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.HiddenColumns;
  47 import jalview.datamodel.PDBEntry;
  48 import jalview.datamodel.Sequence;
  49 import jalview.datamodel.SequenceGroup;
  50 import jalview.datamodel.SequenceI;
  51 import jalview.io.AnnotationFile;
  52 import jalview.io.AppletFormatAdapter;
  53 import jalview.io.DataSourceType;
  54 import jalview.io.FeaturesFile;
  55 import jalview.io.FileFormat;
  56 import jalview.io.FileFormatI;
  57 import jalview.io.FileFormats;
  58 import jalview.io.TCoffeeScoreFile;
  59 import jalview.schemes.Blosum62ColourScheme;
  60 import jalview.schemes.BuriedColourScheme;
  61 import jalview.schemes.ClustalxColourScheme;
  62 import jalview.schemes.ColourSchemeI;
  63 import jalview.schemes.HelixColourScheme;
  64 import jalview.schemes.HydrophobicColourScheme;
  65 import jalview.schemes.NucleotideColourScheme;
  66 import jalview.schemes.PIDColourScheme;
  67 import jalview.schemes.PurinePyrimidineColourScheme;
  68 import jalview.schemes.RNAHelicesColour;
  69 import jalview.schemes.StrandColourScheme;
  70 import jalview.schemes.TCoffeeColourScheme;
  71 import jalview.schemes.TaylorColourScheme;
  72 import jalview.schemes.TurnColourScheme;
  73 import jalview.schemes.ZappoColourScheme;
  74 import jalview.structure.StructureSelectionManager;
  75 import jalview.structures.models.AAStructureBindingModel;
  76 import jalview.util.MappingUtils;
  77 import jalview.util.MessageManager;
  78 import jalview.viewmodel.AlignmentViewport;
  79 import jalview.viewmodel.ViewportRanges;
  80
  81 import java.awt.BorderLayout;
  82 import java.awt.Canvas;
  83 import java.awt.CheckboxMenuItem;
  84 import java.awt.Color;
  85 import java.awt.FlowLayout;
  86 import java.awt.Font;
  87 import java.awt.FontMetrics;
  88 import java.awt.Frame;
  89 import java.awt.Graphics;
  90 import java.awt.Label;
  91 import java.awt.Menu;
  92 import java.awt.MenuBar;
  93 import java.awt.MenuItem;
  94 import java.awt.Panel;
  95 import java.awt.event.ActionEvent;
  96 import java.awt.event.ActionListener;
  97 import java.awt.event.FocusEvent;
  98 import java.awt.event.FocusListener;
  99 import java.awt.event.ItemEvent;
 100 import java.awt.event.ItemListener;
 101 import java.awt.event.KeyEvent;
 102 import java.awt.event.KeyListener;
 103 import java.awt.event.WindowAdapter;
 104 import java.awt.event.WindowEvent;
 105 import java.io.IOException;
 106 import java.net.URL;
 107 import java.net.URLEncoder;
 108 import java.util.Arrays;
 109 import java.util.Deque;
 110 import java.util.HashMap;
 111 import java.util.List;
 112 import java.util.Map;
 113 import java.util.StringTokenizer;
 114 import java.util.Vector;
 115
 116 import org.jmol.viewer.Viewer;
 117
 118 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 119         ItemListener, KeyListener, AlignViewControllerGuiI
 120 {
 121   public AlignViewControllerI avc;
 122
 123   public AlignmentPanel alignPanel;
 124
 125   public AlignViewport viewport;
 126
 127   // width and height may be overridden by applet parameters
 128   int frameWidth = 700;
 129
 130   int frameHeight = 500;
 131
 132   String jalviewServletURL;
 133
 134   /*
 135    * Flag for showing autocalculated consensus above or below other consensus
 136    * rows
 137    */
 138   private boolean showAutoCalculatedAbove;
 139
 140   private SequenceAnnotationOrder annotationSortOrder;
 141
 142   /**
 143    * Constructor that creates the frame and adds it to the display.
 144    *
 145    * @param al
 146    * @param applet
 147    * @param title
 148    * @param embedded
 149    */
 150   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 151           boolean embedded)
 152   {
 153     this(al, applet, title, embedded, true);
 154   }
 155
 156   /**
 157    * Constructor that optionally allows the frame to be displayed or only
 158    * created.
 159    *
 160    * @param al
 161    * @param applet
 162    * @param title
 163    * @param embedded
 164    * @param addToDisplay
 165    */
 166   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 167           boolean embedded, boolean addToDisplay)
 168   {
 169     this(al, null, null, applet, title, embedded, addToDisplay);
 170   }
 171
 172   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 173           HiddenColumns hidden, JalviewLite applet,
 174           String title, boolean embedded)
 175   {
 176     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 177   }
 178
 179   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 180           HiddenColumns hidden, JalviewLite applet,
 181           String title, boolean embedded, boolean addToDisplay)
 182   {
 183     if (applet != null)
 184     {
 185       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 186     }
 187
 188     try
 189     {
 190       jbInit();
 191     } catch (Exception ex)
 192     {
 193       ex.printStackTrace();
 194     }
 195     // need to get window geometry before we calculate alignment layout
 196     if (applet != null)
 197     {
 198       String param;
 199       try
 200       {
 201         param = applet.getParameter("windowWidth");
 202         if (param != null)
 203         {
 204           int width = Integer.parseInt(param);
 205           frameWidth = width;
 206         }
 207         param = applet.getParameter("windowHeight");
 208         if (param != null)
 209         {
 210           int height = Integer.parseInt(param);
 211           frameHeight = height;
 212         }
 213       } catch (Exception ex)
 214       {
 215       }
 216     }
 217     viewport = new AlignViewport(al, applet);
 218
 219     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 220     {
 221       viewport.hideSequence(hiddenSeqs);
 222     }
 223     if (hidden != null)
 224     {
 225       viewport.getAlignment().setHiddenColumns(hidden);
 226     }
 227     viewport.setScaleAboveWrapped(scaleAbove.getState());
 228
 229     alignPanel = new AlignmentPanel(this, viewport);
 230     avc = new jalview.controller.AlignViewController(this, viewport,
 231             alignPanel);
 232     viewport.updateConservation(alignPanel);
 233     viewport.updateConsensus(alignPanel);
 234
 235     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 236     followMouseOverFlag.setState(viewport.isFollowHighlight());
 237     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 238     showGroupConservation.setState(viewport.isShowGroupConservation());
 239     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 240     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 241     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 242     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 243     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 244     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 245     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 246     showAlignmentAnnotations.setState(true);
 247     showSequenceAnnotations.setState(false);
 248
 249     seqLimits.setState(viewport.getShowJVSuffix());
 250
 251     if (applet != null)
 252     {
 253       String param = applet.getParameter("sortBy");
 254       if (param != null)
 255       {
 256         if (param.equalsIgnoreCase("Id"))
 257         {
 258           sortIDMenuItem_actionPerformed();
 259         }
 260         else if (param.equalsIgnoreCase("Pairwise Identity"))
 261         {
 262           sortPairwiseMenuItem_actionPerformed();
 263         }
 264         else if (param.equalsIgnoreCase("Length"))
 265         {
 266           sortLengthMenuItem_actionPerformed();
 267         }
 268       }
 269
 270       param = applet.getParameter("wrap");
 271       if (param != null)
 272       {
 273         if (param.equalsIgnoreCase("true"))
 274         {
 275           wrapMenuItem.setState(true);
 276           wrapMenuItem_actionPerformed();
 277         }
 278       }
 279       param = applet.getParameter("centrecolumnlabels");
 280       if (param != null)
 281       {
 282         centreColumnLabelFlag.setState(true);
 283         centreColumnLabelFlag_stateChanged();
 284       }
 285
 286     }
 287     if (viewport.getAlignment().isNucleotide())
 288     {
 289       conservationMenuItem.setEnabled(false);
 290       clustalColour.setEnabled(false);
 291       BLOSUM62Colour.setEnabled(false);
 292       zappoColour.setEnabled(false);
 293       taylorColour.setEnabled(false);
 294       hydrophobicityColour.setEnabled(false);
 295       helixColour.setEnabled(false);
 296       strandColour.setEnabled(false);
 297       turnColour.setEnabled(false);
 298       buriedColour.setEnabled(false);
 299       viewport.updateStrucConsensus(alignPanel);
 300       if (viewport.getAlignment().hasRNAStructure())
 301       {
 302         RNAHelixColour.setEnabled(true);
 303       }
 304       else
 305       {
 306         RNAHelixColour.setEnabled(false);
 307       }
 308     }
 309     else
 310     {
 311       RNAHelixColour.setEnabled(false);
 312       purinePyrimidineColour.setEnabled(false);
 313       nucleotideColour.setEnabled(false);
 314     }
 315     // Some JVMS send keyevents to Top frame or lowest panel,
 316     // Havent worked out why yet. So add to both this frame and seqCanvas for
 317     // now
 318     this.addKeyListener(this);
 319     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 320     alignPanel.idPanel.idCanvas.addKeyListener(this);
 321     alignPanel.scalePanel.addKeyListener(this);
 322     alignPanel.annotationPanel.addKeyListener(this);
 323     alignPanel.annotationPanelHolder.addKeyListener(this);
 324     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 325     alignPanel.alabels.addKeyListener(this);
 326
 327     setAnnotationsVisibility();
 328
 329     if (addToDisplay)
 330     {
 331       addToDisplay(embedded);
 332     }
 333   }
 334
 335   /**
 336    * @param embedded
 337    */
 338   public void addToDisplay(boolean embedded)
 339   {
 340     createAlignFrameWindow(embedded);
 341     validate();
 342     alignPanel.adjustAnnotationHeight();
 343     alignPanel.paintAlignment(true);
 344   }
 345
 346   public AlignViewport getAlignViewport()
 347   {
 348     return viewport;
 349   }
 350
 351   public SeqCanvas getSeqcanvas()
 352   {
 353     return alignPanel.seqPanel.seqCanvas;
 354   }
 355
 356   /**
 357    * Load a features file onto the alignment
 358    *
 359    * @param file
 360    *          file URL, content, or other resolvable path
 361    * @param type
 362    *          is protocol for accessing data referred to by file
 363    */
 364
 365   public boolean parseFeaturesFile(String file, DataSourceType type)
 366   {
 367     return parseFeaturesFile(file, type, true);
 368   }
 369
 370   /**
 371    * Load a features file onto the alignment
 372    *
 373    * @param file
 374    *          file URL, content, or other resolvable path
 375    * @param sourceType
 376    *          is protocol for accessing data referred to by file
 377    * @param autoenabledisplay
 378    *          when true, display features flag will be automatically enabled if
 379    *          features are loaded
 380    * @return true if data parsed as a features file
 381    */
 382   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 383           boolean autoenabledisplay)
 384   {
 385     boolean featuresFile = false;
 386     try
 387     {
 388       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 389               .getFeatureRenderer().getFeatureColours();
 390       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 391               "relaxedidmatch", false);
 392       featuresFile = new FeaturesFile(file, sourceType).parse(
 393               viewport.getAlignment(), colours, true, relaxedIdMatching);
 394     } catch (Exception ex)
 395     {
 396       ex.printStackTrace();
 397     }
 398
 399     if (featuresFile)
 400     {
 401       if (autoenabledisplay)
 402       {
 403         viewport.setShowSequenceFeatures(true);
 404         sequenceFeatures.setState(true);
 405       }
 406       if (alignPanel.seqPanel.seqCanvas.fr != null)
 407       {
 408         // update the min/max ranges where necessary
 409         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 410       }
 411       if (viewport.featureSettings != null)
 412       {
 413         viewport.featureSettings.refreshTable();
 414       }
 415       alignPanel.paintAlignment(true);
 416       statusBar.setText(MessageManager
 417               .getString("label.successfully_added_features_alignment"));
 418     }
 419     return featuresFile;
 420   }
 421
 422   @Override
 423   public void keyPressed(KeyEvent evt)
 424   {
 425     ViewportRanges ranges = viewport.getRanges();
 426
 427     if (viewport.cursorMode
 428             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 429                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 430                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 431             && Character.isDigit(evt.getKeyChar()))
 432     {
 433       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 434     }
 435
 436     switch (evt.getKeyCode())
 437     {
 438     case 27: // escape key
 439       deselectAllSequenceMenuItem_actionPerformed();
 440
 441       alignPanel.alabels.cancelDrag();
 442       break;
 443     case KeyEvent.VK_X:
 444       if (evt.isControlDown() || evt.isMetaDown())
 445       {
 446         cut_actionPerformed();
 447       }
 448       break;
 449     case KeyEvent.VK_C:
 450       if (viewport.cursorMode && !evt.isControlDown())
 451       {
 452         alignPanel.seqPanel.setCursorColumn();
 453       }
 454       if (evt.isControlDown() || evt.isMetaDown())
 455       {
 456         copy_actionPerformed();
 457       }
 458       break;
 459     case KeyEvent.VK_V:
 460       if (evt.isControlDown())
 461       {
 462         paste(evt.isShiftDown());
 463       }
 464       break;
 465     case KeyEvent.VK_A:
 466       if (evt.isControlDown() || evt.isMetaDown())
 467       {
 468         selectAllSequenceMenuItem_actionPerformed();
 469       }
 470       break;
 471     case KeyEvent.VK_DOWN:
 472       if (viewport.cursorMode)
 473       {
 474         alignPanel.seqPanel.moveCursor(0, 1);
 475       }
 476       else
 477       {
 478         moveSelectedSequences(false);
 479       }
 480       break;
 481
 482     case KeyEvent.VK_UP:
 483       if (viewport.cursorMode)
 484       {
 485         alignPanel.seqPanel.moveCursor(0, -1);
 486       }
 487       else
 488       {
 489         moveSelectedSequences(true);
 490       }
 491       break;
 492
 493     case KeyEvent.VK_LEFT:
 494       if (evt.isAltDown() || !viewport.cursorMode)
 495       {
 496         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 497       }
 498       else
 499       {
 500         alignPanel.seqPanel.moveCursor(-1, 0);
 501       }
 502       break;
 503
 504     case KeyEvent.VK_RIGHT:
 505       if (evt.isAltDown() || !viewport.cursorMode)
 506       {
 507         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 508       }
 509       else
 510       {
 511         alignPanel.seqPanel.moveCursor(1, 0);
 512       }
 513       break;
 514
 515     case KeyEvent.VK_SPACE:
 516       if (viewport.cursorMode)
 517       {
 518         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 519                 || evt.isShiftDown() || evt.isAltDown());
 520       }
 521       break;
 522
 523     case KeyEvent.VK_DELETE:
 524     case KeyEvent.VK_BACK_SPACE:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 528                 || evt.isShiftDown() || evt.isAltDown());
 529       }
 530       else
 531       {
 532         cut_actionPerformed();
 533         alignPanel.seqPanel.seqCanvas.repaint();
 534       }
 535       break;
 536
 537     case KeyEvent.VK_S:
 538       if (viewport.cursorMode)
 539       {
 540         alignPanel.seqPanel.setCursorRow();
 541       }
 542       break;
 543     case KeyEvent.VK_P:
 544       if (viewport.cursorMode)
 545       {
 546         alignPanel.seqPanel.setCursorPosition();
 547       }
 548       break;
 549
 550     case KeyEvent.VK_ENTER:
 551     case KeyEvent.VK_COMMA:
 552       if (viewport.cursorMode)
 553       {
 554         alignPanel.seqPanel.setCursorRowAndColumn();
 555       }
 556       break;
 557
 558     case KeyEvent.VK_Q:
 559       if (viewport.cursorMode)
 560       {
 561         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 562       }
 563       break;
 564     case KeyEvent.VK_M:
 565       if (viewport.cursorMode)
 566       {
 567         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 568       }
 569       break;
 570
 571     case KeyEvent.VK_F2:
 572       viewport.cursorMode = !viewport.cursorMode;
 573       statusBar.setText(MessageManager.formatMessage(
 574               "label.keyboard_editing_mode",
 575               new String[] { (viewport.cursorMode ? "on" : "off") }));
 576       if (viewport.cursorMode)
 577       {
 578         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 579         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 580       }
 581       break;
 582
 583     case KeyEvent.VK_F:
 584       if (evt.isControlDown())
 585       {
 586         findMenuItem_actionPerformed();
 587       }
 588       break;
 589
 590     case KeyEvent.VK_H:
 591     {
 592       boolean toggleSeqs = !evt.isControlDown();
 593       boolean toggleCols = !evt.isShiftDown();
 594       toggleHiddenRegions(toggleSeqs, toggleCols);
 595       break;
 596     }
 597
 598     case KeyEvent.VK_PAGE_UP:
 599       if (viewport.getWrapAlignment())
 600       {
 601         alignPanel.scrollUp(true);
 602       }
 603       else
 604       {
 605         alignPanel.setScrollValues(ranges.getStartRes(),
 606                 2 * ranges.getStartSeq() - ranges.getEndSeq());
 607       }
 608       break;
 609
 610     case KeyEvent.VK_PAGE_DOWN:
 611       if (viewport.getWrapAlignment())
 612       {
 613         alignPanel.scrollUp(false);
 614       }
 615       else
 616       {
 617         alignPanel
 618                 .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
 619       }
 620       break;
 621
 622     case KeyEvent.VK_Z:
 623       if (evt.isControlDown())
 624       {
 625         undoMenuItem_actionPerformed();
 626       }
 627       break;
 628
 629     case KeyEvent.VK_Y:
 630       if (evt.isControlDown())
 631       {
 632         redoMenuItem_actionPerformed();
 633       }
 634       break;
 635
 636     case KeyEvent.VK_L:
 637       if (evt.isControlDown())
 638       {
 639         trimAlignment(true);
 640       }
 641       break;
 642
 643     case KeyEvent.VK_R:
 644       if (evt.isControlDown())
 645       {
 646         trimAlignment(false);
 647       }
 648       break;
 649
 650     case KeyEvent.VK_E:
 651       if (evt.isControlDown())
 652       {
 653         if (evt.isShiftDown())
 654         {
 655           this.removeAllGapsMenuItem_actionPerformed();
 656         }
 657         else
 658         {
 659           removeGappedColumnMenuItem_actionPerformed();
 660         }
 661       }
 662       break;
 663     case KeyEvent.VK_I:
 664       if (evt.isControlDown())
 665       {
 666         if (evt.isAltDown())
 667         {
 668           invertColSel_actionPerformed();
 669         }
 670         else
 671         {
 672           invertSequenceMenuItem_actionPerformed();
 673         }
 674       }
 675       break;
 676
 677     case KeyEvent.VK_G:
 678       if (evt.isControlDown())
 679       {
 680         if (evt.isShiftDown())
 681         {
 682           this.unGroup_actionPerformed();
 683         }
 684         else
 685         {
 686           this.createGroup_actionPerformed();
 687         }
 688       }
 689       break;
 690
 691     case KeyEvent.VK_U:
 692       if (evt.isControlDown())
 693       {
 694         this.deleteGroups_actionPerformed();
 695       }
 696       break;
 697
 698     case KeyEvent.VK_T:
 699       if (evt.isControlDown())
 700       {
 701         newView(null);
 702       }
 703       break;
 704
 705     }
 706     alignPanel.paintAlignment(true);
 707   }
 708
 709   /**
 710    * called by key handler and the hide all/show all menu items
 711    *
 712    * @param toggleSeqs
 713    * @param toggleCols
 714    */
 715   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 716   {
 717     boolean hide = false;
 718     SequenceGroup sg = viewport.getSelectionGroup();
 719     if (!toggleSeqs && !toggleCols)
 720     {
 721       // Hide everything by the current selection - this is a hack - we do the
 722       // invert and then hide
 723       // first check that there will be visible columns after the invert.
