src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.analysis.TreeBuilder;
  26 import jalview.api.AlignViewControllerGuiI;
  27 import jalview.api.AlignViewControllerI;
  28 import jalview.api.AlignViewportI;
  29 import jalview.api.FeatureColourI;
  30 import jalview.api.FeatureRenderer;
  31 import jalview.api.FeatureSettingsControllerI;
  32 import jalview.api.SequenceStructureBinding;
  33 import jalview.bin.JalviewLite;
  34 import jalview.commands.CommandI;
  35 import jalview.commands.EditCommand;
  36 import jalview.commands.EditCommand.Action;
  37 import jalview.commands.OrderCommand;
  38 import jalview.commands.RemoveGapColCommand;
  39 import jalview.commands.RemoveGapsCommand;
  40 import jalview.commands.SlideSequencesCommand;
  41 import jalview.commands.TrimRegionCommand;
  42 import jalview.datamodel.Alignment;
  43 import jalview.datamodel.AlignmentAnnotation;
  44 import jalview.datamodel.AlignmentI;
  45 import jalview.datamodel.AlignmentOrder;
  46 import jalview.datamodel.ColumnSelection;
  47 import jalview.datamodel.PDBEntry;
  48 import jalview.datamodel.Sequence;
  49 import jalview.datamodel.SequenceGroup;
  50 import jalview.datamodel.SequenceI;
  51 import jalview.io.AnnotationFile;
  52 import jalview.io.AppletFormatAdapter;
  53 import jalview.io.DataSourceType;
  54 import jalview.io.FeaturesFile;
  55 import jalview.io.FileFormat;
  56 import jalview.io.FileFormatI;
  57 import jalview.io.FileFormats;
  58 import jalview.io.TCoffeeScoreFile;
  59 import jalview.schemes.Blosum62ColourScheme;
  60 import jalview.schemes.BuriedColourScheme;
  61 import jalview.schemes.ClustalxColourScheme;
  62 import jalview.schemes.ColourSchemeI;
  63 import jalview.schemes.HelixColourScheme;
  64 import jalview.schemes.HydrophobicColourScheme;
  65 import jalview.schemes.NucleotideColourScheme;
  66 import jalview.schemes.PIDColourScheme;
  67 import jalview.schemes.PurinePyrimidineColourScheme;
  68 import jalview.schemes.RNAHelicesColour;
  69 import jalview.schemes.StrandColourScheme;
  70 import jalview.schemes.TCoffeeColourScheme;
  71 import jalview.schemes.TaylorColourScheme;
  72 import jalview.schemes.TurnColourScheme;
  73 import jalview.schemes.ZappoColourScheme;
  74 import jalview.structure.StructureSelectionManager;
  75 import jalview.structures.models.AAStructureBindingModel;
  76 import jalview.util.MappingUtils;
  77 import jalview.util.MessageManager;
  78 import jalview.viewmodel.AlignmentViewport;
  79 import jalview.viewmodel.ViewportRanges;
  80
  81 import java.awt.BorderLayout;
  82 import java.awt.Canvas;
  83 import java.awt.CheckboxMenuItem;
  84 import java.awt.Color;
  85 import java.awt.FlowLayout;
  86 import java.awt.Font;
  87 import java.awt.FontMetrics;
  88 import java.awt.Frame;
  89 import java.awt.Graphics;
  90 import java.awt.Label;
  91 import java.awt.Menu;
  92 import java.awt.MenuBar;
  93 import java.awt.MenuItem;
  94 import java.awt.Panel;
  95 import java.awt.event.ActionEvent;
  96 import java.awt.event.ActionListener;
  97 import java.awt.event.FocusEvent;
  98 import java.awt.event.FocusListener;
  99 import java.awt.event.ItemEvent;
 100 import java.awt.event.ItemListener;
 101 import java.awt.event.KeyEvent;
 102 import java.awt.event.KeyListener;
 103 import java.awt.event.WindowAdapter;
 104 import java.awt.event.WindowEvent;
 105 import java.io.IOException;
 106 import java.net.URL;
 107 import java.net.URLEncoder;
 108 import java.util.Arrays;
 109 import java.util.Deque;
 110 import java.util.HashMap;
 111 import java.util.List;
 112 import java.util.Map;
 113 import java.util.StringTokenizer;
 114 import java.util.Vector;
 115
 116 import org.jmol.viewer.Viewer;
 117
 118 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 119         ItemListener, KeyListener, AlignViewControllerGuiI
 120 {
 121   public AlignViewControllerI avc;
 122
 123   public AlignmentPanel alignPanel;
 124
 125   public AlignViewport viewport;
 126
 127   // width and height may be overridden by applet parameters
 128   int frameWidth = 700;
 129
 130   int frameHeight = 500;
 131
 132   String jalviewServletURL;
 133
 134   /*
 135    * Flag for showing autocalculated consensus above or below other consensus
 136    * rows
 137    */
 138   private boolean showAutoCalculatedAbove;
 139
 140   private SequenceAnnotationOrder annotationSortOrder;
 141
 142   /**
 143    * Constructor that creates the frame and adds it to the display.
 144    *
 145    * @param al
 146    * @param applet
 147    * @param title
 148    * @param embedded
 149    */
 150   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 151           boolean embedded)
 152   {
 153     this(al, applet, title, embedded, true);
 154   }
 155
 156   /**
 157    * Constructor that optionally allows the frame to be displayed or only
 158    * created.
 159    *
 160    * @param al
 161    * @param applet
 162    * @param title
 163    * @param embedded
 164    * @param addToDisplay
 165    */
 166   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 167           boolean embedded, boolean addToDisplay)
 168   {
 169     this(al, null, null, applet, title, embedded, addToDisplay);
 170   }
 171
 172   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 173           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 == grpsFromSelection)
1076     {
1077       makeGrpsFromSelection_actionPerformed();
1078     }
1079     else if (source == deleteGroups)
1080     {
1081       deleteGroups_actionPerformed();
1082     }
1083     else if (source == selectAllSequenceMenuItem)
1084     {
1085       selectAllSequenceMenuItem_actionPerformed();
1086     }
1087     else if (source == deselectAllSequenceMenuItem)
1088     {
1089       deselectAllSequenceMenuItem_actionPerformed();
1090     }
1091     else if (source == invertSequenceMenuItem)
1092     {
1093       invertSequenceMenuItem_actionPerformed();
1094       // uncomment to slave sequence selections in split frame
1095       // viewport.sendSelection();
1096     }
1097     else if (source == invertColSel)
1098     {
1099       viewport.invertColumnSelection();
1100       alignPanel.paintAlignment(true);
1101       viewport.sendSelection();
1102     }
1103     else if (source == remove2LeftMenuItem)
1104     {
1105       trimAlignment(true);
1106     }
1107     else if (source == remove2RightMenuItem)
1108     {
1109       trimAlignment(false);
1110     }
1111     else if (source == removeGappedColumnMenuItem)
1112     {
1113       removeGappedColumnMenuItem_actionPerformed();
1114     }
1115     else if (source == removeAllGapsMenuItem)
1116     {
1117       removeAllGapsMenuItem_actionPerformed();
1118     }
1119     else if (source == findMenuItem)
1120     {
1121       findMenuItem_actionPerformed();
1122     }
1123     else if (source == font)
1124     {
1125       new FontChooser(alignPanel);
1126     }
1127     else if (source == newView)
1128     {
1129       newView(null);
1130     }
1131     else if (source == showColumns)
1132     {
1133       viewport.showAllHiddenColumns();
1134       alignPanel.paintAlignment(true);
1135       viewport.sendSelection();
1136     }
1137     else if (source == showSeqs)
1138     {
1139       viewport.showAllHiddenSeqs();
1140       alignPanel.paintAlignment(true);
1141       // uncomment if we want to slave sequence selections in split frame
1142       // viewport.sendSelection();
1143     }
1144     else if (source == hideColumns)
1145     {
1146       viewport.hideSelectedColumns();
1147       alignPanel.paintAlignment(true);
1148       viewport.sendSelection();
1149     }
1150     else if (source == hideSequences
1151             && viewport.getSelectionGroup() != null)
1152     {
1153       viewport.hideAllSelectedSeqs();
1154       alignPanel.paintAlignment(true);
1155       // uncomment if we want to slave sequence selections in split frame
1156       // viewport.sendSelection();
1157     }
1158     else if (source == hideAllButSelection)
1159     {
1160       toggleHiddenRegions(false, false);
1161       alignPanel.paintAlignment(true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == hideAllSelection)
1165     {
