src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.FileFormatI;
  56 import jalview.io.FileFormats;
  57 import jalview.io.TCoffeeScoreFile;
  58 import jalview.schemes.Blosum62ColourScheme;
  59 import jalview.schemes.BuriedColourScheme;
  60 import jalview.schemes.ClustalxColourScheme;
  61 import jalview.schemes.ColourSchemeI;
  62 import jalview.schemes.HelixColourScheme;
  63 import jalview.schemes.HydrophobicColourScheme;
  64 import jalview.schemes.NucleotideColourScheme;
  65 import jalview.schemes.PIDColourScheme;
  66 import jalview.schemes.PurinePyrimidineColourScheme;
  67 import jalview.schemes.RNAHelicesColour;
  68 import jalview.schemes.StrandColourScheme;
  69 import jalview.schemes.TCoffeeColourScheme;
  70 import jalview.schemes.TaylorColourScheme;
  71 import jalview.schemes.TurnColourScheme;
  72 import jalview.schemes.ZappoColourScheme;
  73 import jalview.structure.StructureSelectionManager;
  74 import jalview.structures.models.AAStructureBindingModel;
  75 import jalview.util.MappingUtils;
  76 import jalview.util.MessageManager;
  77 import jalview.viewmodel.AlignmentViewport;
  78 import jalview.viewmodel.ViewportRanges;
  79
  80 import java.awt.BorderLayout;
  81 import java.awt.Canvas;
  82 import java.awt.CheckboxMenuItem;
  83 import java.awt.Color;
  84 import java.awt.FlowLayout;
  85 import java.awt.Font;
  86 import java.awt.FontMetrics;
  87 import java.awt.Frame;
  88 import java.awt.Graphics;
  89 import java.awt.Label;
  90 import java.awt.Menu;
  91 import java.awt.MenuBar;
  92 import java.awt.MenuItem;
  93 import java.awt.MenuShortcut;
  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           ColumnSelection columnSelection, JalviewLite applet,
 174           String title, boolean embedded)
 175   {
 176     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 177   }
 178
 179   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 180           ColumnSelection columnSelection, 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 (columnSelection != null)
 224     {
 225       viewport.setColumnSelection(columnSelection);
 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.getColumnSelection().getHiddenColumns())
1929       {
1930         copiedHiddenColumns.addElement(new int[] {
1931             region[0] - hiddenOffset, region[1] - hiddenOffset });
1932       }
1933     }
1934     else
1935     {
1936       copiedHiddenColumns = null;
1937     }
1938
1939     for (int i = 0; i < sg.getSize(); i++)
1940     {
1941       SequenceI seq = null;
1942
1943       while (seq == null)
1944       {
1945         if (orderedSeqs.containsKey(index))
1946         {
1947           seq = orderedSeqs.get(index);
1948           index++;
1949           break;
1950         }
1951         else
1952         {
1953           index++;
1954         }
1955       }
1956
1957       // FIND START RES
1958       // Returns residue following index if gap
1959       startRes = seq.findPosition(sg.getStartRes());
1960
1961       // FIND END RES
1962       // Need to find the residue preceeding index if gap
1963       endRes = 0;
1964
1965       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1966       {
1967         ch = seq.getCharAt(j);
1968         if (!jalview.util.Comparison.isGap((ch)))
1969         {
1970           endRes++;
1971         }
1972       }
1973
1974       if (endRes > 0)
1975       {
1976         endRes += seq.getStart() - 1;
1977       }
1978
1979       copiedSequences.append(seq.getName()
1980               + "\t"
1981               + startRes
1982               + "\t"
1983               + endRes
1984               + "\t"
1985               + seq.getSequenceAsString(sg.getStartRes(),
1986                       sg.getEndRes() + 1) + "\n");
1987     }
1988
1989   }
1990
1991   protected void pasteNew_actionPerformed()
1992   {
1993     paste(true);
1994   }
1995
1996   protected void pasteThis_actionPerformed()
1997   {
1998     paste(false);
1999   }
2000
2001   void paste(boolean newAlignment)
2002   {
2003     try
2004     {
2005
2006       if (copiedSequences == null)
2007       {
2008         return;
2009       }
2010
2011       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2012       Vector seqs = new Vector();
2013       while (st.hasMoreElements())
2014       {
2015         String name = st.nextToken();
2016         int start = Integer.parseInt(st.nextToken());
2017         int end = Integer.parseInt(st.nextToken());
2018         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2019       }
2020       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2021       for (int i = 0; i < seqs.size(); i++)
2022       {
2023         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2024       }
2025
2026       if (newAlignment)
2027       {
2028         String newtitle = MessageManager
2029                 .getString("label.copied_sequences");
2030         if (getTitle().startsWith(
2031                 MessageManager.getString("label.copied_sequences")))
2032         {
2033           newtitle = getTitle();
2034         }
2035         else
2036         {
2037           newtitle = newtitle.concat(MessageManager.formatMessage(
2038                   "label.from_msname", new String[] { getTitle() }));
2039         }
2040         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2041                 viewport.applet, newtitle, false);
2042         if (copiedHiddenColumns != null)
2043         {
2044           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2045           {
2046             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2047             af.viewport.hideColumns(region[0], region[1]);
2048           }
2049         }
2050
2051         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2052                 frameHeight);
2053       }
2054       else
2055       {
2056         addSequences(newSeqs);
2057       }
2058
2059     } catch (Exception ex)
2060     {
2061     } // could be anything being pasted in here
2062
2063   }
2064
2065   void addSequences(SequenceI[] seqs)
2066   {
2067     for (int i = 0; i < seqs.length; i++)
2068     {
2069       viewport.getAlignment().addSequence(seqs[i]);
2070     }
2071
2072     // !newAlignment
2073     addHistoryItem(new EditCommand(
2074             MessageManager.getString("label.add_sequences"), Action.PASTE,
2075             seqs, 0, viewport.getAlignment().getWidth(),
2076             viewport.getAlignment()));
2077
2078     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2079     viewport.getAlignment().getWidth();
2080     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2081             .getSequences());
2082
2083   }
2084
2085   protected void cut_actionPerformed()
2086   {
2087     copy_actionPerformed();
2088     delete_actionPerformed();
2089   }
2090
2091   protected void delete_actionPerformed()
2092   {
2093
2094     SequenceGroup sg = viewport.getSelectionGroup();
2095     if (sg == null)
2096     {
2097       return;
2098     }
2099
2100     Vector seqs = new Vector();
2101     SequenceI seq;
2102     for (int i = 0; i < sg.getSize(); i++)
2103     {
2104       seq = sg.getSequenceAt(i);
2105       seqs.addElement(seq);
2106     }
2107
2108     /*
2109      * If the cut affects all sequences, warn, remove highlighted columns
2110      */
2111     if (sg.getSize() == viewport.getAlignment().getHeight())
2112     {
2113       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2114               .getAlignment().getWidth()) ? true : false;
2115       if (isEntireAlignWidth)
2116       {
2117         String title = MessageManager.getString("label.delete_all");
2118         Panel infoPanel = new Panel();
2119         infoPanel.setLayout(new FlowLayout());
2120         infoPanel
2121                 .add(new Label(MessageManager.getString("warn.delete_all")));
2122
2123         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2124         dialog.setMainPanel(infoPanel);
2125         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2126         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2127         dialog.setVisible(true);
2128
2129         if (!dialog.accept)
2130         {
2131           return;
2132         }
2133       }
2134       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2135               sg.getEndRes() + 1);
2136     }
2137
2138     SequenceI[] cut = new SequenceI[seqs.size()];
2139     for (int i = 0; i < seqs.size(); i++)
2140     {
2141       cut[i] = (SequenceI) seqs.elementAt(i);
2142     }
2143
2144     /*
2145      * //ADD HISTORY ITEM
2146      */
2147     addHistoryItem(new EditCommand(
2148             MessageManager.getString("label.cut_sequences"), Action.CUT,
2149             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2150             viewport.getAlignment()));
2151
2152     viewport.setSelectionGroup(null);
2153     viewport.getAlignment().deleteGroup(sg);
2154
2155     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2156             .getSequences());
2157
2158     if (viewport.getAlignment().getHeight() < 1)
2159     {
2160       this.setVisible(false);
2161     }
2162     viewport.sendSelection();
2163   }
2164
2165   /**
2166    * group consensus toggled
2167    *
2168    */
2169   protected void showGroupConsensus_actionPerformed()
2170   {
2171     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2172     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2173
2174   }
2175
2176   /**
2177    * group conservation toggled.
2178    */
2179   protected void showGroupConservation_actionPerformed()
2180   {
2181     viewport.setShowGroupConservation(showGroupConservation.getState());
2182     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183   }
2184
2185   /*
2186    * (non-Javadoc)
2187    *
2188    * @see
2189    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2190    * .event.ActionEvent)
2191    */
2192   protected void showConsensusHistogram_actionPerformed()
2193   {
2194     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2195     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2196   }
2197
2198   /*
2199    * (non-Javadoc)
2200    *
2201    * @see
2202    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2203    * .event.ActionEvent)
2204    */
2205   protected void showSequenceLogo_actionPerformed()
2206   {
2207     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2208     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2209   }
2210
2211   protected void normSequenceLogo_actionPerformed()
2212   {
2213     showSequenceLogo.setState(true);
2214     viewport.setShowSequenceLogo(true);
2215     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2216     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2217   }
2218
2219   protected void applyAutoAnnotationSettings_actionPerformed()
2220   {
2221     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2222   }
2223
2224   protected void makeGrpsFromSelection_actionPerformed()
2225   {
2226     if (avc.makeGroupsFromSelection())
2227     {
2228       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2229       alignPanel.updateAnnotation();
2230       alignPanel.paintAlignment(true);
2231     }
2232   }
2233
2234   protected void createGroup_actionPerformed()
2235   {
2236     avc.createGroup();
2237   }
2238
2239   protected void unGroup_actionPerformed()
2240   {
2241     if (avc.unGroup())
2242     {
2243       alignPanel.alignmentChanged();
2244     }
2245   }
2246
2247   protected void deleteGroups_actionPerformed()
2248   {
2249     if (avc.deleteGroups())
2250     {
2251       alignPanel.alignmentChanged();
2252     }
2253   }
2254
2255   public void selectAllSequenceMenuItem_actionPerformed()
2256   {
2257     SequenceGroup sg = new SequenceGroup();
2258     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2259     {
2260       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2261     }
2262     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2263     viewport.setSelectionGroup(sg);
2264     // JAL-2034 - should delegate to
2265     // alignPanel to decide if overview needs
2266     // updating.