 724       if (viewport.hasSelectedColumns()
 725               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 726                       .getEndRes()))
 727       {
 728         // now invert the sequence set, if required - empty selection implies
 729         // that no hiding is required.
 730         if (sg != null)
 731         {
 732           invertSequenceMenuItem_actionPerformed();
 733           sg = viewport.getSelectionGroup();
 734           toggleSeqs = true;
 735
 736         }
 737         viewport.expandColSelection(sg, true);
 738         // finally invert the column selection and get the new sequence
 739         // selection and indicate it should be hidden.
 740         invertColSel_actionPerformed();
 741         toggleCols = true;
 742       }
 743     }
 744
 745     if (toggleSeqs)
 746     {
 747       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 748       {
 749         hide = true;
 750         viewport.hideAllSelectedSeqs();
 751       }
 752       else if (!(toggleCols && viewport.hasSelectedColumns()))
 753       {
 754         viewport.showAllHiddenSeqs();
 755       }
 756     }
 757
 758     if (toggleCols)
 759     {
 760       if (viewport.hasSelectedColumns())
 761       {
 762         viewport.hideSelectedColumns();
 763         if (!toggleSeqs)
 764         {
 765           viewport.setSelectionGroup(sg);
 766         }
 767       }
 768       else if (!hide)
 769       {
 770         viewport.showAllHiddenColumns();
 771       }
 772       viewport.sendSelection();
 773     }
 774   }
 775
 776   @Override
 777   public void keyReleased(KeyEvent evt)
 778   {
 779   }
 780
 781   @Override
 782   public void keyTyped(KeyEvent evt)
 783   {
 784   }
 785
 786   @Override
 787   public void itemStateChanged(ItemEvent evt)
 788   {
 789     final Object source = evt.getSource();
 790     if (source == displayNonconservedMenuItem)
 791     {
 792       displayNonconservedMenuItem_actionPerformed();
 793     }
 794     else if (source == colourTextMenuItem)
 795     {
 796       colourTextMenuItem_actionPerformed();
 797     }
 798     else if (source == wrapMenuItem)
 799     {
 800       wrapMenuItem_actionPerformed();
 801     }
 802     else if (source == scaleAbove)
 803     {
 804       viewport.setScaleAboveWrapped(scaleAbove.getState());
 805     }
 806     else if (source == scaleLeft)
 807     {
 808       viewport.setScaleLeftWrapped(scaleLeft.getState());
 809     }
 810     else if (source == scaleRight)
 811     {
 812       viewport.setScaleRightWrapped(scaleRight.getState());
 813     }
 814     else if (source == seqLimits)
 815     {
 816       seqLimits_itemStateChanged();
 817     }
 818     else if (source == viewBoxesMenuItem)
 819     {
 820       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 821     }
 822     else if (source == viewTextMenuItem)
 823     {
 824       viewport.setShowText(viewTextMenuItem.getState());
 825     }
 826     else if (source == renderGapsMenuItem)
 827     {
 828       viewport.setRenderGaps(renderGapsMenuItem.getState());
 829     }
 830     else if (source == annotationPanelMenuItem)
 831     {
 832       boolean showAnnotations = annotationPanelMenuItem.getState();
 833       showAlignmentAnnotations.setEnabled(showAnnotations);
 834       showSequenceAnnotations.setEnabled(showAnnotations);
 835       viewport.setShowAnnotation(showAnnotations);
 836       alignPanel.setAnnotationVisible(showAnnotations);
 837     }
 838     else if (source == sequenceFeatures)
 839     {
 840       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 841       alignPanel.seqPanel.seqCanvas.repaint();
 842     }
 843     else if (source == showAlignmentAnnotations)
 844     {
 845       setAnnotationsVisibility();
 846     }
 847     else if (source == showSequenceAnnotations)
 848     {
 849       setAnnotationsVisibility();
 850     }
 851     else if (source == sortAnnBySequence)
 852     {
 853       boolean newState = sortAnnBySequence.getState();
 854       sortAnnByLabel.setState(false);
 855       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 856               : SequenceAnnotationOrder.NONE);
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == sortAnnByLabel)
 860     {
 861       boolean newState = sortAnnByLabel.getState();
 862       sortAnnBySequence.setState(false);
 863       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 864               : SequenceAnnotationOrder.NONE);
 865       setViewportAnnotationOrder();
 866     }
 867     else if (source == showAutoFirst)
 868     {
 869       showAutoLast.setState(!showAutoFirst.getState());
 870       setShowAutoCalculatedAbove(showAutoFirst.getState());
 871       setViewportAnnotationOrder();
 872     }
 873     else if (source == showAutoLast)
 874     {
 875       showAutoFirst.setState(!showAutoLast.getState());
 876       setShowAutoCalculatedAbove(showAutoFirst.getState());
 877       setViewportAnnotationOrder();
 878     }
 879     else if (source == conservationMenuItem)
 880     {
 881       conservationMenuItem_actionPerformed();
 882     }
 883     else if (source == abovePIDThreshold)
 884     {
 885       abovePIDThreshold_actionPerformed();
 886     }
 887     else if (source == applyToAllGroups)
 888     {
 889       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 890     }
 891     else if (source == autoCalculate)
 892     {
 893       viewport.autoCalculateConsensus = autoCalculate.getState();
 894     }
 895     else if (source == sortByTree)
 896     {
 897       viewport.sortByTree = sortByTree.getState();
 898     }
 899     else if (source == this.centreColumnLabelFlag)
 900     {
 901       centreColumnLabelFlag_stateChanged();
 902     }
 903     else if (source == this.followMouseOverFlag)
 904     {
 905       mouseOverFlag_stateChanged();
 906     }
 907     else if (source == showGroupConsensus)
 908     {
 909       showGroupConsensus_actionPerformed();
 910     }
 911     else if (source == showGroupConservation)
 912     {
 913       showGroupConservation_actionPerformed();
 914     }
 915     else if (source == showSequenceLogo)
 916     {
 917       showSequenceLogo_actionPerformed();
 918     }
 919     else if (source == normSequenceLogo)
 920     {
 921       normSequenceLogo_actionPerformed();
 922     }
 923     else if (source == showConsensusHistogram)
 924     {
 925       showConsensusHistogram_actionPerformed();
 926     }
 927     else if (source == applyAutoAnnotationSettings)
 928     {
 929       applyAutoAnnotationSettings_actionPerformed();
 930     }
 931     alignPanel.paintAlignment(true);
 932   }
 933
 934   /**
 935    * Set the visibility state of sequence-related and/or alignment-related
 936    * annotations depending on checkbox selections, and repaint.
 937    *
 938    * @param visible
 939    */
 940   private void setAnnotationsVisibility()
 941   {
 942     boolean showForAlignment = showAlignmentAnnotations.getState();
 943     boolean showForSequences = showSequenceAnnotations.getState();
 944     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 945     {
 946       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 947               .getAlignmentAnnotation())
 948       {
 949         boolean visible = (aa.sequenceRef == null ? showForAlignment
 950                 : showForSequences);
 951         aa.visible = visible;
 952       }
 953     }
 954     alignPanel.validateAnnotationDimensions(true);
 955     validate();
 956     repaint();
 957   }
 958
 959   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 960   {
 961     this.annotationSortOrder = order;
 962   }
 963
 964   /**
 965    * Set flags on the viewport that control annotation ordering
 966    */
 967   private void setViewportAnnotationOrder()
 968   {
 969     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 970     this.alignPanel.av
 971             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 972   }
 973
 974   private void setShowAutoCalculatedAbove(boolean showAbove)
 975   {
 976     this.showAutoCalculatedAbove = showAbove;
 977   }
 978
 979   private void mouseOverFlag_stateChanged()
 980   {
 981     viewport.setFollowHighlight(followMouseOverFlag.getState());
 982     // TODO: could kick the scrollTo mechanism to reset view for current
 983     // searchresults.