1166       SequenceGroup sg = viewport.getSelectionGroup();
1167       viewport.expandColSelection(sg, false);
1168       viewport.hideAllSelectedSeqs();
1169       viewport.hideSelectedColumns();
1170       alignPanel.paintAlignment(true);
1171       viewport.sendSelection();
1172     }
1173     else if (source == showAllHidden)
1174     {
1175       viewport.showAllHiddenColumns();
1176       viewport.showAllHiddenSeqs();
1177       alignPanel.paintAlignment(true);
1178       viewport.sendSelection();
1179     }
1180     else if (source == showGroupConsensus)
1181     {
1182       showGroupConsensus_actionPerformed();
1183     }
1184     else if (source == showGroupConservation)
1185     {
1186       showGroupConservation_actionPerformed();
1187     }
1188     else if (source == showSequenceLogo)
1189     {
1190       showSequenceLogo_actionPerformed();
1191     }
1192     else if (source == normSequenceLogo)
1193     {
1194       normSequenceLogo_actionPerformed();
1195     }
1196     else if (source == showConsensusHistogram)
1197     {
1198       showConsensusHistogram_actionPerformed();
1199     }
1200     else if (source == applyAutoAnnotationSettings)
1201     {
1202       applyAutoAnnotationSettings_actionPerformed();
1203     }
1204     else if (source == featureSettings)
1205     {
1206       new FeatureSettings(alignPanel);
1207     }
1208     else if (source == alProperties)
1209     {
1210       StringBuffer contents = new jalview.io.AlignmentProperties(
1211               viewport.getAlignment()).formatAsString();
1212       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1213       cap.setText(contents.toString());
1214       Frame frame = new Frame();
1215       frame.add(cap);
1216       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1217               "label.alignment_properties", new String[] { getTitle() }),
1218               400, 250);
1219     }
1220     else if (source == overviewMenuItem)
1221     {
1222       overviewMenuItem_actionPerformed();
1223     }
1224     else if (source == noColourmenuItem)
1225     {
1226       changeColour(null);
1227     }
1228     else if (source == clustalColour)
1229     {
1230       abovePIDThreshold.setState(false);
1231       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1232     }
1233     else if (source == zappoColour)
1234     {
1235       changeColour(new ZappoColourScheme());
1236     }
1237     else if (source == taylorColour)
1238     {
1239       changeColour(new TaylorColourScheme());
1240     }
1241     else if (source == hydrophobicityColour)
1242     {
1243       changeColour(new HydrophobicColourScheme());
1244     }
1245     else if (source == helixColour)
1246     {
1247       changeColour(new HelixColourScheme());
1248     }
1249     else if (source == strandColour)
1250     {
1251       changeColour(new StrandColourScheme());
1252     }
1253     else if (source == turnColour)
1254     {
1255       changeColour(new TurnColourScheme());
1256     }
1257     else if (source == buriedColour)
1258     {
1259       changeColour(new BuriedColourScheme());
1260     }
1261     else if (source == nucleotideColour)
1262     {
1263       changeColour(new NucleotideColourScheme());
1264     }
1265     else if (source == purinePyrimidineColour)
1266     {
1267       changeColour(new PurinePyrimidineColourScheme());
1268     }
1269     // else if (source == RNAInteractionColour)
1270     // {
1271     // changeColour(new RNAInteractionColourScheme());
1272     // }
1273     else if (source == RNAHelixColour)
1274     {
1275       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1276       // new RNAHelicesColourChooser(viewport, alignPanel);
1277     }
1278     else if (source == modifyPID)
1279     {
1280       modifyPID_actionPerformed();
1281     }
1282     else if (source == modifyConservation)
1283     {
1284       modifyConservation_actionPerformed();
1285     }
1286     else if (source == userDefinedColour)
1287     {
1288       new UserDefinedColours(alignPanel, null);
1289     }
1290     else if (source == PIDColour)
1291     {
1292       changeColour(new PIDColourScheme());
1293     }
1294     else if (source == BLOSUM62Colour)
1295     {
1296       changeColour(new Blosum62ColourScheme());
1297     }
1298     else if (source == tcoffeeColour)
1299     {
1300       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1301     }
1302     else if (source == annotationColour)
1303     {
1304       new AnnotationColourChooser(viewport, alignPanel);
1305     }
1306     else if (source == annotationColumnSelection)
1307     {
1308       new AnnotationColumnChooser(viewport, alignPanel);
1309     }
1310     else if (source == sortPairwiseMenuItem)
1311     {
1312       sortPairwiseMenuItem_actionPerformed();
1313     }
1314     else if (source == sortIDMenuItem)
1315     {
1316       sortIDMenuItem_actionPerformed();
1317     }
1318     else if (source == sortLengthMenuItem)
1319     {
1320       sortLengthMenuItem_actionPerformed();
1321     }
1322     else if (source == sortGroupMenuItem)
1323     {
1324       sortGroupMenuItem_actionPerformed();
1325     }
1326     else if (source == removeRedundancyMenuItem)
1327     {
1328       removeRedundancyMenuItem_actionPerformed();
1329     }
1330     else if (source == pairwiseAlignmentMenuItem)
1331     {
1332       pairwiseAlignmentMenuItem_actionPerformed();
1333     }
1334     else if (source == PCAMenuItem)
1335     {
1336       PCAMenuItem_actionPerformed();
1337     }
1338     else if (source == averageDistanceTreeMenuItem)
1339     {
1340       averageDistanceTreeMenuItem_actionPerformed();
1341     }
1342     else if (source == neighbourTreeMenuItem)
1343     {
1344       neighbourTreeMenuItem_actionPerformed();
1345     }
1346     else if (source == njTreeBlosumMenuItem)
1347     {
1348       njTreeBlosumMenuItem_actionPerformed();
1349     }
1350     else if (source == avDistanceTreeBlosumMenuItem)
1351     {
1352       avTreeBlosumMenuItem_actionPerformed();
1353     }
1354     else if (source == documentation)
1355     {
1356       documentation_actionPerformed();
1357     }
1358     else if (source == about)
1359     {
1360       about_actionPerformed();
1361     }
1362
1363   }
1364
1365   public void inputText_actionPerformed()
1366   {
1367     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1368     Frame frame = new Frame();
1369     frame.add(cap);
1370     jalview.bin.JalviewLite.addFrame(frame,
1371             MessageManager.getString("label.input_cut_paste"), 500, 500);
1372   }
1373
1374   protected void outputText_actionPerformed(ActionEvent e)
1375   {
1376     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377     Frame frame = new Frame();
1378     frame.add(cap);
1379     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1380             "label.alignment_output_command",
1381             new Object[] { e.getActionCommand() }), 600, 500);
1382
1383     FileFormatI fileFormat = FileFormats.getInstance().forName(
1384             e.getActionCommand());
1385     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1386             fileFormat, viewport.getAlignment(),
1387             viewport.getShowJVSuffix()));
1388   }
1389
1390   public void loadAnnotations()
1391   {
1392     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1393     cap.setText(MessageManager
1394             .getString("label.paste_features_annotations_Tcoffee_here"));
1395     cap.setAnnotationImport();
1396     Frame frame = new Frame();
1397     frame.add(cap);
1398     jalview.bin.JalviewLite.addFrame(frame,
1399             MessageManager.getString("action.paste_annotations"), 400, 300);
1400
1401   }
1402
1403   public String outputAnnotations(boolean displayTextbox)
1404   {
1405     String annotation = new AnnotationFile()
1406             .printAnnotationsForView(viewport);
1407
1408     if (displayTextbox)
1409     {
1410       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1411       Frame frame = new Frame();
1412       frame.add(cap);
1413       jalview.bin.JalviewLite.addFrame(frame,
1414               MessageManager.getString("label.annotations"), 600, 500);
1415       cap.setText(annotation);
1416     }
1417
