonconservedMenuItem);
3756     formatMenu.add(renderGapsMenuItem);
3757     formatMenu.add(centreColumnLabelFlag);
3758
3759     /*
3760      * Colour menu
3761      */
3762     colourMenu.add(applyToAllGroups);
3763     colourMenu.addSeparator();
3764     colourMenu.add(noColourmenuItem);
3765     colourMenu.add(clustalColour);
3766     colourMenu.add(BLOSUM62Colour);
3767     colourMenu.add(PIDColour);
3768     colourMenu.add(zappoColour);
3769     colourMenu.add(taylorColour);
3770     colourMenu.add(hydrophobicityColour);
3771     colourMenu.add(helixColour);
3772     colourMenu.add(strandColour);
3773     colourMenu.add(turnColour);
3774     colourMenu.add(buriedColour);
3775     colourMenu.add(nucleotideColour);
3776     colourMenu.add(purinePyrimidineColour);
3777     // colourMenu.add(RNAInteractionColour);
3778     colourMenu.add(tcoffeeColour);
3779     colourMenu.add(userDefinedColour);
3780     colourMenu.addSeparator();
3781     colourMenu.add(conservationMenuItem);
3782     colourMenu.add(modifyConservation);
3783     colourMenu.add(abovePIDThreshold);
3784     colourMenu.add(modifyPID);
3785     colourMenu.add(annotationColour);
3786     colourMenu.add(RNAHelixColour);
3787
3788     /*
3789      * Calculate menu
3790      */
3791     sortMenu.add(sortIDMenuItem);
3792     sortMenu.add(sortLengthMenuItem);
3793     sortMenu.add(sortByTreeMenu);
3794     sortMenu.add(sortGroupMenuItem);
3795     sortMenu.add(sortPairwiseMenuItem);
3796     calculateMenu.add(sortMenu);
3797     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3798     calculateTreeMenu.add(neighbourTreeMenuItem);
3799     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3800     calculateTreeMenu.add(njTreeBlosumMenuItem);
3801     calculateMenu.add(calculateTreeMenu);
3802     calculateMenu.addSeparator();
3803     calculateMenu.add(pairwiseAlignmentMenuItem);
3804     calculateMenu.add(PCAMenuItem);
3805     calculateMenu.add(autoCalculate);
3806     calculateMenu.add(sortByTree);
3807
3808     /*
3809      * Help menu
3810      */
3811     helpMenu.add(documentation);
3812     helpMenu.add(about);
3813
3814     /*
3815      * Status bar
3816      */
3817     statusBar.setBackground(Color.white);
3818     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3819     statusBar.setText(MessageManager.getString("label.status_bar"));
3820     this.add(statusBar, BorderLayout.SOUTH);
3821   }
3822
3823   @Override
3824   public void setStatus(String string)
3825   {
3826     statusBar.setText(string);
3827   };
3828
3829   MenuItem featureSettings = new MenuItem();
3830
3831   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3832
3833   MenuItem annotationColour = new MenuItem();
3834
3835   MenuItem annotationColumnSelection = new MenuItem();
3836
3837   MenuItem invertColSel = new MenuItem();
3838
3839   MenuItem showColumns = new MenuItem();
3840
3841   MenuItem showSeqs = new MenuItem();
3842
3843   MenuItem hideColumns = new MenuItem();
3844
3845   MenuItem hideSequences = new MenuItem();
3846
3847   MenuItem hideAllButSelection = new MenuItem();
3848
3849   MenuItem hideAllSelection = new MenuItem();
3850
3851   MenuItem showAllHidden = new MenuItem();
3852
3853   MenuItem newView = new MenuItem();
3854
3855   private CheckboxMenuItem showAlignmentAnnotations;
3856
3857   private CheckboxMenuItem showSequenceAnnotations;
3858
3859   private CheckboxMenuItem sortAnnBySequence;
3860
3861   private CheckboxMenuItem sortAnnByLabel;
3862
3863   private CheckboxMenuItem showAutoFirst;
3864
3865   private CheckboxMenuItem showAutoLast;
3866
3867   private SplitFrame splitFrame;
3868
3869   /**
3870    * Attach the alignFrame panels after embedding menus, if necessary. This used
3871    * to be called setEmbedded, but is now creates the dropdown menus in a
3872    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3873    *
3874    * @param reallyEmbedded
3875    *          true to attach the view to the applet area on the page rather than
3876    *          in a new window
3877    */
3878   public void createAlignFrameWindow(boolean reallyEmbedded)
3879   {
3880     if (reallyEmbedded)
3881     {
3882       embedAlignFrameInApplet(viewport.applet);
3883     }
3884     else
3885     {
3886       // //////
3887       // test and embed menu bar if necessary.
