src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.FileFormatI;
  56 import jalview.io.FileFormats;
  57 import jalview.io.TCoffeeScoreFile;
  58 import jalview.schemes.Blosum62ColourScheme;
  59 import jalview.schemes.BuriedColourScheme;
  60 import jalview.schemes.ClustalxColourScheme;
  61 import jalview.schemes.ColourSchemeI;
  62 import jalview.schemes.HelixColourScheme;
  63 import jalview.schemes.HydrophobicColourScheme;
  64 import jalview.schemes.NucleotideColourScheme;
  65 import jalview.schemes.PIDColourScheme;
  66 import jalview.schemes.PurinePyrimidineColourScheme;
  67 import jalview.schemes.RNAHelicesColour;
  68 import jalview.schemes.StrandColourScheme;
  69 import jalview.schemes.TCoffeeColourScheme;
  70 import jalview.schemes.TaylorColourScheme;
  71 import jalview.schemes.TurnColourScheme;
  72 import jalview.schemes.ZappoColourScheme;
  73 import jalview.structure.StructureSelectionManager;
  74 import jalview.structures.models.AAStructureBindingModel;
  75 import jalview.util.MappingUtils;
  76 import jalview.util.MessageManager;
  77 import jalview.viewmodel.AlignmentViewport;
  78
  79 import java.awt.BorderLayout;
  80 import java.awt.Canvas;
  81 import java.awt.CheckboxMenuItem;
  82 import java.awt.Color;
  83 import java.awt.FlowLayout;
  84 import java.awt.Font;
  85 import java.awt.FontMetrics;
  86 import java.awt.Frame;
  87 import java.awt.Graphics;
  88 import java.awt.Label;
  89 import java.awt.Menu;
  90 import java.awt.MenuBar;
  91 import java.awt.MenuItem;
  92 import java.awt.MenuShortcut;
  93 import java.awt.Panel;
  94 import java.awt.event.ActionEvent;
  95 import java.awt.event.ActionListener;
  96 import java.awt.event.FocusEvent;
  97 import java.awt.event.FocusListener;
  98 import java.awt.event.ItemEvent;
  99 import java.awt.event.ItemListener;
 100 import java.awt.event.KeyEvent;
 101 import java.awt.event.KeyListener;
 102 import java.awt.event.WindowAdapter;
 103 import java.awt.event.WindowEvent;
 104 import java.io.IOException;
 105 import java.net.URL;
 106 import java.net.URLEncoder;
 107 import java.util.Arrays;
 108 import java.util.Deque;
 109 import java.util.HashMap;
 110 import java.util.List;
 111 import java.util.Map;
 112 import java.util.StringTokenizer;
 113 import java.util.Vector;
 114
 115 import org.jmol.viewer.Viewer;
 116
 117 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 118         ItemListener, KeyListener, AlignViewControllerGuiI
 119 {
 120   public AlignViewControllerI avc;
 121
 122   public AlignmentPanel alignPanel;
 123
 124   public AlignViewport viewport;
 125
 126   // width and height may be overridden by applet parameters
 127   int frameWidth = 700;
 128
 129   int frameHeight = 500;
 130
 131   String jalviewServletURL;
 132
 133   /*
 134    * Flag for showing autocalculated consensus above or below other consensus
 135    * rows
 136    */
 137   private boolean showAutoCalculatedAbove;
 138
 139   private SequenceAnnotationOrder annotationSortOrder;
 140
 141   /**
 142    * Constructor that creates the frame and adds it to the display.
 143    *
 144    * @param al
 145    * @param applet
 146    * @param title
 147    * @param embedded
 148    */
 149   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 150           boolean embedded)
 151   {
 152     this(al, applet, title, embedded, true);
 153   }
 154
 155   /**
 156    * Constructor that optionally allows the frame to be displayed or only
 157    * created.
 158    *
 159    * @param al
 160    * @param applet
 161    * @param title
 162    * @param embedded
 163    * @param addToDisplay
 164    */
 165   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 166           boolean embedded, boolean addToDisplay)
 167   {
 168     this(al, null, null, applet, title, embedded, addToDisplay);
 169   }
 170
 171   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 172           ColumnSelection columnSelection, JalviewLite applet,
 173           String title, boolean embedded)
 174   {
 175     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 176   }
 177
 178   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 179           ColumnSelection columnSelection, JalviewLite applet,
 180           String title, boolean embedded, boolean addToDisplay)
 181   {
 182     if (applet != null)
 183     {
 184       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 185     }
 186
 187     try
 188     {
 189       jbInit();
 190     } catch (Exception ex)
 191     {
 192       ex.printStackTrace();
 193     }
 194     // need to get window geometry before we calculate alignment layout
 195     if (applet != null)
 196     {
 197       String param;
 198       try
 199       {
 200         param = applet.getParameter("windowWidth");
 201         if (param != null)
 202         {
 203           int width = Integer.parseInt(param);
 204           frameWidth = width;
 205         }
 206         param = applet.getParameter("windowHeight");
 207         if (param != null)
 208         {
 209           int height = Integer.parseInt(param);
 210           frameHeight = height;
 211         }
 212       } catch (Exception ex)
 213       {
 214       }
 215     }
 216     viewport = new AlignViewport(al, applet);
 217
 218     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 219     {
 220       viewport.hideSequence(hiddenSeqs);
 221     }
 222     if (columnSelection != null)
 223     {
 224       viewport.setColumnSelection(columnSelection);
 225     }
 226     viewport.setScaleAboveWrapped(scaleAbove.getState());
 227
 228     alignPanel = new AlignmentPanel(this, viewport);
 229     avc = new jalview.controller.AlignViewController(this, viewport,
 230             alignPanel);
 231     viewport.updateConservation(alignPanel);
 232     viewport.updateConsensus(alignPanel);
 233
 234     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 235     followMouseOverFlag.setState(viewport.isFollowHighlight());
 236     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 237     showGroupConservation.setState(viewport.isShowGroupConservation());
 238     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 239     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 240     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 241     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 242     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 243     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 244     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 245     showAlignmentAnnotations.setState(true);
 246     showSequenceAnnotations.setState(false);
 247
 248     seqLimits.setState(viewport.getShowJVSuffix());
 249
 250     if (applet != null)
 251     {
 252       String param = applet.getParameter("sortBy");
 253       if (param != null)
 254       {
 255         if (param.equalsIgnoreCase("Id"))
 256         {
 257           sortIDMenuItem_actionPerformed();
 258         }
 259         else if (param.equalsIgnoreCase("Pairwise Identity"))
 260         {
 261           sortPairwiseMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Length"))
 264         {
 265           sortLengthMenuItem_actionPerformed();
 266         }
 267       }
 268
 269       param = applet.getParameter("wrap");
 270       if (param != null)
 271       {
 272         if (param.equalsIgnoreCase("true"))
 273         {
 274           wrapMenuItem.setState(true);
 275           wrapMenuItem_actionPerformed();
 276         }
 277       }
 278       param = applet.getParameter("centrecolumnlabels");
 279       if (param != null)
 280       {
 281         centreColumnLabelFlag.setState(true);
 282         centreColumnLabelFlag_stateChanged();
 283       }
 284
 285     }
 286     if (viewport.getAlignment().isNucleotide())
 287     {
 288       conservationMenuItem.setEnabled(false);
 289       clustalColour.setEnabled(false);
 290       BLOSUM62Colour.setEnabled(false);
 291       zappoColour.setEnabled(false);
 292       taylorColour.setEnabled(false);
 293       hydrophobicityColour.setEnabled(false);
 294       helixColour.setEnabled(false);
 295       strandColour.setEnabled(false);
 296       turnColour.setEnabled(false);
 297       buriedColour.setEnabled(false);
 298       viewport.updateStrucConsensus(alignPanel);
 299       if (viewport.getAlignment().hasRNAStructure())
 300       {
 301         RNAHelixColour.setEnabled(true);
 302       }
 303       else
 304       {
 305         RNAHelixColour.setEnabled(false);
 306       }
 307     }
 308     else
 309     {
 310       RNAHelixColour.setEnabled(false);
 311       purinePyrimidineColour.setEnabled(false);
 312       nucleotideColour.setEnabled(false);
 313     }
 314     // Some JVMS send keyevents to Top frame or lowest panel,
 315     // Havent worked out why yet. So add to both this frame and seqCanvas for
 316     // now
 317     this.addKeyListener(this);
 318     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 319     alignPanel.idPanel.idCanvas.addKeyListener(this);
 320     alignPanel.scalePanel.addKeyListener(this);
 321     alignPanel.annotationPanel.addKeyListener(this);
 322     alignPanel.annotationPanelHolder.addKeyListener(this);
 323     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 324     alignPanel.alabels.addKeyListener(this);
 325
 326     setAnnotationsVisibility();
 327
 328     if (addToDisplay)
 329     {
 330       addToDisplay(embedded);
 331     }
 332   }
 333
 334   /**
 335    * @param embedded
 336    */
 337   public void addToDisplay(boolean embedded)
 338   {
 339     createAlignFrameWindow(embedded);
 340     validate();
 341     alignPanel.adjustAnnotationHeight();
 342     alignPanel.paintAlignment(true);
 343   }
 344
 345   public AlignViewport getAlignViewport()
 346   {
 347     return viewport;
 348   }
 349
 350   public SeqCanvas getSeqcanvas()
 351   {
 352     return alignPanel.seqPanel.seqCanvas;
 353   }
 354
 355   /**
 356    * Load a features file onto the alignment
 357    *
 358    * @param file
 359    *          file URL, content, or other resolvable path
 360    * @param type
 361    *          is protocol for accessing data referred to by file
 362    */
 363
 364   public boolean parseFeaturesFile(String file, DataSourceType type)
 365   {
 366     return parseFeaturesFile(file, type, true);
 367   }
 368
 369   /**
 370    * Load a features file onto the alignment
 371    *
 372    * @param file
 373    *          file URL, content, or other resolvable path
 374    * @param sourceType
 375    *          is protocol for accessing data referred to by file
 376    * @param autoenabledisplay
 377    *          when true, display features flag will be automatically enabled if
 378    *          features are loaded
 379    * @return true if data parsed as a features file
 380    */
 381   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 382           boolean autoenabledisplay)
 383   {
 384     boolean featuresFile = false;
 385     try
 386     {
 387       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 388               .getFeatureRenderer().getFeatureColours();
 389       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 390               "relaxedidmatch", false);
 391       featuresFile = new FeaturesFile(file, sourceType).parse(
 392               viewport.getAlignment(), colours, true, relaxedIdMatching);
 393     } catch (Exception ex)
 394     {
 395       ex.printStackTrace();
 396     }
 397
 398     if (featuresFile)
 399     {
 400       if (autoenabledisplay)
 401       {
 402         viewport.setShowSequenceFeatures(true);
 403         sequenceFeatures.setState(true);
 404       }
 405       if (alignPanel.seqPanel.seqCanvas.fr != null)
 406       {
 407         // update the min/max ranges where necessary
 408         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 409       }
 410       if (viewport.featureSettings != null)
 411       {
 412         viewport.featureSettings.refreshTable();
 413       }
 414       alignPanel.paintAlignment(true);
 415       statusBar.setText(MessageManager
 416               .getString("label.successfully_added_features_alignment"));
 417     }
 418     return featuresFile;
 419   }
 420
 421   @Override
 422   public void keyPressed(KeyEvent evt)
 423   {
 424     if (viewport.cursorMode
 425             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 426                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 427                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 428             && Character.isDigit(evt.getKeyChar()))
 429     {
 430       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 431     }
 432
 433     switch (evt.getKeyCode())
 434     {
 435     case 27: // escape key
 436       deselectAllSequenceMenuItem_actionPerformed();
 437
 438       alignPanel.alabels.cancelDrag();
 439       break;
 440     case KeyEvent.VK_X:
 441       if (evt.isControlDown() || evt.isMetaDown())
 442       {
 443         cut_actionPerformed();
 444       }
 445       break;
 446     case KeyEvent.VK_C:
 447       if (viewport.cursorMode && !evt.isControlDown())
 448       {
 449         alignPanel.seqPanel.setCursorColumn();
 450       }
 451       if (evt.isControlDown() || evt.isMetaDown())
 452       {
 453         copy_actionPerformed();
 454       }
 455       break;
 456     case KeyEvent.VK_V:
 457       if (evt.isControlDown())
 458       {
 459         paste(evt.isShiftDown());
 460       }
 461       break;
 462     case KeyEvent.VK_A:
 463       if (evt.isControlDown() || evt.isMetaDown())
 464       {
 465         selectAllSequenceMenuItem_actionPerformed();
 466       }
 467       break;
 468     case KeyEvent.VK_DOWN:
 469       if (viewport.cursorMode)
 470       {
 471         alignPanel.seqPanel.moveCursor(0, 1);
 472       }
 473       else
 474       {
 475         moveSelectedSequences(false);
 476       }
 477       break;
 478
 479     case KeyEvent.VK_UP:
 480       if (viewport.cursorMode)
 481       {
 482         alignPanel.seqPanel.moveCursor(0, -1);
 483       }
 484       else
 485       {
 486         moveSelectedSequences(true);
 487       }
 488       break;
 489
 490     case KeyEvent.VK_LEFT:
 491       if (evt.isAltDown() || !viewport.cursorMode)
 492       {
 493         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 494       }
 495       else
 496       {
 497         alignPanel.seqPanel.moveCursor(-1, 0);
 498       }
 499       break;
 500
 501     case KeyEvent.VK_RIGHT:
 502       if (evt.isAltDown() || !viewport.cursorMode)
 503       {
 504         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 505       }
 506       else
 507       {
 508         alignPanel.seqPanel.moveCursor(1, 0);
 509       }
 510       break;
 511
 512     case KeyEvent.VK_SPACE:
 513       if (viewport.cursorMode)
 514       {
 515         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 516                 || evt.isShiftDown() || evt.isAltDown());
 517       }
 518       break;
 519
 520     case KeyEvent.VK_DELETE:
 521     case KeyEvent.VK_BACK_SPACE:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 525                 || evt.isShiftDown() || evt.isAltDown());
 526       }
 527       else
 528       {
 529         cut_actionPerformed();
 530         alignPanel.seqPanel.seqCanvas.repaint();
 531       }
 532       break;
 533
 534     case KeyEvent.VK_S:
 535       if (viewport.cursorMode)
 536       {
 537         alignPanel.seqPanel.setCursorRow();
 538       }
 539       break;
 540     case KeyEvent.VK_P:
 541       if (viewport.cursorMode)
 542       {
 543         alignPanel.seqPanel.setCursorPosition();
 544       }
 545       break;
 546
 547     case KeyEvent.VK_ENTER:
 548     case KeyEvent.VK_COMMA:
 549       if (viewport.cursorMode)
 550       {
 551         alignPanel.seqPanel.setCursorRowAndColumn();
 552       }
 553       break;
 554
 555     case KeyEvent.VK_Q:
 556       if (viewport.cursorMode)
 557       {
 558         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 559       }
 560       break;
 561     case KeyEvent.VK_M:
 562       if (viewport.cursorMode)
 563       {
 564         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 565       }
 566       break;
 567
 568     case KeyEvent.VK_F2:
 569       viewport.cursorMode = !viewport.cursorMode;
 570       statusBar.setText(MessageManager.formatMessage(
 571               "label.keyboard_editing_mode",
 572               new String[] { (viewport.cursorMode ? "on" : "off") }));
 573       if (viewport.cursorMode)
 574       {
 575         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 576         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 577       }
 578       break;
 579
 580     case KeyEvent.VK_F:
 581       if (evt.isControlDown())
 582       {
 583         findMenuItem_actionPerformed();
 584       }
 585       break;
 586
 587     case KeyEvent.VK_H:
 588     {
 589       boolean toggleSeqs = !evt.isControlDown();
 590       boolean toggleCols = !evt.isShiftDown();
 591       toggleHiddenRegions(toggleSeqs, toggleCols);
 592       break;
 593     }
 594
 595     case KeyEvent.VK_PAGE_UP:
 596       if (viewport.getWrapAlignment())
 597       {
 598         alignPanel.scrollUp(true);
 599       }
 600       else
 601       {
 602         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 603                 - viewport.endSeq + viewport.startSeq);
 604       }
 605       break;
 606
 607     case KeyEvent.VK_PAGE_DOWN:
 608       if (viewport.getWrapAlignment())
 609       {
 610         alignPanel.scrollUp(false);
 611       }
 612       else
 613       {
 614         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 615                 + viewport.endSeq - viewport.startSeq);
 616       }
 617       break;
 618
 619     case KeyEvent.VK_Z:
 620       if (evt.isControlDown())
 621       {
 622         undoMenuItem_actionPerformed();
 623       }
 624       break;
 625
 626     case KeyEvent.VK_Y:
 627       if (evt.isControlDown())
 628       {
 629         redoMenuItem_actionPerformed();
 630       }
 631       break;
 632
 633     case KeyEvent.VK_L:
 634       if (evt.isControlDown())
 635       {
 636         trimAlignment(true);
 637       }
 638       break;
 639
 640     case KeyEvent.VK_R:
 641       if (evt.isControlDown())
 642       {
 643         trimAlignment(false);
 644       }
 645       break;
 646
 647     case KeyEvent.VK_E:
 648       if (evt.isControlDown())
 649       {
 650         if (evt.isShiftDown())
 651         {
 652           this.removeAllGapsMenuItem_actionPerformed();
 653         }
 654         else
 655         {
 656           removeGappedColumnMenuItem_actionPerformed();
 657         }
 658       }
 659       break;
 660     case KeyEvent.VK_I:
 661       if (evt.isControlDown())
 662       {
 663         if (evt.isAltDown())
 664         {
 665           invertColSel_actionPerformed();
 666         }
 667         else
 668         {
 669           invertSequenceMenuItem_actionPerformed();
 670         }
 671       }
 672       break;
 673
 674     case KeyEvent.VK_G:
 675       if (evt.isControlDown())
 676       {
 677         if (evt.isShiftDown())
 678         {
 679           this.unGroup_actionPerformed();
 680         }
 681         else
 682         {
 683           this.createGroup_actionPerformed();
 684         }
 685       }
 686       break;
 687
 688     case KeyEvent.VK_U:
 689       if (evt.isControlDown())
 690       {
 691         this.deleteGroups_actionPerformed();
 692       }
 693       break;
 694
 695     case KeyEvent.VK_T:
 696       if (evt.isControlDown())
 697       {
 698         newView(null);
 699       }
 700       break;
 701
 702     }
 703     alignPanel.paintAlignment(true);
 704   }
 705
 706   /**
 707    * called by key handler and the hide all/show all menu items
 708    *
 709    * @param toggleSeqs
 710    * @param toggleCols
 711    */
 712   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 713   {
 714     boolean hide = false;
 715     SequenceGroup sg = viewport.getSelectionGroup();
 716     if (!toggleSeqs && !toggleCols)
 717     {
 718       // Hide everything by the current selection - this is a hack - we do the
 719       // invert and then hide
 720       // first check that there will be visible columns after the invert.