2267     alignPanel.paintAlignment(false);
2268     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2269     viewport.sendSelection();
2270   }
2271
2272   public void deselectAllSequenceMenuItem_actionPerformed()
2273   {
2274     if (viewport.cursorMode)
2275     {
2276       alignPanel.seqPanel.keyboardNo1 = null;
2277       alignPanel.seqPanel.keyboardNo2 = null;
2278     }
2279     viewport.setSelectionGroup(null);
2280     viewport.getColumnSelection().clear();
2281     viewport.setSelectionGroup(null);
2282     alignPanel.idPanel.idCanvas.searchResults = null;
2283     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2284     // JAL-2034 - should delegate to
2285     // alignPanel to decide if overview needs
2286     // updating.
2287     alignPanel.paintAlignment(false);
2288     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289     viewport.sendSelection();
2290   }
2291
2292   public void invertSequenceMenuItem_actionPerformed()
2293   {
2294     SequenceGroup sg = viewport.getSelectionGroup();
2295     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2296     {
2297       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2298     }
2299
2300     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2301     viewport.sendSelection();
2302   }
2303
2304   public void invertColSel_actionPerformed()
2305   {
2306     viewport.invertColumnSelection();
2307     alignPanel.paintAlignment(true);
2308     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2309     viewport.sendSelection();
2310   }
2311
2312   void trimAlignment(boolean trimLeft)
2313   {
2314     AlignmentI al = viewport.getAlignment();
2315     ViewportRanges ranges = viewport.getRanges();
2316     ColumnSelection colSel = viewport.getColumnSelection();
2317     int column;
2318
2319     if (!colSel.isEmpty())
2320     {
2321       if (trimLeft)
2322       {
2323         column = colSel.getMin();
2324       }
2325       else
2326       {
2327         column = colSel.getMax();
2328       }
2329
2330       SequenceI[] seqs;
2331       if (viewport.getSelectionGroup() != null)
2332       {
2333         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2334                 viewport.getHiddenRepSequences());
2335       }
2336       else
2337       {
2338         seqs = al.getSequencesArray();
2339       }
2340
2341       TrimRegionCommand trimRegion;
2342       if (trimLeft)
2343       {
2344         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2345                 column, al);
2346         ranges.setStartRes(0);
2347       }
2348       else
2349       {
2350         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2351                 column, al);
2352       }
2353
2354       statusBar.setText(MessageManager.formatMessage(
2355               "label.removed_columns",
2356               new String[] { Integer.valueOf(trimRegion.getSize())
2357                       .toString() }));
2358       addHistoryItem(trimRegion);
2359
2360       for (SequenceGroup sg : al.getGroups())
2361       {
2362         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2363                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2364         {
2365           al.deleteGroup(sg);
2366         }
2367       }
2368
2369       viewport.firePropertyChange("alignment", null, al.getSequences());
2370     }
2371   }
2372
2373   public void removeGappedColumnMenuItem_actionPerformed()
2374   {
2375     AlignmentI al = viewport.getAlignment();
2376     ViewportRanges ranges = viewport.getRanges();
2377     int start = 0;
2378     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2379
2380     SequenceI[] seqs;
2381     if (viewport.getSelectionGroup() != null)
2382     {
2383       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2384               viewport.getHiddenRepSequences());
2385       start = viewport.getSelectionGroup().getStartRes();
2386       end = viewport.getSelectionGroup().getEndRes();
2387     }
2388     else
2389     {
2390       seqs = viewport.getAlignment().getSequencesArray();
2391     }
2392
2393     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2394             "Remove Gapped Columns", seqs, start, end,
2395             viewport.getAlignment());
2396
2397     addHistoryItem(removeGapCols);
2398
2399     statusBar.setText(MessageManager.formatMessage(
2400             "label.removed_empty_columns",
2401             new String[] { Integer.valueOf(removeGapCols.getSize())
2402                     .toString() }));
2403
2404     // This is to maintain viewport position on first residue
2405     // of first sequence
2406     SequenceI seq = al.getSequenceAt(0);
2407     int startRes = seq.findPosition(ranges.getStartRes());
2408     // ShiftList shifts;
2409     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2410     // edit.alColumnChanges=shifts.getInverse();
2411     // if (viewport.hasHiddenColumns)
2412     // viewport.getColumnSelection().compensateForEdits(shifts);
2413     ranges.setStartRes(seq.findIndex(startRes) - 1);
2414     viewport.firePropertyChange("alignment", null, al.getSequences());
2415
2416   }
2417
2418   public void removeAllGapsMenuItem_actionPerformed()
2419   {
2420     AlignmentI al = viewport.getAlignment();
2421     ViewportRanges ranges = viewport.getRanges();
2422     int start = 0;
2423     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2424
2425     SequenceI[] seqs;
2426     if (viewport.getSelectionGroup() != null)
2427     {
2428       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2429               viewport.getHiddenRepSequences());
2430       start = viewport.getSelectionGroup().getStartRes();
2431       end = viewport.getSelectionGroup().getEndRes();
2432     }
2433     else
2434     {
2435       seqs = viewport.getAlignment().getSequencesArray();
2436     }
2437
2438     // This is to maintain viewport position on first residue
2439     // of first sequence
2440     SequenceI seq = al.getSequenceAt(0);
2441     int startRes = seq.findPosition(ranges.getStartRes());
2442
2443     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2444             al));
2445
2446     ranges.setStartRes(seq.findIndex(startRes) - 1);
2447
2448     viewport.firePropertyChange("alignment", null, al.getSequences());
2449
2450   }
2451
2452   public void findMenuItem_actionPerformed()
2453   {
2454     new Finder(alignPanel);
2455   }
2456
2457   /**
2458    * create a new view derived from the current view
2459    *
2460    * @param viewtitle
2461    * @return frame for the new view
2462    */
2463   public AlignFrame newView(String viewtitle)
2464   {
2465     AlignmentI newal;
2466     if (viewport.hasHiddenRows())
2467     {
2468       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2469               .getFullAlignment().getSequencesArray());
2470     }
2471     else
2472     {
2473       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2474     }
2475
2476     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2477     {
2478       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2479       {
2480         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2481         {
2482           newal.addAnnotation(viewport.getAlignment()
2483                   .getAlignmentAnnotation()[i]);
2484         }
2485       }
2486     }
2487
2488     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2489
2490     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2491     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2492     PaintRefresher.Register(newaf.alignPanel,
2493             newaf.alignPanel.av.getSequenceSetId());
2494
2495     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2496             newaf.alignPanel.av.getSequenceSetId());
2497     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2498             newaf.alignPanel.av.getSequenceSetId());
2499
2500     Vector comps = (Vector) PaintRefresher.components.get(viewport
2501             .getSequenceSetId());
2502     int viewSize = -1;
2503     for (int i = 0; i < comps.size(); i++)
2504     {
2505       if (comps.elementAt(i) instanceof AlignmentPanel)
2506       {
2507         viewSize++;
2508       }
2509     }
2510
2511     String title = new String(this.getTitle());
2512     if (viewtitle != null)
2513     {
2514       title = viewtitle + " ( " + title + ")";
2515     }
2516     else
2517     {
2518       if (title.indexOf("(View") > -1)
2519       {
2520         title = title.substring(0, title.indexOf("(View"));
2521       }
2522       title += "(View " + viewSize + ")";
2523     }
2524
2525     newaf.setTitle(title.toString());
2526
2527     newaf.viewport.setHistoryList(viewport.getHistoryList());
2528     newaf.viewport.setRedoList(viewport.getRedoList());
2529     return newaf;
2530   }
2531
2532   /**
2533    *
2534    * @return list of feature groups on the view
2535    */
2536   public String[] getFeatureGroups()
2537   {
2538     FeatureRenderer fr = null;
2539     if (alignPanel != null
2540             && (fr = alignPanel.getFeatureRenderer()) != null)
2541     {
2542       List<String> gps = fr.getFeatureGroups();
2543       String[] _gps = gps.toArray(new String[gps.size()]);
2544       return _gps;
2545     }
2546     return null;
2547   }
2548
2549   /**