 984   }
 985
 986   private void centreColumnLabelFlag_stateChanged()
 987   {
 988     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 989     this.alignPanel.annotationPanel.repaint();
 990   }
 991
 992   @Override
 993   public void actionPerformed(ActionEvent evt)
 994   {
 995     viewport.applet.currentAlignFrame = this;
 996
 997     Object source = evt.getSource();
 998
 999     if (source == inputText)
1000     {
1001       inputText_actionPerformed();
1002     }
1003     else if (source == loadTree)
1004     {
1005       loadTree_actionPerformed();
1006     }
1007     else if (source == loadApplication)
1008     {
1009       launchFullApplication();
1010     }
1011     else if (source == loadAnnotations)
1012     {
1013       loadAnnotations();
1014     }
1015     else if (source == outputAnnotations)
1016     {
1017       outputAnnotations(true);
1018     }
1019     else if (source == outputFeatures)
1020     {
1021       outputFeatures(true, "Jalview");
1022     }
1023     else if (source == closeMenuItem)
1024     {
1025       closeMenuItem_actionPerformed();
1026     }
1027     else if (source == copy)
1028     {
1029       copy_actionPerformed();
1030     }
1031     else if (source == undoMenuItem)
1032     {
1033       undoMenuItem_actionPerformed();
1034     }
1035     else if (source == redoMenuItem)
1036     {
1037       redoMenuItem_actionPerformed();
1038     }
1039     else if (source == inputText)
1040     {
1041       inputText_actionPerformed();
1042     }
1043     else if (source == closeMenuItem)
1044     {
1045       closeMenuItem_actionPerformed();
1046     }
1047     else if (source == undoMenuItem)
1048     {
1049       undoMenuItem_actionPerformed();
1050     }
1051     else if (source == redoMenuItem)
1052     {
1053       redoMenuItem_actionPerformed();
1054     }
1055     else if (source == copy)
1056     {
1057       copy_actionPerformed();
1058     }
1059     else if (source == pasteNew)
1060     {
1061       pasteNew_actionPerformed();
1062     }
1063     else if (source == pasteThis)
1064     {
1065       pasteThis_actionPerformed();
1066     }
1067     else if (source == cut)
1068     {
1069       cut_actionPerformed();
1070     }
1071     else if (source == delete)
1072     {
1073       delete_actionPerformed();
1074     }
1075     else if (source == createGroup)
1076     {
1077       createGroup_actionPerformed();
1078     }
1079     else if (source == unGroup)
1080     {
1081       unGroup_actionPerformed();
1082     }
1083     else if (source == grpsFromSelection)
1084     {
1085       makeGrpsFromSelection_actionPerformed();
1086     }
1087     else if (source == deleteGroups)
1088     {
1089       deleteGroups_actionPerformed();
1090     }
1091     else if (source == selectAllSequenceMenuItem)
1092     {
1093       selectAllSequenceMenuItem_actionPerformed();
1094     }
1095     else if (source == deselectAllSequenceMenuItem)
1096     {
1097       deselectAllSequenceMenuItem_actionPerformed();
1098     }
1099     else if (source == invertSequenceMenuItem)
1100     {
1101       invertSequenceMenuItem_actionPerformed();
1102       // uncomment to slave sequence selections in split frame
1103       // viewport.sendSelection();
1104     }
1105     else if (source == invertColSel)
1106     {
1107       viewport.invertColumnSelection();
1108       alignPanel.paintAlignment(true);
1109       viewport.sendSelection();
1110     }
1111     else if (source == remove2LeftMenuItem)
1112     {
1113       trimAlignment(true);
1114     }
1115     else if (source == remove2RightMenuItem)
1116     {
1117       trimAlignment(false);
1118     }
1119     else if (source == removeGappedColumnMenuItem)
1120     {
1121       removeGappedColumnMenuItem_actionPerformed();
1122     }
1123     else if (source == removeAllGapsMenuItem)
1124     {
1125       removeAllGapsMenuItem_actionPerformed();
1126     }
1127     else if (source == findMenuItem)
1128     {
1129       findMenuItem_actionPerformed();
1130     }
1131     else if (source == font)
1132     {
1133       new FontChooser(alignPanel);
1134     }
1135     else if (source == newView)
1136     {
1137       newView(null);
1138     }
1139     else if (source == showColumns)
1140     {
1141       viewport.showAllHiddenColumns();
1142       alignPanel.paintAlignment(true);
1143       viewport.sendSelection();
1144     }
1145     else if (source == showSeqs)
1146     {
1147       viewport.showAllHiddenSeqs();
1148       alignPanel.paintAlignment(true);
1149       // uncomment if we want to slave sequence selections in split frame
1150       // viewport.sendSelection();
1151     }
1152     else if (source == hideColumns)
1153     {
1154       viewport.hideSelectedColumns();
1155       alignPanel.paintAlignment(true);
1156       viewport.sendSelection();
1157     }
1158     else if (source == hideSequences
1159             && viewport.getSelectionGroup() != null)
1160     {
1161       viewport.hideAllSelectedSeqs();
1162       alignPanel.paintAlignment(true);
1163       // uncomment if we want to slave sequence selections in split frame
1164       // viewport.sendSelection();
1165     }
1166     else if (source == hideAllButSelection)
1167     {
1168       toggleHiddenRegions(false, false);
1169       alignPanel.paintAlignment(true);
1170       viewport.sendSelection();
1171     }
1172     else if (source == hideAllSelection)
1173     {
1174       SequenceGroup sg = viewport.getSelectionGroup();
1175       viewport.expandColSelection(sg, false);
1176       viewport.hideAllSelectedSeqs();
1177       viewport.hideSelectedColumns();
1178       alignPanel.paintAlignment(true);
1179       viewport.sendSelection();
1180     }
1181     else if (source == showAllHidden)
1182     {
1183       viewport.showAllHiddenColumns();
1184       viewport.showAllHiddenSeqs();
1185       alignPanel.paintAlignment(true);
1186       viewport.sendSelection();
1187     }
1188     else if (source == showGroupConsensus)
1189     {
1190       showGroupConsensus_actionPerformed();
1191     }
1192     else if (source == showGroupConservation)
1193     {
1194       showGroupConservation_actionPerformed();
1195     }
1196     else if (source == showSequenceLogo)
1197     {
1198       showSequenceLogo_actionPerformed();
1199     }
1200     else if (source == normSequenceLogo)
1201     {
1202       normSequenceLogo_actionPerformed();
1203     }
1204     else if (source == showConsensusHistogram)
1205     {
1206       showConsensusHistogram_actionPerformed();
1207     }
1208     else if (source == applyAutoAnnotationSettings)
1209     {
1210       applyAutoAnnotationSettings_actionPerformed();
1211     }
1212     else if (source == featureSettings)
1213     {
1214       new FeatureSettings(alignPanel);
1215     }
1216     else if (source == alProperties)
1217     {
1218       StringBuffer contents = new jalview.io.AlignmentProperties(
1219               viewport.getAlignment()).formatAsString();
1220       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1221       cap.setText(contents.toString());
1222       Frame frame = new Frame();
1223       frame.add(cap);
1224       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1225               "label.alignment_properties", new String[] { getTitle() }),
1226               400, 250);
1227     }
1228     else if (source == overviewMenuItem)
1229     {
1230       overviewMenuItem_actionPerformed();
1231     }
1232     else if (source == noColourmenuItem)
1233     {
1234       changeColour(null);
1235     }
1236     else if (source == clustalColour)
1237     {
1238       abovePIDThreshold.setState(false);
1239       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1240     }
1241     else if (source == zappoColour)
1242     {
1243       changeColour(new ZappoColourScheme());
1244     }
1245     else if (source == taylorColour)
1246     {
1247       changeColour(new TaylorColourScheme());
1248     }
1249     else if (source == hydrophobicityColour)
1250     {
1251       changeColour(new HydrophobicColourScheme());
1252     }
1253     else if (source == helixColour)
1254     {
1255       changeColour(new HelixColourScheme());
1256     }
1257     else if (source == strandColour)
1258     {
1259       changeColour(new StrandColourScheme());
1260     }
1261     else if (source == turnColour)
1262     {
1263       changeColour(new TurnColourScheme());
1264     }
1265     else if (source == buriedColour)
1266     {
1267       changeColour(new BuriedColourScheme());
1268     }
1269     else if (source == nucleotideColour)
1270     {
1271       changeColour(new NucleotideColourScheme());
1272     }
1273     else if (source == purinePyrimidineColour)
1274     {
1275       changeColour(new PurinePyrimidineColourScheme());
1276     }
1277     // else if (source == RNAInteractionColour)
1278     // {
1279     // changeColour(new RNAInteractionColourScheme());
1280     // }
1281     else if (source == RNAHelixColour)
1282     {
1283       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1284       // new RNAHelicesColourChooser(viewport, alignPanel);
1285     }
1286     else if (source == modifyPID)
1287     {
1288       modifyPID_actionPerformed();
1289     }
1290     else if (source == modifyConservation)
1291     {
1292       modifyConservation_actionPerformed();
1293     }
1294     else if (source == userDefinedColour)
1295     {
1296       new UserDefinedColours(alignPanel, null);
1297     }
1298     else if (source == PIDColour)
1299     {
1300       changeColour(new PIDColourScheme());
1301     }
1302     else if (source == BLOSUM62Colour)
1303     {
1304       changeColour(new Blosum62ColourScheme());
1305     }
1306     else if (source == tcoffeeColour)
1307     {
1308       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1309     }
1310     else if (source == annotationColour)
1311     {
1312       new AnnotationColourChooser(viewport, alignPanel);
1313     }
1314     else if (source == annotationColumnSelection)
1315     {
1316       new AnnotationColumnChooser(viewport, alignPanel);
1317     }
1318     else if (source == sortPairwiseMenuItem)
1319     {
1320       sortPairwiseMenuItem_actionPerformed();
1321     }
1322     else if (source == sortIDMenuItem)
1323     {
1324       sortIDMenuItem_actionPerformed();
1325     }
1326     else if (source == sortLengthMenuItem)
1327     {
1328       sortLengthMenuItem_actionPerformed();
1329     }
1330     else if (source == sortGroupMenuItem)
1331     {
1332       sortGroupMenuItem_actionPerformed();
1333     }
1334     else if (source == removeRedundancyMenuItem)
1335     {
1336       removeRedundancyMenuItem_actionPerformed();
1337     }
1338     else if (source == pairwiseAlignmentMenuItem)
1339     {
1340       pairwiseAlignmentMenuItem_actionPerformed();
1341     }
1342     else if (source == PCAMenuItem)
1343     {
1344       PCAMenuItem_actionPerformed();
1345     }
1346     else if (source == averageDistanceTreeMenuItem)
1347     {
1348       averageDistanceTreeMenuItem_actionPerformed();
1349     }
1350     else if (source == neighbourTreeMenuItem)
1351     {
1352       neighbourTreeMenuItem_actionPerformed();
1353     }
1354     else if (source == njTreeBlosumMenuItem)
1355     {
1356       njTreeBlosumMenuItem_actionPerformed();
1357     }
1358     else if (source == avDistanceTreeBlosumMenuItem)
1359     {
1360       avTreeBlosumMenuItem_actionPerformed();
1361     }
1362     else if (source == documentation)
1363     {
1364       documentation_actionPerformed();
1365     }
1366     else if (source == about)
1367     {
1368       about_actionPerformed();
1369     }
1370
1371   }
1372
1373   public void inputText_actionPerformed()
1374   {
1375     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376     Frame frame = new Frame();
1377     frame.add(cap);
1378     jalview.bin.JalviewLite.addFrame(frame,
1379             MessageManager.getString("label.input_cut_paste"), 500, 500);
1380   }
1381
1382   protected void outputText_actionPerformed(ActionEvent e)
1383   {
1384     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1385     Frame frame = new Frame();
1386     frame.add(cap);
1387     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1388             "label.alignment_output_command",
1389             new Object[] { e.getActionCommand() }), 600, 500);
1390
1391     FileFormatI fileFormat = FileFormats.getInstance().forName(
1392             e.getActionCommand());
1393     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1394             fileFormat, viewport.getAlignment(),
1395             viewport.getShowJVSuffix()));
1396   }
1397
1398   public void loadAnnotations()
1399   {
1400     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1401     cap.setText(MessageManager
1402             .getString("label.paste_features_annotations_Tcoffee_here"));
1403     cap.setAnnotationImport();
1404     Frame frame = new Frame();
1405     frame.add(cap);
1406     jalview.bin.JalviewLite.addFrame(frame,
1407             MessageManager.getString("action.paste_annotations"), 400, 300);
1408
1409   }
1410
1411   public String outputAnnotations(boolean displayTextbox)
1412   {
1413     String annotation = new AnnotationFile()
1414             .printAnnotationsForView(viewport);
1415
1416     if (displayTextbox)
1417     {
1418       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1419       Frame frame = new Frame();
1420       frame.add(cap);
1421       jalview.bin.JalviewLite.addFrame(frame,
1422               MessageManager.getString("label.annotations"), 600, 500);
1423       cap.setText(annotation);
1424     }
1425
1426     return annotation;
1427   }
1428
1429   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1430   {
1431     if (alignPanel.getFeatureRenderer() != null
1432             && viewport.getFeaturesDisplayed() != null)
1433     {
1434       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1435
1436     }
1437     return null;
1438   }
1439
1440   public String outputFeatures(boolean displayTextbox, String format)
1441   {
1442     String features;
1443     FeaturesFile formatter = new FeaturesFile();
1444     if (format.equalsIgnoreCase("Jalview"))
1445     {
1446       features = formatter.printJalviewFormat(viewport.getAlignment()
1447               .getSequencesArray(), getDisplayedFeatureCols());
1448     }
1449     else
1450     {
1451       features = formatter.printGffFormat(viewport.getAlignment()
1452               .getSequencesArray(), getDisplayedFeatureCols());
1453     }
1454
1455     if (displayTextbox)
1456     {
1457       boolean frimport = false;
1458       if (features == null || features.equals("No Features Visible"))
1459       {
1460         features = "# No features visible - paste some and import them here.";
1461         frimport = true;
1462       }
1463
1464       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1465       if (frimport)
1466       {
1467         cap.setAnnotationImport();
1468       }
1469       Frame frame = new Frame();
1470       frame.add(cap);
1471       jalview.bin.JalviewLite.addFrame(frame,
1472               MessageManager.getString("label.features"), 600, 500);
1473       cap.setText(features);
1474     }
1475     else
1476     {
1477       if (features == null)
1478       {
1479         features = "";
1480       }
1481     }
1482
1483     return features;
1484   }
1485
1486   void launchFullApplication()
1487   {
1488     StringBuffer url = new StringBuffer(jalviewServletURL);
1489
1490     // allow servlet parameters to be passed in applet parameter
1491     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1492             : "?";
1493     url.append(firstSep);
1494
1495     url.append("open="
1496             + appendProtocol(viewport.applet.getParameter("file")));
1497
1498     if (viewport.applet.getParameter("features") != null)
1499     {
1500       url.append("&features=");
1501       url.append(appendProtocol(viewport.applet.getParameter("features")));
1502     }
1503
1504     if (viewport.applet.getParameter("annotations") != null)
1505     {
1506       url.append("&annotations=");
1507       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1508     }
1509
1510     if (viewport.applet.getParameter("jnetfile") != null
1511             || viewport.applet.getParameter("jpredfile") != null)
1512     {
1513       url.append("&annotations=");
1514       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1515               .getParameter("jnetfile") : viewport.applet
1516               .getParameter("jpredfile")));
1517     }
1518
1519     if (viewport.applet.getParameter("defaultColour") != null)
1520     {
1521       url.append("&colour="
1522               + removeWhiteSpace(viewport.applet
1523                       .getParameter("defaultColour")));
1524     }
1525
1526     if (viewport.applet.getParameter("userDefinedColour") != null)
1527     {
1528       url.append("&colour="
1529               + removeWhiteSpace(viewport.applet
1530                       .getParameter("userDefinedColour")));
1531     }
1532     if (viewport.applet.getParameter("tree") != null)
1533     {
1534       url.append("&tree="
1535               + appendProtocol(viewport.applet.getParameter("tree")));
1536     }
1537     if (viewport.applet.getParameter("treeFile") != null)
1538     {
1539       url.append("&tree="
1540               + appendProtocol(viewport.applet.getParameter("treeFile")));
1541     }
1542
1543     showURL(url.toString(), "FULL_APP");
1544   }
1545
1546   String removeWhiteSpace(String colour)
1547   {
1548     StringBuffer sb = new StringBuffer();
1549     for (int i = 0; i < colour.length(); i++)
1550     {
1551       if (Character.isWhitespace(colour.charAt(i)))
1552       {
1553         sb.append("%20");
1554       }
1555       else
1556       {
1557         sb.append(colour.charAt(i));
1558       }
1559     }
1560
1561     return sb.toString();
1562   }
1563
1564   String appendProtocol(String url)
1565   {
1566     try
1567     {
1568       new URL(url);
1569       url = URLEncoder.encode(url);
1570     }
1571     /*
1572      * When we finally deprecate 1.1 compatibility, we can start to use
1573      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1574      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1575      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1576      * ex.printStackTrace(); }
1577      */
1578     catch (java.net.MalformedURLException ex)
1579     {
1580       url = viewport.applet.getCodeBase() + url;
1581     }
1582     return url;
1583   }
1584
1585   public void closeMenuItem_actionPerformed()
1586   {
1587     PaintRefresher.RemoveComponent(alignPanel);
1588     if (alignPanel.seqPanel != null
1589             && alignPanel.seqPanel.seqCanvas != null)
1590     {
1591       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1592     }
1593     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1594     {
1595       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1596     }
1597
1598     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1599     {
1600       System.exit(0);
1601     }
1602     else
1603     {
1604     }
1605     viewport = null;
1606     alignPanel = null;
1607     this.dispose();
1608   }
1609
1610   /**
1611    * TODO: JAL-1104
1612    */
1613   void updateEditMenuBar()
1614   {
1615
1616     if (viewport.getHistoryList().size() > 0)
1617     {
1618       undoMenuItem.setEnabled(true);
1619       CommandI command = viewport.getHistoryList().peek();
1620       undoMenuItem.setLabel(MessageManager.formatMessage(
1621               "label.undo_command",
1622               new Object[] { command.getDescription() }));
1623     }
1624     else
1625     {
1626       undoMenuItem.setEnabled(false);
1627       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1628     }
1629
1630     if (viewport.getRedoList().size() > 0)
1631     {
1632       redoMenuItem.setEnabled(true);
1633
1634       CommandI command = viewport.getRedoList().peek();
1635       redoMenuItem.setLabel(MessageManager.formatMessage(
1636               "label.redo_command",
1637               new Object[] { command.getDescription() }));
1638     }
1639     else
1640     {
1641       redoMenuItem.setEnabled(false);
1642       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1643     }
1644   }
1645
1646   /**
1647    * TODO: JAL-1104
1648    */
1649   @Override
1650   public void addHistoryItem(CommandI command)
1651   {
1652     if (command.getSize() > 0)
1653     {
1654       viewport.addToHistoryList(command);
1655       viewport.clearRedoList();
1656       updateEditMenuBar();
1657       viewport.updateHiddenColumns();
1658     }
1659   }
1660
1661   /**
1662    * TODO: JAL-1104 DOCUMENT ME!
1663    *
1664    * @param e
1665    *          DOCUMENT ME!
1666    */
1667   protected void undoMenuItem_actionPerformed()
1668   {
1669     if (viewport.getHistoryList().isEmpty())
1670     {
1671       return;
1672     }
1673
1674     CommandI command = viewport.getHistoryList().pop();
1675     viewport.addToRedoList(command);
1676     command.undoCommand(null);
1677
1678     AlignmentViewport originalSource = getOriginatingSource(command);
1679     // JBPNote Test
1680     if (originalSource != viewport)
1681     {
1682       System.err
1683               .println("Warning: Viewport object mismatch whilst undoing");
1684     }
1685     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1686                                           // viewport.getColumnSelection().getHiddenColumns()
1687                                           // != null;
1688     updateEditMenuBar();
1689     originalSource.firePropertyChange("alignment", null, originalSource
1690             .getAlignment().getSequences());
1691   }
1692
1693   /**
1694    * TODO: JAL-1104 DOCUMENT ME!
1695    *
1696    * @param e
1697    *          DOCUMENT ME!