 721       if (viewport.hasSelectedColumns()
 722               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 723                       .getEndRes()))
 724       {
 725         // now invert the sequence set, if required - empty selection implies
 726         // that no hiding is required.
 727         if (sg != null)
 728         {
 729           invertSequenceMenuItem_actionPerformed();
 730           sg = viewport.getSelectionGroup();
 731           toggleSeqs = true;
 732
 733         }
 734         viewport.expandColSelection(sg, true);
 735         // finally invert the column selection and get the new sequence
 736         // selection and indicate it should be hidden.
 737         invertColSel_actionPerformed();
 738         toggleCols = true;
 739       }
 740     }
 741
 742     if (toggleSeqs)
 743     {
 744       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 745       {
 746         hide = true;
 747         viewport.hideAllSelectedSeqs();
 748       }
 749       else if (!(toggleCols && viewport.hasSelectedColumns()))
 750       {
 751         viewport.showAllHiddenSeqs();
 752       }
 753     }
 754
 755     if (toggleCols)
 756     {
 757       if (viewport.hasSelectedColumns())
 758       {
 759         viewport.hideSelectedColumns();
 760         if (!toggleSeqs)
 761         {
 762           viewport.setSelectionGroup(sg);
 763         }
 764       }
 765       else if (!hide)
 766       {
 767         viewport.showAllHiddenColumns();
 768       }
 769       viewport.sendSelection();
 770     }
 771   }
 772
 773   @Override
 774   public void keyReleased(KeyEvent evt)
 775   {
 776   }
 777
 778   @Override
 779   public void keyTyped(KeyEvent evt)
 780   {
 781   }
 782
 783   @Override
 784   public void itemStateChanged(ItemEvent evt)
 785   {
 786     final Object source = evt.getSource();
 787     if (source == displayNonconservedMenuItem)
 788     {
 789       displayNonconservedMenuItem_actionPerformed();
 790     }
 791     else if (source == colourTextMenuItem)
 792     {
 793       colourTextMenuItem_actionPerformed();
 794     }
 795     else if (source == wrapMenuItem)
 796     {
 797       wrapMenuItem_actionPerformed();
 798     }
 799     else if (source == scaleAbove)
 800     {
 801       viewport.setScaleAboveWrapped(scaleAbove.getState());
 802     }
 803     else if (source == scaleLeft)
 804     {
 805       viewport.setScaleLeftWrapped(scaleLeft.getState());
 806     }
 807     else if (source == scaleRight)
 808     {
 809       viewport.setScaleRightWrapped(scaleRight.getState());
 810     }
 811     else if (source == seqLimits)
 812     {
 813       seqLimits_itemStateChanged();
 814     }
 815     else if (source == viewBoxesMenuItem)
 816     {
 817       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 818     }
 819     else if (source == viewTextMenuItem)
 820     {
 821       viewport.setShowText(viewTextMenuItem.getState());
 822     }
 823     else if (source == renderGapsMenuItem)
 824     {
 825       viewport.setRenderGaps(renderGapsMenuItem.getState());
 826     }
 827     else if (source == annotationPanelMenuItem)
 828     {
 829       boolean showAnnotations = annotationPanelMenuItem.getState();
 830       showAlignmentAnnotations.setEnabled(showAnnotations);
 831       showSequenceAnnotations.setEnabled(showAnnotations);
 832       viewport.setShowAnnotation(showAnnotations);
 833       alignPanel.setAnnotationVisible(showAnnotations);
 834     }
 835     else if (source == sequenceFeatures)
 836     {
 837       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 838       alignPanel.seqPanel.seqCanvas.repaint();
 839     }
 840     else if (source == showAlignmentAnnotations)
 841     {
 842       setAnnotationsVisibility();
 843     }
 844     else if (source == showSequenceAnnotations)
 845     {
 846       setAnnotationsVisibility();
 847     }
 848     else if (source == sortAnnBySequence)
 849     {
 850       boolean newState = sortAnnBySequence.getState();
 851       sortAnnByLabel.setState(false);
 852       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 853               : SequenceAnnotationOrder.NONE);
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == sortAnnByLabel)
 857     {
 858       boolean newState = sortAnnByLabel.getState();
 859       sortAnnBySequence.setState(false);
 860       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 861               : SequenceAnnotationOrder.NONE);
 862       setViewportAnnotationOrder();
 863     }
 864     else if (source == showAutoFirst)
 865     {
 866       showAutoLast.setState(!showAutoFirst.getState());
 867       setShowAutoCalculatedAbove(showAutoFirst.getState());
 868       setViewportAnnotationOrder();
 869     }
 870     else if (source == showAutoLast)
 871     {
 872       showAutoFirst.setState(!showAutoLast.getState());
 873       setShowAutoCalculatedAbove(showAutoFirst.getState());
 874       setViewportAnnotationOrder();
 875     }
 876     else if (source == conservationMenuItem)
 877     {
 878       conservationMenuItem_actionPerformed();
 879     }
 880     else if (source == abovePIDThreshold)
 881     {
 882       abovePIDThreshold_actionPerformed();
 883     }
 884     else if (source == applyToAllGroups)
 885     {
 886       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 887     }
 888     else if (source == autoCalculate)
 889     {
 890       viewport.autoCalculateConsensus = autoCalculate.getState();
 891     }
 892     else if (source == sortByTree)
 893     {
 894       viewport.sortByTree = sortByTree.getState();
 895     }
 896     else if (source == this.centreColumnLabelFlag)
 897     {
 898       centreColumnLabelFlag_stateChanged();
 899     }
 900     else if (source == this.followMouseOverFlag)
 901     {
 902       mouseOverFlag_stateChanged();
 903     }
 904     else if (source == showGroupConsensus)
 905     {
 906       showGroupConsensus_actionPerformed();
 907     }
 908     else if (source == showGroupConservation)
 909     {
 910       showGroupConservation_actionPerformed();
 911     }
 912     else if (source == showSequenceLogo)
 913     {
 914       showSequenceLogo_actionPerformed();
 915     }
 916     else if (source == normSequenceLogo)
 917     {
 918       normSequenceLogo_actionPerformed();
 919     }
 920     else if (source == showConsensusHistogram)
 921     {
 922       showConsensusHistogram_actionPerformed();
 923     }
 924     else if (source == applyAutoAnnotationSettings)
 925     {
 926       applyAutoAnnotationSettings_actionPerformed();
 927     }
 928     alignPanel.paintAlignment(true);
 929   }
 930
 931   /**
 932    * Set the visibility state of sequence-related and/or alignment-related
 933    * annotations depending on checkbox selections, and repaint.
 934    *
 935    * @param visible
 936    */
 937   private void setAnnotationsVisibility()
 938   {
 939     boolean showForAlignment = showAlignmentAnnotations.getState();
 940     boolean showForSequences = showSequenceAnnotations.getState();
 941     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 942     {
 943       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 944               .getAlignmentAnnotation())
 945       {
 946         boolean visible = (aa.sequenceRef == null ? showForAlignment
 947                 : showForSequences);
 948         aa.visible = visible;
 949       }
 950     }
 951     alignPanel.validateAnnotationDimensions(true);
 952     validate();
 953     repaint();
 954   }
 955
 956   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 957   {
 958     this.annotationSortOrder = order;
 959   }
 960
 961   /**
 962    * Set flags on the viewport that control annotation ordering
 963    */
 964   private void setViewportAnnotationOrder()
 965   {
 966     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 967     this.alignPanel.av
 968             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 969   }
 970
 971   private void setShowAutoCalculatedAbove(boolean showAbove)
 972   {
 973     this.showAutoCalculatedAbove = showAbove;
 974   }
 975
 976   private void mouseOverFlag_stateChanged()
 977   {
 978     viewport.setFollowHighlight(followMouseOverFlag.getState());
 979     // TODO: could kick the scrollTo mechanism to reset view for current
 980     // searchresults.
 981   }
 982
 983   private void centreColumnLabelFlag_stateChanged()
 984   {
 985     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 986     this.alignPanel.annotationPanel.repaint();
 987   }
 988
 989   @Override
 990   public void actionPerformed(ActionEvent evt)
 991   {
 992     viewport.applet.currentAlignFrame = this;
 993
 994     Object source = evt.getSource();
 995
 996     if (source == inputText)
 997     {
 998       inputText_actionPerformed();
 999     }
1000     else if (source == loadTree)
1001     {
1002       loadTree_actionPerformed();
1003     }
1004     else if (source == loadApplication)
1005     {
1006       launchFullApplication();
1007     }
1008     else if (source == loadAnnotations)
1009     {
1010       loadAnnotations();
1011     }
1012     else if (source == outputAnnotations)
1013     {
1014       outputAnnotations(true);
1015     }
1016     else if (source == outputFeatures)
1017     {
1018       outputFeatures(true, "Jalview");
1019     }
1020     else if (source == closeMenuItem)
1021     {
1022       closeMenuItem_actionPerformed();
1023     }
1024     else if (source == copy)
1025     {
1026       copy_actionPerformed();
1027     }
1028     else if (source == undoMenuItem)
1029     {
1030       undoMenuItem_actionPerformed();
1031     }
1032     else if (source == redoMenuItem)
1033     {
1034       redoMenuItem_actionPerformed();
1035     }
1036     else if (source == inputText)
1037     {
1038       inputText_actionPerformed();
1039     }
1040     else if (source == closeMenuItem)
1041     {
1042       closeMenuItem_actionPerformed();
1043     }
1044     else if (source == undoMenuItem)
1045     {
1046       undoMenuItem_actionPerformed();
1047     }
1048     else if (source == redoMenuItem)
1049     {
1050       redoMenuItem_actionPerformed();
1051     }
1052     else if (source == copy)
1053     {
1054       copy_actionPerformed();
1055     }
1056     else if (source == pasteNew)
1057     {
1058       pasteNew_actionPerformed();
1059     }
1060     else if (source == pasteThis)
1061     {
1062       pasteThis_actionPerformed();
1063     }
1064     else if (source == cut)
1065     {
1066       cut_actionPerformed();
1067     }
1068     else if (source == delete)
1069     {
1070       delete_actionPerformed();
1071     }
1072     else if (source == createGroup)
1073     {
1074       createGroup_actionPerformed();
1075     }
1076     else if (source == unGroup)
1077     {
1078       unGroup_actionPerformed();
1079     }
1080     else if (source == grpsFromSelection)
1081     {
1082       makeGrpsFromSelection_actionPerformed();
1083     }
1084     else if (source == deleteGroups)
1085     {
1086       deleteGroups_actionPerformed();
1087     }
1088     else if (source == selectAllSequenceMenuItem)
1089     {
1090       selectAllSequenceMenuItem_actionPerformed();
1091     }
1092     else if (source == deselectAllSequenceMenuItem)
1093     {
1094       deselectAllSequenceMenuItem_actionPerformed();
1095     }
1096     else if (source == invertSequenceMenuItem)
1097     {
1098       invertSequenceMenuItem_actionPerformed();
1099       // uncomment to slave sequence selections in split frame
1100       // viewport.sendSelection();
1101     }
1102     else if (source == invertColSel)
1103     {
1104       viewport.invertColumnSelection();
1105       alignPanel.paintAlignment(true);
1106       viewport.sendSelection();
1107     }
1108     else if (source == remove2LeftMenuItem)
1109     {
1110       trimAlignment(true);
1111     }
1112     else if (source == remove2RightMenuItem)
1113     {
1114       trimAlignment(false);
1115     }
1116     else if (source == removeGappedColumnMenuItem)
1117     {
1118       removeGappedColumnMenuItem_actionPerformed();
1119     }
1120     else if (source == removeAllGapsMenuItem)
1121     {
1122       removeAllGapsMenuItem_actionPerformed();
1123     }
1124     else if (source == findMenuItem)
1125     {
1126       findMenuItem_actionPerformed();
1127     }
1128     else if (source == font)
1129     {
1130       new FontChooser(alignPanel);
1131     }
1132     else if (source == newView)
1133     {
1134       newView(null);
1135     }
1136     else if (source == showColumns)
1137     {
1138       viewport.showAllHiddenColumns();
1139       alignPanel.paintAlignment(true);
1140       viewport.sendSelection();
1141     }
1142     else if (source == showSeqs)
1143     {
1144       viewport.showAllHiddenSeqs();
1145       alignPanel.paintAlignment(true);
1146       // uncomment if we want to slave sequence selections in split frame
1147       // viewport.sendSelection();
1148     }
1149     else if (source == hideColumns)
1150     {
1151       viewport.hideSelectedColumns();
1152       alignPanel.paintAlignment(true);
1153       viewport.sendSelection();
1154     }
1155     else if (source == hideSequences
1156             && viewport.getSelectionGroup() != null)
1157     {
1158       viewport.hideAllSelectedSeqs();
1159       alignPanel.paintAlignment(true);
1160       // uncomment if we want to slave sequence selections in split frame
1161       // viewport.sendSelection();
1162     }
1163     else if (source == hideAllButSelection)
1164     {
1165       toggleHiddenRegions(false, false);
1166       alignPanel.paintAlignment(true);
1167       viewport.sendSelection();
1168     }
1169     else if (source == hideAllSelection)
1170     {
1171       SequenceGroup sg = viewport.getSelectionGroup();
1172       viewport.expandColSelection(sg, false);
1173       viewport.hideAllSelectedSeqs();
1174       viewport.hideSelectedColumns();
1175       alignPanel.paintAlignment(true);
1176       viewport.sendSelection();
1177     }
1178     else if (source == showAllHidden)
1179     {
1180       viewport.showAllHiddenColumns();
1181       viewport.showAllHiddenSeqs();
1182       alignPanel.paintAlignment(true);
1183       viewport.sendSelection();
1184     }
1185     else if (source == showGroupConsensus)
1186     {
1187       showGroupConsensus_actionPerformed();
1188     }
1189     else if (source == showGroupConservation)
1190     {
1191       showGroupConservation_actionPerformed();
1192     }
1193     else if (source == showSequenceLogo)
1194     {
1195       showSequenceLogo_actionPerformed();
1196     }
1197     else if (source == normSequenceLogo)
1198     {
1199       normSequenceLogo_actionPerformed();
1200     }
1201     else if (source == showConsensusHistogram)
1202     {
1203       showConsensusHistogram_actionPerformed();
1204     }
1205     else if (source == applyAutoAnnotationSettings)
1206     {
1207       applyAutoAnnotationSettings_actionPerformed();
1208     }
1209     else if (source == featureSettings)
1210     {
1211       new FeatureSettings(alignPanel);
1212     }