2550    * get sequence feature groups that are hidden or shown
2551    *
2552    * @param visible
2553    *          true is visible
2554    * @return list
2555    */
2556   public String[] getFeatureGroupsOfState(boolean visible)
2557   {
2558     FeatureRenderer fr = null;
2559     if (alignPanel != null
2560             && (fr = alignPanel.getFeatureRenderer()) != null)
2561     {
2562       List<String> gps = fr.getGroups(visible);
2563       String[] _gps = gps.toArray(new String[gps.size()]);
2564       return _gps;
2565     }
2566     return null;
2567   }
2568
2569   /**
2570    * Change the display state for the given feature groups
2571    *
2572    * @param groups
2573    *          list of group strings
2574    * @param state
2575    *          visible or invisible
2576    */
2577   public void setFeatureGroupState(String[] groups, boolean state)
2578   {
2579     FeatureRenderer fr = null;
2580     this.sequenceFeatures.setState(true);
2581     viewport.setShowSequenceFeatures(true);
2582     if (alignPanel != null
2583             && (fr = alignPanel.getFeatureRenderer()) != null)
2584     {
2585
2586       fr.setGroupVisibility(Arrays.asList(groups), state);
2587       alignPanel.seqPanel.seqCanvas.repaint();
2588       if (alignPanel.overviewPanel != null)
2589       {
2590         alignPanel.overviewPanel.updateOverviewImage();
2591       }
2592     }
2593   }
2594
2595   public void seqLimits_itemStateChanged()
2596   {
2597     viewport.setShowJVSuffix(seqLimits.getState());
2598     alignPanel.fontChanged();
2599     alignPanel.paintAlignment(true);
2600   }
2601
2602   protected void colourTextMenuItem_actionPerformed()
2603   {
2604     viewport.setColourText(colourTextMenuItem.getState());
2605     alignPanel.paintAlignment(true);
2606   }
2607
2608   protected void displayNonconservedMenuItem_actionPerformed()
2609   {
2610     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2611     alignPanel.paintAlignment(true);
2612   }
2613
2614   protected void wrapMenuItem_actionPerformed()
2615   {
2616     viewport.setWrapAlignment(wrapMenuItem.getState());
2617     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2618     scaleAbove.setEnabled(wrapMenuItem.getState());
2619     scaleLeft.setEnabled(wrapMenuItem.getState());
2620     scaleRight.setEnabled(wrapMenuItem.getState());
2621     alignPanel.paintAlignment(true);
2622   }
2623
2624   public void overviewMenuItem_actionPerformed()
2625   {
2626     if (alignPanel.overviewPanel != null)
2627     {
2628       return;
2629     }
2630
2631     Frame frame = new Frame();
2632     OverviewPanel overview = new OverviewPanel(alignPanel);
2633     frame.add(overview);
2634     // +50 must allow for applet frame window
2635     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2636             "label.overview_params", new String[] { this.getTitle() }),
2637             overview.getPreferredSize().width,
2638             overview.getPreferredSize().height + 50);
2639
2640     frame.pack();
2641     final AlignmentPanel ap = alignPanel;
2642     frame.addWindowListener(new WindowAdapter()
2643     {
2644       @Override
2645       public void windowClosing(WindowEvent e)
2646       {
2647         if (ap != null)
2648         {
2649           ap.setOverviewPanel(null);
2650         }
2651       };
2652     });
2653
2654     alignPanel.setOverviewPanel(overview);
2655
2656   }
2657
2658   @Override
2659   public void changeColour(ColourSchemeI cs)
2660   {
2661     viewport.setGlobalColourScheme(cs);
2662
2663     alignPanel.paintAlignment(true);
2664   }
2665
2666   protected void modifyPID_actionPerformed()
2667   {
2668     if (viewport.getAbovePIDThreshold()
2669             && viewport.getGlobalColourScheme() != null)
2670     {
2671       SliderPanel.setPIDSliderSource(alignPanel,
2672               viewport.getResidueShading(), alignPanel.getViewName());
2673       SliderPanel.showPIDSlider();
2674     }
2675   }
2676
2677   protected void modifyConservation_actionPerformed()
2678   {
2679     if (viewport.getConservationSelected()
2680             && viewport.getGlobalColourScheme() != null)
2681     {
2682       SliderPanel.setConservationSlider(alignPanel,
2683               viewport.getResidueShading(), alignPanel.getViewName());
2684       SliderPanel.showConservationSlider();
2685     }
2686   }
2687
2688   protected void conservationMenuItem_actionPerformed()
2689   {
2690     boolean selected = conservationMenuItem.getState();
2691     modifyConservation.setEnabled(selected);
2692     viewport.setConservationSelected(selected);
2693
2694     // viewport.setAbovePIDThreshold(false);
2695     // abovePIDThreshold.setState(false);
2696
2697     changeColour(viewport.getGlobalColourScheme());
2698
2699     if (selected)
2700     {
2701       modifyConservation_actionPerformed();
2702     }
2703     else
2704     {
2705       SliderPanel.hideConservationSlider();
2706     }
2707   }
2708
2709   public void abovePIDThreshold_actionPerformed()
2710   {
2711     boolean selected = abovePIDThreshold.getState();
2712     modifyPID.setEnabled(selected);
2713     viewport.setAbovePIDThreshold(selected);
2714     // conservationMenuItem.setState(false);
2715     // viewport.setConservationSelected(false);
2716
2717     changeColour(viewport.getGlobalColourScheme());
2718
2719     if (selected)
2720     {
2721       modifyPID_actionPerformed();
2722     }
2723     else
2724     {
2725       SliderPanel.hidePIDSlider();
2726     }
2727   }
2728
2729   public void sortPairwiseMenuItem_actionPerformed()
2730   {
2731     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2732     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2733             .getAlignment().getSequenceAt(0), null);
2734
2735     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2736             viewport.getAlignment()));
2737     alignPanel.paintAlignment(true);
2738   }
2739
2740   public void sortIDMenuItem_actionPerformed()
2741   {
2742     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2743     AlignmentSorter.sortByID(viewport.getAlignment());
2744     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2745             viewport.getAlignment()));
2746     alignPanel.paintAlignment(true);
2747   }
2748
2749   public void sortLengthMenuItem_actionPerformed()
2750   {
2751     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752     AlignmentSorter.sortByLength(viewport.getAlignment());
2753     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2754             viewport.getAlignment()));
2755     alignPanel.paintAlignment(true);
2756   }
2757
2758   public void sortGroupMenuItem_actionPerformed()
2759   {
2760     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2761     AlignmentSorter.sortByGroup(viewport.getAlignment());
2762     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2763             viewport.getAlignment()));
2764     alignPanel.paintAlignment(true);
2765
2766   }
2767
2768   public void removeRedundancyMenuItem_actionPerformed()
2769   {
2770     new RedundancyPanel(alignPanel);
2771   }
2772
2773   public void pairwiseAlignmentMenuItem_actionPerformed()
2774   {
2775     if (viewport.getSelectionGroup() != null
2776             && viewport.getSelectionGroup().getSize() > 1)
2777     {
2778       Frame frame = new Frame();
2779       frame.add(new PairwiseAlignPanel(alignPanel));
2780       jalview.bin.JalviewLite.addFrame(frame,
2781               MessageManager.getString("action.pairwise_alignment"), 600,
2782               500);
2783     }
2784   }
2785
2786   public void PCAMenuItem_actionPerformed()
2787   {
2788     // are the sequences aligned?
2789     if (!viewport.getAlignment().isAligned(false))
2790     {
2791       SequenceI current;
2792       int Width = viewport.getAlignment().getWidth();
2793
2794       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2795       {
2796         current = viewport.getAlignment().getSequenceAt(i);
2797
2798         if (current.getLength() < Width)
2799         {
2800           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2801         }
2802       }
2803       alignPanel.paintAlignment(true);
2804     }
2805
2806     if ((viewport.getSelectionGroup() != null
2807             && viewport.getSelectionGroup().getSize() < 4 && viewport
2808             .getSelectionGroup().getSize() > 0)
2809             || viewport.getAlignment().getHeight() < 4)
2810     {
2811       return;
2812     }
2813
2814     try
2815     {
2816       new PCAPanel(viewport);
2817     } catch (java.lang.OutOfMemoryError ex)
2818     {
2819     }
2820
2821   }
2822
2823   public void averageDistanceTreeMenuItem_actionPerformed()
2824   {
2825     NewTreePanel("AV", "PID", "Average distance tree using PID");
2826   }
2827
2828   public void neighbourTreeMenuItem_actionPerformed()
2829   {
2830     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2831   }
2832
2833   protected void njTreeBlosumMenuItem_actionPerformed()
2834   {
2835     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2836   }
2837
2838   protected void avTreeBlosumMenuItem_actionPerformed()
2839   {
2840     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2841   }
2842
2843   void NewTreePanel(String type, String pwType, String title)
2844   {
2845     // are the sequences aligned?