1698    */
1699   protected void redoMenuItem_actionPerformed()
1700   {
1701     if (viewport.getRedoList().isEmpty())
1702     {
1703       return;
1704     }
1705
1706     CommandI command = viewport.getRedoList().pop();
1707     viewport.addToHistoryList(command);
1708     command.doCommand(null);
1709
1710     AlignmentViewport originalSource = getOriginatingSource(command);
1711     // JBPNote Test
1712     if (originalSource != viewport)
1713     {
1714       System.err
1715               .println("Warning: Viewport object mismatch whilst re-doing");
1716     }
1717     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1718                                           // viewport.getColumnSelection().getHiddenColumns()
1719                                           // != null;
1720
1721     updateEditMenuBar();
1722     originalSource.firePropertyChange("alignment", null, originalSource
1723             .getAlignment().getSequences());
1724   }
1725
1726   AlignmentViewport getOriginatingSource(CommandI command)
1727   {
1728     AlignmentViewport originalSource = null;
1729     // For sequence removal and addition, we need to fire
1730     // the property change event FROM the viewport where the
1731     // original alignment was altered
1732     AlignmentI al = null;
1733     if (command instanceof EditCommand)
1734     {
1735       EditCommand editCommand = (EditCommand) command;
1736       al = editCommand.getAlignment();
1737       Vector comps = (Vector) PaintRefresher.components.get(viewport
1738               .getSequenceSetId());
1739       for (int i = 0; i < comps.size(); i++)
1740       {
1741         if (comps.elementAt(i) instanceof AlignmentPanel)
1742         {
1743           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1744           {
1745             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1746             break;
1747           }
1748         }
1749       }
1750     }
1751
1752     if (originalSource == null)
1753     {
1754       // The original view is closed, we must validate
1755       // the current view against the closed view first
1756       if (al != null)
1757       {
1758         PaintRefresher.validateSequences(al, viewport.getAlignment());
1759       }
1760
1761       originalSource = viewport;
1762     }
1763
1764     return originalSource;
1765   }
1766
1767   /**
1768    * Move the currently selected sequences up or down one position in the
1769    * alignment
1770    *
1771    * @param up
1772    */
1773   public void moveSelectedSequences(boolean up)
1774   {
1775     SequenceGroup sg = viewport.getSelectionGroup();
1776     if (sg == null)
1777     {
1778       return;
1779     }
1780     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1781             up ? null : viewport.getHiddenRepSequences(), up);
1782     alignPanel.paintAlignment(true);
1783
1784     /*
1785      * Also move cDNA/protein complement sequences
1786      */
1787     AlignViewportI complement = viewport.getCodingComplement();
1788     if (complement != null)
1789     {
1790       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1791               viewport, complement);
1792       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1793               up ? null : complement.getHiddenRepSequences(), up);
1794       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1795     }
1796   }
1797
1798   synchronized void slideSequences(boolean right, int size)
1799   {
1800     List<SequenceI> sg = new Vector<SequenceI>();
1801     if (viewport.cursorMode)
1802     {
1803       sg.add(viewport.getAlignment().getSequenceAt(
1804               alignPanel.seqPanel.seqCanvas.cursorY));
1805     }
1806     else if (viewport.getSelectionGroup() != null
1807             && viewport.getSelectionGroup().getSize() != viewport
1808                     .getAlignment().getHeight())
1809     {
1810       sg = viewport.getSelectionGroup().getSequences(
1811               viewport.getHiddenRepSequences());
1812     }
1813
1814     if (sg.size() < 1)
1815     {
1816       return;
1817     }
1818
1819     Vector<SequenceI> invertGroup = new Vector();
1820
1821     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1822     {
1823       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1824       {
1825         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1826       }
1827     }
1828
1829     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1830
1831     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1832             .size()]);
1833     for (int i = 0; i < invertGroup.size(); i++)
1834     {
1835       seqs2[i] = invertGroup.elementAt(i);
1836     }
1837
1838     SlideSequencesCommand ssc;
1839     if (right)
1840     {
1841       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1842               size, viewport.getGapCharacter());
1843     }
1844     else
1845     {
1846       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1847               size, viewport.getGapCharacter());
1848     }
1849
1850     int groupAdjustment = 0;
1851     if (ssc.getGapsInsertedBegin() && right)
1852     {
1853       if (viewport.cursorMode)
1854       {
1855         alignPanel.seqPanel.moveCursor(size, 0);
1856       }
1857       else
1858       {
1859         groupAdjustment = size;
1860       }
1861     }
1862     else if (!ssc.getGapsInsertedBegin() && !right)
1863     {
1864       if (viewport.cursorMode)
1865       {
1866         alignPanel.seqPanel.moveCursor(-size, 0);
1867       }
1868       else
1869       {
1870         groupAdjustment = -size;
1871       }
1872     }
1873
1874     if (groupAdjustment != 0)
1875     {
1876       viewport.getSelectionGroup().setStartRes(
1877               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1878       viewport.getSelectionGroup().setEndRes(
1879               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1880     }
1881
1882     boolean appendHistoryItem = false;
1883     Deque<CommandI> historyList = viewport.getHistoryList();
1884     if (historyList != null && historyList.size() > 0
1885             && historyList.peek() instanceof SlideSequencesCommand)
1886     {
1887       appendHistoryItem = ssc
1888               .appendSlideCommand((SlideSequencesCommand) historyList
1889                       .peek());
1890     }
1891
1892     if (!appendHistoryItem)
1893     {
1894       addHistoryItem(ssc);
1895     }
1896
1897     repaint();
1898   }
1899
1900   static StringBuffer copiedSequences;
1901
1902   static Vector copiedHiddenColumns;
1903
1904   protected void copy_actionPerformed()
1905   {
1906     if (viewport.getSelectionGroup() == null)
1907     {
1908       return;
1909     }
1910
1911     SequenceGroup sg = viewport.getSelectionGroup();
1912     copiedSequences = new StringBuffer();
1913     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1914     for (int i = 0; i < sg.getSize(); i++)
1915     {
1916       SequenceI seq = sg.getSequenceAt(i);
1917       int index = viewport.getAlignment().findIndex(seq);
1918       orderedSeqs.put(index, seq);
1919     }
1920
1921     int index = 0, startRes, endRes;
1922     char ch;
1923
1924     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1925     {
1926       copiedHiddenColumns = new Vector();
1927       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1928       for (int[] region : viewport.getAlignment().getHiddenColumns()
1929               .getHiddenRegions())
1930       {
1931         copiedHiddenColumns.addElement(new int[] {
1932             region[0] - hiddenOffset, region[1] - hiddenOffset });
1933       }
1934     }
1935     else
1936     {
1937       copiedHiddenColumns = null;
1938     }
1939
1940     for (int i = 0; i < sg.getSize(); i++)
1941     {
1942       SequenceI seq = null;
1943
1944       while (seq == null)
1945       {
1946         if (orderedSeqs.containsKey(index))
1947         {
1948           seq = orderedSeqs.get(index);
1949           index++;
1950           break;
1951         }
1952         else
1953         {
1954           index++;
1955         }
1956       }
1957
1958       // FIND START RES
1959       // Returns residue following index if gap
1960       startRes = seq.findPosition(sg.getStartRes());
1961
1962       // FIND END RES
1963       // Need to find the residue preceeding index if gap
1964       endRes = 0;
1965
1966       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1967       {
1968         ch = seq.getCharAt(j);
1969         if (!jalview.util.Comparison.isGap((ch)))
1970         {
1971           endRes++;
1972         }
1973       }
1974
1975       if (endRes > 0)
1976       {
1977         endRes += seq.getStart() - 1;
1978       }
1979
1980       copiedSequences.append(seq.getName()
1981               + "\t"
1982               + startRes
1983               + "\t"
1984               + endRes
1985               + "\t"
1986               + seq.getSequenceAsString(sg.getStartRes(),
1987                       sg.getEndRes() + 1) + "\n");
1988     }
1989
1990   }
1991
1992   protected void pasteNew_actionPerformed()
1993   {
1994     paste(true);
1995   }
1996
1997   protected void pasteThis_actionPerformed()
1998   {
1999     paste(false);
2000   }
2001
2002   void paste(boolean newAlignment)
2003   {
2004     try
2005     {
2006
2007       if (copiedSequences == null)
2008       {
2009         return;
2010       }
2011
2012       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2013       Vector seqs = new Vector();
2014       while (st.hasMoreElements())
2015       {
2016         String name = st.nextToken();
2017         int start = Integer.parseInt(st.nextToken());
2018         int end = Integer.parseInt(st.nextToken());
2019         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2020       }
2021       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2022       for (int i = 0; i < seqs.size(); i++)
2023       {
2024         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2025       }
2026
2027       if (newAlignment)
2028       {
2029         String newtitle = MessageManager
2030                 .getString("label.copied_sequences");
2031         if (getTitle().startsWith(
2032                 MessageManager.getString("label.copied_sequences")))
2033         {
2034           newtitle = getTitle();
2035         }
2036         else
2037         {
2038           newtitle = newtitle.concat(MessageManager.formatMessage(
2039                   "label.from_msname", new String[] { getTitle() }));
2040         }
2041         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2042                 viewport.applet, newtitle, false);
2043         if (copiedHiddenColumns != null)
2044         {
2045           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2046           {
2047             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2048             af.viewport.hideColumns(region[0], region[1]);
2049           }
2050         }
2051
2052         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2053                 frameHeight);
2054       }
2055       else
2056       {
2057         addSequences(newSeqs);
2058       }
2059
2060     } catch (Exception ex)
2061     {
2062     } // could be anything being pasted in here
2063
2064   }
2065
2066   void addSequences(SequenceI[] seqs)
2067   {
2068     for (int i = 0; i < seqs.length; i++)
2069     {
2070       viewport.getAlignment().addSequence(seqs[i]);
2071     }
2072
2073     // !newAlignment
2074     addHistoryItem(new EditCommand(
2075             MessageManager.getString("label.add_sequences"), Action.PASTE,
2076             seqs, 0, viewport.getAlignment().getWidth(),
2077             viewport.getAlignment()));
2078
2079     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2080     viewport.getAlignment().getWidth();
2081     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2082             .getSequences());
2083
2084   }
2085
2086   protected void cut_actionPerformed()
2087   {
2088     copy_actionPerformed();
2089     delete_actionPerformed();
2090   }
2091
2092   protected void delete_actionPerformed()
2093   {
2094
2095     SequenceGroup sg = viewport.getSelectionGroup();
2096     if (sg == null)
2097     {
2098       return;
2099     }
2100
2101     Vector seqs = new Vector();
2102     SequenceI seq;
2103     for (int i = 0; i < sg.getSize(); i++)
2104     {
2105       seq = sg.getSequenceAt(i);
2106       seqs.addElement(seq);
2107     }
2108
2109     /*
2110      * If the cut affects all sequences, warn, remove highlighted columns
2111      */
2112     if (sg.getSize() == viewport.getAlignment().getHeight())
2113     {
2114       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2115               .getAlignment().getWidth()) ? true : false;
2116       if (isEntireAlignWidth)
2117       {
2118         String title = MessageManager.getString("label.delete_all");
2119         Panel infoPanel = new Panel();
2120         infoPanel.setLayout(new FlowLayout());
2121         infoPanel
2122                 .add(new Label(MessageManager.getString("warn.delete_all")));
2123
2124         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2125         dialog.setMainPanel(infoPanel);
2126         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2127         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2128         dialog.setVisible(true);
2129
2130         if (!dialog.accept)
2131         {
2132           return;
2133         }
2134       }
2135       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2136               sg.getEndRes() + 1);
2137     }
2138
2139     SequenceI[] cut = new SequenceI[seqs.size()];
2140     for (int i = 0; i < seqs.size(); i++)
2141     {
2142       cut[i] = (SequenceI) seqs.elementAt(i);
2143     }
2144
2145     /*
2146      * //ADD HISTORY ITEM
2147      */
2148     addHistoryItem(new EditCommand(
2149             MessageManager.getString("label.cut_sequences"), Action.CUT,
2150             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2151             viewport.getAlignment()));
2152
2153     viewport.setSelectionGroup(null);
2154     viewport.getAlignment().deleteGroup(sg);
2155
2156     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2157             .getSequences());
2158
2159     if (viewport.getAlignment().getHeight() < 1)
2160     {
2161       this.setVisible(false);
2162     }
2163     viewport.sendSelection();
2164   }
2165
2166   /**
2167    * group consensus toggled
2168    *
2169    */
2170   protected void showGroupConsensus_actionPerformed()
2171   {
2172     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2173     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174
2175   }
2176
2177   /**
2178    * group conservation toggled.
2179    */
2180   protected void showGroupConservation_actionPerformed()
2181   {
2182     viewport.setShowGroupConservation(showGroupConservation.getState());
2183     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184   }
2185
2186   /*
2187    * (non-Javadoc)
2188    *
2189    * @see
2190    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2191    * .event.ActionEvent)
2192    */
2193   protected void showConsensusHistogram_actionPerformed()
2194   {
2195     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197   }
2198
2199   /*
2200    * (non-Javadoc)
2201    *
2202    * @see
2203    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2204    * .event.ActionEvent)
2205    */
2206   protected void showSequenceLogo_actionPerformed()
2207   {
2208     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2209     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2210   }
2211
2212   protected void normSequenceLogo_actionPerformed()
2213   {
2214     showSequenceLogo.setState(true);
2215     viewport.setShowSequenceLogo(true);
2216     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2217     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2218   }
2219
2220   protected void applyAutoAnnotationSettings_actionPerformed()
2221   {
2222     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2223   }
2224
2225   protected void makeGrpsFromSelection_actionPerformed()
2226   {
2227     if (avc.makeGroupsFromSelection())
2228     {
2229       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2230       alignPanel.updateAnnotation();
2231       alignPanel.paintAlignment(true);
2232     }
2233   }
2234
2235   protected void createGroup_actionPerformed()
2236   {
2237     avc.createGroup();
2238   }
2239
2240   protected void unGroup_actionPerformed()
2241   {
2242     if (avc.unGroup())
2243     {
2244       alignPanel.alignmentChanged();
2245     }
2246   }
2247
2248   protected void deleteGroups_actionPerformed()
2249   {
2250     if (avc.deleteGroups())
2251     {
2252       alignPanel.alignmentChanged();
2253     }
2254   }
2255
2256   public void selectAllSequenceMenuItem_actionPerformed()
2257   {
2258     SequenceGroup sg = new SequenceGroup();
2259     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2260     {
2261       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2262     }
2263     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2264     viewport.setSelectionGroup(sg);
2265     // JAL-2034 - should delegate to
2266     // alignPanel to decide if overview needs
2267     // updating.
2268     alignPanel.paintAlignment(false);
2269     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2270     viewport.sendSelection();
2271   }
2272
2273   public void deselectAllSequenceMenuItem_actionPerformed()
2274   {
2275     if (viewport.cursorMode)
2276     {
2277       alignPanel.seqPanel.keyboardNo1 = null;
2278       alignPanel.seqPanel.keyboardNo2 = null;
2279     }
2280     viewport.setSelectionGroup(null);
2281     viewport.getColumnSelection().clear();
2282     viewport.setSelectionGroup(null);
2283     alignPanel.idPanel.idCanvas.searchResults = null;
2284     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2285     // JAL-2034 - should delegate to
2286     // alignPanel to decide if overview needs
2287     // updating.
