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