1418     return annotation;
1419   }
1420
1421   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1422   {
1423     if (alignPanel.getFeatureRenderer() != null
1424             && viewport.getFeaturesDisplayed() != null)
1425     {
1426       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1427
1428     }
1429     return null;
1430   }
1431
1432   public String outputFeatures(boolean displayTextbox, String format)
1433   {
1434     String features;
1435     FeaturesFile formatter = new FeaturesFile();
1436     if (format.equalsIgnoreCase("Jalview"))
1437     {
1438       features = formatter.printJalviewFormat(viewport.getAlignment()
1439               .getSequencesArray(), getDisplayedFeatureCols());
1440     }
1441     else
1442     {
1443       features = formatter.printGffFormat(viewport.getAlignment()
1444               .getSequencesArray(), getDisplayedFeatureCols());
1445     }
1446
1447     if (displayTextbox)
1448     {
1449       boolean frimport = false;
1450       if (features == null || features.equals("No Features Visible"))
1451       {
1452         features = "# No features visible - paste some and import them here.";
1453         frimport = true;
1454       }
1455
1456       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1457       if (frimport)
1458       {
1459         cap.setAnnotationImport();
1460       }
1461       Frame frame = new Frame();
1462       frame.add(cap);
1463       jalview.bin.JalviewLite.addFrame(frame,
1464               MessageManager.getString("label.features"), 600, 500);
1465       cap.setText(features);
1466     }
1467     else
1468     {
1469       if (features == null)
1470       {
1471         features = "";
1472       }
1473     }
1474
1475     return features;
1476   }
1477
1478   void launchFullApplication()
1479   {
1480     StringBuffer url = new StringBuffer(jalviewServletURL);
1481
1482     // allow servlet parameters to be passed in applet parameter
1483     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1484             : "?";
1485     url.append(firstSep);
1486
1487     url.append("open="
1488             + appendProtocol(viewport.applet.getParameter("file")));
1489
1490     if (viewport.applet.getParameter("features") != null)
1491     {
1492       url.append("&features=");
1493       url.append(appendProtocol(viewport.applet.getParameter("features")));
1494     }
1495
1496     if (viewport.applet.getParameter("annotations") != null)
1497     {
1498       url.append("&annotations=");
1499       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1500     }
1501
1502     if (viewport.applet.getParameter("jnetfile") != null
1503             || viewport.applet.getParameter("jpredfile") != null)
1504     {
1505       url.append("&annotations=");
1506       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1507               .getParameter("jnetfile") : viewport.applet
1508               .getParameter("jpredfile")));
1509     }
1510
1511     if (viewport.applet.getParameter("defaultColour") != null)
1512     {
1513       url.append("&colour="
1514               + removeWhiteSpace(viewport.applet
1515                       .getParameter("defaultColour")));
1516     }
1517
1518     if (viewport.applet.getParameter("userDefinedColour") != null)
1519     {
1520       url.append("&colour="
1521               + removeWhiteSpace(viewport.applet
1522                       .getParameter("userDefinedColour")));
1523     }
1524     if (viewport.applet.getParameter("tree") != null)
1525     {
1526       url.append("&tree="
1527               + appendProtocol(viewport.applet.getParameter("tree")));
1528     }
1529     if (viewport.applet.getParameter("treeFile") != null)
1530     {
1531       url.append("&tree="
1532               + appendProtocol(viewport.applet.getParameter("treeFile")));
1533     }
1534
1535     showURL(url.toString(), "FULL_APP");
1536   }
1537
1538   String removeWhiteSpace(String colour)
1539   {
1540     StringBuffer sb = new StringBuffer();
1541     for (int i = 0; i < colour.length(); i++)
1542     {
1543       if (Character.isWhitespace(colour.charAt(i)))
1544       {
1545         sb.append("%20");
1546       }
1547       else
1548       {
1549         sb.append(colour.charAt(i));
1550       }
1551     }
1552
1553     return sb.toString();
1554   }
1555
1556   String appendProtocol(String url)
1557   {
1558     try
1559     {
1560       new URL(url);
1561       url = URLEncoder.encode(url);
1562     }
1563     /*
1564      * When we finally deprecate 1.1 compatibility, we can start to use
1565      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1566      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1567      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1568      * ex.printStackTrace(); }
1569      */
1570     catch (java.net.MalformedURLException ex)
1571     {
1572       url = viewport.applet.getCodeBase() + url;
1573     }
1574     return url;
1575   }
1576
1577   public void closeMenuItem_actionPerformed()
1578   {
1579     PaintRefresher.RemoveComponent(alignPanel);
1580     if (alignPanel.seqPanel != null
1581             && alignPanel.seqPanel.seqCanvas != null)
1582     {
1583       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1584     }
1585     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1586     {
1587       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1588     }
1589
1590     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1591     {
1592       System.exit(0);
1593     }
1594     else
1595     {
1596     }
1597     viewport = null;
1598     alignPanel = null;
1599     this.dispose();
1600   }
1601
1602   /**
1603    * TODO: JAL-1104
1604    */
1605   void updateEditMenuBar()
1606   {
1607
1608     if (viewport.getHistoryList().size() > 0)
1609     {
1610       undoMenuItem.setEnabled(true);
1611       CommandI command = viewport.getHistoryList().peek();
1612       undoMenuItem.setLabel(MessageManager.formatMessage(
1613               "label.undo_command",
1614               new Object[] { command.getDescription() }));
1615     }
1616     else
1617     {
1618       undoMenuItem.setEnabled(false);
1619       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1620     }
1621
1622     if (viewport.getRedoList().size() > 0)
1623     {
1624       redoMenuItem.setEnabled(true);
1625
1626       CommandI command = viewport.getRedoList().peek();
1627       redoMenuItem.setLabel(MessageManager.formatMessage(
1628               "label.redo_command",
1629               new Object[] { command.getDescription() }));
1630     }
1631     else
1632     {
1633       redoMenuItem.setEnabled(false);
1634       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1635     }
1636   }
1637
1638   /**
1639    * TODO: JAL-1104
1640    */
1641   @Override
1642   public void addHistoryItem(CommandI command)
1643   {
1644     if (command.getSize() > 0)
1645     {
1646       viewport.addToHistoryList(command);
1647       viewport.clearRedoList();
1648       updateEditMenuBar();
1649       viewport.updateHiddenColumns();
1650     }
1651   }
1652
1653   /**
1654    * TODO: JAL-1104 DOCUMENT ME!
1655    *
1656    * @param e
1657    *          DOCUMENT ME!
1658    */
1659   protected void undoMenuItem_actionPerformed()
1660   {
1661     if (viewport.getHistoryList().isEmpty())
1662     {
1663       return;
1664     }
1665
1666     CommandI command = viewport.getHistoryList().pop();
1667     viewport.addToRedoList(command);
1668     command.undoCommand(null);
1669
1670     AlignmentViewport originalSource = getOriginatingSource(command);
1671     // JBPNote Test
1672     if (originalSource != viewport)
1673     {
1674       System.err
1675               .println("Warning: Viewport object mismatch whilst undoing");
1676     }
1677     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1678                                           // viewport.getColumnSelection().getHiddenColumns()
1679                                           // != null;
1680     updateEditMenuBar();
1681     originalSource.firePropertyChange("alignment", null, originalSource
1682             .getAlignment().getSequences());
1683   }
1684
1685   /**
1686    * TODO: JAL-1104 DOCUMENT ME!