1213     else if (source == alProperties)
1214     {
1215       StringBuffer contents = new jalview.io.AlignmentProperties(
1216               viewport.getAlignment()).formatAsString();
1217       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1218       cap.setText(contents.toString());
1219       Frame frame = new Frame();
1220       frame.add(cap);
1221       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1222               "label.alignment_properties", new String[] { getTitle() }),
1223               400, 250);
1224     }
1225     else if (source == overviewMenuItem)
1226     {
1227       overviewMenuItem_actionPerformed();
1228     }
1229     else if (source == noColourmenuItem)
1230     {
1231       changeColour(null);
1232     }
1233     else if (source == clustalColour)
1234     {
1235       abovePIDThreshold.setState(false);
1236       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1237     }
1238     else if (source == zappoColour)
1239     {
1240       changeColour(new ZappoColourScheme());
1241     }
1242     else if (source == taylorColour)
1243     {
1244       changeColour(new TaylorColourScheme());
1245     }
1246     else if (source == hydrophobicityColour)
1247     {
1248       changeColour(new HydrophobicColourScheme());
1249     }
1250     else if (source == helixColour)
1251     {
1252       changeColour(new HelixColourScheme());
1253     }
1254     else if (source == strandColour)
1255     {
1256       changeColour(new StrandColourScheme());
1257     }
1258     else if (source == turnColour)
1259     {
1260       changeColour(new TurnColourScheme());
1261     }
1262     else if (source == buriedColour)
1263     {
1264       changeColour(new BuriedColourScheme());
1265     }
1266     else if (source == nucleotideColour)
1267     {
1268       changeColour(new NucleotideColourScheme());
1269     }
1270     else if (source == purinePyrimidineColour)
1271     {
1272       changeColour(new PurinePyrimidineColourScheme());
1273     }
1274     // else if (source == RNAInteractionColour)
1275     // {
1276     // changeColour(new RNAInteractionColourScheme());
1277     // }
1278     else if (source == RNAHelixColour)
1279     {
1280       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1281       // new RNAHelicesColourChooser(viewport, alignPanel);
1282     }
1283     else if (source == modifyPID)
1284     {
1285       modifyPID_actionPerformed();
1286     }
1287     else if (source == modifyConservation)
1288     {
1289       modifyConservation_actionPerformed();
1290     }
1291     else if (source == userDefinedColour)
1292     {
1293       new UserDefinedColours(alignPanel, null);
1294     }
1295     else if (source == PIDColour)
1296     {
1297       changeColour(new PIDColourScheme());
1298     }
1299     else if (source == BLOSUM62Colour)
1300     {
1301       changeColour(new Blosum62ColourScheme());
1302     }
1303     else if (source == tcoffeeColour)
1304     {
1305       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1306     }
1307     else if (source == annotationColour)
1308     {
1309       new AnnotationColourChooser(viewport, alignPanel);
1310     }
1311     else if (source == annotationColumnSelection)
1312     {
1313       new AnnotationColumnChooser(viewport, alignPanel);
1314     }
1315     else if (source == sortPairwiseMenuItem)
1316     {
1317       sortPairwiseMenuItem_actionPerformed();
1318     }
1319     else if (source == sortIDMenuItem)
1320     {
1321       sortIDMenuItem_actionPerformed();
1322     }
1323     else if (source == sortLengthMenuItem)
1324     {
1325       sortLengthMenuItem_actionPerformed();
1326     }
1327     else if (source == sortGroupMenuItem)
1328     {
1329       sortGroupMenuItem_actionPerformed();
1330     }
1331     else if (source == removeRedundancyMenuItem)
1332     {
1333       removeRedundancyMenuItem_actionPerformed();
1334     }
1335     else if (source == pairwiseAlignmentMenuItem)
1336     {
1337       pairwiseAlignmentMenuItem_actionPerformed();
1338     }
1339     else if (source == PCAMenuItem)
1340     {
1341       PCAMenuItem_actionPerformed();
1342     }
1343     else if (source == averageDistanceTreeMenuItem)
1344     {
1345       averageDistanceTreeMenuItem_actionPerformed();
1346     }
1347     else if (source == neighbourTreeMenuItem)
1348     {
1349       neighbourTreeMenuItem_actionPerformed();
1350     }
1351     else if (source == njTreeBlosumMenuItem)
1352     {
1353       njTreeBlosumMenuItem_actionPerformed();
1354     }
1355     else if (source == avDistanceTreeBlosumMenuItem)
1356     {
1357       avTreeBlosumMenuItem_actionPerformed();
1358     }
1359     else if (source == documentation)
1360     {
1361       documentation_actionPerformed();
1362     }
1363     else if (source == about)
1364     {
1365       about_actionPerformed();
1366     }
1367
1368   }
1369
1370   public void inputText_actionPerformed()
1371   {
1372     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1373     Frame frame = new Frame();
1374     frame.add(cap);
1375     jalview.bin.JalviewLite.addFrame(frame,
1376             MessageManager.getString("label.input_cut_paste"), 500, 500);
1377   }
1378
1379   protected void outputText_actionPerformed(ActionEvent e)
1380   {
1381     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1382     Frame frame = new Frame();
1383     frame.add(cap);
1384     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1385             "label.alignment_output_command",
1386             new Object[] { e.getActionCommand() }), 600, 500);
1387
1388     FileFormatI fileFormat = FileFormats.getInstance().forName(
1389             e.getActionCommand());
1390     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1391             fileFormat, viewport.getAlignment(),
1392             viewport.getShowJVSuffix()));
1393   }
1394
1395   public void loadAnnotations()
1396   {
1397     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1398     cap.setText(MessageManager
1399             .getString("label.paste_features_annotations_Tcoffee_here"));
1400     cap.setAnnotationImport();
1401     Frame frame = new Frame();
1402     frame.add(cap);
1403     jalview.bin.JalviewLite.addFrame(frame,
1404             MessageManager.getString("action.paste_annotations"), 400, 300);
1405
1406   }
1407
1408   public String outputAnnotations(boolean displayTextbox)
1409   {
1410     String annotation = new AnnotationFile()
1411             .printAnnotationsForView(viewport);
1412
1413     if (displayTextbox)
1414     {
1415       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1416       Frame frame = new Frame();
1417       frame.add(cap);
1418       jalview.bin.JalviewLite.addFrame(frame,
1419               MessageManager.getString("label.annotations"), 600, 500);
1420       cap.setText(annotation);
1421     }
1422
1423     return annotation;
1424   }
1425
1426   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1427   {
1428     if (alignPanel.getFeatureRenderer() != null
1429             && viewport.getFeaturesDisplayed() != null)
1430     {
1431       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1432
1433     }
1434     return null;
1435   }
1436
1437   public String outputFeatures(boolean displayTextbox, String format)
1438   {
1439     String features;
1440     FeaturesFile formatter = new FeaturesFile();
1441     if (format.equalsIgnoreCase("Jalview"))
1442     {
1443       features = formatter.printJalviewFormat(viewport.getAlignment()
1444               .getSequencesArray(), getDisplayedFeatureCols());
1445     }
1446     else
1447     {
1448       features = formatter.printGffFormat(viewport.getAlignment()
1449               .getSequencesArray(), getDisplayedFeatureCols());
1450     }
1451
1452     if (displayTextbox)
1453     {
1454       boolean frimport = false;
1455       if (features == null || features.equals("No Features Visible"))
1456       {
1457         features = "# No features visible - paste some and import them here.";
1458         frimport = true;
1459       }
1460
1461       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1462       if (frimport)
1463       {
1464         cap.setAnnotationImport();
1465       }
1466       Frame frame = new Frame();
1467       frame.add(cap);
1468       jalview.bin.JalviewLite.addFrame(frame,
1469               MessageManager.getString("label.features"), 600, 500);
1470       cap.setText(features);
1471     }
1472     else
1473     {
1474       if (features == null)
1475       {
1476         features = "";
1477       }
1478     }
1479
1480     return features;
1481   }
1482
1483   void launchFullApplication()
1484   {
1485     StringBuffer url = new StringBuffer(jalviewServletURL);
1486
1487     // allow servlet parameters to be passed in applet parameter
1488     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1489             : "?";
1490     url.append(firstSep);
1491
1492     url.append("open="
1493             + appendProtocol(viewport.applet.getParameter("file")));
1494
1495     if (viewport.applet.getParameter("features") != null)
1496     {
1497       url.append("&features=");
1498       url.append(appendProtocol(viewport.applet.getParameter("features")));
1499     }
1500
1501     if (viewport.applet.getParameter("annotations") != null)
1502     {
1503       url.append("&annotations=");
1504       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1505     }
1506
1507     if (viewport.applet.getParameter("jnetfile") != null
1508             || viewport.applet.getParameter("jpredfile") != null)
1509     {
1510       url.append("&annotations=");
1511       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1512               .getParameter("jnetfile") : viewport.applet
1513               .getParameter("jpredfile")));
1514     }
1515
1516     if (viewport.applet.getParameter("defaultColour") != null)
1517     {
1518       url.append("&colour="
1519               + removeWhiteSpace(viewport.applet
1520                       .getParameter("defaultColour")));
1521     }
1522
1523     if (viewport.applet.getParameter("userDefinedColour") != null)
1524     {
1525       url.append("&colour="
1526               + removeWhiteSpace(viewport.applet
1527                       .getParameter("userDefinedColour")));
1528     }
1529     if (viewport.applet.getParameter("tree") != null)
1530     {
1531       url.append("&tree="
1532               + appendProtocol(viewport.applet.getParameter("tree")));
1533     }
1534     if (viewport.applet.getParameter("treeFile") != null)
1535     {
1536       url.append("&tree="
1537               + appendProtocol(viewport.applet.getParameter("treeFile")));
1538     }
1539
1540     showURL(url.toString(), "FULL_APP");
1541   }
1542
1543   String removeWhiteSpace(String colour)
1544   {
1545     StringBuffer sb = new StringBuffer();
1546     for (int i = 0; i < colour.length(); i++)
1547     {
1548       if (Character.isWhitespace(colour.charAt(i)))
1549       {
1550         sb.append("%20");
1551       }
1552       else
1553       {
1554         sb.append(colour.charAt(i));
1555       }
1556     }
1557
1558     return sb.toString();
1559   }
1560
1561   String appendProtocol(String url)
1562   {
1563     try
1564     {
1565       new URL(url);
1566       url = URLEncoder.encode(url);
1567     }
1568     /*
1569      * When we finally deprecate 1.1 compatibility, we can start to use
1570      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1571      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1572      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1573      * ex.printStackTrace(); }
1574      */
1575     catch (java.net.MalformedURLException ex)
1576     {
1577       url = viewport.applet.getCodeBase() + url;
1578     }
1579     return url;
1580   }
1581
1582   public void closeMenuItem_actionPerformed()
1583   {
1584     PaintRefresher.RemoveComponent(alignPanel);
1585     if (alignPanel.seqPanel != null
1586             && alignPanel.seqPanel.seqCanvas != null)
1587     {
1588       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1589     }
1590     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1591     {
1592       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1593     }
1594
1595     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1596     {
1597       System.exit(0);
1598     }
1599     else
1600     {
1601     }
1602     viewport = null;
1603     alignPanel = null;
1604     this.dispose();
1605   }
1606
1607   /**
1608    * TODO: JAL-1104
1609    */
1610   void updateEditMenuBar()
1611   {
1612
1613     if (viewport.getHistoryList().size() > 0)
1614     {
1615       undoMenuItem.setEnabled(true);
1616       CommandI command = viewport.getHistoryList().peek();
1617       undoMenuItem.setLabel(MessageManager.formatMessage(
1618               "label.undo_command",
1619               new Object[] { command.getDescription() }));
1620     }
1621     else
1622     {
1623       undoMenuItem.setEnabled(false);
1624       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1625     }
1626
1627     if (viewport.getRedoList().size() > 0)
1628     {
1629       redoMenuItem.setEnabled(true);
1630
1631       CommandI command = viewport.getRedoList().peek();
1632       redoMenuItem.setLabel(MessageManager.formatMessage(
1633               "label.redo_command",
1634               new Object[] { command.getDescription() }));
1635     }
1636     else
1637     {
1638       redoMenuItem.setEnabled(false);
1639       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1640     }
1641   }
1642
1643   /**
1644    * TODO: JAL-1104
1645    */
1646   @Override
1647   public void addHistoryItem(CommandI command)
1648   {
1649     if (command.getSize() > 0)
1650     {
1651       viewport.addToHistoryList(command);
1652       viewport.clearRedoList();
1653       updateEditMenuBar();
1654       viewport.updateHiddenColumns();
1655     }
1656   }
1657
1658   /**
1659    * TODO: JAL-1104 DOCUMENT ME!
1660    *
1661    * @param e
1662    *          DOCUMENT ME!
1663    */
1664   protected void undoMenuItem_actionPerformed()
1665   {
1666     if (viewport.getHistoryList().isEmpty())
1667     {
1668       return;
1669     }
1670
1671     CommandI command = viewport.getHistoryList().pop();
1672     viewport.addToRedoList(command);
1673     command.undoCommand(null);
1674
1675     AlignmentViewport originalSource = getOriginatingSource(command);
1676     // JBPNote Test
1677     if (originalSource != viewport)
1678     {
1679       System.err
1680               .println("Warning: Viewport object mismatch whilst undoing");
1681     }
1682     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1683                                           // viewport.getColumnSelection().getHiddenColumns()
1684                                           // != null;
1685     updateEditMenuBar();
1686     originalSource.firePropertyChange("alignment", null, originalSource
1687             .getAlignment().getSequences());
1688   }
1689
1690   /**
1691    * TODO: JAL-1104 DOCUMENT ME!
1692    *
1693    * @param e
1694    *          DOCUMENT ME!