2846     if (!viewport.getAlignment().isAligned(false))
2847     {
2848       SequenceI current;
2849       int Width = viewport.getAlignment().getWidth();
2850
2851       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2852       {
2853         current = viewport.getAlignment().getSequenceAt(i);
2854
2855         if (current.getLength() < Width)
2856         {
2857           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2858         }
2859       }
2860       alignPanel.paintAlignment(true);
2861
2862     }
2863
2864     if ((viewport.getSelectionGroup() != null && viewport
2865             .getSelectionGroup().getSize() > 1)
2866             || (viewport.getAlignment().getHeight() > 1))
2867     {
2868       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2869
2870       addTreeMenuItem(tp, title);
2871
2872       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2873     }
2874   }
2875
2876   void loadTree_actionPerformed()
2877   {
2878     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2879     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2880     cap.setTreeImport();
2881     Frame frame = new Frame();
2882     frame.add(cap);
2883     jalview.bin.JalviewLite.addFrame(frame,
2884             MessageManager.getString("label.paste_newick_file"), 400, 300);
2885   }
2886
2887   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2888   {
2889     TreePanel tp = new TreePanel(alignPanel, treeFile,
2890             MessageManager.getString("label.load_tree_from_file"), tree);
2891     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2892     addTreeMenuItem(tp, treeFile);
2893   }
2894
2895   /**
2896    * sort the alignment using the given treePanel
2897    *
2898    * @param treePanel
2899    *          tree used to sort view
2900    * @param title
2901    *          string used for undo event name
2902    */
2903   public void sortByTree(TreePanel treePanel, String title)
2904   {
2905     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2906     AlignmentSorter
2907             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2908     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2909     // HistoryItem.SORT));
2910     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2911             "label.order_by_params", new String[] { title }), oldOrder,
2912             viewport.getAlignment()));
2913     alignPanel.paintAlignment(true);
2914   }
2915
2916   /**
2917    * Do any automatic reordering of the alignment and add the necessary bits to
2918    * the menu structure for the new tree
2919    *
2920    * @param treePanel
2921    * @param title
2922    */
2923   protected void addTreeMenuItem(final TreePanel treePanel,
2924           final String title)
2925   {
2926     final MenuItem item = new MenuItem(title);
2927     sortByTreeMenu.add(item);
2928     item.addActionListener(new java.awt.event.ActionListener()
2929     {
2930       @Override
2931       public void actionPerformed(ActionEvent evt)
2932       {
2933         sortByTree(treePanel, title); // treePanel.getTitle());
2934       }
2935     });
2936
2937     treePanel.addWindowListener(new WindowAdapter()
2938     {
2939       @Override
2940       public void windowOpened(WindowEvent e)
2941       {
2942         if (viewport.sortByTree)
2943         {
2944           sortByTree(treePanel, title);
2945         }
2946         super.windowOpened(e);
2947       }
2948
2949       @Override
2950       public void windowClosing(WindowEvent e)
2951       {
2952         sortByTreeMenu.remove(item);
2953       };
2954     });
2955   }
2956
2957   public boolean sortBy(AlignmentOrder alorder, String undoname)
2958   {
2959     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2960     if (viewport.applet.debug)
2961     {
2962       System.err.println("Sorting " + alorder.getOrder().size()
2963               + " in alignment '" + getTitle() + "'");
2964     }
2965     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2966     if (undoname != null)
2967     {
2968       addHistoryItem(new OrderCommand(undoname, oldOrder,
2969               viewport.getAlignment()));
2970     }
2971     alignPanel.paintAlignment(true);
2972     return true;
2973   }
2974
2975   protected void documentation_actionPerformed()
2976   {
2977     alignPanel.av.applet.openJalviewHelpUrl();
2978   }
2979
2980   protected void about_actionPerformed()
2981   {
2982
2983     class AboutPanel extends Canvas
2984     {
2985       String version;
2986
2987       String builddate;
2988
2989       public AboutPanel(String version, String builddate)
2990       {
2991         this.version = version;
2992         this.builddate = builddate;
2993       }
2994
2995       @Override
2996       public void paint(Graphics g)
2997       {
2998         g.setColor(Color.white);
2999         g.fillRect(0, 0, getSize().width, getSize().height);
3000         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3001         FontMetrics fm = g.getFontMetrics();
3002         int fh = fm.getHeight();
3003         int y = 5, x = 7;
3004         g.setColor(Color.black);
3005         // TODO: update this text for each release or centrally store it for
3006         // lite and application
3007         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3008         g.drawString(MessageManager.formatMessage(
3009                 "label.jalviewLite_release", new String[] { version }), x,
3010                 y += fh);
3011         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3012         g.drawString(MessageManager.formatMessage(
3013                 "label.jaview_build_date", new String[] { builddate }), x,
3014                 y += fh);
3015         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3016         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3017                 x, y += fh * 1.5);
3018         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3019                 x + 50, y += fh + 8);
3020         g.drawString(
3021                 MessageManager.getString("label.jalview_dev_managers"), x,
3022                 y += fh);
3023         g.drawString(MessageManager
3024                 .getString("label.jalview_distribution_lists"), x, y += fh);
3025         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3026                 x, y += fh + 8);
3027         g.drawString(
3028                 MessageManager.getString("label.jalview_cite_1_authors"),
3029                 x, y += fh);
3030         g.drawString(
3031                 MessageManager.getString("label.jalview_cite_1_title"), x,
3032                 y += fh);
3033         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3034                 x, y += fh);
3035       }
3036     }
3037
3038     Frame frame = new Frame();
3039     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3040             .getBuildDate()));
3041     jalview.bin.JalviewLite.addFrame(frame,
3042             MessageManager.getString("label.jalview"), 580, 220);
3043
3044   }
3045
3046   public void showURL(String url, String target)
3047   {
3048     if (viewport.applet == null)
3049     {
3050       System.out.println("Not running as applet - no browser available.");
3051     }
3052     else
3053     {
3054       viewport.applet.showURL(url, target);
3055     }
3056   }
3057
3058   // ////////////////////////////////////////////////////////////////////////////////
3059   // JBuilder Graphics here
3060
3061   MenuBar alignFrameMenuBar = new MenuBar();
3062
3063   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3064
3065   MenuItem loadApplication = new MenuItem(
3066           MessageManager.getString("label.view_full_application"));
3067
3068   MenuItem loadTree = new MenuItem(
3069           MessageManager.getString("label.load_associated_tree"));
3070
3071   MenuItem loadAnnotations = new MenuItem(
3072           MessageManager.getString("label.load_features_annotations"));
3073
3074   MenuItem outputFeatures = new MenuItem(
3075           MessageManager.getString("label.export_features"));
3076
3077   MenuItem outputAnnotations = new MenuItem(
3078           MessageManager.getString("label.export_annotations"));
3079
3080   MenuItem closeMenuItem = new MenuItem(
3081           MessageManager.getString("action.close"));
3082
3083   MenuItem selectAllSequenceMenuItem = new MenuItem(
3084           MessageManager.getString("action.select_all"));
3085
3086   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3087           MessageManager.getString("action.deselect_all"));
3088
3089   MenuItem invertSequenceMenuItem = new MenuItem(
3090           MessageManager.getString("action.invert_selection"));
3091
3092   MenuItem remove2LeftMenuItem = new MenuItem();
3093
3094   MenuItem remove2RightMenuItem = new MenuItem();
3095
3096   MenuItem removeGappedColumnMenuItem = new MenuItem();
3097
3098   MenuItem removeAllGapsMenuItem = new MenuItem();
3099
3100   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3101
3102   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3103
3104   MenuItem sortPairwiseMenuItem = new MenuItem();
3105
3106   MenuItem sortIDMenuItem = new MenuItem();
3107
3108   MenuItem sortLengthMenuItem = new MenuItem();
3109
3110   MenuItem sortGroupMenuItem = new MenuItem();
3111
3112   MenuItem removeRedundancyMenuItem = new MenuItem();
3113
3114   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3115
3116   MenuItem PCAMenuItem = new MenuItem();
3117
3118   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3119
3120   MenuItem neighbourTreeMenuItem = new MenuItem();
3121
3122   BorderLayout borderLayout1 = new BorderLayout();
3123
3124   public Label statusBar = new Label();
3125
3126   MenuItem clustalColour = new MenuItem();
3127
3128   MenuItem zappoColour = new MenuItem();
3129
3130   MenuItem taylorColour = new MenuItem();
3131
3132   MenuItem hydrophobicityColour = new MenuItem();
3133
3134   MenuItem helixColour = new MenuItem();
3135
3136   MenuItem strandColour = new MenuItem();
3137
3138   MenuItem turnColour = new MenuItem();
3139
3140   MenuItem buriedColour = new MenuItem();
3141
3142   MenuItem purinePyrimidineColour = new MenuItem();
3143
3144   // MenuItem RNAInteractionColour = new MenuItem();
3145
3146   MenuItem RNAHelixColour = new MenuItem();
3147
3148   MenuItem userDefinedColour = new MenuItem();
3149
3150   MenuItem PIDColour = new MenuItem();
3151
3152   MenuItem BLOSUM62Colour = new MenuItem();
3153
3154   MenuItem tcoffeeColour = new MenuItem();
3155
3156   MenuItem njTreeBlosumMenuItem = new MenuItem();
3157
3158   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3159
3160   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3161
3162   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3163
3164   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3165
3166   MenuItem alProperties = new MenuItem(
3167           MessageManager.getString("label.alignment_props"));
3168
3169   MenuItem overviewMenuItem = new MenuItem();
3170