1687    *
1688    * @param e
1689    *          DOCUMENT ME!
1690    */
1691   protected void redoMenuItem_actionPerformed()
1692   {
1693     if (viewport.getRedoList().isEmpty())
1694     {
1695       return;
1696     }
1697
1698     CommandI command = viewport.getRedoList().pop();
1699     viewport.addToHistoryList(command);
1700     command.doCommand(null);
1701
1702     AlignmentViewport originalSource = getOriginatingSource(command);
1703     // JBPNote Test
1704     if (originalSource != viewport)
1705     {
1706       System.err
1707               .println("Warning: Viewport object mismatch whilst re-doing");
1708     }
1709     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1710                                           // viewport.getColumnSelection().getHiddenColumns()
1711                                           // != null;
1712
1713     updateEditMenuBar();
1714     originalSource.firePropertyChange("alignment", null, originalSource
1715             .getAlignment().getSequences());
1716   }
1717
1718   AlignmentViewport getOriginatingSource(CommandI command)
1719   {
1720     AlignmentViewport originalSource = null;
1721     // For sequence removal and addition, we need to fire
1722     // the property change event FROM the viewport where the
1723     // original alignment was altered
1724     AlignmentI al = null;
1725     if (command instanceof EditCommand)
1726     {
1727       EditCommand editCommand = (EditCommand) command;
1728       al = editCommand.getAlignment();
1729       Vector comps = (Vector) PaintRefresher.components.get(viewport
1730               .getSequenceSetId());
1731       for (int i = 0; i < comps.size(); i++)
1732       {
1733         if (comps.elementAt(i) instanceof AlignmentPanel)
1734         {
1735           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1736           {
1737             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1738             break;
1739           }
1740         }
1741       }
1742     }
1743
1744     if (originalSource == null)
1745     {
1746       // The original view is closed, we must validate
1747       // the current view against the closed view first
1748       if (al != null)
1749       {
1750         PaintRefresher.validateSequences(al, viewport.getAlignment());
1751       }
1752
1753       originalSource = viewport;
1754     }
1755
1756     return originalSource;
1757   }
1758
1759   /**
1760    * Move the currently selected sequences up or down one position in the
1761    * alignment
1762    *
1763    * @param up
1764    */
1765   public void moveSelectedSequences(boolean up)
1766   {
1767     SequenceGroup sg = viewport.getSelectionGroup();
1768     if (sg == null)
1769     {
1770       return;
1771     }
1772     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1773             up ? null : viewport.getHiddenRepSequences(), up);
1774     alignPanel.paintAlignment(true);
1775
1776     /*
1777      * Also move cDNA/protein complement sequences
1778      */
1779     AlignViewportI complement = viewport.getCodingComplement();
1780     if (complement != null)
1781     {
1782       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1783               viewport, complement);
1784       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1785               up ? null : complement.getHiddenRepSequences(), up);
1786       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1787     }
1788   }
1789
1790   synchronized void slideSequences(boolean right, int size)
1791   {
1792     List<SequenceI> sg = new Vector<SequenceI>();
1793     if (viewport.cursorMode)
1794     {
1795       sg.add(viewport.getAlignment().getSequenceAt(
1796               alignPanel.seqPanel.seqCanvas.cursorY));
1797     }
1798     else if (viewport.getSelectionGroup() != null
1799             && viewport.getSelectionGroup().getSize() != viewport
1800                     .getAlignment().getHeight())
1801     {
1802       sg = viewport.getSelectionGroup().getSequences(
1803               viewport.getHiddenRepSequences());
1804     }
1805
1806     if (sg.size() < 1)
1807     {
1808       return;
1809     }
1810
1811     Vector<SequenceI> invertGroup = new Vector();
1812
1813     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1814     {
1815       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1816       {
1817         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1818       }
1819     }
1820
1821     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1822
1823     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1824             .size()]);
1825     for (int i = 0; i < invertGroup.size(); i++)
1826     {
1827       seqs2[i] = invertGroup.elementAt(i);
1828     }
1829
1830     SlideSequencesCommand ssc;
1831     if (right)
1832     {
1833       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1834               size, viewport.getGapCharacter());
1835     }
1836     else
1837     {
1838       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1839               size, viewport.getGapCharacter());
1840     }
1841
1842     int groupAdjustment = 0;
1843     if (ssc.getGapsInsertedBegin() && right)
1844     {
1845       if (viewport.cursorMode)
1846       {
1847         alignPanel.seqPanel.moveCursor(size, 0);
1848       }
1849       else
1850       {
1851         groupAdjustment = size;
1852       }
1853     }
1854     else if (!ssc.getGapsInsertedBegin() && !right)
1855     {
1856       if (viewport.cursorMode)
1857       {
1858         alignPanel.seqPanel.moveCursor(-size, 0);
1859       }
1860       else
1861       {
1862         groupAdjustment = -size;
1863       }
1864     }
1865
1866     if (groupAdjustment != 0)
1867     {
1868       viewport.getSelectionGroup().setStartRes(
1869               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1870       viewport.getSelectionGroup().setEndRes(
1871               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1872     }
1873
1874     boolean appendHistoryItem = false;
1875     Deque<CommandI> historyList = viewport.getHistoryList();
1876     if (historyList != null && historyList.size() > 0
1877             && historyList.peek() instanceof SlideSequencesCommand)
1878     {
1879       appendHistoryItem = ssc
1880               .appendSlideCommand((SlideSequencesCommand) historyList
1881                       .peek());
1882     }
1883
1884     if (!appendHistoryItem)
1885     {
1886       addHistoryItem(ssc);
1887     }
1888
1889     repaint();
1890   }
1891
1892   static StringBuffer copiedSequences;
1893
1894   static Vector copiedHiddenColumns;
1895
1896   protected void copy_actionPerformed()
1897   {
1898     if (viewport.getSelectionGroup() == null)
1899     {
1900       return;
1901     }
1902
1903     SequenceGroup sg = viewport.getSelectionGroup();
1904     copiedSequences = new StringBuffer();
1905     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1906     for (int i = 0; i < sg.getSize(); i++)
1907     {
1908       SequenceI seq = sg.getSequenceAt(i);
1909       int index = viewport.getAlignment().findIndex(seq);
1910       orderedSeqs.put(index, seq);
1911     }
1912
1913     int index = 0, startRes, endRes;
1914     char ch;
1915
1916     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1917     {
1918       copiedHiddenColumns = new Vector();
1919       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1920       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1921       {
1922         copiedHiddenColumns.addElement(new int[] {
1923             region[0] - hiddenOffset, region[1] - hiddenOffset });
1924       }
1925     }
1926     else
1927     {
1928       copiedHiddenColumns = null;
1929     }
1930
1931     for (int i = 0; i < sg.getSize(); i++)
1932     {
1933       SequenceI seq = null;
1934
1935       while (seq == null)
1936       {
1937         if (orderedSeqs.containsKey(index))
1938         {
1939           seq = orderedSeqs.get(index);
1940           index++;
1941           break;
1942         }
1943         else
1944         {
1945           index++;
1946         }
1947       }
1948
1949       // FIND START RES
1950       // Returns residue following index if gap
1951       startRes = seq.findPosition(sg.getStartRes());
1952
1953       // FIND END RES
1954       // Need to find the residue preceeding index if gap
1955       endRes = 0;
1956
1957       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1958       {
1959         ch = seq.getCharAt(j);
1960         if (!jalview.util.Comparison.isGap((ch)))
1961         {
1962           endRes++;
1963         }
1964       }
1965
1966       if (endRes > 0)
1967       {
1968         endRes += seq.getStart() - 1;
1969       }
1970
1971       copiedSequences.append(seq.getName()
1972               + "\t"
1973               + startRes
1974               + "\t"
1975               + endRes
1976               + "\t"
1977               + seq.getSequenceAsString(sg.getStartRes(),
1978                       sg.getEndRes() + 1) + "\n");
1979     }
1980
1981   }
1982
1983   protected void pasteNew_actionPerformed()