3888       //
3889       if (embedMenuIfNeeded(alignPanel))
3890       {
3891         /*
3892          * adjust for status bar height too. ? pointless as overridden by layout
3893          * manager
3894          */
3895         alignPanel.setSize(getSize().width,
3896                 getSize().height - statusBar.getHeight());
3897       }
3898       add(statusBar, BorderLayout.SOUTH);
3899       add(alignPanel, BorderLayout.CENTER);
3900       // and register with the applet so it can pass external API calls to us
3901       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3902               frameHeight);
3903     }
3904   }
3905
3906   /**
3907    * Add the components of this AlignFrame to the applet container.
3908    *
3909    * @param theApplet
3910    */
3911   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3912   {
3913     // ////
3914     // Explicitly build the embedded menu panel for the on-page applet
3915     //
3916     // view cannot be closed if its actually on the page
3917     fileMenu.remove(closeMenuItem);
3918     fileMenu.remove(3); // Remove Separator
3919     // construct embedded menu, using default font
3920     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3921     // and actually add the components to the applet area
3922     theApplet.setLayout(new BorderLayout());
3923     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3924     theApplet.add(statusBar, BorderLayout.SOUTH);
3925     // TODO should size be left to the layout manager?
3926     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3927             - embeddedMenu.getHeight() - statusBar.getHeight());
3928     theApplet.add(alignPanel, BorderLayout.CENTER);
3929     final AlignFrame me = this;
3930     theApplet.addFocusListener(new FocusListener()
3931     {
3932
3933       @Override
3934       public void focusLost(FocusEvent e)
3935       {
3936         if (theApplet.currentAlignFrame == me)
3937         {
3938           theApplet.currentAlignFrame = null;
3939         }
3940       }
3941
3942       @Override
3943       public void focusGained(FocusEvent e)
3944       {
3945         theApplet.currentAlignFrame = me;
3946       }
3947     });
3948     theApplet.validate();
3949   }
3950
3951   /**
3952    * create a new binding between structures in an existing jmol viewer instance
3953    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3954    * this does not open a new Jmol window, or modify the display of the
3955    * structures in the original jmol window. Note This method doesn't work
3956    * without an additional javascript library to exchange messages between the
3957    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3958    *
3959    * @param viewer
3960    *          JmolViewer instance
3961    * @param sequenceIds
3962    *          - sequence Ids to search for associations
3963    */
3964   public SequenceStructureBinding addStructureViewInstance(
3965           Object jmolviewer, String[] sequenceIds)
3966   {
3967     Viewer viewer = null;
3968     try
3969     {
3970       viewer = (Viewer) jmolviewer;
3971     } catch (ClassCastException ex)
3972     {
3973       System.err.println(
3974               "Unsupported viewer object :" + jmolviewer.getClass());
3975     }
3976     if (viewer == null)
3977     {
3978       System.err.println("Can't use this object as a structure viewer:"
3979               + jmolviewer.getClass());
3980       return null;
3981     }
3982     SequenceI[] seqs = null;
3983     if (sequenceIds == null || sequenceIds.length == 0)
3984     {
3985       seqs = viewport.getAlignment().getSequencesArray();
3986     }
3987     else
3988     {
3989       Vector sqi = new Vector();
3990       AlignmentI al = viewport.getAlignment();
3991       for (int sid = 0; sid < sequenceIds.length; sid++)
3992       {
3993         SequenceI sq = al.findName(sequenceIds[sid]);
3994         if (sq != null)
3995         {
3996           sqi.addElement(sq);
3997         }
3998       }
3999       if (sqi.size() > 0)
4000       {
4001         seqs = new SequenceI[sqi.size()];
4002         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4003         {
4004           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4005         }
4006       }
4007       else
4008       {
4009         return null;
4010       }
4011     }
4012     AAStructureBindingModel jmv = null;
4013     // TODO: search for a jmv that involves viewer
4014     if (jmv == null)
4015     { // create a new viewer/jalview binding.