2288     alignPanel.paintAlignment(false);
2289     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2290     viewport.sendSelection();
2291   }
2292
2293   public void invertSequenceMenuItem_actionPerformed()
2294   {
2295     SequenceGroup sg = viewport.getSelectionGroup();
2296     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2297     {
2298       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2299     }
2300
2301     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2302     viewport.sendSelection();
2303   }
2304
2305   public void invertColSel_actionPerformed()
2306   {
2307     viewport.invertColumnSelection();
2308     alignPanel.paintAlignment(true);
2309     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2310     viewport.sendSelection();
2311   }
2312
2313   void trimAlignment(boolean trimLeft)
2314   {
2315     AlignmentI al = viewport.getAlignment();
2316     ViewportRanges ranges = viewport.getRanges();
2317     ColumnSelection colSel = viewport.getColumnSelection();
2318     int column;
2319
2320     if (!colSel.isEmpty())
2321     {
2322       if (trimLeft)
2323       {
2324         column = colSel.getMin();
2325       }
2326       else
2327       {
2328         column = colSel.getMax();
2329       }
2330
2331       SequenceI[] seqs;
2332       if (viewport.getSelectionGroup() != null)
2333       {
2334         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2335                 viewport.getHiddenRepSequences());
2336       }
2337       else
2338       {
2339         seqs = al.getSequencesArray();
2340       }
2341
2342       TrimRegionCommand trimRegion;
2343       if (trimLeft)
2344       {
2345         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2346                 column, al);
2347         ranges.setStartRes(0);
2348       }
2349       else
2350       {
2351         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2352                 column, al);
2353       }
2354
2355       statusBar.setText(MessageManager.formatMessage(
2356               "label.removed_columns",
2357               new String[] { Integer.valueOf(trimRegion.getSize())
2358                       .toString() }));
2359       addHistoryItem(trimRegion);
2360
2361       for (SequenceGroup sg : al.getGroups())
2362       {
2363         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2364                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2365         {
2366           al.deleteGroup(sg);
2367         }
2368       }
2369
2370       viewport.firePropertyChange("alignment", null, al.getSequences());
2371     }
2372   }
2373
2374   public void removeGappedColumnMenuItem_actionPerformed()
2375   {
2376     AlignmentI al = viewport.getAlignment();
2377     ViewportRanges ranges = viewport.getRanges();
2378     int start = 0;
2379     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2380
2381     SequenceI[] seqs;
2382     if (viewport.getSelectionGroup() != null)
2383     {
2384       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2385               viewport.getHiddenRepSequences());
2386       start = viewport.getSelectionGroup().getStartRes();
2387       end = viewport.getSelectionGroup().getEndRes();
2388     }
2389     else
2390     {
2391       seqs = viewport.getAlignment().getSequencesArray();
2392     }
2393
2394     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2395             "Remove Gapped Columns", seqs, start, end,
2396             viewport.getAlignment());
2397
2398     addHistoryItem(removeGapCols);
2399
2400     statusBar.setText(MessageManager.formatMessage(
2401             "label.removed_empty_columns",
2402             new String[] { Integer.valueOf(removeGapCols.getSize())
2403                     .toString() }));
2404
2405     // This is to maintain viewport position on first residue
2406     // of first sequence
2407     SequenceI seq = al.getSequenceAt(0);
2408     int startRes = seq.findPosition(ranges.getStartRes());
2409     // ShiftList shifts;
2410     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2411     // edit.alColumnChanges=shifts.getInverse();
2412     // if (viewport.hasHiddenColumns)
2413     // viewport.getColumnSelection().compensateForEdits(shifts);
2414     ranges.setStartRes(seq.findIndex(startRes) - 1);
2415     viewport.firePropertyChange("alignment", null, al.getSequences());
2416
2417   }
2418
2419   public void removeAllGapsMenuItem_actionPerformed()
2420   {
2421     AlignmentI al = viewport.getAlignment();
2422     ViewportRanges ranges = viewport.getRanges();
2423     int start = 0;
2424     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2425
2426     SequenceI[] seqs;
2427     if (viewport.getSelectionGroup() != null)
2428     {
2429       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2430               viewport.getHiddenRepSequences());
2431       start = viewport.getSelectionGroup().getStartRes();
2432       end = viewport.getSelectionGroup().getEndRes();
2433     }
2434     else
2435     {
2436       seqs = viewport.getAlignment().getSequencesArray();
2437     }
2438
2439     // This is to maintain viewport position on first residue
2440     // of first sequence
2441     SequenceI seq = al.getSequenceAt(0);
2442     int startRes = seq.findPosition(ranges.getStartRes());
2443
2444     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2445             al));
2446
2447     ranges.setStartRes(seq.findIndex(startRes) - 1);
2448
2449     viewport.firePropertyChange("alignment", null, al.getSequences());
2450
2451   }
2452
2453   public void findMenuItem_actionPerformed()
2454   {
2455     new Finder(alignPanel);
2456   }
2457
2458   /**
2459    * create a new view derived from the current view
2460    *
2461    * @param viewtitle
2462    * @return frame for the new view
2463    */
2464   public AlignFrame newView(String viewtitle)
2465   {
2466     AlignmentI newal;
2467     if (viewport.hasHiddenRows())
2468     {
2469       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2470               .getFullAlignment().getSequencesArray());
2471     }
2472     else
2473     {
2474       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2475     }
2476
2477     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2478     {
2479       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2480       {
2481         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2482         {
2483           newal.addAnnotation(viewport.getAlignment()
2484                   .getAlignmentAnnotation()[i]);
2485         }
2486       }
2487     }
2488
2489     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2490
2491     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2492     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2493     PaintRefresher.Register(newaf.alignPanel,
2494             newaf.alignPanel.av.getSequenceSetId());
2495
2496     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2497             newaf.alignPanel.av.getSequenceSetId());
2498     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2499             newaf.alignPanel.av.getSequenceSetId());
2500
2501     Vector comps = (Vector) PaintRefresher.components.get(viewport
2502             .getSequenceSetId());
2503     int viewSize = -1;
2504     for (int i = 0; i < comps.size(); i++)
2505     {
2506       if (comps.elementAt(i) instanceof AlignmentPanel)
2507       {
2508         viewSize++;
2509       }
2510     }
2511
2512     String title = new String(this.getTitle());
2513     if (viewtitle != null)
2514     {
2515       title = viewtitle + " ( " + title + ")";
2516     }
2517     else
2518     {
2519       if (title.indexOf("(View") > -1)
2520       {
2521         title = title.substring(0, title.indexOf("(View"));
2522       }
2523       title += "(View " + viewSize + ")";
2524     }
2525
2526     newaf.setTitle(title.toString());
2527
2528     newaf.viewport.setHistoryList(viewport.getHistoryList());
2529     newaf.viewport.setRedoList(viewport.getRedoList());
2530     return newaf;
2531   }
2532
2533   /**
2534    *
2535    * @return list of feature groups on the view
2536    */
2537   public String[] getFeatureGroups()
2538   {
2539     FeatureRenderer fr = null;
2540     if (alignPanel != null
2541             && (fr = alignPanel.getFeatureRenderer()) != null)
2542     {
2543       List<String> gps = fr.getFeatureGroups();
2544       String[] _gps = gps.toArray(new String[gps.size()]);
2545       return _gps;
2546     }
2547     return null;
2548   }
2549
2550   /**
2551    * get sequence feature groups that are hidden or shown
2552    *
2553    * @param visible
2554    *          true is visible
2555    * @return list
2556    */
2557   public String[] getFeatureGroupsOfState(boolean visible)
2558   {
2559     FeatureRenderer fr = null;
2560     if (alignPanel != null
2561             && (fr = alignPanel.getFeatureRenderer()) != null)
2562     {
2563       List<String> gps = fr.getGroups(visible);
2564       String[] _gps = gps.toArray(new String[gps.size()]);
2565       return _gps;
2566     }
2567     return null;
2568   }
2569
2570   /**
2571    * Change the display state for the given feature groups
2572    *
2573    * @param groups
2574    *          list of group strings
2575    * @param state
2576    *          visible or invisible
2577    */
2578   public void setFeatureGroupState(String[] groups, boolean state)
2579   {
2580     FeatureRenderer fr = null;
2581     this.sequenceFeatures.setState(true);
2582     viewport.setShowSequenceFeatures(true);
2583     if (alignPanel != null
2584             && (fr = alignPanel.getFeatureRenderer()) != null)
2585     {
2586
2587       fr.setGroupVisibility(Arrays.asList(groups), state);
2588       alignPanel.seqPanel.seqCanvas.repaint();
2589       if (alignPanel.overviewPanel != null)
2590       {
2591         alignPanel.overviewPanel.updateOverviewImage();
2592       }
2593     }
2594   }
2595
2596   public void seqLimits_itemStateChanged()
2597   {
2598     viewport.setShowJVSuffix(seqLimits.getState());
2599     alignPanel.fontChanged();
2600     alignPanel.paintAlignment(true);
2601   }
2602
2603   protected void colourTextMenuItem_actionPerformed()
2604   {
2605     viewport.setColourText(colourTextMenuItem.getState());
2606     alignPanel.paintAlignment(true);
2607   }
2608
2609   protected void displayNonconservedMenuItem_actionPerformed()
2610   {
2611     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2612     alignPanel.paintAlignment(true);
2613   }
2614
2615   protected void wrapMenuItem_actionPerformed()
2616   {
2617     viewport.setWrapAlignment(wrapMenuItem.getState());
2618     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2619     scaleAbove.setEnabled(wrapMenuItem.getState());
2620     scaleLeft.setEnabled(wrapMenuItem.getState());
2621     scaleRight.setEnabled(wrapMenuItem.getState());
2622     alignPanel.paintAlignment(true);
2623   }
2624
2625   public void overviewMenuItem_actionPerformed()
2626   {
2627     if (alignPanel.overviewPanel != null)
2628     {
2629       return;
2630     }
2631
2632     Frame frame = new Frame();
2633     OverviewPanel overview = new OverviewPanel(alignPanel);
2634     frame.add(overview);
2635     // +50 must allow for applet frame window
2636     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2637             "label.overview_params", new String[] { this.getTitle() }),
2638             overview.getPreferredSize().width,
2639             overview.getPreferredSize().height + 50);
2640
2641     frame.pack();
2642     final AlignmentPanel ap = alignPanel;
2643     frame.addWindowListener(new WindowAdapter()
2644     {
2645       @Override
2646       public void windowClosing(WindowEvent e)
2647       {
2648         if (ap != null)
2649         {
2650           ap.setOverviewPanel(null);
2651         }
2652       };
2653     });
2654
2655     alignPanel.setOverviewPanel(overview);
2656
2657   }
2658
2659   @Override
2660   public void changeColour(ColourSchemeI cs)
2661   {
2662     viewport.setGlobalColourScheme(cs);
2663
2664     alignPanel.paintAlignment(true);
2665   }
2666
2667   protected void modifyPID_actionPerformed()
2668   {
2669     if (viewport.getAbovePIDThreshold()
2670             && viewport.getGlobalColourScheme() != null)
2671     {
2672       SliderPanel.setPIDSliderSource(alignPanel,
2673               viewport.getResidueShading(), alignPanel.getViewName());
2674       SliderPanel.showPIDSlider();
2675     }
2676   }
2677
2678   protected void modifyConservation_actionPerformed()
2679   {
2680     if (viewport.getConservationSelected()
2681             && viewport.getGlobalColourScheme() != null)
2682     {
2683       SliderPanel.setConservationSlider(alignPanel,
2684               viewport.getResidueShading(), alignPanel.getViewName());
2685       SliderPanel.showConservationSlider();
2686     }
2687   }
2688
2689   protected void conservationMenuItem_actionPerformed()
2690   {
2691     boolean selected = conservationMenuItem.getState();
2692     modifyConservation.setEnabled(selected);
2693     viewport.setConservationSelected(selected);
2694     viewport.getResidueShading().setConservationApplied(selected);
2695
2696     changeColour(viewport.getGlobalColourScheme());
2697
2698     if (selected)
2699     {
2700       modifyConservation_actionPerformed();
2701     }
2702     else
2703     {
2704       SliderPanel.hideConservationSlider();
2705     }
2706   }
2707
2708   public void abovePIDThreshold_actionPerformed()
2709   {
2710     boolean selected = abovePIDThreshold.getState();
2711     modifyPID.setEnabled(selected);
2712     viewport.setAbovePIDThreshold(selected);
2713     if (!selected)
2714     {
2715       viewport.getResidueShading().setThreshold(0,
2716               viewport.isIgnoreGapsConsensus());
2717     }
2718
2719     changeColour(viewport.getGlobalColourScheme());
2720
2721     if (selected)
2722     {
2723       modifyPID_actionPerformed();
2724     }
2725     else
2726     {
2727       SliderPanel.hidePIDSlider();
2728     }
2729   }
2730
2731   public void sortPairwiseMenuItem_actionPerformed()
2732   {
2733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2735             .getAlignment().getSequenceAt(0), null);
2736
2737     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2738             viewport.getAlignment()));
2739     alignPanel.paintAlignment(true);
2740   }
2741
2742   public void sortIDMenuItem_actionPerformed()
2743   {
2744     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2745     AlignmentSorter.sortByID(viewport.getAlignment());
2746     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2747             viewport.getAlignment()));
2748     alignPanel.paintAlignment(true);
2749   }
2750
2751   public void sortLengthMenuItem_actionPerformed()
2752   {
2753     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2754     AlignmentSorter.sortByLength(viewport.getAlignment());
2755     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2756             viewport.getAlignment()));
2757     alignPanel.paintAlignment(true);
2758   }
2759
2760   public void sortGroupMenuItem_actionPerformed()
2761   {
2762     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2763     AlignmentSorter.sortByGroup(viewport.getAlignment());
2764     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2765             viewport.getAlignment()));
2766     alignPanel.paintAlignment(true);
2767
2768   }
2769
2770   public void removeRedundancyMenuItem_actionPerformed()
2771   {
2772     new RedundancyPanel(alignPanel);
2773   }
2774
2775   public void pairwiseAlignmentMenuItem_actionPerformed()
2776   {
2777     if (viewport.getSelectionGroup() != null
2778             && viewport.getSelectionGroup().getSize() > 1)
2779     {
2780       Frame frame = new Frame();
2781       frame.add(new PairwiseAlignPanel(alignPanel));
2782       jalview.bin.JalviewLite.addFrame(frame,
2783               MessageManager.getString("action.pairwise_alignment"), 600,
2784               500);
2785     }
2786   }
2787
2788   public void PCAMenuItem_actionPerformed()
2789   {
2790     // are the sequences aligned?
2791     if (!viewport.getAlignment().isAligned(false))
2792     {
2793       SequenceI current;
2794       int Width = viewport.getAlignment().getWidth();
2795
2796       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2797       {
2798         current = viewport.getAlignment().getSequenceAt(i);
2799
2800         if (current.getLength() < Width)
2801         {
2802           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2803         }
2804       }
2805       alignPanel.paintAlignment(true);
2806     }
2807
2808     if ((viewport.getSelectionGroup() != null
2809             && viewport.getSelectionGroup().getSize() < 4 && viewport
2810             .getSelectionGroup().getSize() > 0)
2811             || viewport.getAlignment().getHeight() < 4)
2812     {
2813       return;
2814     }
2815
2816     try
2817     {
2818       new PCAPanel(viewport);
2819     } catch (java.lang.OutOfMemoryError ex)
2820     {
2821     }
2822
2823   }
2824
2825   public void averageDistanceTreeMenuItem_actionPerformed()
2826   {
2827     NewTreePanel("AV", "PID", "Average distance tree using PID");
2828   }
2829
2830   public void neighbourTreeMenuItem_actionPerformed()
2831   {
2832     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2833   }
2834
2835   protected void njTreeBlosumMenuItem_actionPerformed()
2836   {
2837     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2838   }
2839
2840   protected void avTreeBlosumMenuItem_actionPerformed()
2841   {
2842     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2843   }
2844
2845   void NewTreePanel(String type, String pwType, String title)
2846   {
2847     // are the sequences aligned?