1695    */
1696   protected void redoMenuItem_actionPerformed()
1697   {
1698     if (viewport.getRedoList().isEmpty())
1699     {
1700       return;
1701     }
1702
1703     CommandI command = viewport.getRedoList().pop();
1704     viewport.addToHistoryList(command);
1705     command.doCommand(null);
1706
1707     AlignmentViewport originalSource = getOriginatingSource(command);
1708     // JBPNote Test
1709     if (originalSource != viewport)
1710     {
1711       System.err
1712               .println("Warning: Viewport object mismatch whilst re-doing");
1713     }
1714     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1715                                           // viewport.getColumnSelection().getHiddenColumns()
1716                                           // != null;
1717
1718     updateEditMenuBar();
1719     originalSource.firePropertyChange("alignment", null, originalSource
1720             .getAlignment().getSequences());
1721   }
1722
1723   AlignmentViewport getOriginatingSource(CommandI command)
1724   {
1725     AlignmentViewport originalSource = null;
1726     // For sequence removal and addition, we need to fire
1727     // the property change event FROM the viewport where the
1728     // original alignment was altered
1729     AlignmentI al = null;
1730     if (command instanceof EditCommand)
1731     {
1732       EditCommand editCommand = (EditCommand) command;
1733       al = editCommand.getAlignment();
1734       Vector comps = (Vector) PaintRefresher.components.get(viewport
1735               .getSequenceSetId());
1736       for (int i = 0; i < comps.size(); i++)
1737       {
1738         if (comps.elementAt(i) instanceof AlignmentPanel)
1739         {
1740           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1741           {
1742             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1743             break;
1744           }
1745         }
1746       }
1747     }
1748
1749     if (originalSource == null)
1750     {
1751       // The original view is closed, we must validate
1752       // the current view against the closed view first
1753       if (al != null)
1754       {
1755         PaintRefresher.validateSequences(al, viewport.getAlignment());
1756       }
1757
1758       originalSource = viewport;
1759     }
1760
1761     return originalSource;
1762   }
1763
1764   /**
1765    * Move the currently selected sequences up or down one position in the
1766    * alignment
1767    *
1768    * @param up
1769    */
1770   public void moveSelectedSequences(boolean up)
1771   {
1772     SequenceGroup sg = viewport.getSelectionGroup();
1773     if (sg == null)
1774     {
1775       return;
1776     }
1777     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1778             up ? null : viewport.getHiddenRepSequences(), up);
1779     alignPanel.paintAlignment(true);
1780
1781     /*
1782      * Also move cDNA/protein complement sequences
1783      */
1784     AlignViewportI complement = viewport.getCodingComplement();
1785     if (complement != null)
1786     {
1787       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1788               viewport, complement);
1789       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1790               up ? null : complement.getHiddenRepSequences(), up);
1791       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1792     }
1793   }
1794
1795   synchronized void slideSequences(boolean right, int size)
1796   {
1797     List<SequenceI> sg = new Vector<SequenceI>();
1798     if (viewport.cursorMode)
1799     {
1800       sg.add(viewport.getAlignment().getSequenceAt(
1801               alignPanel.seqPanel.seqCanvas.cursorY));
1802     }
1803     else if (viewport.getSelectionGroup() != null
1804             && viewport.getSelectionGroup().getSize() != viewport
1805                     .getAlignment().getHeight())
1806     {
1807       sg = viewport.getSelectionGroup().getSequences(
1808               viewport.getHiddenRepSequences());
1809     }
1810
1811     if (sg.size() < 1)
1812     {
1813       return;
1814     }
1815
1816     Vector<SequenceI> invertGroup = new Vector();
1817
1818     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1819     {
1820       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1821       {
1822         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1823       }
1824     }
1825
1826     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1827
1828     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1829             .size()]);
1830     for (int i = 0; i < invertGroup.size(); i++)
1831     {
1832       seqs2[i] = invertGroup.elementAt(i);
1833     }
1834
1835     SlideSequencesCommand ssc;
1836     if (right)
1837     {
1838       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1839               size, viewport.getGapCharacter());
1840     }
1841     else
1842     {
1843       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1844               size, viewport.getGapCharacter());
1845     }
1846
1847     int groupAdjustment = 0;
1848     if (ssc.getGapsInsertedBegin() && right)
1849     {
1850       if (viewport.cursorMode)
1851       {
1852         alignPanel.seqPanel.moveCursor(size, 0);
1853       }
1854       else
1855       {
1856         groupAdjustment = size;
1857       }
1858     }
1859     else if (!ssc.getGapsInsertedBegin() && !right)
1860     {
1861       if (viewport.cursorMode)
1862       {
1863         alignPanel.seqPanel.moveCursor(-size, 0);
1864       }
1865       else
1866       {
1867         groupAdjustment = -size;
1868       }
1869     }
1870
1871     if (groupAdjustment != 0)
1872     {
1873       viewport.getSelectionGroup().setStartRes(
1874               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1875       viewport.getSelectionGroup().setEndRes(
1876               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1877     }
1878
1879     boolean appendHistoryItem = false;
1880     Deque<CommandI> historyList = viewport.getHistoryList();
1881     if (historyList != null && historyList.size() > 0
1882             && historyList.peek() instanceof SlideSequencesCommand)
1883     {
1884       appendHistoryItem = ssc
1885               .appendSlideCommand((SlideSequencesCommand) historyList
1886                       .peek());
1887     }
1888
1889     if (!appendHistoryItem)
1890     {
1891       addHistoryItem(ssc);
1892     }
1893
1894     repaint();
1895   }
1896
1897   static StringBuffer copiedSequences;
1898
1899   static Vector copiedHiddenColumns;
1900
1901   protected void copy_actionPerformed()
1902   {
1903     if (viewport.getSelectionGroup() == null)
1904     {
1905       return;
1906     }
1907
1908     SequenceGroup sg = viewport.getSelectionGroup();
1909     copiedSequences = new StringBuffer();
1910     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1911     for (int i = 0; i < sg.getSize(); i++)
1912     {
1913       SequenceI seq = sg.getSequenceAt(i);
1914       int index = viewport.getAlignment().findIndex(seq);
1915       orderedSeqs.put(index, seq);
1916     }
1917
1918     int index = 0, startRes, endRes;
1919     char ch;
1920
1921     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1922     {
1923       copiedHiddenColumns = new Vector();
1924       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1925       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1926       {
1927         copiedHiddenColumns.addElement(new int[] {
1928             region[0] - hiddenOffset, region[1] - hiddenOffset });
1929       }
1930     }
1931     else
1932     {
1933       copiedHiddenColumns = null;
1934     }
1935
1936     for (int i = 0; i < sg.getSize(); i++)
1937     {
1938       SequenceI seq = null;
1939
1940       while (seq == null)
1941       {
1942         if (orderedSeqs.containsKey(index))
1943         {
1944           seq = orderedSeqs.get(index);
1945           index++;
1946           break;
1947         }
1948         else
1949         {
1950           index++;
1951         }
1952       }
1953
1954       // FIND START RES
1955       // Returns residue following index if gap
1956       startRes = seq.findPosition(sg.getStartRes());
1957
1958       // FIND END RES
1959       // Need to find the residue preceeding index if gap
1960       endRes = 0;
1961
1962       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1963       {
1964         ch = seq.getCharAt(j);
1965         if (!jalview.util.Comparison.isGap((ch)))
1966         {
1967           endRes++;
1968         }
1969       }
1970
1971       if (endRes > 0)
1972       {
1973         endRes += seq.getStart() - 1;
1974       }
1975
1976       copiedSequences.append(seq.getName()
1977               + "\t"
1978               + startRes
1979               + "\t"
1980               + endRes
1981               + "\t"
1982               + seq.getSequenceAsString(sg.getStartRes(),
1983                       sg.getEndRes() + 1) + "\n");
1984     }
1985
1986   }
1987
1988   protected void pasteNew_actionPerformed()
1989   {
1990     paste(true);
1991   }
1992
1993   protected void pasteThis_actionPerformed()
1994   {
1995     paste(false);
1996   }
1997
1998   void paste(boolean newAlignment)
1999   {
2000     try
2001     {
2002
2003       if (copiedSequences == null)
2004       {
2005         return;
2006       }
2007
2008       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2009       Vector seqs = new Vector();
2010       while (st.hasMoreElements())
2011       {
2012         String name = st.nextToken();
2013         int start = Integer.parseInt(st.nextToken());
2014         int end = Integer.parseInt(st.nextToken());
2015         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2016       }
2017       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2018       for (int i = 0; i < seqs.size(); i++)
2019       {
2020         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2021       }
2022
2023       if (newAlignment)
2024       {
2025         String newtitle = MessageManager
2026                 .getString("label.copied_sequences");
2027         if (getTitle().startsWith(
2028                 MessageManager.getString("label.copied_sequences")))
2029         {
2030           newtitle = getTitle();
2031         }
2032         else
2033         {
2034           newtitle = newtitle.concat(MessageManager.formatMessage(
2035                   "label.from_msname", new String[] { getTitle() }));
2036         }
2037         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2038                 viewport.applet, newtitle, false);
2039         if (copiedHiddenColumns != null)
2040         {
2041           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2042           {
2043             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2044             af.viewport.hideColumns(region[0], region[1]);
2045           }
2046         }
2047
2048         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2049                 frameHeight);
2050       }
2051       else
2052       {
2053         addSequences(newSeqs);
2054       }
2055
2056     } catch (Exception ex)
2057     {
2058     } // could be anything being pasted in here
2059
2060   }
2061
2062   void addSequences(SequenceI[] seqs)
2063   {
2064     for (int i = 0; i < seqs.length; i++)
2065     {
2066       viewport.getAlignment().addSequence(seqs[i]);
2067     }
2068
2069     // !newAlignment
2070     addHistoryItem(new EditCommand(
2071             MessageManager.getString("label.add_sequences"), Action.PASTE,
2072             seqs, 0, viewport.getAlignment().getWidth(),
2073             viewport.getAlignment()));
2074
2075     viewport.setEndSeq(viewport.getAlignment().getHeight());
2076     viewport.getAlignment().getWidth();
2077     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2078             .getSequences());
2079
2080   }
2081
2082   protected void cut_actionPerformed()
2083   {
2084     copy_actionPerformed();
2085     delete_actionPerformed();
2086   }
2087
2088   protected void delete_actionPerformed()
2089   {
2090
2091     SequenceGroup sg = viewport.getSelectionGroup();
2092     if (sg == null)
2093     {
2094       return;
2095     }
2096
2097     Vector seqs = new Vector();
2098     SequenceI seq;
2099     for (int i = 0; i < sg.getSize(); i++)
2100     {
2101       seq = sg.getSequenceAt(i);
2102       seqs.addElement(seq);
2103     }
2104
2105     /*
2106      * If the cut affects all sequences, warn, remove highlighted columns
2107      */
2108     if (sg.getSize() == viewport.getAlignment().getHeight())
2109     {
2110       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2111               .getAlignment().getWidth()) ? true : false;
2112       if (isEntireAlignWidth)
2113       {
2114         String title = MessageManager.getString("label.delete_all");
2115         Panel infoPanel = new Panel();
2116         infoPanel.setLayout(new FlowLayout());
2117         infoPanel
2118                 .add(new Label(MessageManager.getString("warn.delete_all")));
2119
2120         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2121         dialog.setMainPanel(infoPanel);
2122         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2123         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2124         dialog.setVisible(true);
2125
2126         if (!dialog.accept)
2127         {
2128           return;
2129         }
2130       }
2131       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2132               sg.getEndRes() + 1);
2133     }
2134
2135     SequenceI[] cut = new SequenceI[seqs.size()];
2136     for (int i = 0; i < seqs.size(); i++)
2137     {
2138       cut[i] = (SequenceI) seqs.elementAt(i);
2139     }
2140
2141     /*
2142      * //ADD HISTORY ITEM
2143      */
2144     addHistoryItem(new EditCommand(
2145             MessageManager.getString("label.cut_sequences"), Action.CUT,
2146             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2147             viewport.getAlignment()));
2148
2149     viewport.setSelectionGroup(null);
2150     viewport.getAlignment().deleteGroup(sg);
2151
2152     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2153             .getSequences());
2154
2155     if (viewport.getAlignment().getHeight() < 1)
2156     {
2157       this.setVisible(false);
2158     }
2159     viewport.sendSelection();
2160   }
2161
2162   /**
2163    * group consensus toggled
2164    *
2165    */
2166   protected void showGroupConsensus_actionPerformed()
2167   {
2168     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2169     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2170
2171   }
2172
2173   /**
2174    * group conservation toggled.
2175    */
2176   protected void showGroupConservation_actionPerformed()
2177   {
2178     viewport.setShowGroupConservation(showGroupConservation.getState());
2179     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180   }
2181
2182   /*
2183    * (non-Javadoc)
2184    *
2185    * @see
2186    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2187    * .event.ActionEvent)
2188    */
2189   protected void showConsensusHistogram_actionPerformed()
2190   {
2191     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2192     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2193   }
2194
2195   /*
2196    * (non-Javadoc)
2197    *
2198    * @see
2199    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2200    * .event.ActionEvent)
2201    */
2202   protected void showSequenceLogo_actionPerformed()
2203   {
2204     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2205     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2206   }
2207
2208   protected void normSequenceLogo_actionPerformed()
2209   {
2210     showSequenceLogo.setState(true);
2211     viewport.setShowSequenceLogo(true);
2212     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2213     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2214   }
2215
2216   protected void applyAutoAnnotationSettings_actionPerformed()
2217   {
2218     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2219   }
2220
2221   protected void makeGrpsFromSelection_actionPerformed()
2222   {
2223     if (avc.makeGroupsFromSelection())
2224     {
2225       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2226       alignPanel.updateAnnotation();
2227       alignPanel.paintAlignment(true);
2228     }
2229   }
2230
2231   protected void createGroup_actionPerformed()
2232   {
2233     avc.createGroup();
2234   }
2235
2236   protected void unGroup_actionPerformed()
2237   {
2238     if (avc.unGroup())
2239     {
2240       alignPanel.alignmentChanged();
2241     }
2242   }
2243
2244   protected void deleteGroups_actionPerformed()
2245   {
2246     if (avc.deleteGroups())
2247     {
2248       alignPanel.alignmentChanged();
2249     }
2250   }
2251
2252   public void selectAllSequenceMenuItem_actionPerformed()
2253   {
2254     SequenceGroup sg = new SequenceGroup();
2255     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2256     {
2257       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2258     }
2259     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2260     viewport.setSelectionGroup(sg);
2261     // JAL-2034 - should delegate to
2262     // alignPanel to decide if overview needs
2263     // updating.
2264     alignPanel.paintAlignment(false);
2265     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2266     viewport.sendSelection();
2267   }
2268
2269   public void deselectAllSequenceMenuItem_actionPerformed()
2270   {
2271     if (viewport.cursorMode)
2272     {
2273       alignPanel.seqPanel.keyboardNo1 = null;
2274       alignPanel.seqPanel.keyboardNo2 = null;
2275     }
2276     viewport.setSelectionGroup(null);
2277     viewport.getColumnSelection().clear();
2278     viewport.setSelectionGroup(null);
2279     alignPanel.idPanel.idCanvas.searchResults = null;
2280     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2281     // JAL-2034 - should delegate to
2282     // alignPanel to decide if overview needs
2283     // updating.