3171   MenuItem undoMenuItem = new MenuItem();
3172
3173   MenuItem redoMenuItem = new MenuItem();
3174
3175   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3176
3177   MenuItem noColourmenuItem = new MenuItem();
3178
3179   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3180
3181   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3182
3183   MenuItem findMenuItem = new MenuItem();
3184
3185   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3186
3187   MenuItem nucleotideColour = new MenuItem();
3188
3189   MenuItem deleteGroups = new MenuItem();
3190
3191   MenuItem grpsFromSelection = new MenuItem();
3192
3193   MenuItem createGroup = new MenuItem();
3194
3195   MenuItem unGroup = new MenuItem();
3196
3197   MenuItem delete = new MenuItem();
3198
3199   MenuItem copy = new MenuItem();
3200
3201   MenuItem cut = new MenuItem();
3202
3203   Menu pasteMenu = new Menu();
3204
3205   MenuItem pasteNew = new MenuItem();
3206
3207   MenuItem pasteThis = new MenuItem();
3208
3209   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3210
3211   MenuItem font = new MenuItem();
3212
3213   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3218
3219   MenuItem modifyPID = new MenuItem();
3220
3221   MenuItem modifyConservation = new MenuItem();
3222
3223   CheckboxMenuItem autoCalculate = null;
3224
3225   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3226           "Sort Alignment With New Tree", true);
3227
3228   Menu sortByTreeMenu = new Menu();
3229
3230   MenuItem inputText = new MenuItem();
3231
3232   MenuItem documentation = new MenuItem();
3233
3234   MenuItem about = new MenuItem();
3235
3236   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3237
3238   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3253
3254   /**
3255    * Initialise menus and other items
3256    *
3257    * @throws Exception
3258    */
3259   private void jbInit() throws Exception
3260   {
3261     setMenuBar(alignFrameMenuBar);
3262
3263     /*
3264      * Configure File menu items and actions
3265      */
3266     inputText
3267             .setLabel(MessageManager.getString("label.input_from_textbox"));
3268     inputText.addActionListener(this);
3269     Menu outputTextboxMenu = new Menu(
3270             MessageManager.getString("label.out_to_textbox"));
3271     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3272     {
3273       MenuItem item = new MenuItem(ff);
3274
3275       item.addActionListener(new java.awt.event.ActionListener()
3276       {
3277         @Override
3278         public void actionPerformed(ActionEvent e)
3279         {
3280           outputText_actionPerformed(e);
3281         }
3282       });
3283
3284       outputTextboxMenu.add(item);
3285     }
3286     closeMenuItem.addActionListener(this);
3287     loadApplication.addActionListener(this);
3288     loadTree.addActionListener(this);
3289     loadAnnotations.addActionListener(this);
3290     outputFeatures.addActionListener(this);
3291     outputAnnotations.addActionListener(this);
3292
3293     /*
3294      * Configure Edit menu items and actions
3295      */
3296     undoMenuItem.setEnabled(false);
3297     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3298     undoMenuItem.addActionListener(this);
3299     redoMenuItem.setEnabled(false);
3300     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3301     redoMenuItem.addActionListener(this);
3302     copy.setLabel(MessageManager.getString("action.copy"));
3303     copy.addActionListener(this);
3304     cut.setLabel(MessageManager.getString("action.cut"));
3305     cut.addActionListener(this);
3306     delete.setLabel(MessageManager.getString("action.delete"));
3307     delete.addActionListener(this);
3308     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3309     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3310     pasteNew.addActionListener(this);
3311     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3312     pasteThis.addActionListener(this);
3313     remove2LeftMenuItem.setLabel(MessageManager
3314             .getString("action.remove_left"));
3315     remove2LeftMenuItem.addActionListener(this);
3316     remove2RightMenuItem.setLabel(MessageManager
3317             .getString("action.remove_right"));
3318     remove2RightMenuItem.addActionListener(this);
3319     removeGappedColumnMenuItem.setLabel(MessageManager
3320             .getString("action.remove_empty_columns"));
3321     removeGappedColumnMenuItem.addActionListener(this);
3322     removeAllGapsMenuItem.setLabel(MessageManager
3323             .getString("action.remove_all_gaps"));
3324     removeAllGapsMenuItem.addActionListener(this);
3325     removeRedundancyMenuItem.setLabel(MessageManager
3326             .getString("action.remove_redundancy"));
3327     removeRedundancyMenuItem.addActionListener(this);
3328
3329     /*
3330      * Configure Select menu items and actions
3331      */
3332     findMenuItem.setLabel(MessageManager.getString("action.find"));
3333     findMenuItem.addActionListener(this);
3334     selectAllSequenceMenuItem.addActionListener(this);
3335     deselectAllSequenceMenuItem.addActionListener(this);
3336     invertSequenceMenuItem.setLabel(MessageManager
3337             .getString("action.invert_sequence_selection"));
3338     invertSequenceMenuItem.addActionListener(this);
3339     invertColSel.setLabel(MessageManager
3340             .getString("action.invert_column_selection"));
3341     invertColSel.addActionListener(this);
3342     deleteGroups.setLabel(MessageManager
3343             .getString("action.undefine_groups"));
3344     deleteGroups.addActionListener(this);
3345     grpsFromSelection.setLabel(MessageManager
3346             .getString("action.make_groups_selection"));
3347     grpsFromSelection.addActionListener(this);
3348     createGroup.setLabel(MessageManager.getString("action.create_group"));
3349     createGroup.addActionListener(this);
3350     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3351     unGroup.addActionListener(this);
3352
3353     annotationColumnSelection.setLabel(MessageManager
3354             .getString("action.select_by_annotation"));
3355     annotationColumnSelection.addActionListener(this);
3356
3357     /*
3358      * Configure View menu items and actions
3359      */
3360     newView.setLabel(MessageManager.getString("action.new_view"));
3361     newView.addActionListener(this);
3362     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3363     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3364     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3365     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3366     hideColumns
3367             .setLabel(MessageManager.getString("label.selected_columns"));
3368     hideSequences.setLabel(MessageManager
3369             .getString("label.selected_sequences"));
3370     hideAllButSelection.setLabel(MessageManager
3371             .getString("label.all_but_selected_region"));
3372     hideAllSelection.setLabel(MessageManager
3373             .getString("label.selected_region"));
3374     showAllHidden.setLabel(MessageManager
3375             .getString("label.all_sequences_columns"));
3376     showColumns.addActionListener(this);
3377     showSeqs.addActionListener(this);
3378     hideColumns.addActionListener(this);
3379     hideSequences.addActionListener(this);
3380     hideAllButSelection.addActionListener(this);
3381     hideAllSelection.addActionListener(this);
3382     showAllHidden.addActionListener(this);
3383     featureSettings.setLabel(MessageManager
3384             .getString("action.feature_settings"));
3385     featureSettings.addActionListener(this);
3386     sequenceFeatures.setLabel(MessageManager
3387             .getString("label.show_sequence_features"));
3388     sequenceFeatures.addItemListener(this);
3389     sequenceFeatures.setState(false);
3390     followMouseOverFlag.setLabel(MessageManager
3391             .getString("label.automatic_scrolling"));
3392     followMouseOverFlag.addItemListener(this);
3393     alProperties.addActionListener(this);
3394     overviewMenuItem.setLabel(MessageManager
3395             .getString("label.overview_window"));
3396     overviewMenuItem.addActionListener(this);
3397
3398     /*
3399      * Configure Annotations menu items and actions
3400      */
3401     annotationPanelMenuItem.setLabel(MessageManager
3402             .getString("label.show_annotations"));
3403     annotationPanelMenuItem.addItemListener(this);
3404     showGroupConsensus.setLabel(MessageManager
3405             .getString("label.group_consensus"));
3406     showGroupConservation.setLabel(MessageManager
3407             .getString("label.group_conservation"));
3408     showConsensusHistogram.setLabel(MessageManager
3409             .getString("label.show_consensus_histogram"));
3410     showSequenceLogo.setLabel(MessageManager
3411             .getString("label.show_consensus_logo"));
3412     normSequenceLogo.setLabel(MessageManager
3413             .getString("label.norm_consensus_logo"));
3414     applyAutoAnnotationSettings.setLabel(MessageManager
3415             .getString("label.apply_all_groups"));
3416     applyAutoAnnotationSettings.setState(true);
3417     Menu autoAnnMenu = new Menu(
3418             MessageManager.getString("label.autocalculated_annotation"));
3419     showGroupConsensus.addItemListener(this);
3420     showGroupConservation.addItemListener(this);
3421     showConsensusHistogram.addItemListener(this);
3422     showSequenceLogo.addItemListener(this);
3423     normSequenceLogo.addItemListener(this);
3424     applyAutoAnnotationSettings.addItemListener(this);
3425     showAlignmentAnnotations = new CheckboxMenuItem(
3426             MessageManager.getString("label.show_all_al_annotations"));
3427     showSequenceAnnotations = new CheckboxMenuItem(
3428             MessageManager.getString("label.show_all_seq_annotations"));
3429     sortAnnBySequence = new CheckboxMenuItem(
3430             MessageManager.getString("label.sort_annotations_by_sequence"));
3431     sortAnnByLabel = new CheckboxMenuItem(
3432             MessageManager.getString("label.sort_annotations_by_label"));
3433     showAutoFirst = new CheckboxMenuItem(
3434             MessageManager.getString("label.show_first"));
3435     showAutoFirst.setState(false); // pending applet parameter
3436     setShowAutoCalculatedAbove(showAutoFirst.getState());
3437     showAutoLast = new CheckboxMenuItem(
3438             MessageManager.getString("label.show_last"));
3439     showAutoLast.setState(!showAutoFirst.getState());
3440     showAlignmentAnnotations.addItemListener(this);
3441     showSequenceAnnotations.addItemListener(this);
3442     sortAnnBySequence.addItemListener(this);
3443     sortAnnByLabel.addItemListener(this);
3444     showAutoFirst.addItemListener(this);
3445     showAutoLast.addItemListener(this);
3446
3447     /*
3448      * Configure Format menu items and actions
3449      */
3450     font.setLabel(MessageManager.getString("action.font"));