1984   {
1985     paste(true);
1986   }
1987
1988   protected void pasteThis_actionPerformed()
1989   {
1990     paste(false);
1991   }
1992
1993   void paste(boolean newAlignment)
1994   {
1995     try
1996     {
1997
1998       if (copiedSequences == null)
1999       {
2000         return;
2001       }
2002
2003       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2004       Vector seqs = new Vector();
2005       while (st.hasMoreElements())
2006       {
2007         String name = st.nextToken();
2008         int start = Integer.parseInt(st.nextToken());
2009         int end = Integer.parseInt(st.nextToken());
2010         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2011       }
2012       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2013       for (int i = 0; i < seqs.size(); i++)
2014       {
2015         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2016       }
2017
2018       if (newAlignment)
2019       {
2020         String newtitle = MessageManager
2021                 .getString("label.copied_sequences");
2022         if (getTitle().startsWith(
2023                 MessageManager.getString("label.copied_sequences")))
2024         {
2025           newtitle = getTitle();
2026         }
2027         else
2028         {
2029           newtitle = newtitle.concat(MessageManager.formatMessage(
2030                   "label.from_msname", new String[] { getTitle() }));
2031         }
2032         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2033                 viewport.applet, newtitle, false);
2034         if (copiedHiddenColumns != null)
2035         {
2036           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2037           {
2038             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2039             af.viewport.hideColumns(region[0], region[1]);
2040           }
2041         }
2042
2043         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2044                 frameHeight);
2045       }
2046       else
2047       {
2048         addSequences(newSeqs);
2049       }
2050
2051     } catch (Exception ex)
2052     {
2053     } // could be anything being pasted in here
2054
2055   }
2056
2057   void addSequences(SequenceI[] seqs)
2058   {
2059     for (int i = 0; i < seqs.length; i++)
2060     {
2061       viewport.getAlignment().addSequence(seqs[i]);
2062     }
2063
2064     // !newAlignment
2065     addHistoryItem(new EditCommand(
2066             MessageManager.getString("label.add_sequences"), Action.PASTE,
2067             seqs, 0, viewport.getAlignment().getWidth(),
2068             viewport.getAlignment()));
2069
2070     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2071     viewport.getAlignment().getWidth();
2072     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2073             .getSequences());
2074
2075   }
2076
2077   protected void cut_actionPerformed()
2078   {
2079     copy_actionPerformed();
2080     delete_actionPerformed();
2081   }
2082
2083   protected void delete_actionPerformed()
2084   {
2085
2086     SequenceGroup sg = viewport.getSelectionGroup();
2087     if (sg == null)
2088     {
2089       return;
2090     }
2091
2092     Vector seqs = new Vector();
2093     SequenceI seq;
2094     for (int i = 0; i < sg.getSize(); i++)
2095     {
2096       seq = sg.getSequenceAt(i);
2097       seqs.addElement(seq);
2098     }
2099
2100     /*
2101      * If the cut affects all sequences, warn, remove highlighted columns
2102      */
2103     if (sg.getSize() == viewport.getAlignment().getHeight())
2104     {
2105       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2106               .getAlignment().getWidth()) ? true : false;
2107       if (isEntireAlignWidth)
2108       {
2109         String title = MessageManager.getString("label.delete_all");
2110         Panel infoPanel = new Panel();
2111         infoPanel.setLayout(new FlowLayout());
2112         infoPanel
2113                 .add(new Label(MessageManager.getString("warn.delete_all")));
2114
2115         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2116         dialog.setMainPanel(infoPanel);
2117         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2118         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2119         dialog.setVisible(true);
2120
2121         if (!dialog.accept)
2122         {
2123           return;
2124         }
2125       }
2126       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2127               sg.getEndRes() + 1);
2128     }
2129
2130     SequenceI[] cut = new SequenceI[seqs.size()];
2131     for (int i = 0; i < seqs.size(); i++)
2132     {
2133       cut[i] = (SequenceI) seqs.elementAt(i);
2134     }
2135
2136     /*
2137      * //ADD HISTORY ITEM
2138      */
2139     addHistoryItem(new EditCommand(
2140             MessageManager.getString("label.cut_sequences"), Action.CUT,
2141             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2142             viewport.getAlignment()));
2143
2144     viewport.setSelectionGroup(null);
2145     viewport.getAlignment().deleteGroup(sg);
2146
2147     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2148             .getSequences());
2149
2150     if (viewport.getAlignment().getHeight() < 1)
2151     {
2152       this.setVisible(false);
2153     }
2154     viewport.sendSelection();
2155   }
2156
2157   /**
2158    * group consensus toggled
2159    *
2160    */
2161   protected void showGroupConsensus_actionPerformed()
2162   {
2163     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2164     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2165
2166   }
2167
2168   /**
2169    * group conservation toggled.
2170    */
2171   protected void showGroupConservation_actionPerformed()
2172   {
2173     viewport.setShowGroupConservation(showGroupConservation.getState());
2174     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2175   }
2176
2177   /*
2178    * (non-Javadoc)
2179    *
2180    * @see
2181    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2182    * .event.ActionEvent)
2183    */
2184   protected void showConsensusHistogram_actionPerformed()
2185   {
2186     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2187     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188   }
2189
2190   /*
2191    * (non-Javadoc)
2192    *
2193    * @see
2194    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2195    * .event.ActionEvent)
2196    */
2197   protected void showSequenceLogo_actionPerformed()
2198   {
2199     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2200     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2201   }
2202
2203   protected void normSequenceLogo_actionPerformed()
2204   {
2205     showSequenceLogo.setState(true);
2206     viewport.setShowSequenceLogo(true);
2207     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2208     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2209   }
2210
2211   protected void applyAutoAnnotationSettings_actionPerformed()
2212   {
2213     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2214   }
2215
2216   protected void makeGrpsFromSelection_actionPerformed()
2217   {
2218     if (avc.makeGroupsFromSelection())
2219     {
2220       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2221       alignPanel.updateAnnotation();
2222       alignPanel.paintAlignment(true);
2223     }
2224   }
2225
2226   protected void createGroup_actionPerformed()
2227   {
2228     avc.createGroup();
2229   }
2230
2231   protected void unGroup_actionPerformed()
2232   {
2233     if (avc.unGroup())
2234     {
2235       alignPanel.alignmentChanged();
2236     }
2237   }
2238
2239   protected void deleteGroups_actionPerformed()
2240   {
2241     if (avc.deleteGroups())
2242     {
2243       alignPanel.alignmentChanged();
2244     }
2245   }
2246
2247   public void selectAllSequenceMenuItem_actionPerformed()
2248   {
2249     SequenceGroup sg = new SequenceGroup();
2250     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2251     {
2252       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2253     }
2254     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2255     viewport.setSelectionGroup(sg);
2256     // JAL-2034 - should delegate to
2257     // alignPanel to decide if overview needs
2258     // updating.
2259     alignPanel.paintAlignment(false);
2260     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2261     viewport.sendSelection();
2262   }
2263
2264   public void deselectAllSequenceMenuItem_actionPerformed()
2265   {
2266     if (viewport.cursorMode)
2267     {
2268       alignPanel.seqPanel.keyboardNo1 = null;
2269       alignPanel.seqPanel.keyboardNo2 = null;
2270     }
2271     viewport.setSelectionGroup(null);
2272     viewport.getColumnSelection().clear();
2273     viewport.setSelectionGroup(null);
2274     alignPanel.idPanel.idCanvas.searchResults = null;
2275     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2276     // JAL-2034 - should delegate to
2277     // alignPanel to decide if overview needs
2278     // updating.