2284     alignPanel.paintAlignment(false);
2285     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2286     viewport.sendSelection();
2287   }
2288
2289   public void invertSequenceMenuItem_actionPerformed()
2290   {
2291     SequenceGroup sg = viewport.getSelectionGroup();
2292     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2293     {
2294       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2295     }
2296
2297     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2298     viewport.sendSelection();
2299   }
2300
2301   public void invertColSel_actionPerformed()
2302   {
2303     viewport.invertColumnSelection();
2304     alignPanel.paintAlignment(true);
2305     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2306     viewport.sendSelection();
2307   }
2308
2309   void trimAlignment(boolean trimLeft)
2310   {
2311     ColumnSelection colSel = viewport.getColumnSelection();
2312     int column;
2313
2314     if (!colSel.isEmpty())
2315     {
2316       if (trimLeft)
2317       {
2318         column = colSel.getMin();
2319       }
2320       else
2321       {
2322         column = colSel.getMax();
2323       }
2324
2325       SequenceI[] seqs;
2326       if (viewport.getSelectionGroup() != null)
2327       {
2328         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2329                 viewport.getHiddenRepSequences());
2330       }
2331       else
2332       {
2333         seqs = viewport.getAlignment().getSequencesArray();
2334       }
2335
2336       TrimRegionCommand trimRegion;
2337       if (trimLeft)
2338       {
2339         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2340                 column, viewport.getAlignment());
2341         viewport.setStartRes(0);
2342       }
2343       else
2344       {
2345         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2346                 column, viewport.getAlignment());
2347       }
2348
2349       statusBar.setText(MessageManager.formatMessage(
2350               "label.removed_columns",
2351               new String[] { Integer.valueOf(trimRegion.getSize())
2352                       .toString() }));
2353       addHistoryItem(trimRegion);
2354
2355       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2356       {
2357         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2358                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2359         {
2360           viewport.getAlignment().deleteGroup(sg);
2361         }
2362       }
2363
2364       viewport.firePropertyChange("alignment", null, viewport
2365               .getAlignment().getSequences());
2366     }
2367   }
2368
2369   public void removeGappedColumnMenuItem_actionPerformed()
2370   {
2371     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2372
2373     SequenceI[] seqs;
2374     if (viewport.getSelectionGroup() != null)
2375     {
2376       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2377               viewport.getHiddenRepSequences());
2378       start = viewport.getSelectionGroup().getStartRes();
2379       end = viewport.getSelectionGroup().getEndRes();
2380     }
2381     else
2382     {
2383       seqs = viewport.getAlignment().getSequencesArray();
2384     }
2385
2386     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2387             "Remove Gapped Columns", seqs, start, end,
2388             viewport.getAlignment());
2389
2390     addHistoryItem(removeGapCols);
2391
2392     statusBar.setText(MessageManager.formatMessage(
2393             "label.removed_empty_columns",
2394             new String[] { Integer.valueOf(removeGapCols.getSize())
2395                     .toString() }));
2396
2397     // This is to maintain viewport position on first residue
2398     // of first sequence
2399     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2400     int startRes = seq.findPosition(viewport.startRes);
2401     // ShiftList shifts;
2402     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2403     // edit.alColumnChanges=shifts.getInverse();
2404     // if (viewport.hasHiddenColumns)
2405     // viewport.getColumnSelection().compensateForEdits(shifts);
2406     viewport.setStartRes(seq.findIndex(startRes) - 1);
2407     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2408             .getSequences());
2409
2410   }
2411
2412   public void removeAllGapsMenuItem_actionPerformed()
2413   {
2414     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2415
2416     SequenceI[] seqs;
2417     if (viewport.getSelectionGroup() != null)
2418     {
2419       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2420               viewport.getHiddenRepSequences());
2421       start = viewport.getSelectionGroup().getStartRes();
2422       end = viewport.getSelectionGroup().getEndRes();
2423     }
2424     else
2425     {
2426       seqs = viewport.getAlignment().getSequencesArray();
2427     }
2428
2429     // This is to maintain viewport position on first residue
2430     // of first sequence
2431     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2432     int startRes = seq.findPosition(viewport.startRes);
2433
2434     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2435             viewport.getAlignment()));
2436
2437     viewport.setStartRes(seq.findIndex(startRes) - 1);
2438
2439     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2440             .getSequences());
2441
2442   }
2443
2444   public void findMenuItem_actionPerformed()
2445   {
2446     new Finder(alignPanel);
2447   }
2448
2449   /**
2450    * create a new view derived from the current view
2451    *
2452    * @param viewtitle
2453    * @return frame for the new view
2454    */
2455   public AlignFrame newView(String viewtitle)
2456   {
2457     AlignmentI newal;
2458     if (viewport.hasHiddenRows())
2459     {
2460       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2461               .getFullAlignment().getSequencesArray());
2462     }
2463     else
2464     {
2465       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2466     }
2467
2468     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2469     {
2470       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2471       {
2472         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2473         {
2474           newal.addAnnotation(viewport.getAlignment()
2475                   .getAlignmentAnnotation()[i]);
2476         }
2477       }
2478     }
2479
2480     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2481
2482     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2483     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2484     PaintRefresher.Register(newaf.alignPanel,
2485             newaf.alignPanel.av.getSequenceSetId());
2486
2487     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2488             newaf.alignPanel.av.getSequenceSetId());
2489     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2490             newaf.alignPanel.av.getSequenceSetId());
2491
2492     Vector comps = (Vector) PaintRefresher.components.get(viewport
2493             .getSequenceSetId());
2494     int viewSize = -1;
2495     for (int i = 0; i < comps.size(); i++)
2496     {
2497       if (comps.elementAt(i) instanceof AlignmentPanel)
2498       {
2499         viewSize++;
2500       }
2501     }
2502
2503     String title = new String(this.getTitle());
2504     if (viewtitle != null)
2505     {
2506       title = viewtitle + " ( " + title + ")";
2507     }
2508     else
2509     {
2510       if (title.indexOf("(View") > -1)
2511       {
2512         title = title.substring(0, title.indexOf("(View"));
2513       }
2514       title += "(View " + viewSize + ")";
2515     }
2516
2517     newaf.setTitle(title.toString());
2518
2519     newaf.viewport.setHistoryList(viewport.getHistoryList());
2520     newaf.viewport.setRedoList(viewport.getRedoList());
2521     return newaf;
2522   }
2523
2524   /**
2525    *
2526    * @return list of feature groups on the view
2527    */
2528   public String[] getFeatureGroups()
2529   {
2530     FeatureRenderer fr = null;
2531     if (alignPanel != null
2532             && (fr = alignPanel.getFeatureRenderer()) != null)
2533     {
2534       List<String> gps = fr.getFeatureGroups();
2535       String[] _gps = gps.toArray(new String[gps.size()]);
2536       return _gps;
2537     }
2538     return null;
2539   }
2540
2541   /**
2542    * get sequence feature groups that are hidden or shown
2543    *
2544    * @param visible
2545    *          true is visible
2546    * @return list
2547    */
2548   public String[] getFeatureGroupsOfState(boolean visible)
2549   {
2550     FeatureRenderer fr = null;
2551     if (alignPanel != null
2552             && (fr = alignPanel.getFeatureRenderer()) != null)
2553     {
2554       List<String> gps = fr.getGroups(visible);
2555       String[] _gps = gps.toArray(new String[gps.size()]);
2556       return _gps;
2557     }
2558     return null;
2559   }
2560
2561   /**
2562    * Change the display state for the given feature groups
2563    *
2564    * @param groups
2565    *          list of group strings
2566    * @param state
2567    *          visible or invisible
2568    */
2569   public void setFeatureGroupState(String[] groups, boolean state)
2570   {
2571     FeatureRenderer fr = null;
2572     this.sequenceFeatures.setState(true);
2573     viewport.setShowSequenceFeatures(true);
2574     if (alignPanel != null
2575             && (fr = alignPanel.getFeatureRenderer()) != null)
2576     {
2577
2578       fr.setGroupVisibility(Arrays.asList(groups), state);
2579       alignPanel.seqPanel.seqCanvas.repaint();
2580       if (alignPanel.overviewPanel != null)
2581       {
2582         alignPanel.overviewPanel.updateOverviewImage();
2583       }
2584     }
2585   }
2586
2587   public void seqLimits_itemStateChanged()
2588   {
2589     viewport.setShowJVSuffix(seqLimits.getState());
2590     alignPanel.fontChanged();
2591     alignPanel.paintAlignment(true);
2592   }
2593
2594   protected void colourTextMenuItem_actionPerformed()
2595   {
2596     viewport.setColourText(colourTextMenuItem.getState());
2597     alignPanel.paintAlignment(true);
2598   }
2599
2600   protected void displayNonconservedMenuItem_actionPerformed()
2601   {
2602     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2603     alignPanel.paintAlignment(true);
2604   }
2605
2606   protected void wrapMenuItem_actionPerformed()
2607   {
2608     viewport.setWrapAlignment(wrapMenuItem.getState());
2609     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2610     scaleAbove.setEnabled(wrapMenuItem.getState());
2611     scaleLeft.setEnabled(wrapMenuItem.getState());
2612     scaleRight.setEnabled(wrapMenuItem.getState());
2613     alignPanel.paintAlignment(true);
2614   }
2615
2616   public void overviewMenuItem_actionPerformed()
2617   {
2618     if (alignPanel.overviewPanel != null)
2619     {
2620       return;
2621     }
2622
2623     Frame frame = new Frame();
2624     OverviewPanel overview = new OverviewPanel(alignPanel);
2625     frame.add(overview);
2626     // +50 must allow for applet frame window
2627     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2628             "label.overview_params", new String[] { this.getTitle() }),
2629             overview.getPreferredSize().width,
2630             overview.getPreferredSize().height + 50);
2631
2632     frame.pack();
2633     final AlignmentPanel ap = alignPanel;
2634     frame.addWindowListener(new WindowAdapter()
2635     {
2636       @Override
2637       public void windowClosing(WindowEvent e)
2638       {
2639         if (ap != null)
2640         {
2641           ap.setOverviewPanel(null);
2642         }
2643       };
2644     });
2645
2646     alignPanel.setOverviewPanel(overview);
2647
2648   }
2649
2650   @Override
2651   public void changeColour(ColourSchemeI cs)
2652   {
2653     viewport.setGlobalColourScheme(cs);
2654
2655     alignPanel.paintAlignment(true);
2656   }
2657
2658   protected void modifyPID_actionPerformed()
2659   {
2660     if (viewport.getAbovePIDThreshold()
2661             && viewport.getGlobalColourScheme() != null)
2662     {
2663       SliderPanel.setPIDSliderSource(alignPanel,
2664               viewport.getResidueShading(), alignPanel.getViewName());
2665       SliderPanel.showPIDSlider();
2666     }
2667   }
2668
2669   protected void modifyConservation_actionPerformed()
2670   {
2671     if (viewport.getConservationSelected()
2672             && viewport.getGlobalColourScheme() != null)
2673     {
2674       SliderPanel.setConservationSlider(alignPanel,
2675               viewport.getResidueShading(), alignPanel.getViewName());
2676       SliderPanel.showConservationSlider();
2677     }
2678   }
2679
2680   protected void conservationMenuItem_actionPerformed()
2681   {
2682     boolean selected = conservationMenuItem.getState();
2683     modifyConservation.setEnabled(selected);
2684     viewport.setConservationSelected(selected);
2685
2686     // viewport.setAbovePIDThreshold(false);
2687     // abovePIDThreshold.setState(false);
2688
2689     changeColour(viewport.getGlobalColourScheme());
2690
2691     if (selected)
2692     {
2693       modifyConservation_actionPerformed();
2694     }
2695     else
2696     {
2697       SliderPanel.hideConservationSlider();
2698     }
2699   }
2700
2701   public void abovePIDThreshold_actionPerformed()
2702   {
2703     boolean selected = abovePIDThreshold.getState();
2704     modifyPID.setEnabled(selected);
2705     viewport.setAbovePIDThreshold(selected);
2706     // conservationMenuItem.setState(false);
2707     // viewport.setConservationSelected(false);
2708
2709     changeColour(viewport.getGlobalColourScheme());
2710
2711     if (selected)
2712     {
2713       modifyPID_actionPerformed();
2714     }
2715     else
2716     {
2717       SliderPanel.hidePIDSlider();
2718     }
2719   }
2720
2721   public void sortPairwiseMenuItem_actionPerformed()
2722   {
2723     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2724     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2725             .getAlignment().getSequenceAt(0), null);
2726
2727     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2728             viewport.getAlignment()));
2729     alignPanel.paintAlignment(true);
2730   }
2731
2732   public void sortIDMenuItem_actionPerformed()
2733   {
2734     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2735     AlignmentSorter.sortByID(viewport.getAlignment());
2736     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2737             viewport.getAlignment()));
2738     alignPanel.paintAlignment(true);
2739   }
2740
2741   public void sortLengthMenuItem_actionPerformed()
2742   {
2743     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2744     AlignmentSorter.sortByLength(viewport.getAlignment());
2745     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2746             viewport.getAlignment()));
2747     alignPanel.paintAlignment(true);
2748   }
2749
2750   public void sortGroupMenuItem_actionPerformed()
2751   {
2752     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2753     AlignmentSorter.sortByGroup(viewport.getAlignment());
2754     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2755             viewport.getAlignment()));
2756     alignPanel.paintAlignment(true);
2757
2758   }
2759
2760   public void removeRedundancyMenuItem_actionPerformed()
2761   {
2762     new RedundancyPanel(alignPanel);
2763   }
2764
2765   public void pairwiseAlignmentMenuItem_actionPerformed()
2766   {
2767     if (viewport.getSelectionGroup() != null
2768             && viewport.getSelectionGroup().getSize() > 1)
2769     {
2770       Frame frame = new Frame();
2771       frame.add(new PairwiseAlignPanel(alignPanel));
2772       jalview.bin.JalviewLite.addFrame(frame,
2773               MessageManager.getString("action.pairwise_alignment"), 600,
2774               500);
2775     }
2776   }
2777
2778   public void PCAMenuItem_actionPerformed()
2779   {
2780     // are the sequences aligned?
2781     if (!viewport.getAlignment().isAligned(false))
2782     {
2783       SequenceI current;
2784       int Width = viewport.getAlignment().getWidth();
2785
2786       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2787       {
2788         current = viewport.getAlignment().getSequenceAt(i);
2789
2790         if (current.getLength() < Width)
2791         {
2792           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2793         }
2794       }
2795       alignPanel.paintAlignment(true);
2796     }
2797
2798     if ((viewport.getSelectionGroup() != null
2799             && viewport.getSelectionGroup().getSize() < 4 && viewport
2800             .getSelectionGroup().getSize() > 0)
2801             || viewport.getAlignment().getHeight() < 4)
2802     {
2803       return;
2804     }
2805
2806     try
2807     {
2808       new PCAPanel(viewport);
2809     } catch (java.lang.OutOfMemoryError ex)
2810     {
2811     }
2812
2813   }
2814
2815   public void averageDistanceTreeMenuItem_actionPerformed()
2816   {
2817     NewTreePanel("AV", "PID", "Average distance tree using PID");
2818   }
2819
2820   public void neighbourTreeMenuItem_actionPerformed()
2821   {
2822     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2823   }
2824
2825   protected void njTreeBlosumMenuItem_actionPerformed()
2826   {
2827     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2828   }
2829
2830   protected void avTreeBlosumMenuItem_actionPerformed()
2831   {
2832     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2833   }
2834
2835   void NewTreePanel(String type, String pwType, String title)
2836   {
2837     // are the sequences aligned?