2848     if (!viewport.getAlignment().isAligned(false))
2849     {
2850       SequenceI current;
2851       int Width = viewport.getAlignment().getWidth();
2852
2853       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2854       {
2855         current = viewport.getAlignment().getSequenceAt(i);
2856
2857         if (current.getLength() < Width)
2858         {
2859           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2860         }
2861       }
2862       alignPanel.paintAlignment(true);
2863
2864     }
2865
2866     if ((viewport.getSelectionGroup() != null && viewport
2867             .getSelectionGroup().getSize() > 1)
2868             || (viewport.getAlignment().getHeight() > 1))
2869     {
2870       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2871
2872       addTreeMenuItem(tp, title);
2873
2874       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2875     }
2876   }
2877
2878   void loadTree_actionPerformed()
2879   {
2880     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2881     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2882     cap.setTreeImport();
2883     Frame frame = new Frame();
2884     frame.add(cap);
2885     jalview.bin.JalviewLite.addFrame(frame,
2886             MessageManager.getString("label.paste_newick_file"), 400, 300);
2887   }
2888
2889   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2890   {
2891     TreePanel tp = new TreePanel(alignPanel, treeFile,
2892             MessageManager.getString("label.load_tree_from_file"), tree);
2893     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2894     addTreeMenuItem(tp, treeFile);
2895   }
2896
2897   /**
2898    * sort the alignment using the given treePanel
2899    *
2900    * @param treePanel
2901    *          tree used to sort view
2902    * @param title
2903    *          string used for undo event name
2904    */
2905   public void sortByTree(TreePanel treePanel, String title)
2906   {
2907     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2908     AlignmentSorter
2909             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2910     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2911     // HistoryItem.SORT));
2912     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2913             "label.order_by_params", new String[] { title }), oldOrder,
2914             viewport.getAlignment()));
2915     alignPanel.paintAlignment(true);
2916   }
2917
2918   /**
2919    * Do any automatic reordering of the alignment and add the necessary bits to
2920    * the menu structure for the new tree
2921    *
2922    * @param treePanel
2923    * @param title
2924    */
2925   protected void addTreeMenuItem(final TreePanel treePanel,
2926           final String title)
2927   {
2928     final MenuItem item = new MenuItem(title);
2929     sortByTreeMenu.add(item);
2930     item.addActionListener(new java.awt.event.ActionListener()
2931     {
2932       @Override
2933       public void actionPerformed(ActionEvent evt)
2934       {
2935         sortByTree(treePanel, title); // treePanel.getTitle());
2936       }
2937     });
2938
2939     treePanel.addWindowListener(new WindowAdapter()
2940     {
2941       @Override
2942       public void windowOpened(WindowEvent e)
2943       {
2944         if (viewport.sortByTree)
2945         {
2946           sortByTree(treePanel, title);
2947         }
2948         super.windowOpened(e);
2949       }
2950
2951       @Override
2952       public void windowClosing(WindowEvent e)
2953       {
2954         sortByTreeMenu.remove(item);
2955       };
2956     });
2957   }
2958
2959   public boolean sortBy(AlignmentOrder alorder, String undoname)
2960   {
2961     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2962     if (viewport.applet.debug)
2963     {
2964       System.err.println("Sorting " + alorder.getOrder().size()
2965               + " in alignment '" + getTitle() + "'");
2966     }
2967     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2968     if (undoname != null)
2969     {
2970       addHistoryItem(new OrderCommand(undoname, oldOrder,
2971               viewport.getAlignment()));
2972     }
2973     alignPanel.paintAlignment(true);
2974     return true;
2975   }
2976
2977   protected void documentation_actionPerformed()
2978   {
2979     alignPanel.av.applet.openJalviewHelpUrl();
2980   }
2981
2982   protected void about_actionPerformed()
2983   {
2984
2985     class AboutPanel extends Canvas
2986     {
2987       String version;
2988
2989       String builddate;
2990
2991       public AboutPanel(String version, String builddate)
2992       {
2993         this.version = version;
2994         this.builddate = builddate;
2995       }
2996
2997       @Override
2998       public void paint(Graphics g)
2999       {
3000         g.setColor(Color.white);
3001         g.fillRect(0, 0, getSize().width, getSize().height);
3002         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3003         FontMetrics fm = g.getFontMetrics();
3004         int fh = fm.getHeight();
3005         int y = 5, x = 7;
3006         g.setColor(Color.black);
3007         // TODO: update this text for each release or centrally store it for
3008         // lite and application
3009         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3010         g.drawString(MessageManager.formatMessage(
3011                 "label.jalviewLite_release", new String[] { version }), x,
3012                 y += fh);
3013         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3014         g.drawString(MessageManager.formatMessage(
3015                 "label.jaview_build_date", new String[] { builddate }), x,
3016                 y += fh);
3017         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3018         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3019                 x, y += fh * 1.5);
3020         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3021                 x + 50, y += fh + 8);
3022         g.drawString(
3023                 MessageManager.getString("label.jalview_dev_managers"), x,
3024                 y += fh);
3025         g.drawString(MessageManager
3026                 .getString("label.jalview_distribution_lists"), x, y += fh);
3027         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3028                 x, y += fh + 8);
3029         g.drawString(
3030                 MessageManager.getString("label.jalview_cite_1_authors"),
3031                 x, y += fh);
3032         g.drawString(
3033                 MessageManager.getString("label.jalview_cite_1_title"), x,
3034                 y += fh);
3035         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3036                 x, y += fh);
3037       }
3038     }
3039
3040     Frame frame = new Frame();
3041     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3042             .getBuildDate()));
3043     jalview.bin.JalviewLite.addFrame(frame,
3044             MessageManager.getString("label.jalview"), 580, 220);
3045
3046   }
3047
3048   public void showURL(String url, String target)
3049   {
3050     if (viewport.applet == null)
3051     {
3052       System.out.println("Not running as applet - no browser available.");
3053     }
3054     else
3055     {
3056       viewport.applet.showURL(url, target);
3057     }
3058   }
3059
3060   // ////////////////////////////////////////////////////////////////////////////////
3061   // JBuilder Graphics here
3062
3063   MenuBar alignFrameMenuBar = new MenuBar();
3064
3065   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3066
3067   MenuItem loadApplication = new MenuItem(
3068           MessageManager.getString("label.view_full_application"));
3069
3070   MenuItem loadTree = new MenuItem(
3071           MessageManager.getString("label.load_associated_tree"));
3072
3073   MenuItem loadAnnotations = new MenuItem(
3074           MessageManager.getString("label.load_features_annotations"));
3075
3076   MenuItem outputFeatures = new MenuItem(
3077           MessageManager.getString("label.export_features"));
3078
3079   MenuItem outputAnnotations = new MenuItem(
3080           MessageManager.getString("label.export_annotations"));
3081
3082   MenuItem closeMenuItem = new MenuItem(
3083           MessageManager.getString("action.close"));
3084
3085   MenuItem selectAllSequenceMenuItem = new MenuItem(
3086           MessageManager.getString("action.select_all"));
3087
3088   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3089           MessageManager.getString("action.deselect_all"));
3090
3091   MenuItem invertSequenceMenuItem = new MenuItem(
3092           MessageManager.getString("action.invert_selection"));
3093
3094   MenuItem remove2LeftMenuItem = new MenuItem();
3095
3096   MenuItem remove2RightMenuItem = new MenuItem();
3097
3098   MenuItem removeGappedColumnMenuItem = new MenuItem();
3099
3100   MenuItem removeAllGapsMenuItem = new MenuItem();
3101
3102   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3103
3104   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3105
3106   MenuItem sortPairwiseMenuItem = new MenuItem();
3107
3108   MenuItem sortIDMenuItem = new MenuItem();
3109
3110   MenuItem sortLengthMenuItem = new MenuItem();
3111
3112   MenuItem sortGroupMenuItem = new MenuItem();
3113
3114   MenuItem removeRedundancyMenuItem = new MenuItem();
3115
3116   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3117
3118   MenuItem PCAMenuItem = new MenuItem();
3119
3120   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3121
3122   MenuItem neighbourTreeMenuItem = new MenuItem();
3123
3124   BorderLayout borderLayout1 = new BorderLayout();
3125
3126   public Label statusBar = new Label();
3127
3128   MenuItem clustalColour = new MenuItem();
3129
3130   MenuItem zappoColour = new MenuItem();
3131
3132   MenuItem taylorColour = new MenuItem();
3133
3134   MenuItem hydrophobicityColour = new MenuItem();
3135
3136   MenuItem helixColour = new MenuItem();
3137
3138   MenuItem strandColour = new MenuItem();
3139
3140   MenuItem turnColour = new MenuItem();
3141
3142   MenuItem buriedColour = new MenuItem();
3143
3144   MenuItem purinePyrimidineColour = new MenuItem();
3145
3146   // MenuItem RNAInteractionColour = new MenuItem();
3147
3148   MenuItem RNAHelixColour = new MenuItem();
3149
3150   MenuItem userDefinedColour = new MenuItem();
3151
3152   MenuItem PIDColour = new MenuItem();
3153
3154   MenuItem BLOSUM62Colour = new MenuItem();
3155
3156   MenuItem tcoffeeColour = new MenuItem();
3157
3158   MenuItem njTreeBlosumMenuItem = new MenuItem();
3159
3160   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3161
3162   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3163
3164   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3165
3166   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3167
3168   MenuItem alProperties = new MenuItem(
3169           MessageManager.getString("label.alignment_props"));
3170
3171   MenuItem overviewMenuItem = new MenuItem();
3172
3173   MenuItem undoMenuItem = new MenuItem();
3174
3175   MenuItem redoMenuItem = new MenuItem();
3176
3177   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3178
3179   MenuItem noColourmenuItem = new MenuItem();
3180
3181   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3182
3183   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3184
3185   MenuItem findMenuItem = new MenuItem();
3186
3187   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3188
3189   MenuItem nucleotideColour = new MenuItem();
3190
3191   MenuItem deleteGroups = new MenuItem();
3192
3193   MenuItem grpsFromSelection = new MenuItem();
3194
3195   MenuItem createGroup = new MenuItem();
3196
3197   MenuItem unGroup = new MenuItem();
3198
3199   MenuItem delete = new MenuItem();
3200
3201   MenuItem copy = new MenuItem();
3202
3203   MenuItem cut = new MenuItem();
3204
3205   Menu pasteMenu = new Menu();
3206
3207   MenuItem pasteNew = new MenuItem();
3208
3209   MenuItem pasteThis = new MenuItem();
3210
3211   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3212
3213   MenuItem font = new MenuItem();
3214
3215   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3220
3221   MenuItem modifyPID = new MenuItem();
3222
3223   MenuItem modifyConservation = new MenuItem();
3224
3225   CheckboxMenuItem autoCalculate = null;
3226
3227   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3228           "Sort Alignment With New Tree", true);
3229
3230   Menu sortByTreeMenu = new Menu();
3231
3232   MenuItem inputText = new MenuItem();
3233
3234   MenuItem documentation = new MenuItem();
3235
3236   MenuItem about = new MenuItem();
3237
3238   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3253
3254   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3255
3256   /**
3257    * Initialise menus and other items
3258    *
3259    * @throws Exception
3260    */
3261   private void jbInit() throws Exception
3262   {
3263     setMenuBar(alignFrameMenuBar);
3264
3265     /*
3266      * Configure File menu items and actions
3267      */
3268     inputText
3269             .setLabel(MessageManager.getString("label.input_from_textbox"));
3270     inputText.addActionListener(this);
3271     Menu outputTextboxMenu = new Menu(
3272             MessageManager.getString("label.out_to_textbox"));
3273     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3274     {
3275       MenuItem item = new MenuItem(ff);
3276
3277       item.addActionListener(new java.awt.event.ActionListener()
3278       {
3279         @Override
3280         public void actionPerformed(ActionEvent e)
3281         {
3282           outputText_actionPerformed(e);
3283         }
3284       });
3285
3286       outputTextboxMenu.add(item);
3287     }
3288     closeMenuItem.addActionListener(this);
3289     loadApplication.addActionListener(this);
3290     loadTree.addActionListener(this);
3291     loadAnnotations.addActionListener(this);
3292     outputFeatures.addActionListener(this);
3293     outputAnnotations.addActionListener(this);
3294
3295     /*
3296      * Configure Edit menu items and actions
3297      */
3298     undoMenuItem.setEnabled(false);
3299     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3300     undoMenuItem.addActionListener(this);
3301     redoMenuItem.setEnabled(false);
3302     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3303     redoMenuItem.addActionListener(this);
3304     copy.setLabel(MessageManager.getString("action.copy"));
3305     copy.addActionListener(this);
3306     cut.setLabel(MessageManager.getString("action.cut"));
3307     cut.addActionListener(this);
3308     delete.setLabel(MessageManager.getString("action.delete"));
3309     delete.addActionListener(this);
3310     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3311     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3312     pasteNew.addActionListener(this);
3313     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3314     pasteThis.addActionListener(this);
3315     remove2LeftMenuItem.setLabel(MessageManager
3316             .getString("action.remove_left"));
3317     remove2LeftMenuItem.addActionListener(this);
3318     remove2RightMenuItem.setLabel(MessageManager
3319             .getString("action.remove_right"));
3320     remove2RightMenuItem.addActionListener(this);
3321     removeGappedColumnMenuItem.setLabel(MessageManager
3322             .getString("action.remove_empty_columns"));
3323     removeGappedColumnMenuItem.addActionListener(this);
3324     removeAllGapsMenuItem.setLabel(MessageManager
3325             .getString("action.remove_all_gaps"));
3326     removeAllGapsMenuItem.addActionListener(this);
3327     removeRedundancyMenuItem.setLabel(MessageManager
3328             .getString("action.remove_redundancy"));
3329     removeRedundancyMenuItem.addActionListener(this);
3330
3331     /*
3332      * Configure Select menu items and actions
3333      */
3334     findMenuItem.setLabel(MessageManager.getString("action.find"));
3335     findMenuItem.addActionListener(this);
3336     selectAllSequenceMenuItem.addActionListener(this);
3337     deselectAllSequenceMenuItem.addActionListener(this);
3338     invertSequenceMenuItem.setLabel(MessageManager
3339             .getString("action.invert_sequence_selection"));
3340     invertSequenceMenuItem.addActionListener(this);
3341     invertColSel.setLabel(MessageManager
3342             .getString("action.invert_column_selection"));
3343     invertColSel.addActionListener(this);
3344     deleteGroups.setLabel(MessageManager
3345             .getString("action.undefine_groups"));
3346     deleteGroups.addActionListener(this);
3347     grpsFromSelection.setLabel(MessageManager
3348             .getString("action.make_groups_selection"));
3349     grpsFromSelection.addActionListener(this);
3350     createGroup.setLabel(MessageManager.getString("action.create_group"));
3351     createGroup.addActionListener(this);
3352     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3353     unGroup.addActionListener(this);
3354
3355     annotationColumnSelection.setLabel(MessageManager
3356             .getString("action.select_by_annotation"));
3357     annotationColumnSelection.addActionListener(this);
3358
3359     /*
3360      * Configure View menu items and actions
3361      */
3362     newView.setLabel(MessageManager.getString("action.new_view"));
3363     newView.addActionListener(this);
3364     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3365     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3366     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3367     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3368     hideColumns
3369             .setLabel(MessageManager.getString("label.selected_columns"));
3370     hideSequences.setLabel(MessageManager
3371             .getString("label.selected_sequences"));
3372     hideAllButSelection.setLabel(MessageManager
3373             .getString("label.all_but_selected_region"));
3374     hideAllSelection.setLabel(MessageManager
3375             .getString("label.selected_region"));
3376     showAllHidden.setLabel(MessageManager
3377             .getString("label.all_sequences_columns"));
3378     showColumns.addActionListener(this);
3379     showSeqs.addActionListener(this);
3380     hideColumns.addActionListener(this);
3381     hideSequences.addActionListener(this);
3382     hideAllButSelection.addActionListener(this);
3383     hideAllSelection.addActionListener(this);
3384     showAllHidden.addActionListener(this);
3385     featureSettings.setLabel(MessageManager
3386             .getString("action.feature_settings"));
3387     featureSettings.addActionListener(this);
3388     sequenceFeatures.setLabel(MessageManager
3389             .getString("label.show_sequence_features"));
3390     sequenceFeatures.addItemListener(this);
3391     sequenceFeatures.setState(false);
3392     followMouseOverFlag.setLabel(MessageManager
3393             .getString("label.automatic_scrolling"));
3394     followMouseOverFlag.addItemListener(this);
3395     alProperties.addActionListener(this);
3396     overviewMenuItem.setLabel(MessageManager
3397             .getString("label.overview_window"));
3398     overviewMenuItem.addActionListener(this);
3399
3400     /*
3401      * Configure Annotations menu items and actions
3402      */
3403     annotationPanelMenuItem.setLabel(MessageManager
3404             .getString("label.show_annotations"));
3405     annotationPanelMenuItem.addItemListener(this);
3406     showGroupConsensus.setLabel(MessageManager
3407             .getString("label.group_consensus"));
3408     showGroupConservation.setLabel(MessageManager
3409             .getString("label.group_conservation"));