2279     alignPanel.paintAlignment(false);
2280     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281     viewport.sendSelection();
2282   }
2283
2284   public void invertSequenceMenuItem_actionPerformed()
2285   {
2286     SequenceGroup sg = viewport.getSelectionGroup();
2287     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2288     {
2289       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2290     }
2291
2292     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2293     viewport.sendSelection();
2294   }
2295
2296   public void invertColSel_actionPerformed()
2297   {
2298     viewport.invertColumnSelection();
2299     alignPanel.paintAlignment(true);
2300     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2301     viewport.sendSelection();
2302   }
2303
2304   void trimAlignment(boolean trimLeft)
2305   {
2306     AlignmentI al = viewport.getAlignment();
2307     ViewportRanges ranges = viewport.getRanges();
2308     ColumnSelection colSel = viewport.getColumnSelection();
2309     int column;
2310
2311     if (!colSel.isEmpty())
2312     {
2313       if (trimLeft)
2314       {
2315         column = colSel.getMin();
2316       }
2317       else
2318       {
2319         column = colSel.getMax();
2320       }
2321
2322       SequenceI[] seqs;
2323       if (viewport.getSelectionGroup() != null)
2324       {
2325         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2326                 viewport.getHiddenRepSequences());
2327       }
2328       else
2329       {
2330         seqs = al.getSequencesArray();
2331       }
2332
2333       TrimRegionCommand trimRegion;
2334       if (trimLeft)
2335       {
2336         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2337                 column, al);
2338         ranges.setStartRes(0);
2339       }
2340       else
2341       {
2342         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2343                 column, al);
2344       }
2345
2346       statusBar.setText(MessageManager.formatMessage(
2347               "label.removed_columns",
2348               new String[] { Integer.valueOf(trimRegion.getSize())
2349                       .toString() }));
2350       addHistoryItem(trimRegion);
2351
2352       for (SequenceGroup sg : al.getGroups())
2353       {
2354         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2355                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2356         {
2357           al.deleteGroup(sg);
2358         }
2359       }
2360
2361       viewport.firePropertyChange("alignment", null, al.getSequences());
2362     }
2363   }
2364
2365   public void removeGappedColumnMenuItem_actionPerformed()
2366   {
2367     AlignmentI al = viewport.getAlignment();
2368     ViewportRanges ranges = viewport.getRanges();
2369     int start = 0;
2370     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2371
2372     SequenceI[] seqs;
2373     if (viewport.getSelectionGroup() != null)
2374     {
2375       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2376               viewport.getHiddenRepSequences());
2377       start = viewport.getSelectionGroup().getStartRes();
2378       end = viewport.getSelectionGroup().getEndRes();
2379     }
2380     else
2381     {
2382       seqs = viewport.getAlignment().getSequencesArray();
2383     }
2384
2385     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2386             "Remove Gapped Columns", seqs, start, end,
2387             viewport.getAlignment());
2388
2389     addHistoryItem(removeGapCols);
2390
2391     statusBar.setText(MessageManager.formatMessage(
2392             "label.removed_empty_columns",
2393             new String[] { Integer.valueOf(removeGapCols.getSize())
2394                     .toString() }));
2395
2396     // This is to maintain viewport position on first residue
2397     // of first sequence
2398     SequenceI seq = al.getSequenceAt(0);
2399     int startRes = seq.findPosition(ranges.getStartRes());
2400     // ShiftList shifts;
2401     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2402     // edit.alColumnChanges=shifts.getInverse();
2403     // if (viewport.hasHiddenColumns)
2404     // viewport.getColumnSelection().compensateForEdits(shifts);
2405     ranges.setStartRes(seq.findIndex(startRes) - 1);
2406     viewport.firePropertyChange("alignment", null, al.getSequences());
2407
2408   }
2409
2410   public void removeAllGapsMenuItem_actionPerformed()
2411   {
2412     AlignmentI al = viewport.getAlignment();
2413     ViewportRanges ranges = viewport.getRanges();
2414     int start = 0;
2415     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2416
2417     SequenceI[] seqs;
2418     if (viewport.getSelectionGroup() != null)
2419     {
2420       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2421               viewport.getHiddenRepSequences());
2422       start = viewport.getSelectionGroup().getStartRes();
2423       end = viewport.getSelectionGroup().getEndRes();
2424     }
2425     else
2426     {
2427       seqs = viewport.getAlignment().getSequencesArray();
2428     }
2429
2430     // This is to maintain viewport position on first residue
2431     // of first sequence
2432     SequenceI seq = al.getSequenceAt(0);
2433     int startRes = seq.findPosition(ranges.getStartRes());
2434
2435     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2436             al));
2437
2438     ranges.setStartRes(seq.findIndex(startRes) - 1);
2439
2440     viewport.firePropertyChange("alignment", null, al.getSequences());
2441
2442   }
2443
2444   public void findMenuItem_actionPerformed()
2445   {
2446     new Finder(alignPanel);
2447   }
2448
2449   /**
2450    * create a new view derived from the current view
2451    *
2452    * @param viewtitle
2453    * @return frame for the new view
2454    */
2455   public AlignFrame newView(String viewtitle)
2456   {
2457     AlignmentI newal;
2458     if (viewport.hasHiddenRows())
2459     {
2460       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2461               .getFullAlignment().getSequencesArray());
2462     }
2463     else
2464     {
2465       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2466     }
2467
2468     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2469     {
2470       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2471       {
2472         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2473         {
2474           newal.addAnnotation(viewport.getAlignment()
2475                   .getAlignmentAnnotation()[i]);
2476         }
2477       }
2478     }
2479
2480     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2481
2482     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2483     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2484     PaintRefresher.Register(newaf.alignPanel,
2485             newaf.alignPanel.av.getSequenceSetId());
2486
2487     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2488             newaf.alignPanel.av.getSequenceSetId());
2489     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2490             newaf.alignPanel.av.getSequenceSetId());
2491
2492     Vector comps = (Vector) PaintRefresher.components.get(viewport
2493             .getSequenceSetId());
2494     int viewSize = -1;
2495     for (int i = 0; i < comps.size(); i++)
2496     {
2497       if (comps.elementAt(i) instanceof AlignmentPanel)
2498       {
2499         viewSize++;
2500       }
2501     }
2502
2503     String title = new String(this.getTitle());
2504     if (viewtitle != null)
2505     {
2506       title = viewtitle + " ( " + title + ")";
2507     }
2508     else
2509     {
2510       if (title.indexOf("(View") > -1)
2511       {
2512         title = title.substring(0, title.indexOf("(View"));
2513       }
2514       title += "(View " + viewSize + ")";
2515     }
2516
2517     newaf.setTitle(title.toString());
2518
2519     newaf.viewport.setHistoryList(viewport.getHistoryList());
2520     newaf.viewport.setRedoList(viewport.getRedoList());
2521     return newaf;
2522   }
2523
2524   /**
2525    *
2526    * @return list of feature groups on the view