2838     if (!viewport.getAlignment().isAligned(false))
2839     {
2840       SequenceI current;
2841       int Width = viewport.getAlignment().getWidth();
2842
2843       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2844       {
2845         current = viewport.getAlignment().getSequenceAt(i);
2846
2847         if (current.getLength() < Width)
2848         {
2849           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2850         }
2851       }
2852       alignPanel.paintAlignment(true);
2853
2854     }
2855
2856     if ((viewport.getSelectionGroup() != null && viewport
2857             .getSelectionGroup().getSize() > 1)
2858             || (viewport.getAlignment().getHeight() > 1))
2859     {
2860       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2861
2862       addTreeMenuItem(tp, title);
2863
2864       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2865     }
2866   }
2867
2868   void loadTree_actionPerformed()
2869   {
2870     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2871     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2872     cap.setTreeImport();
2873     Frame frame = new Frame();
2874     frame.add(cap);
2875     jalview.bin.JalviewLite.addFrame(frame,
2876             MessageManager.getString("label.paste_newick_file"), 400, 300);
2877   }
2878
2879   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2880   {
2881     TreePanel tp = new TreePanel(alignPanel, treeFile,
2882             MessageManager.getString("label.load_tree_from_file"), tree);
2883     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2884     addTreeMenuItem(tp, treeFile);
2885   }
2886
2887   /**
2888    * sort the alignment using the given treePanel
2889    *
2890    * @param treePanel
2891    *          tree used to sort view
2892    * @param title
2893    *          string used for undo event name
2894    */
2895   public void sortByTree(TreePanel treePanel, String title)
2896   {
2897     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2898     AlignmentSorter
2899             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2900     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2901     // HistoryItem.SORT));
2902     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2903             "label.order_by_params", new String[] { title }), oldOrder,
2904             viewport.getAlignment()));
2905     alignPanel.paintAlignment(true);
2906   }
2907
2908   /**
2909    * Do any automatic reordering of the alignment and add the necessary bits to
2910    * the menu structure for the new tree
2911    *
2912    * @param treePanel
2913    * @param title
2914    */
2915   protected void addTreeMenuItem(final TreePanel treePanel,
2916           final String title)
2917   {
2918     final MenuItem item = new MenuItem(title);
2919     sortByTreeMenu.add(item);
2920     item.addActionListener(new java.awt.event.ActionListener()
2921     {
2922       @Override
2923       public void actionPerformed(ActionEvent evt)
2924       {
2925         sortByTree(treePanel, title); // treePanel.getTitle());
2926       }
2927     });
2928
2929     treePanel.addWindowListener(new WindowAdapter()
2930     {
2931       @Override
2932       public void windowOpened(WindowEvent e)
2933       {
2934         if (viewport.sortByTree)
2935         {
2936           sortByTree(treePanel, title);
2937         }
2938         super.windowOpened(e);
2939       }
2940
2941       @Override
2942       public void windowClosing(WindowEvent e)
2943       {
2944         sortByTreeMenu.remove(item);
2945       };
2946     });
2947   }
2948
2949   public boolean sortBy(AlignmentOrder alorder, String undoname)
2950   {
2951     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2952     if (viewport.applet.debug)
2953     {
2954       System.err.println("Sorting " + alorder.getOrder().size()
2955               + " in alignment '" + getTitle() + "'");
2956     }
2957     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2958     if (undoname != null)
2959     {
2960       addHistoryItem(new OrderCommand(undoname, oldOrder,
2961               viewport.getAlignment()));
2962     }
2963     alignPanel.paintAlignment(true);
2964     return true;
2965   }
2966
2967   protected void documentation_actionPerformed()
2968   {
2969     alignPanel.av.applet.openJalviewHelpUrl();
2970   }
2971
2972   protected void about_actionPerformed()
2973   {
2974
2975     class AboutPanel extends Canvas
2976     {
2977       String version;
2978
2979       String builddate;
2980
2981       public AboutPanel(String version, String builddate)
2982       {
2983         this.version = version;
2984         this.builddate = builddate;
2985       }
2986
2987       @Override
2988       public void paint(Graphics g)
2989       {
2990         g.setColor(Color.white);
2991         g.fillRect(0, 0, getSize().width, getSize().height);
2992         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2993         FontMetrics fm = g.getFontMetrics();
2994         int fh = fm.getHeight();
2995         int y = 5, x = 7;
2996         g.setColor(Color.black);
2997         // TODO: update this text for each release or centrally store it for
2998         // lite and application
2999         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3000         g.drawString(MessageManager.formatMessage(
3001                 "label.jalviewLite_release", new String[] { version }), x,
3002                 y += fh);
3003         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3004         g.drawString(MessageManager.formatMessage(
3005                 "label.jaview_build_date", new String[] { builddate }), x,
3006                 y += fh);
3007         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3008         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3009                 x, y += fh * 1.5);
3010         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3011                 x + 50, y += fh + 8);
3012         g.drawString(
3013                 MessageManager.getString("label.jalview_dev_managers"), x,
3014                 y += fh);
3015         g.drawString(MessageManager
3016                 .getString("label.jalview_distribution_lists"), x, y += fh);
3017         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3018                 x, y += fh + 8);
3019         g.drawString(
3020                 MessageManager.getString("label.jalview_cite_1_authors"),
3021                 x, y += fh);
3022         g.drawString(
3023                 MessageManager.getString("label.jalview_cite_1_title"), x,
3024                 y += fh);
3025         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3026                 x, y += fh);
3027       }
3028     }
3029
3030     Frame frame = new Frame();
3031     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3032             .getBuildDate()));
3033     jalview.bin.JalviewLite.addFrame(frame,
3034             MessageManager.getString("label.jalview"), 580, 220);
3035
3036   }
3037
3038   public void showURL(String url, String target)
3039   {
3040     if (viewport.applet == null)
3041     {
3042       System.out.println("Not running as applet - no browser available.");
3043     }
3044     else
3045     {
3046       viewport.applet.showURL(url, target);
3047     }
3048   }
3049
3050   // ////////////////////////////////////////////////////////////////////////////////
3051   // JBuilder Graphics here
3052
3053   MenuBar alignFrameMenuBar = new MenuBar();
3054
3055   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3056
3057   MenuItem loadApplication = new MenuItem(
3058           MessageManager.getString("label.view_full_application"));
3059
3060   MenuItem loadTree = new MenuItem(
3061           MessageManager.getString("label.load_associated_tree"));
3062
3063   MenuItem loadAnnotations = new MenuItem(
3064           MessageManager.getString("label.load_features_annotations"));
3065
3066   MenuItem outputFeatures = new MenuItem(
3067           MessageManager.getString("label.export_features"));
3068
3069   MenuItem outputAnnotations = new MenuItem(
3070           MessageManager.getString("label.export_annotations"));
3071
3072   MenuItem closeMenuItem = new MenuItem(
3073           MessageManager.getString("action.close"));
3074
3075   MenuItem selectAllSequenceMenuItem = new MenuItem(
3076           MessageManager.getString("action.select_all"));
3077
3078   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3079           MessageManager.getString("action.deselect_all"));
3080
3081   MenuItem invertSequenceMenuItem = new MenuItem(
3082           MessageManager.getString("action.invert_selection"));
3083
3084   MenuItem remove2LeftMenuItem = new MenuItem();
3085
3086   MenuItem remove2RightMenuItem = new MenuItem();
3087
3088   MenuItem removeGappedColumnMenuItem = new MenuItem();
3089
3090   MenuItem removeAllGapsMenuItem = new MenuItem();
3091
3092   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3093
3094   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3095
3096   MenuItem sortPairwiseMenuItem = new MenuItem();
3097
3098   MenuItem sortIDMenuItem = new MenuItem();
3099
3100   MenuItem sortLengthMenuItem = new MenuItem();
3101
3102   MenuItem sortGroupMenuItem = new MenuItem();
3103
3104   MenuItem removeRedundancyMenuItem = new MenuItem();
3105
3106   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3107
3108   MenuItem PCAMenuItem = new MenuItem();
3109
3110   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3111
3112   MenuItem neighbourTreeMenuItem = new MenuItem();
3113
3114   BorderLayout borderLayout1 = new BorderLayout();
3115
3116   public Label statusBar = new Label();
3117
3118   MenuItem clustalColour = new MenuItem();
3119
3120   MenuItem zappoColour = new MenuItem();
3121
3122   MenuItem taylorColour = new MenuItem();
3123
3124   MenuItem hydrophobicityColour = new MenuItem();
3125
3126   MenuItem helixColour = new MenuItem();
3127
3128   MenuItem strandColour = new MenuItem();
3129
3130   MenuItem turnColour = new MenuItem();
3131
3132   MenuItem buriedColour = new MenuItem();
3133
3134   MenuItem purinePyrimidineColour = new MenuItem();
3135
3136   // MenuItem RNAInteractionColour = new MenuItem();
3137
3138   MenuItem RNAHelixColour = new MenuItem();
3139
3140   MenuItem userDefinedColour = new MenuItem();
3141
3142   MenuItem PIDColour = new MenuItem();
3143
3144   MenuItem BLOSUM62Colour = new MenuItem();
3145
3146   MenuItem tcoffeeColour = new MenuItem();
3147
3148   MenuItem njTreeBlosumMenuItem = new MenuItem();
3149
3150   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3151
3152   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3153
3154   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3155
3156   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3157
3158   MenuItem alProperties = new MenuItem(
3159           MessageManager.getString("label.alignment_props"));
3160
3161   MenuItem overviewMenuItem = new MenuItem();
3162
3163   MenuItem undoMenuItem = new MenuItem();
3164
3165   MenuItem redoMenuItem = new MenuItem();
3166
3167   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3168
3169   MenuItem noColourmenuItem = new MenuItem();
3170
3171   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3174
3175   MenuItem findMenuItem = new MenuItem();
3176
3177   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3178
3179   MenuItem nucleotideColour = new MenuItem();
3180
3181   MenuItem deleteGroups = new MenuItem();
3182
3183   MenuItem grpsFromSelection = new MenuItem();
3184
3185   MenuItem createGroup = new MenuItem();
3186
3187   MenuItem unGroup = new MenuItem();
3188
3189   MenuItem delete = new MenuItem();
3190
3191   MenuItem copy = new MenuItem();
3192
3193   MenuItem cut = new MenuItem();
3194
3195   Menu pasteMenu = new Menu();
3196
3197   MenuItem pasteNew = new MenuItem();
3198
3199   MenuItem pasteThis = new MenuItem();
3200
3201   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3202
3203   MenuItem font = new MenuItem();
3204
3205   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3206
3207   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3208
3209   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3210
3211   MenuItem modifyPID = new MenuItem();
3212
3213   MenuItem modifyConservation = new MenuItem();
3214
3215   CheckboxMenuItem autoCalculate = null;
3216
3217   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3218           "Sort Alignment With New Tree", true);
3219
3220   Menu sortByTreeMenu = new Menu();
3221
3222   MenuItem inputText = new MenuItem();
3223
3224   MenuItem documentation = new MenuItem();
3225
3226   MenuItem about = new MenuItem();
3227
3228   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3229
3230   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3231
3232   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3233
3234   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3235
3236   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3237
3238   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3245
3246   /**
3247    * Initialise menus and other items
3248    *
3249    * @throws Exception
3250    */
3251   private void jbInit() throws Exception
3252   {
3253     setMenuBar(alignFrameMenuBar);
3254
3255     /*
3256      * Configure File menu items and actions
3257      */
3258     inputText
3259             .setLabel(MessageManager.getString("label.input_from_textbox"));
3260     inputText.addActionListener(this);
3261     Menu outputTextboxMenu = new Menu(
3262             MessageManager.getString("label.out_to_textbox"));
3263     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3264     {
3265       MenuItem item = new MenuItem(ff);
3266
3267       item.addActionListener(new java.awt.event.ActionListener()
3268       {
3269         @Override
3270         public void actionPerformed(ActionEvent e)
3271         {
3272           outputText_actionPerformed(e);
3273         }
3274       });
3275
3276       outputTextboxMenu.add(item);
3277     }
3278     closeMenuItem.addActionListener(this);
3279     loadApplication.addActionListener(this);
3280     loadTree.addActionListener(this);
3281     loadAnnotations.addActionListener(this);
3282     outputFeatures.addActionListener(this);
3283     outputAnnotations.addActionListener(this);
3284
3285     /*
3286      * Configure Edit menu items and actions
3287      */
3288     undoMenuItem.setEnabled(false);
3289     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3290     undoMenuItem.addActionListener(this);
3291     redoMenuItem.setEnabled(false);
3292     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3293     redoMenuItem.addActionListener(this);
3294     copy.setLabel(MessageManager.getString("action.copy"));
3295     copy.addActionListener(this);
3296     cut.setLabel(MessageManager.getString("action.cut"));
3297     cut.addActionListener(this);
3298     delete.setLabel(MessageManager.getString("action.delete"));
3299     delete.addActionListener(this);
3300     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3301     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3302     pasteNew.addActionListener(this);
3303     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3304     pasteThis.addActionListener(this);
3305     remove2LeftMenuItem.setLabel(MessageManager
3306             .getString("action.remove_left"));
3307     remove2LeftMenuItem.addActionListener(this);
3308     remove2RightMenuItem.setLabel(MessageManager
3309             .getString("action.remove_right"));
3310     remove2RightMenuItem.addActionListener(this);
3311     removeGappedColumnMenuItem.setLabel(MessageManager
3312             .getString("action.remove_empty_columns"));
3313     removeGappedColumnMenuItem.addActionListener(this);
3314     removeAllGapsMenuItem.setLabel(MessageManager
3315             .getString("action.remove_all_gaps"));
3316     removeAllGapsMenuItem.addActionListener(this);
3317     removeRedundancyMenuItem.setLabel(MessageManager
3318             .getString("action.remove_redundancy"));
3319     removeRedundancyMenuItem.addActionListener(this);
3320
3321     /*
3322      * Configure Select menu items and actions
3323      */
3324     findMenuItem.setLabel(MessageManager.getString("action.find"));
3325     findMenuItem.addActionListener(this);
3326     selectAllSequenceMenuItem.addActionListener(this);
3327     deselectAllSequenceMenuItem.addActionListener(this);
3328     invertSequenceMenuItem.setLabel(MessageManager
3329             .getString("action.invert_sequence_selection"));
3330     invertSequenceMenuItem.addActionListener(this);
3331     invertColSel.setLabel(MessageManager
3332             .getString("action.invert_column_selection"));
3333     invertColSel.addActionListener(this);
3334     deleteGroups.setLabel(MessageManager
3335             .getString("action.undefine_groups"));
3336     deleteGroups.addActionListener(this);
3337     grpsFromSelection.setLabel(MessageManager
3338             .getString("action.make_groups_selection"));
3339     grpsFromSelection.addActionListener(this);
3340     createGroup.setLabel(MessageManager.getString("action.create_group"));
3341     createGroup.addActionListener(this);
3342     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3343     unGroup.addActionListener(this);
3344
3345     annotationColumnSelection.setLabel(MessageManager
3346             .getString("action.select_by_annotation"));
3347     annotationColumnSelection.addActionListener(this);
3348
3349     /*
3350      * Configure View menu items and actions
3351      */
3352     newView.setLabel(MessageManager.getString("action.new_view"));
3353     newView.addActionListener(this);
3354     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3355     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3356     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3357     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3358     hideColumns
3359             .setLabel(MessageManager.getString("label.selected_columns"));
3360     hideSequences.setLabel(MessageManager
3361             .getString("label.selected_sequences"));
3362     hideAllButSelection.setLabel(MessageManager
3363             .getString("label.all_but_selected_region"));
3364     hideAllSelection.setLabel(MessageManager
3365             .getString("label.selected_region"));
3366     showAllHidden.setLabel(MessageManager
3367             .getString("label.all_sequences_columns"));
3368     showColumns.addActionListener(this);
3369     showSeqs.addActionListener(this);
3370     hideColumns.addActionListener(this);
3371     hideSequences.addActionListener(this);
3372     hideAllButSelection.addActionListener(this);
3373     hideAllSelection.addActionListener(this);
3374     showAllHidden.addActionListener(this);
3375     featureSettings.setLabel(MessageManager
3376             .getString("action.feature_settings"));
3377     featureSettings.addActionListener(this);
3378     sequenceFeatures.setLabel(MessageManager
3379             .getString("label.show_sequence_features"));
3380     sequenceFeatures.addItemListener(this);
3381     sequenceFeatures.setState(false);
3382     followMouseOverFlag.setLabel(MessageManager
3383             .getString("label.automatic_scrolling"));
3384     followMouseOverFlag.addItemListener(this);
3385     alProperties.addActionListener(this);
3386     overviewMenuItem.setLabel(MessageManager
3387             .getString("label.overview_window"));
3388     overviewMenuItem.addActionListener(this);
3389
3390     /*
3391      * Configure Annotations menu items and actions
3392      */
3393     annotationPanelMenuItem.setLabel(MessageManager
3394             .getString("label.show_annotations"));
3395     annotationPanelMenuItem.addItemListener(this);
3396     showGroupConsensus.setLabel(MessageManager