4016       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4017     }
4018     return jmv;
4019
4020   }
4021
4022   /**
4023    * bind a pdb file to a sequence in the current view
4024    *
4025    * @param sequenceId
4026    *          - sequenceId within the dataset.
4027    * @param pdbEntryString
4028    *          - the short name for the PDB file
4029    * @param pdbFile
4030    *          - pdb file - either a URL or a valid PDB file.
4031    * @return true if binding was as success TODO: consider making an exception
4032    *         structure for indicating when PDB parsing or sequenceId location
4033    *         fails.
4034    */
4035   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4036           String pdbFile)
4037   {
4038     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4039     boolean needtoadd = false;
4040     if (toaddpdb != null)
4041     {
4042       Vector pdbe = toaddpdb.getAllPDBEntries();
4043       PDBEntry pdbentry = null;
4044       if (pdbe != null && pdbe.size() > 0)
4045       {
4046         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4047         {
4048           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4049           if (!pdbentry.getId().equals(pdbEntryString)
4050                   && !pdbentry.getFile().equals(pdbFile))
4051           {
4052             pdbentry = null;
4053           }
4054           else
4055           {
4056             continue;
4057           }
4058         }
4059       }
4060       if (pdbentry == null)
4061       {
4062         pdbentry = new PDBEntry();
4063         pdbentry.setId(pdbEntryString);
4064         pdbentry.setFile(pdbFile);
4065         needtoadd = true; // add this new entry to sequence.
4066       }
4067       // resolve data source
4068       // TODO: this code should be a refactored to an io package
4069       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4070               FileFormat.PDB);
4071       if (protocol == null)
4072       {
4073         return false;
4074       }
4075       if (needtoadd)
4076       {
4077         pdbentry.setProperty("protocol", protocol);
4078         toaddpdb.addPDBId(pdbentry);
4079         alignPanel.getStructureSelectionManager()
4080                 .registerPDBEntry(pdbentry);
4081       }
4082     }
4083     return true;
4084   }
4085
4086   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4087   {
4088     if (seqs != null)
4089     {
4090       Vector sequences = new Vector();
4091       for (int i = 0; i < seqs.length; i++)
4092       {
4093         if (seqs[i] != null)
4094         {
4095           sequences
4096                   .addElement(new Object[]
4097                   { seqs[i], (chains != null) ? chains[i] : null });
4098         }
4099       }
4100       seqs = new SequenceI[sequences.size()];
4101       chains = new String[sequences.size()];
4102       for (int i = 0, isize = sequences.size(); i < isize; i++)
4103       {
4104         Object[] oj = (Object[]) sequences.elementAt(i);
4105
4106         seqs[i] = (SequenceI) oj[0];
4107         chains[i] = (String) oj[1];
4108       }
4109     }
4110     return new Object[] { seqs, chains };
4111
4112   }
4113
4114   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4115           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4116   {
4117     // Scrub any null sequences from the array
4118     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4119     seqs = (SequenceI[]) sqch[0];
4120     chains = (String[]) sqch[1];
4121     if (seqs == null || seqs.length == 0)
4122     {
4123       System.err.println(
4124               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4125     }
4126     if (protocol == null)
4127     {
4128       String sourceType = (String) pdb.getProperty("protocol");
4129       try
4130       {
4131         protocol = DataSourceType.valueOf(sourceType);
4132       } catch (IllegalArgumentException e)
4133       {
4134         // ignore
4135       }
4136       if (protocol == null)
4137       {
4138         System.err.println("Couldn't work out protocol to open structure: "
4139                 + pdb.getId());
4140         return;
4141       }
4142     }
4143     if (applet.useXtrnalSviewer)
4144     {
4145       // register the association(s) and quit, don't create any windows.
4146       if (StructureSelectionManager.getStructureSelectionManager(applet)
4147               .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4148       {
4149         System.err.println("Failed to map " + pdb.getFile() + " ("
4150                 + protocol + ") to any sequences");
4151       }
4152       return;
4153     }
4154     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4155     {
4156       // can only do alignments with Jmol
4157       // find the last jmol window assigned to this alignment
4158       AppletJmol ajm = null, tajm;
4159       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4160       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4161       {
4162         tajm = (AppletJmol) jmols.elementAt(i);
4163         if (tajm.ap.alignFrame == this)
4164         {
4165           ajm = tajm;
4166           break;
4167         }
4168       }
4169       if (ajm != null)
4170       {
4171         System.err.println(
4172                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4173         // try and add the pdb structure
4174         // ajm.addS
4175         ajm = null;
4176       }
4177     }
4178     // otherwise, create a new window
4179     if (applet.jmolAvailable)
4180     {
4181       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4182       applet.lastFrameX += 40;
4183       applet.lastFrameY += 40;
4184     }
4185     else
4186     {
4187       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4188     }
4189
4190   }
4191
4192   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4193           SequenceI[][] seqs, String[][] chains, String[] protocols)
4194   {
4195     // TODO Auto-generated method stub
4196     System.err.println("Aligned Structure View: Not yet implemented.");
4197   }
4198
4199   /**
4200    * modify the current selection, providing the user has not made a selection
4201    * already.