3410     showConsensusHistogram.setLabel(MessageManager
3411             .getString("label.show_consensus_histogram"));
3412     showSequenceLogo.setLabel(MessageManager
3413             .getString("label.show_consensus_logo"));
3414     normSequenceLogo.setLabel(MessageManager
3415             .getString("label.norm_consensus_logo"));
3416     applyAutoAnnotationSettings.setLabel(MessageManager
3417             .getString("label.apply_all_groups"));
3418     applyAutoAnnotationSettings.setState(true);
3419     Menu autoAnnMenu = new Menu(
3420             MessageManager.getString("label.autocalculated_annotation"));
3421     showGroupConsensus.addItemListener(this);
3422     showGroupConservation.addItemListener(this);
3423     showConsensusHistogram.addItemListener(this);
3424     showSequenceLogo.addItemListener(this);
3425     normSequenceLogo.addItemListener(this);
3426     applyAutoAnnotationSettings.addItemListener(this);
3427     showAlignmentAnnotations = new CheckboxMenuItem(
3428             MessageManager.getString("label.show_all_al_annotations"));
3429     showSequenceAnnotations = new CheckboxMenuItem(
3430             MessageManager.getString("label.show_all_seq_annotations"));
3431     sortAnnBySequence = new CheckboxMenuItem(
3432             MessageManager.getString("label.sort_annotations_by_sequence"));
3433     sortAnnByLabel = new CheckboxMenuItem(
3434             MessageManager.getString("label.sort_annotations_by_label"));
3435     showAutoFirst = new CheckboxMenuItem(
3436             MessageManager.getString("label.show_first"));
3437     showAutoFirst.setState(false); // pending applet parameter
3438     setShowAutoCalculatedAbove(showAutoFirst.getState());
3439     showAutoLast = new CheckboxMenuItem(
3440             MessageManager.getString("label.show_last"));
3441     showAutoLast.setState(!showAutoFirst.getState());
3442     showAlignmentAnnotations.addItemListener(this);
3443     showSequenceAnnotations.addItemListener(this);
3444     sortAnnBySequence.addItemListener(this);
3445     sortAnnByLabel.addItemListener(this);
3446     showAutoFirst.addItemListener(this);
3447     showAutoLast.addItemListener(this);
3448
3449     /*
3450      * Configure Format menu items and actions
3451      */
3452     font.setLabel(MessageManager.getString("action.font"));
3453     font.addActionListener(this);
3454     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3455     scaleAbove.setState(true);
3456     scaleAbove.setEnabled(false);
3457     scaleAbove.addItemListener(this);
3458     scaleLeft.setEnabled(false);
3459     scaleLeft.setState(true);
3460     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3461     scaleLeft.addItemListener(this);
3462     scaleRight.setEnabled(false);
3463     scaleRight.setState(true);
3464     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3465     scaleRight.addItemListener(this);
3466     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3467     viewBoxesMenuItem.setState(true);
3468     viewBoxesMenuItem.addItemListener(this);
3469     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3470     viewTextMenuItem.setState(true);
3471     viewTextMenuItem.addItemListener(this);
3472     colourTextMenuItem.setLabel(MessageManager
3473             .getString("label.colour_text"));
3474     colourTextMenuItem.addItemListener(this);
3475     displayNonconservedMenuItem.setLabel(MessageManager
3476             .getString("label.show_non_conserved"));
3477     displayNonconservedMenuItem.addItemListener(this);
3478     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3479     wrapMenuItem.addItemListener(this);
3480     renderGapsMenuItem.setLabel(MessageManager
3481             .getString("action.show_gaps"));
3482     renderGapsMenuItem.setState(true);
3483     renderGapsMenuItem.addItemListener(this);
3484     centreColumnLabelFlag.setLabel(MessageManager
3485             .getString("label.centre_column_labels"));
3486     centreColumnLabelFlag.addItemListener(this);
3487     seqLimits.setState(true);
3488     seqLimits.setLabel(MessageManager
3489             .getString("label.show_sequence_limits"));
3490     seqLimits.addItemListener(this);
3491
3492     /*
3493      * Configure Colour menu items and actions
3494      */
3495     applyToAllGroups.setLabel(MessageManager
3496             .getString("label.apply_colour_to_all_groups"));
3497     applyToAllGroups.setState(true);
3498     applyToAllGroups.addItemListener(this);
3499     clustalColour.setLabel(MessageManager
3500             .getString("label.colourScheme_clustal"));
3501     clustalColour.addActionListener(this);
3502     zappoColour.setLabel(MessageManager
3503             .getString("label.colourScheme_zappo"));
3504     zappoColour.addActionListener(this);
3505     taylorColour.setLabel(MessageManager
3506             .getString("label.colourScheme_taylor"));
3507     taylorColour.addActionListener(this);
3508     hydrophobicityColour.setLabel(MessageManager
3509             .getString("label.colourScheme_hydrophobic"));
3510     hydrophobicityColour.addActionListener(this);
3511     helixColour.setLabel(MessageManager
3512             .getString("label.colourScheme_helix_propensity"));
3513     helixColour.addActionListener(this);
3514     strandColour.setLabel(MessageManager
3515             .getString("label.colourScheme_strand_propensity"));
3516     strandColour.addActionListener(this);
3517     turnColour.setLabel(MessageManager
3518             .getString("label.colourScheme_turn_propensity"));
3519     turnColour.addActionListener(this);
3520     buriedColour.setLabel(MessageManager
3521             .getString("label.colourScheme_buried_index"));
3522     buriedColour.addActionListener(this);
3523     purinePyrimidineColour.setLabel(MessageManager
3524             .getString("label.colourScheme_purine/pyrimidine"));
3525     purinePyrimidineColour.addActionListener(this);
3526     // RNAInteractionColour.setLabel(MessageManager
3527     // .getString("label.rna_interaction"));
3528     // RNAInteractionColour.addActionListener(this);
3529     RNAHelixColour.setLabel(MessageManager
3530             .getString("label.colourScheme_rna_helices"));
3531     RNAHelixColour.addActionListener(this);
3532     userDefinedColour.setLabel(MessageManager
3533             .getString("action.user_defined"));
3534     userDefinedColour.addActionListener(this);
3535     PIDColour.setLabel(MessageManager
3536             .getString("label.colourScheme_%_identity"));
3537     PIDColour.addActionListener(this);
3538     BLOSUM62Colour.setLabel(MessageManager
3539             .getString("label.colourScheme_blosum62"));
3540     BLOSUM62Colour.addActionListener(this);
3541     tcoffeeColour.setLabel(MessageManager
3542             .getString("label.colourScheme_t-coffee_scores"));
3543     // it will be enabled only if a score file is provided
3544     tcoffeeColour.setEnabled(false);
3545     tcoffeeColour.addActionListener(this);
3546     conservationMenuItem.setLabel(MessageManager
3547             .getString("action.by_conservation"));
3548     conservationMenuItem.addItemListener(this);
3549     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3550     noColourmenuItem.addActionListener(this);
3551     abovePIDThreshold.setLabel(MessageManager
3552             .getString("label.above_identity_threshold"));
3553     abovePIDThreshold.addItemListener(this);
3554     nucleotideColour.setLabel(MessageManager
3555             .getString("label.colourScheme_nucleotide"));
3556     nucleotideColour.addActionListener(this);
3557     modifyPID.setLabel(MessageManager
3558             .getString("label.modify_identity_threshold"));
3559     modifyPID.setEnabled(abovePIDThreshold.getState());
3560     modifyPID.addActionListener(this);
3561     modifyConservation.setLabel(MessageManager
3562             .getString("label.modify_conservation_threshold"));
3563     modifyConservation.setEnabled(conservationMenuItem.getState());
3564     modifyConservation.addActionListener(this);
3565     annotationColour.setLabel(MessageManager
3566             .getString("action.by_annotation"));
3567     annotationColour.addActionListener(this);
3568
3569     /*
3570      * Configure Calculate menu items and actions
3571      */
3572     sortPairwiseMenuItem.setLabel(MessageManager
3573             .getString("action.by_pairwise_id"));
3574     sortPairwiseMenuItem.addActionListener(this);
3575     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3576     sortIDMenuItem.addActionListener(this);
3577     sortLengthMenuItem.setLabel(MessageManager
3578             .getString("action.by_length"));
3579     sortLengthMenuItem.addActionListener(this);
3580     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3581     sortGroupMenuItem.addActionListener(this);
3582     pairwiseAlignmentMenuItem.setLabel(MessageManager
3583             .getString("action.pairwise_alignment"));
3584     pairwiseAlignmentMenuItem.addActionListener(this);
3585     PCAMenuItem.setLabel(MessageManager
3586             .getString("label.principal_component_analysis"));
3587     PCAMenuItem.addActionListener(this);
3588     autoCalculate = new CheckboxMenuItem(
3589             MessageManager.getString("label.autocalculate_consensus"), true);
3590     averageDistanceTreeMenuItem.setLabel(MessageManager
3591             .getString("label.average_distance_identity"));
3592     averageDistanceTreeMenuItem.addActionListener(this);
3593     neighbourTreeMenuItem.setLabel(MessageManager
3594             .getString("label.neighbour_joining_identity"));
3595     neighbourTreeMenuItem.addActionListener(this);
3596     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3597             .getString("label.average_distance_blosum62"));
3598     avDistanceTreeBlosumMenuItem.addActionListener(this);
3599     njTreeBlosumMenuItem.setLabel(MessageManager
3600             .getString("label.neighbour_blosum62"));
3601     njTreeBlosumMenuItem.addActionListener(this);
3602     sortByTreeMenu.setLabel(MessageManager
3603             .getString("action.by_tree_order"));
3604     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3605     Menu calculateTreeMenu = new Menu(
3606             MessageManager.getString("action.calculate_tree"));
3607     autoCalculate.addItemListener(this);
3608     sortByTree.addItemListener(this);
3609
3610     /*
3611      * Configure Help menu items and actions
3612      */
3613     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3614     documentation.setLabel(MessageManager.getString("label.documentation"));
3615     documentation.addActionListener(this);
3616     about.setLabel(MessageManager.getString("label.about"));
3617     about.addActionListener(this);
3618
3619     /*
3620      * Add top level menus to frame
3621      */
3622     alignFrameMenuBar.add(fileMenu);
3623     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3624     alignFrameMenuBar.add(editMenu);
3625     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3626     alignFrameMenuBar.add(selectMenu);
3627     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3628     alignFrameMenuBar.add(viewMenu);
3629     Menu annotationsMenu = new Menu(
3630             MessageManager.getString("action.annotations"));
3631     alignFrameMenuBar.add(annotationsMenu);
3632     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3633     alignFrameMenuBar.add(formatMenu);
3634     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3635     alignFrameMenuBar.add(colourMenu);
3636     Menu calculateMenu = new Menu(
3637             MessageManager.getString("action.calculate"));
3638     alignFrameMenuBar.add(calculateMenu);
3639     alignFrameMenuBar.add(helpMenu);
3640
3641     /*
3642      * File menu
3643      */
3644     fileMenu.add(inputText);
3645     fileMenu.add(loadTree);
3646     fileMenu.add(loadAnnotations);
3647     fileMenu.addSeparator();
3648     fileMenu.add(outputTextboxMenu);
3649     fileMenu.add(outputFeatures);
3650     fileMenu.add(outputAnnotations);
3651     if (jalviewServletURL != null)
3652     {
3653       fileMenu.add(loadApplication);
3654     }
3655     fileMenu.addSeparator();
3656     fileMenu.add(closeMenuItem);
3657
3658     /*
3659      * Edit menu
3660      */
3661     editMenu.add(undoMenuItem);
3662     editMenu.add(redoMenuItem);
3663     editMenu.add(cut);
3664     editMenu.add(copy);
3665     pasteMenu.add(pasteNew);
3666     pasteMenu.add(pasteThis);
3667     editMenu.add(pasteMenu);
3668     editMenu.add(delete);
3669     editMenu.addSeparator();
3670     editMenu.add(remove2LeftMenuItem);
3671     editMenu.add(remove2RightMenuItem);
3672     editMenu.add(removeGappedColumnMenuItem);
3673     editMenu.add(removeAllGapsMenuItem);
3674     editMenu.add(removeRedundancyMenuItem);
3675
3676     /*
3677      * Select menu
3678      */
3679     selectMenu.add(findMenuItem);
3680     selectMenu.addSeparator();
3681     selectMenu.add(selectAllSequenceMenuItem);
3682     selectMenu.add(deselectAllSequenceMenuItem);
3683     selectMenu.add(invertSequenceMenuItem);
3684     selectMenu.add(invertColSel);
3685     selectMenu.add(createGroup);
3686     selectMenu.add(unGroup);
3687     selectMenu.add(grpsFromSelection);
3688     selectMenu.add(deleteGroups);
3689     selectMenu.add(annotationColumnSelection);
3690
3691     /*
3692      * View menu
3693      */
3694     viewMenu.add(newView);
3695     viewMenu.addSeparator();
3696     showMenu.add(showColumns);
3697     showMenu.add(showSeqs);
3698     showMenu.add(showAllHidden);
3699     viewMenu.add(showMenu);
3700     hideMenu.add(hideColumns);
3701     hideMenu.add(hideSequences);
3702     hideMenu.add(hideAllSelection);
3703     hideMenu.add(hideAllButSelection);
3704     viewMenu.add(hideMenu);
3705     viewMenu.addSeparator();
3706     viewMenu.add(followMouseOverFlag);
3707     viewMenu.addSeparator();
3708     viewMenu.add(sequenceFeatures);
3709     viewMenu.add(featureSettings);
3710     viewMenu.addSeparator();
3711     viewMenu.add(alProperties);
3712     viewMenu.addSeparator();
3713     viewMenu.add(overviewMenuItem);
3714
3715     /*
3716      * Annotations menu
3717      */
3718     annotationsMenu.add(annotationPanelMenuItem);
3719     annotationsMenu.addSeparator();
3720     annotationsMenu.add(showAlignmentAnnotations);
3721     annotationsMenu.add(showSequenceAnnotations);
3722     annotationsMenu.add(sortAnnBySequence);
3723     annotationsMenu.add(sortAnnByLabel);
3724     annotationsMenu.addSeparator();
3725     autoAnnMenu.add(showAutoFirst);
3726     autoAnnMenu.add(showAutoLast);
3727     autoAnnMenu.addSeparator();
3728     autoAnnMenu.add(applyAutoAnnotationSettings);
3729     autoAnnMenu.add(showConsensusHistogram);
3730     autoAnnMenu.add(showSequenceLogo);
3731     autoAnnMenu.add(normSequenceLogo);
3732     autoAnnMenu.addSeparator();
3733     autoAnnMenu.add(showGroupConservation);
3734     autoAnnMenu.add(showGroupConsensus);
3735     annotationsMenu.add(autoAnnMenu);
3736
3737     /*
3738      * Format menu
3739      */
3740     formatMenu.add(font);
3741     formatMenu.add(seqLimits);
3742     formatMenu.add(wrapMenuItem);
3743     formatMenu.add(scaleAbove);
3744     formatMenu.add(scaleLeft);
3745     formatMenu.add(scaleRight);
3746     formatMenu.add(viewBoxesMenuItem);
3747     formatMenu.add(viewTextMenuItem);
3748     formatMenu.add(colourTextMenuItem);
3749     formatMenu.add(displayNonconservedMenuItem);
3750     formatMenu.add(renderGapsMenuItem);
3751     formatMenu.add(centreColumnLabelFlag);
3752
3753     /*
3754      * Colour menu
3755      */
3756     colourMenu.add(applyToAllGroups);
3757     colourMenu.addSeparator();
3758     colourMenu.add(noColourmenuItem);
3759     colourMenu.add(clustalColour);
3760     colourMenu.add(BLOSUM62Colour);
3761     colourMenu.add(PIDColour);
3762     colourMenu.add(zappoColour);
3763     colourMenu.add(taylorColour);
3764     colourMenu.add(hydrophobicityColour);
3765     colourMenu.add(helixColour);
3766     colourMenu.add(strandColour);
3767     colourMenu.add(turnColour);
3768     colourMenu.add(buriedColour);
3769     colourMenu.add(nucleotideColour);
3770     colourMenu.add(purinePyrimidineColour);
3771     // colourMenu.add(RNAInteractionColour);
3772     colourMenu.add(tcoffeeColour);
3773     colourMenu.add(userDefinedColour);
3774     colourMenu.addSeparator();
3775     colourMenu.add(conservationMenuItem);
3776     colourMenu.add(modifyConservation);
3777     colourMenu.add(abovePIDThreshold);
3778     colourMenu.add(modifyPID);
3779     colourMenu.add(annotationColour);
3780     colourMenu.add(RNAHelixColour);
3781
3782     /*
3783      * Calculate menu
3784      */
3785     sortMenu.add(sortIDMenuItem);
3786     sortMenu.add(sortLengthMenuItem);
3787     sortMenu.add(sortByTreeMenu);
3788     sortMenu.add(sortGroupMenuItem);
3789     sortMenu.add(sortPairwiseMenuItem);
3790     calculateMenu.add(sortMenu);
3791     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3792     calculateTreeMenu.add(neighbourTreeMenuItem);
3793     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3794     calculateTreeMenu.add(njTreeBlosumMenuItem);
3795     calculateMenu.add(calculateTreeMenu);
3796     calculateMenu.addSeparator();
3797     calculateMenu.add(pairwiseAlignmentMenuItem);
3798     calculateMenu.add(PCAMenuItem);
3799     calculateMenu.add(autoCalculate);
3800     calculateMenu.add(sortByTree);
3801
3802     /*
3803      * Help menu
3804      */
3805     helpMenu.add(documentation);
3806     helpMenu.add(about);
3807
3808     /*
3809      * Status bar
3810      */
3811     statusBar.setBackground(Color.white);
3812     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3813     statusBar.setText(MessageManager.getString("label.status_bar"));
3814     this.add(statusBar, BorderLayout.SOUTH);
3815   }
3816
3817   @Override
3818   public void setStatus(String string)
3819   {
3820     statusBar.setText(string);
3821   };
3822
3823   MenuItem featureSettings = new MenuItem();
3824
3825   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3826
3827   MenuItem annotationColour = new MenuItem();
3828
3829   MenuItem annotationColumnSelection = new MenuItem();
3830
3831   MenuItem invertColSel = new MenuItem();
3832
3833   MenuItem showColumns = new MenuItem();
3834
3835   MenuItem showSeqs = new MenuItem();
3836
3837   MenuItem hideColumns = new MenuItem();
3838
3839   MenuItem hideSequences = new MenuItem();
3840
3841   MenuItem hideAllButSelection = new MenuItem();
3842
3843   MenuItem hideAllSelection = new MenuItem();
3844
3845   MenuItem showAllHidden = new MenuItem();
3846
3847   MenuItem newView = new MenuItem();
3848
3849   private CheckboxMenuItem showAlignmentAnnotations;
3850
3851   private CheckboxMenuItem showSequenceAnnotations;
3852
3853   private CheckboxMenuItem sortAnnBySequence;
3854
3855   private CheckboxMenuItem sortAnnByLabel;
3856
3857   private CheckboxMenuItem showAutoFirst;
3858
3859   private CheckboxMenuItem showAutoLast;
3860
3861   private SplitFrame splitFrame;
3862
3863   /**
3864    * Attach the alignFrame panels after embedding menus, if necessary. This used
3865    * to be called setEmbedded, but is now creates the dropdown menus in a
3866    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3867    *
3868    * @param reallyEmbedded
3869    *          true to attach the view to the applet area on the page rather than
3870    *          in a new window
3871    */
3872   public void createAlignFrameWindow(boolean reallyEmbedded)
3873   {
3874     if (reallyEmbedded)
3875     {
3876       embedAlignFrameInApplet(viewport.applet);
3877     }
3878     else
3879     {
3880       // //////
3881       // test and embed menu bar if necessary.