3397             .getString("label.group_consensus"));
3398     showGroupConservation.setLabel(MessageManager
3399             .getString("label.group_conservation"));
3400     showConsensusHistogram.setLabel(MessageManager
3401             .getString("label.show_consensus_histogram"));
3402     showSequenceLogo.setLabel(MessageManager
3403             .getString("label.show_consensus_logo"));
3404     normSequenceLogo.setLabel(MessageManager
3405             .getString("label.norm_consensus_logo"));
3406     applyAutoAnnotationSettings.setLabel(MessageManager
3407             .getString("label.apply_all_groups"));
3408     applyAutoAnnotationSettings.setState(true);
3409     Menu autoAnnMenu = new Menu(
3410             MessageManager.getString("label.autocalculated_annotation"));
3411     showGroupConsensus.addItemListener(this);
3412     showGroupConservation.addItemListener(this);
3413     showConsensusHistogram.addItemListener(this);
3414     showSequenceLogo.addItemListener(this);
3415     normSequenceLogo.addItemListener(this);
3416     applyAutoAnnotationSettings.addItemListener(this);
3417     showAlignmentAnnotations = new CheckboxMenuItem(
3418             MessageManager.getString("label.show_all_al_annotations"));
3419     showSequenceAnnotations = new CheckboxMenuItem(
3420             MessageManager.getString("label.show_all_seq_annotations"));
3421     sortAnnBySequence = new CheckboxMenuItem(
3422             MessageManager.getString("label.sort_annotations_by_sequence"));
3423     sortAnnByLabel = new CheckboxMenuItem(
3424             MessageManager.getString("label.sort_annotations_by_label"));
3425     showAutoFirst = new CheckboxMenuItem(
3426             MessageManager.getString("label.show_first"));
3427     showAutoFirst.setState(false); // pending applet parameter
3428     setShowAutoCalculatedAbove(showAutoFirst.getState());
3429     showAutoLast = new CheckboxMenuItem(
3430             MessageManager.getString("label.show_last"));
3431     showAutoLast.setState(!showAutoFirst.getState());
3432     showAlignmentAnnotations.addItemListener(this);
3433     showSequenceAnnotations.addItemListener(this);
3434     sortAnnBySequence.addItemListener(this);
3435     sortAnnByLabel.addItemListener(this);
3436     showAutoFirst.addItemListener(this);
3437     showAutoLast.addItemListener(this);
3438
3439     /*
3440      * Configure Format menu items and actions
3441      */
3442     font.setLabel(MessageManager.getString("action.font"));
3443     font.addActionListener(this);
3444     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3445     scaleAbove.setState(true);
3446     scaleAbove.setEnabled(false);
3447     scaleAbove.addItemListener(this);
3448     scaleLeft.setEnabled(false);
3449     scaleLeft.setState(true);
3450     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3451     scaleLeft.addItemListener(this);
3452     scaleRight.setEnabled(false);
3453     scaleRight.setState(true);
3454     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3455     scaleRight.addItemListener(this);
3456     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3457     viewBoxesMenuItem.setState(true);
3458     viewBoxesMenuItem.addItemListener(this);
3459     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3460     viewTextMenuItem.setState(true);
3461     viewTextMenuItem.addItemListener(this);
3462     colourTextMenuItem.setLabel(MessageManager
3463             .getString("label.colour_text"));
3464     colourTextMenuItem.addItemListener(this);
3465     displayNonconservedMenuItem.setLabel(MessageManager
3466             .getString("label.show_non_conserved"));
3467     displayNonconservedMenuItem.addItemListener(this);
3468     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3469     wrapMenuItem.addItemListener(this);
3470     renderGapsMenuItem.setLabel(MessageManager
3471             .getString("action.show_gaps"));
3472     renderGapsMenuItem.setState(true);
3473     renderGapsMenuItem.addItemListener(this);
3474     centreColumnLabelFlag.setLabel(MessageManager
3475             .getString("label.centre_column_labels"));
3476     centreColumnLabelFlag.addItemListener(this);
3477     seqLimits.setState(true);
3478     seqLimits.setLabel(MessageManager
3479             .getString("label.show_sequence_limits"));
3480     seqLimits.addItemListener(this);
3481
3482     /*
3483      * Configure Colour menu items and actions
3484      */
3485     applyToAllGroups.setLabel(MessageManager
3486             .getString("label.apply_colour_to_all_groups"));
3487     applyToAllGroups.setState(true);
3488     applyToAllGroups.addItemListener(this);
3489     clustalColour.setLabel(MessageManager
3490             .getString("label.colourScheme_clustal"));
3491     clustalColour.addActionListener(this);
3492     zappoColour.setLabel(MessageManager
3493             .getString("label.colourScheme_zappo"));
3494     zappoColour.addActionListener(this);
3495     taylorColour.setLabel(MessageManager
3496             .getString("label.colourScheme_taylor"));
3497     taylorColour.addActionListener(this);
3498     hydrophobicityColour.setLabel(MessageManager
3499             .getString("label.colourScheme_hydrophobic"));
3500     hydrophobicityColour.addActionListener(this);
3501     helixColour.setLabel(MessageManager
3502             .getString("label.colourScheme_helix_propensity"));
3503     helixColour.addActionListener(this);
3504     strandColour.setLabel(MessageManager
3505             .getString("label.colourScheme_strand_propensity"));
3506     strandColour.addActionListener(this);
3507     turnColour.setLabel(MessageManager
3508             .getString("label.colourScheme_turn_propensity"));
3509     turnColour.addActionListener(this);
3510     buriedColour.setLabel(MessageManager
3511             .getString("label.colourScheme_buried_index"));
3512     buriedColour.addActionListener(this);
3513     purinePyrimidineColour.setLabel(MessageManager
3514             .getString("label.colourScheme_purine/pyrimidine"));
3515     purinePyrimidineColour.addActionListener(this);
3516     // RNAInteractionColour.setLabel(MessageManager
3517     // .getString("label.rna_interaction"));
3518     // RNAInteractionColour.addActionListener(this);
3519     RNAHelixColour.setLabel(MessageManager
3520             .getString("label.colourScheme_rna_helices"));
3521     RNAHelixColour.addActionListener(this);
3522     userDefinedColour.setLabel(MessageManager
3523             .getString("action.user_defined"));
3524     userDefinedColour.addActionListener(this);
3525     PIDColour.setLabel(MessageManager
3526             .getString("label.colourScheme_%_identity"));
3527     PIDColour.addActionListener(this);
3528     BLOSUM62Colour.setLabel(MessageManager
3529             .getString("label.colourScheme_blosum62"));
3530     BLOSUM62Colour.addActionListener(this);
3531     tcoffeeColour.setLabel(MessageManager
3532             .getString("label.colourScheme_t-coffee_scores"));
3533     // it will be enabled only if a score file is provided
3534     tcoffeeColour.setEnabled(false);
3535     tcoffeeColour.addActionListener(this);
3536     conservationMenuItem.setLabel(MessageManager
3537             .getString("action.by_conservation"));
3538     conservationMenuItem.addItemListener(this);
3539     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3540     noColourmenuItem.addActionListener(this);
3541     abovePIDThreshold.setLabel(MessageManager
3542             .getString("label.above_identity_threshold"));
3543     abovePIDThreshold.addItemListener(this);
3544     nucleotideColour.setLabel(MessageManager
3545             .getString("label.colourScheme_nucleotide"));
3546     nucleotideColour.addActionListener(this);
3547     modifyPID.setLabel(MessageManager
3548             .getString("label.modify_identity_threshold"));
3549     modifyPID.setEnabled(abovePIDThreshold.getState());
3550     modifyPID.addActionListener(this);
3551     modifyConservation.setLabel(MessageManager
3552             .getString("label.modify_conservation_threshold"));
3553     modifyConservation.setEnabled(conservationMenuItem.getState());
3554     modifyConservation.addActionListener(this);
3555     annotationColour.setLabel(MessageManager
3556             .getString("action.by_annotation"));
3557     annotationColour.addActionListener(this);
3558
3559     /*
3560      * Configure Calculate menu items and actions
3561      */
3562     sortPairwiseMenuItem.setLabel(MessageManager
3563             .getString("action.by_pairwise_id"));
3564     sortPairwiseMenuItem.addActionListener(this);
3565     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3566     sortIDMenuItem.addActionListener(this);
3567     sortLengthMenuItem.setLabel(MessageManager
3568             .getString("action.by_length"));
3569     sortLengthMenuItem.addActionListener(this);
3570     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3571     sortGroupMenuItem.addActionListener(this);
3572     pairwiseAlignmentMenuItem.setLabel(MessageManager
3573             .getString("action.pairwise_alignment"));
3574     pairwiseAlignmentMenuItem.addActionListener(this);
3575     PCAMenuItem.setLabel(MessageManager
3576             .getString("label.principal_component_analysis"));
3577     PCAMenuItem.addActionListener(this);
3578     autoCalculate = new CheckboxMenuItem(
3579             MessageManager.getString("label.autocalculate_consensus"), true);
3580     averageDistanceTreeMenuItem.setLabel(MessageManager
3581             .getString("label.average_distance_identity"));
3582     averageDistanceTreeMenuItem.addActionListener(this);
3583     neighbourTreeMenuItem.setLabel(MessageManager
3584             .getString("label.neighbour_joining_identity"));
3585     neighbourTreeMenuItem.addActionListener(this);
3586     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3587             .getString("label.average_distance_blosum62"));
3588     avDistanceTreeBlosumMenuItem.addActionListener(this);
3589     njTreeBlosumMenuItem.setLabel(MessageManager
3590             .getString("label.neighbour_blosum62"));
3591     njTreeBlosumMenuItem.addActionListener(this);
3592     sortByTreeMenu.setLabel(MessageManager
3593             .getString("action.by_tree_order"));
3594     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3595     Menu calculateTreeMenu = new Menu(
3596             MessageManager.getString("action.calculate_tree"));
3597     autoCalculate.addItemListener(this);
3598     sortByTree.addItemListener(this);
3599
3600     /*
3601      * Configure Help menu items and actions
3602      */
3603     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3604     documentation.setLabel(MessageManager.getString("label.documentation"));
3605     documentation.addActionListener(this);
3606     about.setLabel(MessageManager.getString("label.about"));
3607     about.addActionListener(this);
3608
3609     /*
3610      * Add top level menus to frame
3611      */
3612     alignFrameMenuBar.add(fileMenu);
3613     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3614     alignFrameMenuBar.add(editMenu);
3615     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3616     alignFrameMenuBar.add(selectMenu);
3617     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3618     alignFrameMenuBar.add(viewMenu);
3619     Menu annotationsMenu = new Menu(
3620             MessageManager.getString("action.annotations"));
3621     alignFrameMenuBar.add(annotationsMenu);
3622     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3623     alignFrameMenuBar.add(formatMenu);
3624     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3625     alignFrameMenuBar.add(colourMenu);
3626     Menu calculateMenu = new Menu(
3627             MessageManager.getString("action.calculate"));
3628     alignFrameMenuBar.add(calculateMenu);
3629     alignFrameMenuBar.add(helpMenu);
3630
3631     /*
3632      * File menu
3633      */
3634     fileMenu.add(inputText);
3635     fileMenu.add(loadTree);
3636     fileMenu.add(loadAnnotations);
3637     fileMenu.addSeparator();
3638     fileMenu.add(outputTextboxMenu);
3639     fileMenu.add(outputFeatures);
3640     fileMenu.add(outputAnnotations);
3641     if (jalviewServletURL != null)
3642     {
3643       fileMenu.add(loadApplication);
3644     }
3645     fileMenu.addSeparator();
3646     fileMenu.add(closeMenuItem);
3647
3648     /*
3649      * Edit menu
3650      */
3651     editMenu.add(undoMenuItem);
3652     editMenu.add(redoMenuItem);
3653     editMenu.add(cut);
3654     editMenu.add(copy);
3655     pasteMenu.add(pasteNew);
3656     pasteMenu.add(pasteThis);
3657     editMenu.add(pasteMenu);
3658     editMenu.add(delete);
3659     editMenu.addSeparator();
3660     editMenu.add(remove2LeftMenuItem);
3661     editMenu.add(remove2RightMenuItem);
3662     editMenu.add(removeGappedColumnMenuItem);
3663     editMenu.add(removeAllGapsMenuItem);
3664     editMenu.add(removeRedundancyMenuItem);
3665
3666     /*
3667      * Select menu
3668      */
3669     selectMenu.add(findMenuItem);
3670     selectMenu.addSeparator();
3671     selectMenu.add(selectAllSequenceMenuItem);
3672     selectMenu.add(deselectAllSequenceMenuItem);
3673     selectMenu.add(invertSequenceMenuItem);
3674     selectMenu.add(invertColSel);
3675     selectMenu.add(createGroup);
3676     selectMenu.add(unGroup);
3677     selectMenu.add(grpsFromSelection);
3678     selectMenu.add(deleteGroups);
3679     selectMenu.add(annotationColumnSelection);
3680
3681     /*
3682      * View menu
3683      */
3684     viewMenu.add(newView);
3685     viewMenu.addSeparator();
3686     showMenu.add(showColumns);
3687     showMenu.add(showSeqs);
3688     showMenu.add(showAllHidden);
3689     viewMenu.add(showMenu);
3690     hideMenu.add(hideColumns);
3691     hideMenu.add(hideSequences);
3692     hideMenu.add(hideAllSelection);
3693     hideMenu.add(hideAllButSelection);
3694     viewMenu.add(hideMenu);
3695     viewMenu.addSeparator();
3696     viewMenu.add(followMouseOverFlag);
3697     viewMenu.addSeparator();
3698     viewMenu.add(sequenceFeatures);
3699     viewMenu.add(featureSettings);
3700     viewMenu.addSeparator();
3701     viewMenu.add(alProperties);
3702     viewMenu.addSeparator();
3703     viewMenu.add(overviewMenuItem);
3704
3705     /*
3706      * Annotations menu
3707      */
3708     annotationsMenu.add(annotationPanelMenuItem);
3709     annotationsMenu.addSeparator();
3710     annotationsMenu.add(showAlignmentAnnotations);
3711     annotationsMenu.add(showSequenceAnnotations);
3712     annotationsMenu.add(sortAnnBySequence);
3713     annotationsMenu.add(sortAnnByLabel);
3714     annotationsMenu.addSeparator();
3715     autoAnnMenu.add(showAutoFirst);
3716     autoAnnMenu.add(showAutoLast);
3717     autoAnnMenu.addSeparator();
3718     autoAnnMenu.add(applyAutoAnnotationSettings);
3719     autoAnnMenu.add(showConsensusHistogram);
3720     autoAnnMenu.add(showSequenceLogo);
3721     autoAnnMenu.add(normSequenceLogo);
3722     autoAnnMenu.addSeparator();
3723     autoAnnMenu.add(showGroupConservation);
3724     autoAnnMenu.add(showGroupConsensus);
3725     annotationsMenu.add(autoAnnMenu);
3726
3727     /*
3728      * Format menu
3729      */
3730     formatMenu.add(font);
3731     formatMenu.add(seqLimits);
3732     formatMenu.add(wrapMenuItem);
3733     formatMenu.add(scaleAbove);
3734     formatMenu.add(scaleLeft);
3735     formatMenu.add(scaleRight);
3736     formatMenu.add(viewBoxesMenuItem);
3737     formatMenu.add(viewTextMenuItem);
3738     formatMenu.add(colourTextMenuItem);
3739     formatMenu.add(displayNonconservedMenuItem);
3740     formatMenu.add(renderGapsMenuItem);
3741     formatMenu.add(centreColumnLabelFlag);
3742
3743     /*
3744      * Colour menu
3745      */
3746     colourMenu.add(applyToAllGroups);
3747     colourMenu.addSeparator();
3748     colourMenu.add(noColourmenuItem);
3749     colourMenu.add(clustalColour);
3750     colourMenu.add(BLOSUM62Colour);
3751     colourMenu.add(PIDColour);
3752     colourMenu.add(zappoColour);
3753     colourMenu.add(taylorColour);
3754     colourMenu.add(hydrophobicityColour);
3755     colourMenu.add(helixColour);
3756     colourMenu.add(strandColour);
3757     colourMenu.add(turnColour);
3758     colourMenu.add(buriedColour);
3759     colourMenu.add(nucleotideColour);
3760     colourMenu.add(purinePyrimidineColour);
3761     // colourMenu.add(RNAInteractionColour);
3762     colourMenu.add(tcoffeeColour);
3763     colourMenu.add(userDefinedColour);
3764     colourMenu.addSeparator();
3765     colourMenu.add(conservationMenuItem);
3766     colourMenu.add(modifyConservation);
3767     colourMenu.add(abovePIDThreshold);
3768     colourMenu.add(modifyPID);
3769     colourMenu.add(annotationColour);
3770     colourMenu.add(RNAHelixColour);
3771
3772     /*
3773      * Calculate menu
3774      */
3775     sortMenu.add(sortIDMenuItem);
3776     sortMenu.add(sortLengthMenuItem);
3777     sortMenu.add(sortByTreeMenu);
3778     sortMenu.add(sortGroupMenuItem);
3779     sortMenu.add(sortPairwiseMenuItem);
3780     calculateMenu.add(sortMenu);
3781     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3782     calculateTreeMenu.add(neighbourTreeMenuItem);
3783     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3784     calculateTreeMenu.add(njTreeBlosumMenuItem);
3785     calculateMenu.add(calculateTreeMenu);
3786     calculateMenu.addSeparator();
3787     calculateMenu.add(pairwiseAlignmentMenuItem);
3788     calculateMenu.add(PCAMenuItem);
3789     calculateMenu.add(autoCalculate);
3790     calculateMenu.add(sortByTree);
3791
3792     /*
3793      * Help menu
3794      */
3795     helpMenu.add(documentation);
3796     helpMenu.add(about);
3797
3798     /*
3799      * Status bar
3800      */
3801     statusBar.setBackground(Color.white);
3802     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3803     statusBar.setText(MessageManager.getString("label.status_bar"));
3804     this.add(statusBar, BorderLayout.SOUTH);
3805   }
3806
3807   @Override
3808   public void setStatus(String string)
3809   {
3810     statusBar.setText(string);
3811   };
3812
3813   MenuItem featureSettings = new MenuItem();
3814
3815   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3816
3817   MenuItem annotationColour = new MenuItem();
3818
3819   MenuItem annotationColumnSelection = new MenuItem();
3820
3821   MenuItem invertColSel = new MenuItem();
3822
3823   MenuItem showColumns = new MenuItem();
3824
3825   MenuItem showSeqs = new MenuItem();
3826
3827   MenuItem hideColumns = new MenuItem();
3828
3829   MenuItem hideSequences = new MenuItem();
3830
3831   MenuItem hideAllButSelection = new MenuItem();
3832
3833   MenuItem hideAllSelection = new MenuItem();
3834
3835   MenuItem showAllHidden = new MenuItem();
3836
3837   MenuItem newView = new MenuItem();
3838
3839   private CheckboxMenuItem showAlignmentAnnotations;
3840
3841   private CheckboxMenuItem showSequenceAnnotations;
3842
3843   private CheckboxMenuItem sortAnnBySequence;
3844
3845   private CheckboxMenuItem sortAnnByLabel;
3846
3847   private CheckboxMenuItem showAutoFirst;
3848
3849   private CheckboxMenuItem showAutoLast;
3850
3851   private SplitFrame splitFrame;
3852
3853   /**
3854    * Attach the alignFrame panels after embedding menus, if necessary. This used
3855    * to be called setEmbedded, but is now creates the dropdown menus in a
3856    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3857    *
3858    * @param reallyEmbedded
3859    *          true to attach the view to the applet area on the page rather than
3860    *          in a new window
3861    */
3862   public void createAlignFrameWindow(boolean reallyEmbedded)
3863   {
3864     if (reallyEmbedded)
3865     {
3866       embedAlignFrameInApplet(viewport.applet);
3867     }
3868     else
3869     {
3870       // //////
3871       // test and embed menu bar if necessary.