2527    */
2528   public String[] getFeatureGroups()
2529   {
2530     FeatureRenderer fr = null;
2531     if (alignPanel != null
2532             && (fr = alignPanel.getFeatureRenderer()) != null)
2533     {
2534       List<String> gps = fr.getFeatureGroups();
2535       String[] _gps = gps.toArray(new String[gps.size()]);
2536       return _gps;
2537     }
2538     return null;
2539   }
2540
2541   /**
2542    * get sequence feature groups that are hidden or shown
2543    *
2544    * @param visible
2545    *          true is visible
2546    * @return list
2547    */
2548   public String[] getFeatureGroupsOfState(boolean visible)
2549   {
2550     FeatureRenderer fr = null;
2551     if (alignPanel != null
2552             && (fr = alignPanel.getFeatureRenderer()) != null)
2553     {
2554       List<String> gps = fr.getGroups(visible);
2555       String[] _gps = gps.toArray(new String[gps.size()]);
2556       return _gps;
2557     }
2558     return null;
2559   }
2560
2561   /**
2562    * Change the display state for the given feature groups
2563    *
2564    * @param groups
2565    *          list of group strings
2566    * @param state
2567    *          visible or invisible
2568    */
2569   public void setFeatureGroupState(String[] groups, boolean state)
2570   {
2571     FeatureRenderer fr = null;
2572     this.sequenceFeatures.setState(true);
2573     viewport.setShowSequenceFeatures(true);
2574     if (alignPanel != null
2575             && (fr = alignPanel.getFeatureRenderer()) != null)
2576     {
2577
2578       fr.setGroupVisibility(Arrays.asList(groups), state);
2579       alignPanel.seqPanel.seqCanvas.repaint();
2580       if (alignPanel.overviewPanel != null)
2581       {
2582         alignPanel.overviewPanel.updateOverviewImage();
2583       }
2584     }
2585   }
2586
2587   public void seqLimits_itemStateChanged()
2588   {
2589     viewport.setShowJVSuffix(seqLimits.getState());
2590     alignPanel.fontChanged();
2591     alignPanel.paintAlignment(true);
2592   }
2593
2594   protected void colourTextMenuItem_actionPerformed()
2595   {
2596     viewport.setColourText(colourTextMenuItem.getState());
2597     alignPanel.paintAlignment(true);
2598   }
2599
2600   protected void displayNonconservedMenuItem_actionPerformed()
2601   {
2602     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2603     alignPanel.paintAlignment(true);
2604   }
2605
2606   protected void wrapMenuItem_actionPerformed()
2607   {
2608     viewport.setWrapAlignment(wrapMenuItem.getState());
2609     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2610     scaleAbove.setEnabled(wrapMenuItem.getState());
2611     scaleLeft.setEnabled(wrapMenuItem.getState());
2612     scaleRight.setEnabled(wrapMenuItem.getState());
2613     alignPanel.paintAlignment(true);
2614   }
2615
2616   public void overviewMenuItem_actionPerformed()
2617   {
2618     if (alignPanel.overviewPanel != null)
2619     {
2620       return;
2621     }
2622
2623     Frame frame = new Frame();
2624     OverviewPanel overview = new OverviewPanel(alignPanel);
2625     frame.add(overview);
2626     // +50 must allow for applet frame window
2627     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2628             "label.overview_params", new String[] { this.getTitle() }),
2629             overview.getPreferredSize().width,
2630             overview.getPreferredSize().height + 50);
2631
2632     frame.pack();
2633     final AlignmentPanel ap = alignPanel;
2634     frame.addWindowListener(new WindowAdapter()
2635     {
2636       @Override
2637       public void windowClosing(WindowEvent e)
2638       {
2639         if (ap != null)
2640         {
2641           ap.setOverviewPanel(null);
2642         }
2643       };
2644     });
2645
2646     alignPanel.setOverviewPanel(overview);
2647
2648   }
2649
2650   @Override
2651   public void changeColour(ColourSchemeI cs)
2652   {
2653     viewport.setGlobalColourScheme(cs);
2654
2655     alignPanel.paintAlignment(true);
2656   }
2657
2658   protected void modifyPID_actionPerformed()
2659   {
2660     if (viewport.getAbovePIDThreshold()
2661             && viewport.getGlobalColourScheme() != null)
2662     {
2663       SliderPanel.setPIDSliderSource(alignPanel,
2664               viewport.getResidueShading(), alignPanel.getViewName());
2665       SliderPanel.showPIDSlider();
2666     }
2667   }
2668
2669   protected void modifyConservation_actionPerformed()
2670   {
2671     if (viewport.getConservationSelected()
2672             && viewport.getGlobalColourScheme() != null)
2673     {
2674       SliderPanel.setConservationSlider(alignPanel,
2675               viewport.getResidueShading(), alignPanel.getViewName());
2676       SliderPanel.showConservationSlider();
2677     }
2678   }
2679
2680   protected void conservationMenuItem_actionPerformed()
2681   {
2682     boolean selected = conservationMenuItem.getState();
2683     modifyConservation.setEnabled(selected);
2684     viewport.setConservationSelected(selected);
2685
2686     // viewport.setAbovePIDThreshold(false);
2687     // abovePIDThreshold.setState(false);
2688
2689     changeColour(viewport.getGlobalColourScheme());
2690
2691     if (selected)
2692     {
2693       modifyConservation_actionPerformed();
2694     }
2695     else
2696     {
2697       SliderPanel.hideConservationSlider();
2698     }
2699   }
2700
2701   public void abovePIDThreshold_actionPerformed()
2702   {
2703     boolean selected = abovePIDThreshold.getState();
2704     modifyPID.setEnabled(selected);
2705     viewport.setAbovePIDThreshold(selected);
2706     // conservationMenuItem.setState(false);
2707     // viewport.setConservationSelected(false);
2708
2709     changeColour(viewport.getGlobalColourScheme());
2710
2711     if (selected)
2712     {
2713       modifyPID_actionPerformed();
2714     }
2715     else
2716     {
2717       SliderPanel.hidePIDSlider();
2718     }
2719   }
2720
2721   public void sortPairwiseMenuItem_actionPerformed()
2722   {
2723     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2724     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2725             .getAlignment().getSequenceAt(0));
2726
2727     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2728             viewport.getAlignment()));
2729     alignPanel.paintAlignment(true);
2730   }
2731
2732   public void sortIDMenuItem_actionPerformed()
2733   {
2734     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2735     AlignmentSorter.sortByID(viewport.getAlignment());
2736     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2737             viewport.getAlignment()));
2738     alignPanel.paintAlignment(true);
2739   }
2740
2741   public void sortLengthMenuItem_actionPerformed()
2742   {
2743     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2744     AlignmentSorter.sortByLength(viewport.getAlignment());
2745     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2746             viewport.getAlignment()));
2747     alignPanel.paintAlignment(true);
2748   }
2749
2750   public void sortGroupMenuItem_actionPerformed()
2751   {
2752     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2753     AlignmentSorter.sortByGroup(viewport.getAlignment());
2754     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2755             viewport.getAlignment()));
2756     alignPanel.paintAlignment(true);
2757
2758   }
2759
2760   public void removeRedundancyMenuItem_actionPerformed()
2761   {
2762     new RedundancyPanel(alignPanel);
2763   }
2764
2765   public void pairwiseAlignmentMenuItem_actionPerformed()
2766   {
2767     if (viewport.getSelectionGroup() != null
2768             && viewport.getSelectionGroup().getSize() > 1)
2769     {
2770       Frame frame = new Frame();
2771       frame.add(new PairwiseAlignPanel(alignPanel));
2772       jalview.bin.JalviewLite.addFrame(frame,
2773               MessageManager.getString("action.pairwise_alignment"), 600,
2774               500);
2775     }
2776   }
2777
2778   public void PCAMenuItem_actionPerformed()
2779   {
2780     // are the sequences aligned?