4202    *
4203    * @param sel
4204    *          - sequences from this alignment
4205    * @param csel
4206    *          - columns to be selected on the alignment
4207    */
4208   public void select(SequenceGroup sel, ColumnSelection csel,
4209           HiddenColumns hidden)
4210   {
4211     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4212   }
4213
4214   public void scrollTo(int row, int column)
4215   {
4216     alignPanel.seqPanel.scrollTo(row, column);
4217   }
4218
4219   public void scrollToRow(int row)
4220   {
4221     alignPanel.seqPanel.scrollToRow(row);
4222   }
4223
4224   public void scrollToColumn(int column)
4225   {
4226     alignPanel.seqPanel.scrollToColumn(column);
4227   }
4228
4229   /**
4230    * @return the alignments unique ID.
4231    */
4232   public String getSequenceSetId()
4233   {
4234     return viewport.getSequenceSetId();
4235   }
4236
4237   /**
4238    * Load the (T-Coffee) score file from the specified url
4239    *
4240    * @param source
4241    *          File/URL/T-COFFEE score file contents
4242    * @throws IOException
4243    * @return true if alignment was annotated with data from source
4244    */
4245   public boolean loadScoreFile(String source) throws IOException
4246   {
4247
4248     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4249             AppletFormatAdapter.checkProtocol(source));
4250     if (!file.isValid())
4251     {
4252       // TODO: raise dialog for gui
4253       System.err.println("Problems parsing T-Coffee scores: "
4254               + file.getWarningMessage());
4255       System.err.println("Origin was:\n" + source);
4256       return false;
4257     }
4258
4259     /*
4260      * check that the score matrix matches the alignment dimensions
4261      */
4262     AlignmentI aln;
4263     if ((aln = viewport.getAlignment()) != null
4264             && (aln.getHeight() != file.getHeight()
4265                     || aln.getWidth() != file.getWidth()))
4266     {
4267       // TODO: raise a dialog box here rather than bomb out.
4268       System.err.println(
4269               "The scores matrix does not match the alignment dimensions");
4270
4271     }
4272
4273     // TODO add parameter to indicate if matching should be done
4274     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4275     {
4276       alignPanel.fontChanged();
4277       tcoffeeColour.setEnabled(true);
4278       // switch to this color
4279       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4280       return true;
4281     }
4282     else
4283     {
4284       System.err.println("Problems resolving T-Coffee scores:");
4285       if (file.getWarningMessage() != null)
4286       {
4287         System.err.println(file.getWarningMessage());
4288       }
4289     }
4290     return false;
4291   }
4292
4293   public SplitFrame getSplitFrame()
4294   {
4295     return this.splitFrame;
4296   }
4297
4298   public void setSplitFrame(SplitFrame sf)
4299   {
4300     this.splitFrame = sf;
4301   }
4302
4303   // may not need this
4304   @Override
4305   public void setShowSeqFeatures(boolean b)
4306   {
4307     // showSeqFeatures.setSelected(b);
4308     viewport.setShowSequenceFeatures(b);
4309
4310   }
4311
4312   @Override
4313   public void setMenusForViewport()
4314   {
4315     // setMenusFromViewport(viewport);
4316
4317   }
4318
4319   @Override
4320   public void refreshFeatureUI(boolean enableIfNecessary)
4321   {
4322     if (enableIfNecessary)
4323     {
4324       sequenceFeatures.setState(true);
4325       alignPanel.av.setShowSequenceFeatures(true);
4326     }
4327   }
4328
4329   @Override
4330   public FeatureSettingsControllerI getFeatureSettingsUI()
4331   {
4332     return alignPanel.av.featureSettings;
4333   }
4334
4335 }