3872       //
3873       if (embedMenuIfNeeded(alignPanel))
3874       {
3875         /*
3876          * adjust for status bar height too. ? pointless as overridden by layout
3877          * manager
3878          */
3879         alignPanel.setSize(getSize().width,
3880                 getSize().height - statusBar.getHeight());
3881       }
3882       add(statusBar, BorderLayout.SOUTH);
3883       add(alignPanel, BorderLayout.CENTER);
3884       // and register with the applet so it can pass external API calls to us
3885       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3886               frameHeight);
3887     }
3888   }
3889
3890   /**
3891    * Add the components of this AlignFrame to the applet container.
3892    *
3893    * @param theApplet
3894    */
3895   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3896   {
3897     // ////
3898     // Explicitly build the embedded menu panel for the on-page applet
3899     //
3900     // view cannot be closed if its actually on the page
3901     fileMenu.remove(closeMenuItem);
3902     fileMenu.remove(3); // Remove Separator
3903     // construct embedded menu, using default font
3904     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3905     // and actually add the components to the applet area
3906     theApplet.setLayout(new BorderLayout());
3907     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3908     theApplet.add(statusBar, BorderLayout.SOUTH);
3909     // TODO should size be left to the layout manager?
3910     alignPanel.setSize(theApplet.getSize().width,
3911             theApplet.getSize().height - embeddedMenu.getHeight()
3912                     - statusBar.getHeight());
3913     theApplet.add(alignPanel, BorderLayout.CENTER);
3914     final AlignFrame me = this;
3915     theApplet.addFocusListener(new FocusListener()
3916     {
3917
3918       @Override
3919       public void focusLost(FocusEvent e)
3920       {
3921         if (theApplet.currentAlignFrame == me)
3922         {
3923           theApplet.currentAlignFrame = null;
3924         }
3925       }
3926
3927       @Override
3928       public void focusGained(FocusEvent e)
3929       {
3930         theApplet.currentAlignFrame = me;
3931       }
3932     });
3933     theApplet.validate();
3934   }
3935
3936   /**
3937    * create a new binding between structures in an existing jmol viewer instance
3938    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3939    * this does not open a new Jmol window, or modify the display of the
3940    * structures in the original jmol window. Note This method doesn't work
3941    * without an additional javascript library to exchange messages between the
3942    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3943    *
3944    * @param viewer
3945    *          JmolViewer instance
3946    * @param sequenceIds
3947    *          - sequence Ids to search for associations
3948    */
3949   public SequenceStructureBinding addStructureViewInstance(
3950           Object jmolviewer, String[] sequenceIds)
3951   {
3952     Viewer viewer = null;
3953     try
3954     {
3955       viewer = (Viewer) jmolviewer;
3956     } catch (ClassCastException ex)
3957     {
3958       System.err.println("Unsupported viewer object :"
3959               + jmolviewer.getClass());
3960     }
3961     if (viewer == null)
3962     {
3963       System.err.println("Can't use this object as a structure viewer:"
3964               + jmolviewer.getClass());
3965       return null;
3966     }
3967     SequenceI[] seqs = null;
3968     if (sequenceIds == null || sequenceIds.length == 0)
3969     {
3970       seqs = viewport.getAlignment().getSequencesArray();
3971     }
3972     else
3973     {
3974       Vector sqi = new Vector();
3975       AlignmentI al = viewport.getAlignment();
3976       for (int sid = 0; sid < sequenceIds.length; sid++)
3977       {
3978         SequenceI sq = al.findName(sequenceIds[sid]);
3979         if (sq != null)
3980         {
3981           sqi.addElement(sq);
3982         }
3983       }
3984       if (sqi.size() > 0)
3985       {
3986         seqs = new SequenceI[sqi.size()];
3987         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3988         {
3989           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3990         }
3991       }
3992       else
3993       {
3994         return null;
3995       }
3996     }
3997     AAStructureBindingModel jmv = null;
3998     // TODO: search for a jmv that involves viewer
3999     if (jmv == null)
4000     { // create a new viewer/jalview binding.
4001       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4002     }
4003     return jmv;
4004
4005   }
4006
4007   /**
4008    * bind a pdb file to a sequence in the current view
4009    *
4010    * @param sequenceId
4011    *          - sequenceId within the dataset.
4012    * @param pdbEntryString
4013    *          - the short name for the PDB file
4014    * @param pdbFile
4015    *          - pdb file - either a URL or a valid PDB file.
4016    * @return true if binding was as success TODO: consider making an exception
4017    *         structure for indicating when PDB parsing or sequenceId location
4018    *         fails.
4019    */
4020   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4021           String pdbFile)
4022   {
4023     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4024     boolean needtoadd = false;
4025     if (toaddpdb != null)
4026     {
4027       Vector pdbe = toaddpdb.getAllPDBEntries();
4028       PDBEntry pdbentry = null;
4029       if (pdbe != null && pdbe.size() > 0)
4030       {
4031         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4032         {
4033           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4034           if (!pdbentry.getId().equals(pdbEntryString)
4035                   && !pdbentry.getFile().equals(pdbFile))
4036           {
4037             pdbentry = null;
4038           }
4039           else
4040           {
4041             continue;
4042           }
4043         }
4044       }
4045       if (pdbentry == null)
4046       {
4047         pdbentry = new PDBEntry();
4048         pdbentry.setId(pdbEntryString);
4049         pdbentry.setFile(pdbFile);
4050         needtoadd = true; // add this new entry to sequence.
4051       }
4052       // resolve data source
4053       // TODO: this code should be a refactored to an io package
4054       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4055               pdbFile, FileFormat.PDB);
4056       if (protocol == null)
4057       {
4058         return false;
4059       }
4060       if (needtoadd)
4061       {
4062         pdbentry.setProperty("protocol", protocol);
4063         toaddpdb.addPDBId(pdbentry);
4064         alignPanel.getStructureSelectionManager()
4065                 .registerPDBEntry(pdbentry);
4066       }
4067     }
4068     return true;
4069   }
4070
4071   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4072   {
4073     if (seqs != null)
4074     {
4075       Vector sequences = new Vector();
4076       for (int i = 0; i < seqs.length; i++)
4077       {
4078         if (seqs[i] != null)
4079         {
4080           sequences.addElement(new Object[] { seqs[i],
4081               (chains != null) ? chains[i] : null });
4082         }
4083       }
4084       seqs = new SequenceI[sequences.size()];
4085       chains = new String[sequences.size()];
4086       for (int i = 0, isize = sequences.size(); i < isize; i++)
4087       {
4088         Object[] oj = (Object[]) sequences.elementAt(i);
4089
4090         seqs[i] = (SequenceI) oj[0];
4091         chains[i] = (String) oj[1];
4092       }
4093     }
4094     return new Object[] { seqs, chains };
4095
4096   }
4097
4098   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4099           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4100   {
4101     // Scrub any null sequences from the array
4102     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4103     seqs = (SequenceI[]) sqch[0];
4104     chains = (String[]) sqch[1];
4105     if (seqs == null || seqs.length == 0)
4106     {
4107       System.err
4108               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4109     }
4110     if (protocol == null)
4111     {
4112       String sourceType = (String) pdb.getProperty("protocol");
4113       try
4114       {
4115         protocol = DataSourceType.valueOf(sourceType);
4116       } catch (IllegalArgumentException e)
4117       {
4118         // ignore
4119       }
4120       if (protocol == null)
4121       {
4122         System.err.println("Couldn't work out protocol to open structure: "
4123                 + pdb.getId());
4124         return;
4125       }
4126     }
4127     if (applet.useXtrnalSviewer)
4128     {
4129       // register the association(s) and quit, don't create any windows.
4130       if (StructureSelectionManager.getStructureSelectionManager(applet)
4131               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4132       {
4133         System.err.println("Failed to map " + pdb.getFile() + " ("
4134                 + protocol + ") to any sequences");
4135       }
4136       return;
4137     }
4138     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4139     {
4140       // can only do alignments with Jmol
4141       // find the last jmol window assigned to this alignment
4142       AppletJmol ajm = null, tajm;
4143       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4144       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4145       {
4146         tajm = (AppletJmol) jmols.elementAt(i);
4147         if (tajm.ap.alignFrame == this)
4148         {
4149           ajm = tajm;
4150           break;
4151         }
4152       }
4153       if (ajm != null)
4154       {
4155         System.err
4156                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4157         // try and add the pdb structure
4158         // ajm.addS
4159         ajm = null;
4160       }
4161     }
4162     // otherwise, create a new window
4163     if (applet.jmolAvailable)
4164     {
4165       new AppletJmol(pdb, seqs, chains, alignPanel,
4166               protocol);
4167       applet.lastFrameX += 40;
4168       applet.lastFrameY += 40;
4169     }
4170     else
4171     {
4172       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4173     }
4174
4175   }
4176
4177   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4178           SequenceI[][] seqs, String[][] chains, String[] protocols)
4179   {
4180     // TODO Auto-generated method stub
4181     System.err.println("Aligned Structure View: Not yet implemented.");
4182   }
4183
4184   /**
4185    * modify the current selection, providing the user has not made a selection
4186    * already.
4187    *
4188    * @param sel
4189    *          - sequences from this alignment
4190    * @param csel
4191    *          - columns to be selected on the alignment
4192    */
4193   public void select(SequenceGroup sel, ColumnSelection csel)
4194   {
4195     alignPanel.seqPanel.selection(sel, csel, null);
4196   }
4197
4198   public void scrollTo(int row, int column)
4199   {
4200     alignPanel.seqPanel.scrollTo(row, column);
4201   }
4202
4203   public void scrollToRow(int row)
4204   {
4205     alignPanel.seqPanel.scrollToRow(row);
4206   }
4207
4208   public void scrollToColumn(int column)
4209   {
4210     alignPanel.seqPanel.scrollToColumn(column);
4211   }
4212
4213   /**
4214    * @return the alignments unique ID.
4215    */
4216   public String getSequenceSetId()
4217   {
4218     return viewport.getSequenceSetId();
4219   }
4220
4221   /**
4222    * Load the (T-Coffee) score file from the specified url
4223    *
4224    * @param source
4225    *          File/URL/T-COFFEE score file contents
4226    * @throws IOException
4227    * @return true if alignment was annotated with data from source
4228    */
4229   public boolean loadScoreFile(String source) throws IOException
4230   {
4231
4232     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4233             AppletFormatAdapter.checkProtocol(source));
4234     if (!file.isValid())
4235     {
4236       // TODO: raise dialog for gui
4237       System.err.println("Problems parsing T-Coffee scores: "
4238               + file.getWarningMessage());
4239       System.err.println("Origin was:\n" + source);
4240       return false;
4241     }
4242
4243     /*
4244      * check that the score matrix matches the alignment dimensions
4245      */
4246     AlignmentI aln;
4247     if ((aln = viewport.getAlignment()) != null
4248             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4249                     .getWidth()))
4250     {
4251       // TODO: raise a dialog box here rather than bomb out.
4252       System.err
4253               .println("The scores matrix does not match the alignment dimensions");
4254
4255     }
4256
4257     // TODO add parameter to indicate if matching should be done
4258     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4259     {
4260       alignPanel.fontChanged();
4261       tcoffeeColour.setEnabled(true);
4262       // switch to this color
4263       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4264       return true;
4265     }
4266     else
4267     {
4268       System.err.println("Problems resolving T-Coffee scores:");
4269       if (file.getWarningMessage() != null)
4270       {
4271         System.err.println(file.getWarningMessage());
4272       }
4273     }
4274     return false;
4275   }
4276
4277   public SplitFrame getSplitFrame()
4278   {
4279     return this.splitFrame;
4280   }
4281
4282   public void setSplitFrame(SplitFrame sf)
4283   {
4284     this.splitFrame = sf;
4285   }
4286
4287   // may not need this
4288   @Override
4289   public void setShowSeqFeatures(boolean b)
4290   {
4291     // showSeqFeatures.setSelected(b);
4292     viewport.setShowSequenceFeatures(b);
4293
4294   }
4295
4296   @Override
4297   public void setMenusForViewport()
4298   {
4299     // setMenusFromViewport(viewport);
4300
4301   }
4302
4303   @Override
4304   public void refreshFeatureUI(boolean enableIfNecessary)
4305   {
4306     if (enableIfNecessary)
4307     {
4308       sequenceFeatures.setState(true);
4309       alignPanel.av.setShowSequenceFeatures(true);
4310     }
4311   }
4312
4313   @Override
4314   public FeatureSettingsControllerI getFeatureSettingsUI()
4315   {
4316     return alignPanel.av.featureSettings;
4317   }
4318
4319 }