3451     font.addActionListener(this);
3452     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3453     scaleAbove.setState(true);
3454     scaleAbove.setEnabled(false);
3455     scaleAbove.addItemListener(this);
3456     scaleLeft.setEnabled(false);
3457     scaleLeft.setState(true);
3458     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3459     scaleLeft.addItemListener(this);
3460     scaleRight.setEnabled(false);
3461     scaleRight.setState(true);
3462     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3463     scaleRight.addItemListener(this);
3464     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3465     viewBoxesMenuItem.setState(true);
3466     viewBoxesMenuItem.addItemListener(this);
3467     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3468     viewTextMenuItem.setState(true);
3469     viewTextMenuItem.addItemListener(this);
3470     colourTextMenuItem.setLabel(MessageManager
3471             .getString("label.colour_text"));
3472     colourTextMenuItem.addItemListener(this);
3473     displayNonconservedMenuItem.setLabel(MessageManager
3474             .getString("label.show_non_conserved"));
3475     displayNonconservedMenuItem.addItemListener(this);
3476     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3477     wrapMenuItem.addItemListener(this);
3478     renderGapsMenuItem.setLabel(MessageManager
3479             .getString("action.show_gaps"));
3480     renderGapsMenuItem.setState(true);
3481     renderGapsMenuItem.addItemListener(this);
3482     centreColumnLabelFlag.setLabel(MessageManager
3483             .getString("label.centre_column_labels"));
3484     centreColumnLabelFlag.addItemListener(this);
3485     seqLimits.setState(true);
3486     seqLimits.setLabel(MessageManager
3487             .getString("label.show_sequence_limits"));
3488     seqLimits.addItemListener(this);
3489
3490     /*
3491      * Configure Colour menu items and actions
3492      */
3493     applyToAllGroups.setLabel(MessageManager
3494             .getString("label.apply_colour_to_all_groups"));
3495     applyToAllGroups.setState(true);
3496     applyToAllGroups.addItemListener(this);
3497     clustalColour.setLabel(MessageManager
3498             .getString("label.colourScheme_clustal"));
3499     clustalColour.addActionListener(this);
3500     zappoColour.setLabel(MessageManager
3501             .getString("label.colourScheme_zappo"));
3502     zappoColour.addActionListener(this);
3503     taylorColour.setLabel(MessageManager
3504             .getString("label.colourScheme_taylor"));
3505     taylorColour.addActionListener(this);
3506     hydrophobicityColour.setLabel(MessageManager
3507             .getString("label.colourScheme_hydrophobic"));
3508     hydrophobicityColour.addActionListener(this);
3509     helixColour.setLabel(MessageManager
3510             .getString("label.colourScheme_helix_propensity"));
3511     helixColour.addActionListener(this);
3512     strandColour.setLabel(MessageManager
3513             .getString("label.colourScheme_strand_propensity"));
3514     strandColour.addActionListener(this);
3515     turnColour.setLabel(MessageManager
3516             .getString("label.colourScheme_turn_propensity"));
3517     turnColour.addActionListener(this);
3518     buriedColour.setLabel(MessageManager
3519             .getString("label.colourScheme_buried_index"));
3520     buriedColour.addActionListener(this);
3521     purinePyrimidineColour.setLabel(MessageManager
3522             .getString("label.colourScheme_purine/pyrimidine"));
3523     purinePyrimidineColour.addActionListener(this);
3524     // RNAInteractionColour.setLabel(MessageManager
3525     // .getString("label.rna_interaction"));
3526     // RNAInteractionColour.addActionListener(this);
3527     RNAHelixColour.setLabel(MessageManager
3528             .getString("label.colourScheme_rna_helices"));
3529     RNAHelixColour.addActionListener(this);
3530     userDefinedColour.setLabel(MessageManager
3531             .getString("action.user_defined"));
3532     userDefinedColour.addActionListener(this);
3533     PIDColour.setLabel(MessageManager
3534             .getString("label.colourScheme_%_identity"));
3535     PIDColour.addActionListener(this);
3536     BLOSUM62Colour.setLabel(MessageManager
3537             .getString("label.colourScheme_blosum62"));
3538     BLOSUM62Colour.addActionListener(this);
3539     tcoffeeColour.setLabel(MessageManager
3540             .getString("label.colourScheme_t-coffee_scores"));
3541     // it will be enabled only if a score file is provided
3542     tcoffeeColour.setEnabled(false);
3543     tcoffeeColour.addActionListener(this);
3544     conservationMenuItem.setLabel(MessageManager
3545             .getString("action.by_conservation"));
3546     conservationMenuItem.addItemListener(this);
3547     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3548     noColourmenuItem.addActionListener(this);
3549     abovePIDThreshold.setLabel(MessageManager
3550             .getString("label.above_identity_threshold"));
3551     abovePIDThreshold.addItemListener(this);
3552     nucleotideColour.setLabel(MessageManager
3553             .getString("label.colourScheme_nucleotide"));
3554     nucleotideColour.addActionListener(this);
3555     modifyPID.setLabel(MessageManager
3556             .getString("label.modify_identity_threshold"));
3557     modifyPID.setEnabled(abovePIDThreshold.getState());
3558     modifyPID.addActionListener(this);
3559     modifyConservation.setLabel(MessageManager
3560             .getString("label.modify_conservation_threshold"));
3561     modifyConservation.setEnabled(conservationMenuItem.getState());
3562     modifyConservation.addActionListener(this);
3563     annotationColour.setLabel(MessageManager
3564             .getString("action.by_annotation"));
3565     annotationColour.addActionListener(this);
3566
3567     /*
3568      * Configure Calculate menu items and actions
3569      */
3570     sortPairwiseMenuItem.setLabel(MessageManager
3571             .getString("action.by_pairwise_id"));
3572     sortPairwiseMenuItem.addActionListener(this);
3573     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3574     sortIDMenuItem.addActionListener(this);
3575     sortLengthMenuItem.setLabel(MessageManager
3576             .getString("action.by_length"));
3577     sortLengthMenuItem.addActionListener(this);
3578     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3579     sortGroupMenuItem.addActionListener(this);
3580     pairwiseAlignmentMenuItem.setLabel(MessageManager
3581             .getString("action.pairwise_alignment"));
3582     pairwiseAlignmentMenuItem.addActionListener(this);
3583     PCAMenuItem.setLabel(MessageManager
3584             .getString("label.principal_component_analysis"));
3585     PCAMenuItem.addActionListener(this);
3586     autoCalculate = new CheckboxMenuItem(
3587             MessageManager.getString("label.autocalculate_consensus"), true);
3588     averageDistanceTreeMenuItem.setLabel(MessageManager
3589             .getString("label.average_distance_identity"));
3590     averageDistanceTreeMenuItem.addActionListener(this);
3591     neighbourTreeMenuItem.setLabel(MessageManager
3592             .getString("label.neighbour_joining_identity"));
3593     neighbourTreeMenuItem.addActionListener(this);
3594     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3595             .getString("label.average_distance_blosum62"));
3596     avDistanceTreeBlosumMenuItem.addActionListener(this);
3597     njTreeBlosumMenuItem.setLabel(MessageManager
3598             .getString("label.neighbour_blosum62"));
3599     njTreeBlosumMenuItem.addActionListener(this);
3600     sortByTreeMenu.setLabel(MessageManager
3601             .getString("action.by_tree_order"));
3602     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3603     Menu calculateTreeMenu = new Menu(
3604             MessageManager.getString("action.calculate_tree"));
3605     autoCalculate.addItemListener(this);
3606     sortByTree.addItemListener(this);
3607
3608     /*
3609      * Configure Help menu items and actions
3610      */
3611     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3612     documentation.setLabel(MessageManager.getString("label.documentation"));
3613     documentation.addActionListener(this);
3614     about.setLabel(MessageManager.getString("label.about"));
3615     about.addActionListener(this);
3616
3617     /*
3618      * Add top level menus to frame
3619      */
3620     alignFrameMenuBar.add(fileMenu);
3621     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3622     alignFrameMenuBar.add(editMenu);
3623     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3624     alignFrameMenuBar.add(selectMenu);
3625     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3626     alignFrameMenuBar.add(viewMenu);
3627     Menu annotationsMenu = new Menu(
3628             MessageManager.getString("action.annotations"));
3629     alignFrameMenuBar.add(annotationsMenu);
3630     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3631     alignFrameMenuBar.add(formatMenu);
3632     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3633     alignFrameMenuBar.add(colourMenu);
3634     Menu calculateMenu = new Menu(
3635             MessageManager.getString("action.calculate"));
3636     alignFrameMenuBar.add(calculateMenu);
3637     alignFrameMenuBar.add(helpMenu);
3638
3639     /*
3640      * File menu
3641      */
3642     fileMenu.add(inputText);
3643     fileMenu.add(loadTree);
3644     fileMenu.add(loadAnnotations);
3645     fileMenu.addSeparator();
3646     fileMenu.add(outputTextboxMenu);
3647     fileMenu.add(outputFeatures);
3648     fileMenu.add(outputAnnotations);
3649     if (jalviewServletURL != null)
3650     {
3651       fileMenu.add(loadApplication);
3652     }
3653     fileMenu.addSeparator();
3654     fileMenu.add(closeMenuItem);
3655
3656     /*
3657      * Edit menu
3658      */
3659     editMenu.add(undoMenuItem);
3660     editMenu.add(redoMenuItem);
3661     editMenu.add(cut);
3662     editMenu.add(copy);
3663     pasteMenu.add(pasteNew);
3664     pasteMenu.add(pasteThis);
3665     editMenu.add(pasteMenu);
3666     editMenu.add(delete);
3667     editMenu.addSeparator();
3668     editMenu.add(remove2LeftMenuItem);
3669     editMenu.add(remove2RightMenuItem);
3670     editMenu.add(removeGappedColumnMenuItem);
3671     editMenu.add(removeAllGapsMenuItem);
3672     editMenu.add(removeRedundancyMenuItem);
3673
3674     /*
3675      * Select menu
3676      */
3677     selectMenu.add(findMenuItem);
3678     selectMenu.addSeparator();
3679     selectMenu.add(selectAllSequenceMenuItem);
3680     selectMenu.add(deselectAllSequenceMenuItem);
3681     selectMenu.add(invertSequenceMenuItem);
3682     selectMenu.add(invertColSel);
3683     selectMenu.add(createGroup);
3684     selectMenu.add(unGroup);
3685     selectMenu.add(grpsFromSelection);
3686     selectMenu.add(deleteGroups);