3882       //
3883       if (embedMenuIfNeeded(alignPanel))
3884       {
3885         /*
3886          * adjust for status bar height too. ? pointless as overridden by layout
3887          * manager
3888          */
3889         alignPanel.setSize(getSize().width,
3890                 getSize().height - statusBar.getHeight());
3891       }
3892       add(statusBar, BorderLayout.SOUTH);
3893       add(alignPanel, BorderLayout.CENTER);
3894       // and register with the applet so it can pass external API calls to us
3895       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3896               frameHeight);
3897     }
3898   }
3899
3900   /**
3901    * Add the components of this AlignFrame to the applet container.
3902    *
3903    * @param theApplet
3904    */
3905   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3906   {
3907     // ////
3908     // Explicitly build the embedded menu panel for the on-page applet
3909     //
3910     // view cannot be closed if its actually on the page
3911     fileMenu.remove(closeMenuItem);
3912     fileMenu.remove(3); // Remove Separator
3913     // construct embedded menu, using default font
3914     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3915     // and actually add the components to the applet area
3916     theApplet.setLayout(new BorderLayout());
3917     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3918     theApplet.add(statusBar, BorderLayout.SOUTH);
3919     // TODO should size be left to the layout manager?
3920     alignPanel.setSize(theApplet.getSize().width,
3921             theApplet.getSize().height - embeddedMenu.getHeight()
3922                     - statusBar.getHeight());
3923     theApplet.add(alignPanel, BorderLayout.CENTER);
3924     final AlignFrame me = this;
3925     theApplet.addFocusListener(new FocusListener()
3926     {
3927
3928       @Override
3929       public void focusLost(FocusEvent e)
3930       {
3931         if (theApplet.currentAlignFrame == me)
3932         {
3933           theApplet.currentAlignFrame = null;
3934         }
3935       }
3936
3937       @Override
3938       public void focusGained(FocusEvent e)
3939       {
3940         theApplet.currentAlignFrame = me;
3941       }
3942     });
3943     theApplet.validate();
3944   }
3945
3946   /**
3947    * create a new binding between structures in an existing jmol viewer instance
3948    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3949    * this does not open a new Jmol window, or modify the display of the
3950    * structures in the original jmol window. Note This method doesn't work
3951    * without an additional javascript library to exchange messages between the
3952    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3953    *
3954    * @param viewer
3955    *          JmolViewer instance
3956    * @param sequenceIds
3957    *          - sequence Ids to search for associations
3958    */
3959   public SequenceStructureBinding addStructureViewInstance(
3960           Object jmolviewer, String[] sequenceIds)
3961   {
3962     Viewer viewer = null;
3963     try
3964     {
3965       viewer = (Viewer) jmolviewer;
3966     } catch (ClassCastException ex)
3967     {
3968       System.err.println("Unsupported viewer object :"
3969               + jmolviewer.getClass());
3970     }
3971     if (viewer == null)
3972     {
3973       System.err.println("Can't use this object as a structure viewer:"
3974               + jmolviewer.getClass());
3975       return null;
3976     }
3977     SequenceI[] seqs = null;
3978     if (sequenceIds == null || sequenceIds.length == 0)
3979     {
3980       seqs = viewport.getAlignment().getSequencesArray();
3981     }
3982     else
3983     {
3984       Vector sqi = new Vector();
3985       AlignmentI al = viewport.getAlignment();
3986       for (int sid = 0; sid < sequenceIds.length; sid++)
3987       {
3988         SequenceI sq = al.findName(sequenceIds[sid]);
3989         if (sq != null)
3990         {
3991           sqi.addElement(sq);
3992         }
3993       }
3994       if (sqi.size() > 0)
3995       {
3996         seqs = new SequenceI[sqi.size()];
3997         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3998         {
3999           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4000         }
4001       }
4002       else
4003       {
4004         return null;
4005       }
4006     }
4007     AAStructureBindingModel jmv = null;
4008     // TODO: search for a jmv that involves viewer
4009     if (jmv == null)
4010     { // create a new viewer/jalview binding.
4011       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4012     }
4013     return jmv;
4014
4015   }
4016
4017   /**
4018    * bind a pdb file to a sequence in the current view
4019    *
4020    * @param sequenceId
4021    *          - sequenceId within the dataset.
4022    * @param pdbEntryString
4023    *          - the short name for the PDB file
4024    * @param pdbFile
4025    *          - pdb file - either a URL or a valid PDB file.
4026    * @return true if binding was as success TODO: consider making an exception
4027    *         structure for indicating when PDB parsing or sequenceId location
4028    *         fails.
4029    */
4030   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4031           String pdbFile)
4032   {
4033     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4034     boolean needtoadd = false;
4035     if (toaddpdb != null)
4036     {
4037       Vector pdbe = toaddpdb.getAllPDBEntries();
4038       PDBEntry pdbentry = null;
4039       if (pdbe != null && pdbe.size() > 0)
4040       {
4041         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4042         {
4043           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4044           if (!pdbentry.getId().equals(pdbEntryString)
4045                   && !pdbentry.getFile().equals(pdbFile))
4046           {
4047             pdbentry = null;
4048           }
4049           else
4050           {
4051             continue;
4052           }
4053         }
4054       }
4055       if (pdbentry == null)
4056       {
4057         pdbentry = new PDBEntry();
4058         pdbentry.setId(pdbEntryString);
4059         pdbentry.setFile(pdbFile);
4060         needtoadd = true; // add this new entry to sequence.
4061       }
4062       // resolve data source
4063       // TODO: this code should be a refactored to an io package
4064       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4065               pdbFile, FileFormat.PDB);
4066       if (protocol == null)
4067       {
4068         return false;
4069       }
4070       if (needtoadd)
4071       {
4072         pdbentry.setProperty("protocol", protocol);
4073         toaddpdb.addPDBId(pdbentry);
4074         alignPanel.getStructureSelectionManager()
4075                 .registerPDBEntry(pdbentry);
4076       }
4077     }
4078     return true;
4079   }
4080
4081   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4082   {
4083     if (seqs != null)
4084     {
4085       Vector sequences = new Vector();
4086       for (int i = 0; i < seqs.length; i++)
4087       {
4088         if (seqs[i] != null)
4089         {
4090           sequences.addElement(new Object[] { seqs[i],
4091               (chains != null) ? chains[i] : null });
4092         }
4093       }
4094       seqs = new SequenceI[sequences.size()];
4095       chains = new String[sequences.size()];
4096       for (int i = 0, isize = sequences.size(); i < isize; i++)
4097       {
4098         Object[] oj = (Object[]) sequences.elementAt(i);
4099
4100         seqs[i] = (SequenceI) oj[0];
4101         chains[i] = (String) oj[1];
4102       }
4103     }
4104     return new Object[] { seqs, chains };
4105
4106   }
4107
4108   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4109           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4110   {
4111     // Scrub any null sequences from the array
4112     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4113     seqs = (SequenceI[]) sqch[0];
4114     chains = (String[]) sqch[1];
4115     if (seqs == null || seqs.length == 0)
4116     {
4117       System.err
4118               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4119     }
4120     if (protocol == null)
4121     {
4122       String sourceType = (String) pdb.getProperty("protocol");
4123       try
4124       {
4125         protocol = DataSourceType.valueOf(sourceType);
4126       } catch (IllegalArgumentException e)
4127       {
4128         // ignore
4129       }
4130       if (protocol == null)
4131       {
4132         System.err.println("Couldn't work out protocol to open structure: "
4133                 + pdb.getId());
4134         return;
4135       }
4136     }
4137     if (applet.useXtrnalSviewer)
4138     {
4139       // register the association(s) and quit, don't create any windows.
4140       if (StructureSelectionManager.getStructureSelectionManager(applet)
4141               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4142       {
4143         System.err.println("Failed to map " + pdb.getFile() + " ("
4144                 + protocol + ") to any sequences");
4145       }
4146       return;
4147     }
4148     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4149     {
4150       // can only do alignments with Jmol
4151       // find the last jmol window assigned to this alignment
4152       AppletJmol ajm = null, tajm;
4153       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4154       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4155       {
4156         tajm = (AppletJmol) jmols.elementAt(i);
4157         if (tajm.ap.alignFrame == this)
4158         {
4159           ajm = tajm;
4160           break;
4161         }
4162       }
4163       if (ajm != null)
4164       {
4165         System.err
4166                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4167         // try and add the pdb structure
4168         // ajm.addS
4169         ajm = null;
4170       }
4171     }
4172     // otherwise, create a new window
4173     if (applet.jmolAvailable)
4174     {
4175       new AppletJmol(pdb, seqs, chains, alignPanel,
4176               protocol);
4177       applet.lastFrameX += 40;
4178       applet.lastFrameY += 40;
4179     }
4180     else
4181     {
4182       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4183     }
4184
4185   }
4186
4187   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4188           SequenceI[][] seqs, String[][] chains, String[] protocols)
4189   {
4190     // TODO Auto-generated method stub
4191     System.err.println("Aligned Structure View: Not yet implemented.");
4192   }
4193
4194   /**
4195    * modify the current selection, providing the user has not made a selection
4196    * already.
4197    *
4198    * @param sel
4199    *          - sequences from this alignment
4200    * @param csel
4201    *          - columns to be selected on the alignment
4202    */
4203   public void select(SequenceGroup sel, ColumnSelection csel,
4204           HiddenColumns hidden)
4205   {
4206     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4207   }
4208
4209   public void scrollTo(int row, int column)
4210   {
4211     alignPanel.seqPanel.scrollTo(row, column);
4212   }
4213
4214   public void scrollToRow(int row)
4215   {
4216     alignPanel.seqPanel.scrollToRow(row);
4217   }
4218
4219   public void scrollToColumn(int column)
4220   {
4221     alignPanel.seqPanel.scrollToColumn(column);
4222   }
4223
4224   /**
4225    * @return the alignments unique ID.
4226    */
4227   public String getSequenceSetId()
4228   {
4229     return viewport.getSequenceSetId();
4230   }
4231
4232   /**
4233    * Load the (T-Coffee) score file from the specified url
4234    *
4235    * @param source
4236    *          File/URL/T-COFFEE score file contents
4237    * @throws IOException
4238    * @return true if alignment was annotated with data from source
4239    */
4240   public boolean loadScoreFile(String source) throws IOException
4241   {
4242
4243     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4244             AppletFormatAdapter.checkProtocol(source));
4245     if (!file.isValid())
4246     {
4247       // TODO: raise dialog for gui
4248       System.err.println("Problems parsing T-Coffee scores: "
4249               + file.getWarningMessage());
4250       System.err.println("Origin was:\n" + source);
4251       return false;
4252     }
4253
4254     /*
4255      * check that the score matrix matches the alignment dimensions
4256      */
4257     AlignmentI aln;
4258     if ((aln = viewport.getAlignment()) != null
4259             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4260                     .getWidth()))
4261     {
4262       // TODO: raise a dialog box here rather than bomb out.
4263       System.err
4264               .println("The scores matrix does not match the alignment dimensions");
4265
4266     }
4267
4268     // TODO add parameter to indicate if matching should be done
4269     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4270     {
4271       alignPanel.fontChanged();
4272       tcoffeeColour.setEnabled(true);
4273       // switch to this color
4274       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4275       return true;
4276     }
4277     else
4278     {
4279       System.err.println("Problems resolving T-Coffee scores:");
4280       if (file.getWarningMessage() != null)
4281       {
4282         System.err.println(file.getWarningMessage());
4283       }
4284     }
4285     return false;
4286   }
4287
4288   public SplitFrame getSplitFrame()
4289   {
4290     return this.splitFrame;
4291   }
4292
4293   public void setSplitFrame(SplitFrame sf)
4294   {
4295     this.splitFrame = sf;
4296   }
4297
4298   // may not need this
4299   @Override
4300   public void setShowSeqFeatures(boolean b)
4301   {
4302     // showSeqFeatures.setSelected(b);
4303     viewport.setShowSequenceFeatures(b);
4304
4305   }
4306
4307   @Override
4308   public void setMenusForViewport()
4309   {
4310     // setMenusFromViewport(viewport);
4311
4312   }
4313
4314   @Override
4315   public void refreshFeatureUI(boolean enableIfNecessary)
4316   {
4317     if (enableIfNecessary)
4318     {
4319       sequenceFeatures.setState(true);
4320       alignPanel.av.setShowSequenceFeatures(true);
4321     }
4322   }
4323
4324   @Override
4325   public FeatureSettingsControllerI getFeatureSettingsUI()
4326   {
4327     return alignPanel.av.featureSettings;
4328   }
4329
4330 }