3687     selectMenu.add(annotationColumnSelection);
3688
3689     /*
3690      * View menu
3691      */
3692     viewMenu.add(newView);
3693     viewMenu.addSeparator();
3694     showMenu.add(showColumns);
3695     showMenu.add(showSeqs);
3696     showMenu.add(showAllHidden);
3697     viewMenu.add(showMenu);
3698     hideMenu.add(hideColumns);
3699     hideMenu.add(hideSequences);
3700     hideMenu.add(hideAllSelection);
3701     hideMenu.add(hideAllButSelection);
3702     viewMenu.add(hideMenu);
3703     viewMenu.addSeparator();
3704     viewMenu.add(followMouseOverFlag);
3705     viewMenu.addSeparator();
3706     viewMenu.add(sequenceFeatures);
3707     viewMenu.add(featureSettings);
3708     viewMenu.addSeparator();
3709     viewMenu.add(alProperties);
3710     viewMenu.addSeparator();
3711     viewMenu.add(overviewMenuItem);
3712
3713     /*
3714      * Annotations menu
3715      */
3716     annotationsMenu.add(annotationPanelMenuItem);
3717     annotationsMenu.addSeparator();
3718     annotationsMenu.add(showAlignmentAnnotations);
3719     annotationsMenu.add(showSequenceAnnotations);
3720     annotationsMenu.add(sortAnnBySequence);
3721     annotationsMenu.add(sortAnnByLabel);
3722     annotationsMenu.addSeparator();
3723     autoAnnMenu.add(showAutoFirst);
3724     autoAnnMenu.add(showAutoLast);
3725     autoAnnMenu.addSeparator();
3726     autoAnnMenu.add(applyAutoAnnotationSettings);
3727     autoAnnMenu.add(showConsensusHistogram);
3728     autoAnnMenu.add(showSequenceLogo);
3729     autoAnnMenu.add(normSequenceLogo);
3730     autoAnnMenu.addSeparator();
3731     autoAnnMenu.add(showGroupConservation);
3732     autoAnnMenu.add(showGroupConsensus);
3733     annotationsMenu.add(autoAnnMenu);
3734
3735     /*
3736      * Format menu
3737      */
3738     formatMenu.add(font);
3739     formatMenu.add(seqLimits);
3740     formatMenu.add(wrapMenuItem);
3741     formatMenu.add(scaleAbove);
3742     formatMenu.add(scaleLeft);
3743     formatMenu.add(scaleRight);
3744     formatMenu.add(viewBoxesMenuItem);
3745     formatMenu.add(viewTextMenuItem);
3746     formatMenu.add(colourTextMenuItem);
3747     formatMenu.add(displayNonconservedMenuItem);
3748     formatMenu.add(renderGapsMenuItem);
3749     formatMenu.add(centreColumnLabelFlag);
3750
3751     /*
3752      * Colour menu
3753      */
3754     colourMenu.add(applyToAllGroups);
3755     colourMenu.addSeparator();
3756     colourMenu.add(noColourmenuItem);
3757     colourMenu.add(clustalColour);
3758     colourMenu.add(BLOSUM62Colour);
3759     colourMenu.add(PIDColour);
3760     colourMenu.add(zappoColour);
3761     colourMenu.add(taylorColour);
3762     colourMenu.add(hydrophobicityColour);
3763     colourMenu.add(helixColour);
3764     colourMenu.add(strandColour);
3765     colourMenu.add(turnColour);
3766     colourMenu.add(buriedColour);
3767     colourMenu.add(nucleotideColour);
3768     colourMenu.add(purinePyrimidineColour);
3769     // colourMenu.add(RNAInteractionColour);
3770     colourMenu.add(tcoffeeColour);
3771     colourMenu.add(userDefinedColour);
3772     colourMenu.addSeparator();
3773     colourMenu.add(conservationMenuItem);
3774     colourMenu.add(modifyConservation);
3775     colourMenu.add(abovePIDThreshold);
3776     colourMenu.add(modifyPID);
3777     colourMenu.add(annotationColour);
3778     colourMenu.add(RNAHelixColour);
3779
3780     /*
3781      * Calculate menu
3782      */
3783     sortMenu.add(sortIDMenuItem);
3784     sortMenu.add(sortLengthMenuItem);
3785     sortMenu.add(sortByTreeMenu);
3786     sortMenu.add(sortGroupMenuItem);
3787     sortMenu.add(sortPairwiseMenuItem);
3788     calculateMenu.add(sortMenu);
3789     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3790     calculateTreeMenu.add(neighbourTreeMenuItem);
3791     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3792     calculateTreeMenu.add(njTreeBlosumMenuItem);
3793     calculateMenu.add(calculateTreeMenu);
3794     calculateMenu.addSeparator();
3795     calculateMenu.add(pairwiseAlignmentMenuItem);
3796     calculateMenu.add(PCAMenuItem);
3797     calculateMenu.add(autoCalculate);
3798     calculateMenu.add(sortByTree);
3799
3800     /*
3801      * Help menu
3802      */
3803     helpMenu.add(documentation);
3804     helpMenu.add(about);
3805
3806     /*
3807      * Status bar
3808      */
3809     statusBar.setBackground(Color.white);
3810     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3811     statusBar.setText(MessageManager.getString("label.status_bar"));
3812     this.add(statusBar, BorderLayout.SOUTH);
3813   }
3814
3815   @Override
3816   public void setStatus(String string)
3817   {
3818     statusBar.setText(string);
3819   };
3820
3821   MenuItem featureSettings = new MenuItem();
3822
3823   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3824
3825   MenuItem annotationColour = new MenuItem();
3826
3827   MenuItem annotationColumnSelection = new MenuItem();
3828
3829   MenuItem invertColSel = new MenuItem();
3830
3831   MenuItem showColumns = new MenuItem();
3832
3833   MenuItem showSeqs = new MenuItem();
3834
3835   MenuItem hideColumns = new MenuItem();
3836
3837   MenuItem hideSequences = new MenuItem();
3838
3839   MenuItem hideAllButSelection = new MenuItem();
3840
3841   MenuItem hideAllSelection = new MenuItem();
3842
3843   MenuItem showAllHidden = new MenuItem();
3844
3845   MenuItem newView = new MenuItem();
3846
3847   private CheckboxMenuItem showAlignmentAnnotations;
3848
3849   private CheckboxMenuItem showSequenceAnnotations;
3850
3851   private CheckboxMenuItem sortAnnBySequence;
3852
3853   private CheckboxMenuItem sortAnnByLabel;
3854
3855   private CheckboxMenuItem showAutoFirst;
3856
3857   private CheckboxMenuItem showAutoLast;
3858
3859   private SplitFrame splitFrame;
3860
3861   /**
3862    * Attach the alignFrame panels after embedding menus, if necessary. This used
3863    * to be called setEmbedded, but is now creates the dropdown menus in a
3864    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3865    *
3866    * @param reallyEmbedded
3867    *          true to attach the view to the applet area on the page rather than
3868    *          in a new window
3869    */
3870   public void createAlignFrameWindow(boolean reallyEmbedded)
3871   {
3872     if (reallyEmbedded)
3873     {
3874       embedAlignFrameInApplet(viewport.applet);
3875     }
3876     else
3877     {
3878       // //////
3879       // test and embed menu bar if necessary.
3880       //
3881       if (embedMenuIfNeeded(alignPanel))
3882       {
3883         /*
3884          * adjust for status bar height too. ? pointless as overridden by layout
3885          * manager
3886          */
3887         alignPanel.setSize(getSize().width,
3888                 getSize().height - statusBar.getHeight());
3889       }
3890       add(statusBar, BorderLayout.SOUTH);
3891       add(alignPanel, BorderLayout.CENTER);
3892       // and register with the applet so it can pass external API calls to us
3893       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3894               frameHeight);
3895     }
3896   }
3897
3898   /**
3899    * Add the components of this AlignFrame to the applet container.
3900    *
3901    * @param theApplet
3902    */
3903   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3904   {
3905     // ////
3906     // Explicitly build the embedded menu panel for the on-page applet
3907     //
3908     // view cannot be closed if its actually on the page
3909     fileMenu.remove(closeMenuItem);
3910     fileMenu.remove(3); // Remove Separator
3911     // construct embedded menu, using default font
3912     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3913     // and actually add the components to the applet area
3914     theApplet.setLayout(new BorderLayout());
3915     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3916     theApplet.add(statusBar, BorderLayout.SOUTH);
3917     // TODO should size be left to the layout manager?
3918     alignPanel.setSize(theApplet.getSize().width,
3919             theApplet.getSize().height - embeddedMenu.getHeight()
3920                     - statusBar.getHeight());
3921     theApplet.add(alignPanel, BorderLayout.CENTER);
3922     final AlignFrame me = this;
3923     theApplet.addFocusListener(new FocusListener()
3924     {
3925
3926       @Override
3927       public void focusLost(FocusEvent e)
3928       {
3929         if (theApplet.currentAlignFrame == me)
3930         {
3931           theApplet.currentAlignFrame = null;
3932         }
3933       }
3934
3935       @Override
3936       public void focusGained(FocusEvent e)
3937       {
3938         theApplet.currentAlignFrame = me;
3939       }
3940     });
3941     theApplet.validate();
3942   }
3943
3944   /**
3945    * create a new binding between structures in an existing jmol viewer instance
3946    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3947    * this does not open a new Jmol window, or modify the display of the
3948    * structures in the original jmol window. Note This method doesn't work
3949    * without an additional javascript library to exchange messages between the
3950    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3951    *
3952    * @param viewer
3953    *          JmolViewer instance
3954    * @param sequenceIds
3955    *          - sequence Ids to search for associations
3956    */
3957   public SequenceStructureBinding addStructureViewInstance(
3958           Object jmolviewer, String[] sequenceIds)
3959   {
3960     Viewer viewer = null;
3961     try
3962     {
3963       viewer = (Viewer) jmolviewer;
3964     } catch (ClassCastException ex)
3965     {
3966       System.err.println("Unsupported viewer object :"
3967               + jmolviewer.getClass());
3968     }
3969     if (viewer == null)
3970     {
3971       System.err.println("Can't use this object as a structure viewer:"
3972               + jmolviewer.getClass());
3973       return null;
3974     }
3975     SequenceI[] seqs = null;
3976     if (sequenceIds == null || sequenceIds.length == 0)
3977     {
3978       seqs = viewport.getAlignment().getSequencesArray();
3979     }
3980     else
3981     {
3982       Vector sqi = new Vector();
3983       AlignmentI al = viewport.getAlignment();
3984       for (int sid = 0; sid < sequenceIds.length; sid++)
3985       {
3986         SequenceI sq = al.findName(sequenceIds[sid]);
3987         if (sq != null)
3988         {
3989           sqi.addElement(sq);
3990         }
3991       }
3992       if (sqi.size() > 0)
3993       {
3994         seqs = new SequenceI[sqi.size()];
3995         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3996         {
3997           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3998         }
3999       }
4000       else
4001       {
4002         return null;
4003       }
4004     }
4005     AAStructureBindingModel jmv = null;
4006     // TODO: search for a jmv that involves viewer
4007     if (jmv == null)
4008     { // create a new viewer/jalview binding.
4009       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4010     }
4011     return jmv;
4012
4013   }
4014
4015   /**
4016    * bind a pdb file to a sequence in the current view
4017    *
4018    * @param sequenceId
4019    *          - sequenceId within the dataset.
4020    * @param pdbEntryString
4021    *          - the short name for the PDB file
4022    * @param pdbFile
4023    *          - pdb file - either a URL or a valid PDB file.
4024    * @return true if binding was as success TODO: consider making an exception
4025    *         structure for indicating when PDB parsing or sequenceId location
4026    *         fails.
4027    */
4028   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4029           String pdbFile)
4030   {
4031     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4032     boolean needtoadd = false;
4033     if (toaddpdb != null)
4034     {
4035       Vector pdbe = toaddpdb.getAllPDBEntries();
4036       PDBEntry pdbentry = null;
4037       if (pdbe != null && pdbe.size() > 0)
4038       {
4039         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4040         {
4041           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4042           if (!pdbentry.getId().equals(pdbEntryString)
4043                   && !pdbentry.getFile().equals(pdbFile))
4044           {
4045             pdbentry = null;
4046           }
4047           else
4048           {
4049             continue;
4050           }
4051         }
4052       }
4053       if (pdbentry == null)
4054       {
4055         pdbentry = new PDBEntry();
4056         pdbentry.setId(pdbEntryString);
4057         pdbentry.setFile(pdbFile);
4058         needtoadd = true; // add this new entry to sequence.
4059       }
4060       // resolve data source
4061       // TODO: this code should be a refactored to an io package
4062       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4063               pdbFile, FileFormat.PDB);
4064       if (protocol == null)
4065       {
4066         return false;
4067       }
4068       if (needtoadd)
4069       {
4070         pdbentry.setProperty("protocol", protocol);
4071         toaddpdb.addPDBId(pdbentry);
4072         alignPanel.getStructureSelectionManager()
4073                 .registerPDBEntry(pdbentry);
4074       }
4075     }
4076     return true;
4077   }
4078
4079   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4080   {
4081     if (seqs != null)
4082     {
4083       Vector sequences = new Vector();
4084       for (int i = 0; i < seqs.length; i++)
4085       {
4086         if (seqs[i] != null)
4087         {
4088           sequences.addElement(new Object[] { seqs[i],
4089               (chains != null) ? chains[i] : null });
4090         }
4091       }
4092       seqs = new SequenceI[sequences.size()];
4093       chains = new String[sequences.size()];
4094       for (int i = 0, isize = sequences.size(); i < isize; i++)
4095       {
4096         Object[] oj = (Object[]) sequences.elementAt(i);
4097
4098         seqs[i] = (SequenceI) oj[0];
4099         chains[i] = (String) oj[1];
4100       }
4101     }
4102     return new Object[] { seqs, chains };
4103
4104   }
4105
4106   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4107           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4108   {
4109     // Scrub any null sequences from the array
4110     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4111     seqs = (SequenceI[]) sqch[0];
4112     chains = (String[]) sqch[1];
4113     if (seqs == null || seqs.length == 0)
4114     {
4115       System.err
4116               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4117     }
4118     if (protocol == null)
4119     {
4120       String sourceType = (String) pdb.getProperty("protocol");
4121       try
4122       {
4123         protocol = DataSourceType.valueOf(sourceType);
4124       } catch (IllegalArgumentException e)
4125       {
4126         // ignore
4127       }
4128       if (protocol == null)
4129       {
4130         System.err.println("Couldn't work out protocol to open structure: "
4131                 + pdb.getId());
4132         return;
4133       }
4134     }
4135     if (applet.useXtrnalSviewer)
4136     {
4137       // register the association(s) and quit, don't create any windows.
4138       if (StructureSelectionManager.getStructureSelectionManager(applet)
4139               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4140       {
4141         System.err.println("Failed to map " + pdb.getFile() + " ("
4142                 + protocol + ") to any sequences");
4143       }
4144       return;
4145     }
4146     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4147     {
4148       // can only do alignments with Jmol
4149       // find the last jmol window assigned to this alignment
4150       AppletJmol ajm = null, tajm;
4151       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4152       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4153       {
4154         tajm = (AppletJmol) jmols.elementAt(i);
4155         if (tajm.ap.alignFrame == this)
4156         {
4157           ajm = tajm;
4158           break;
4159         }
4160       }
4161       if (ajm != null)
4162       {
4163         System.err
4164                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4165         // try and add the pdb structure
4166         // ajm.addS
4167         ajm = null;
4168       }
4169     }
4170     // otherwise, create a new window
4171     if (applet.jmolAvailable)
4172     {
4173       new AppletJmol(pdb, seqs, chains, alignPanel,
4174               protocol);
4175       applet.lastFrameX += 40;
4176       applet.lastFrameY += 40;
4177     }
4178     else
4179     {
4180       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4181     }
4182
4183   }
4184
4185   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4186           SequenceI[][] seqs, String[][] chains, String[] protocols)
4187   {
4188     // TODO Auto-generated method stub
4189     System.err.println("Aligned Structure View: Not yet implemented.");
4190   }
4191
4192   /**
4193    * modify the current selection, providing the user has not made a selection
4194    * already.
4195    *
4196    * @param sel
4197    *          - sequences from this alignment
4198    * @param csel
4199    *          - columns to be selected on the alignment
4200    */
4201   public void select(SequenceGroup sel, ColumnSelection csel)
4202   {
4203     alignPanel.seqPanel.selection(sel, csel, null);
4204   }
4205
4206   public void scrollTo(int row, int column)
4207   {
4208     alignPanel.seqPanel.scrollTo(row, column);
4209   }
4210
4211   public void scrollToRow(int row)
4212   {
4213     alignPanel.seqPanel.scrollToRow(row);
4214   }
4215
4216   public void scrollToColumn(int column)
4217   {
4218     alignPanel.seqPanel.scrollToColumn(column);
4219   }
4220
4221   /**
4222    * @return the alignments unique ID.
4223    */
4224   public String getSequenceSetId()
4225   {
4226     return viewport.getSequenceSetId();
4227   }
4228
4229   /**
4230    * Load the (T-Coffee) score file from the specified url
4231    *
4232    * @param source
4233    *          File/URL/T-COFFEE score file contents
4234    * @throws IOException
4235    * @return true if alignment was annotated with data from source
4236    */
4237   public boolean loadScoreFile(String source) throws IOException
4238   {
4239
4240     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4241             AppletFormatAdapter.checkProtocol(source));
4242     if (!file.isValid())
4243     {
4244       // TODO: raise dialog for gui
4245       System.err.println("Problems parsing T-Coffee scores: "
4246               + file.getWarningMessage());
4247       System.err.println("Origin was:\n" + source);
4248       return false;
4249     }
4250
4251     /*
4252      * check that the score matrix matches the alignment dimensions
4253      */
4254     AlignmentI aln;
4255     if ((aln = viewport.getAlignment()) != null
4256             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4257                     .getWidth()))
4258     {
4259       // TODO: raise a dialog box here rather than bomb out.
4260       System.err
4261               .println("The scores matrix does not match the alignment dimensions");
4262
4263     }
4264
4265     // TODO add parameter to indicate if matching should be done
4266     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4267     {
4268       alignPanel.fontChanged();
4269       tcoffeeColour.setEnabled(true);
4270       // switch to this color
4271       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4272       return true;
4273     }
4274     else
4275     {
4276       System.err.println("Problems resolving T-Coffee scores:");
4277       if (file.getWarningMessage() != null)
4278       {
4279         System.err.println(file.getWarningMessage());
4280       }
4281     }
4282     return false;
4283   }
4284
4285   public SplitFrame getSplitFrame()
4286   {
4287     return this.splitFrame;
4288   }
4289
4290   public void setSplitFrame(SplitFrame sf)
4291   {
4292     this.splitFrame = sf;
4293   }
4294
4295   // may not need this
4296   @Override
4297   public void setShowSeqFeatures(boolean b)
4298   {
4299     // showSeqFeatures.setSelected(b);
4300     viewport.setShowSequenceFeatures(b);
4301
4302   }
4303
4304   @Override
4305   public void setMenusForViewport()
4306   {
4307     // setMenusFromViewport(viewport);
4308
4309   }
4310
4311   @Override
4312   public void refreshFeatureUI(boolean enableIfNecessary)
4313   {
4314     if (enableIfNecessary)
4315     {
4316       sequenceFeatures.setState(true);
4317       alignPanel.av.setShowSequenceFeatures(true);
4318     }
4319   }
4320
4321   @Override
4322   public FeatureSettingsControllerI getFeatureSettingsUI()
4323   {
4324     return alignPanel.av.featureSettings;
4325   }
4326
4327 }