2781     if (!viewport.getAlignment().isAligned(false))
2782     {
2783       SequenceI current;
2784       int Width = viewport.getAlignment().getWidth();
2785
2786       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2787       {
2788         current = viewport.getAlignment().getSequenceAt(i);
2789
2790         if (current.getLength() < Width)
2791         {
2792           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2793         }
2794       }
2795       alignPanel.paintAlignment(true);
2796     }
2797
2798     if ((viewport.getSelectionGroup() != null
2799             && viewport.getSelectionGroup().getSize() < 4 && viewport
2800             .getSelectionGroup().getSize() > 0)
2801             || viewport.getAlignment().getHeight() < 4)
2802     {
2803       return;
2804     }
2805
2806     try
2807     {
2808       new PCAPanel(viewport);
2809     } catch (java.lang.OutOfMemoryError ex)
2810     {
2811     }
2812
2813   }
2814
2815   public void averageDistanceTreeMenuItem_actionPerformed()
2816   {
2817     NewTreePanel(TreeBuilder.AVERAGE_DISTANCE, "PID",
2818             "Average distance tree using PID");
2819   }
2820
2821   public void neighbourTreeMenuItem_actionPerformed()
2822   {
2823     NewTreePanel(TreeBuilder.NEIGHBOUR_JOINING, "PID",
2824             "Neighbour joining tree using PID");
2825   }
2826
2827   protected void njTreeBlosumMenuItem_actionPerformed()
2828   {
2829     NewTreePanel(TreeBuilder.NEIGHBOUR_JOINING, "BL",
2830             "Neighbour joining tree using BLOSUM62");
2831   }
2832
2833   protected void avTreeBlosumMenuItem_actionPerformed()
2834   {
2835     NewTreePanel(TreeBuilder.AVERAGE_DISTANCE, "BL",
2836             "Average distance tree using BLOSUM62");
2837   }
2838
2839   void NewTreePanel(String type, String pwType, String title)
2840   {
2841     // are the sequences aligned?
2842     if (!viewport.getAlignment().isAligned(false))
2843     {
2844       SequenceI current;
2845       int Width = viewport.getAlignment().getWidth();
2846
2847       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2848       {
2849         current = viewport.getAlignment().getSequenceAt(i);
2850
2851         if (current.getLength() < Width)
2852         {
2853           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2854         }
2855       }
2856       alignPanel.paintAlignment(true);
2857
2858     }
2859
2860     if ((viewport.getSelectionGroup() != null && viewport
2861             .getSelectionGroup().getSize() > 1)
2862             || (viewport.getAlignment().getHeight() > 1))
2863     {
2864       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2865
2866       addTreeMenuItem(tp, title);
2867
2868       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2869     }
2870   }
2871
2872   void loadTree_actionPerformed()
2873   {
2874     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2875     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2876     cap.setTreeImport();
2877     Frame frame = new Frame();
2878     frame.add(cap);
2879     jalview.bin.JalviewLite.addFrame(frame,
2880             MessageManager.getString("label.paste_newick_file"), 400, 300);
2881   }
2882
2883   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2884   {
2885     TreePanel tp = new TreePanel(alignPanel, treeFile,
2886             MessageManager.getString("label.load_tree_from_file"), tree);
2887     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2888     addTreeMenuItem(tp, treeFile);
2889   }
2890
2891   /**
2892    * sort the alignment using the given treePanel
2893    *
2894    * @param treePanel
2895    *          tree used to sort view
2896    * @param title
2897    *          string used for undo event name
2898    */
2899   public void sortByTree(TreePanel treePanel, String title)
2900   {
2901     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2902     AlignmentSorter
2903             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2904     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2905     // HistoryItem.SORT));
2906     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2907             "label.order_by_params", new String[] { title }), oldOrder,
2908             viewport.getAlignment()));
2909     alignPanel.paintAlignment(true);
2910   }
2911
2912   /**
2913    * Do any automatic reordering of the alignment and add the necessary bits to
2914    * the menu structure for the new tree
2915    *
2916    * @param treePanel
2917    * @param title
2918    */
2919   protected void addTreeMenuItem(final TreePanel treePanel,
2920           final String title)
2921   {
2922     final MenuItem item = new MenuItem(title);
2923     sortByTreeMenu.add(item);
2924     item.addActionListener(new java.awt.event.ActionListener()
2925     {
2926       @Override
2927       public void actionPerformed(ActionEvent evt)
2928       {
2929         sortByTree(treePanel, title); // treePanel.getTitle());
2930       }
2931     });
2932
2933     treePanel.addWindowListener(new WindowAdapter()
2934     {
2935       @Override
2936       public void windowOpened(WindowEvent e)
2937       {
2938         if (viewport.sortByTree)
2939         {
2940           sortByTree(treePanel, title);
2941         }
2942         super.windowOpened(e);
2943       }
2944
2945       @Override
2946       public void windowClosing(WindowEvent e)
2947       {
2948         sortByTreeMenu.remove(item);
2949       };
2950     });
2951   }
2952
2953   public boolean sortBy(AlignmentOrder alorder, String undoname)
2954   {
2955     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2956     if (viewport.applet.debug)
2957     {
2958       System.err.println("Sorting " + alorder.getOrder().size()
2959               + " in alignment '" + getTitle() + "'");
2960     }
2961     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2962     if (undoname != null)
2963     {
2964       addHistoryItem(new OrderCommand(undoname, oldOrder,
2965               viewport.getAlignment()));
2966     }
2967     alignPanel.paintAlignment(true);
2968     return true;
2969   }
2970
2971   protected void documentation_actionPerformed()
2972   {
2973     alignPanel.av.applet.openJalviewHelpUrl();
2974   }
2975
2976   protected void about_actionPerformed()
2977   {
2978
2979     class AboutPanel extends Canvas
2980     {
2981       String version;
2982
2983       String builddate;
2984
2985       public AboutPanel(String version, String builddate)
2986       {
2987         this.version = version;
2988         this.builddate = builddate;
2989       }
2990
2991       @Override
2992       public void paint(Graphics g)
2993       {
2994         g.setColor(Color.white);
2995         g.fillRect(0, 0, getSize().width, getSize().height);
2996         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2997         FontMetrics fm = g.getFontMetrics();
2998         int fh = fm.getHeight();
2999         int y = 5, x = 7;
3000         g.setColor(Color.black);
3001         // TODO: update this text for each release or centrally store it for
3002         // lite and application
3003         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3004         g.drawString(MessageManager.formatMessage(
3005                 "label.jalviewLite_release", new String[] { version }), x,
3006                 y += fh);
3007         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3008         g.drawString(MessageManager.formatMessage(
3009                 "label.jaview_build_date", new String[] { builddate }), x,
3010                 y += fh);
3011         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3012         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3013                 x, y += fh * 1.5);
3014         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3015                 x + 50, y += fh + 8);
3016         g.drawString(
3017                 MessageManager.getString("label.jalview_dev_managers"), x,
3018                 y += fh);
3019         g.drawString(MessageManager
3020                 .getString("label.jalview_distribution_lists"), x, y += fh);
3021         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3022                 x, y += fh + 8);
3023         g.drawString(
3024                 MessageManager.getString("label.jalview_cite_1_authors"),
3025                 x, y += fh);
3026         g.drawString(
3027                 MessageManager.getString("label.jalview_cite_1_title"), x,
3028                 y += fh);
3029         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3030                 x, y += fh);
3031       }
3032     }
3033
3034     Frame frame = new Frame();
3035     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3036             .getBuildDate()));
3037     jalview.bin.JalviewLite.addFrame(frame,
3038             MessageManager.getString("label.jalview"), 580, 220);
3039
3040   }
3041
3042   public void showURL(String url, String target)
3043   {
3044     if (viewport.applet == null)
3045     {
3046       System.out.println("Not running as applet - no browser available.");
3047     }
3048     else
3049     {
3050       viewport.applet.showURL(url, target);
3051     }
3052   }
3053
3054   // ////////////////////////////////////////////////////////////////////////////////
3055   // JBuilder Graphics here
3056
3057   MenuBar alignFrameMenuBar = new MenuBar();
3058
3059   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3060
3061   MenuItem loadApplication = new MenuItem(
3062           MessageManager.getString("label.view_full_application"));
3063
3064   MenuItem loadTree = new MenuItem(
3065           MessageManager.getString("label.load_associated_tree"));
3066
3067   MenuItem loadAnnotations = new MenuItem(
3068           MessageManager.getString("label.load_features_annotations"));
3069
3070   MenuItem outputFeatures = new MenuItem(
3071           MessageManager.getString("label.export_features"));
3072
3073   MenuItem outputAnnotations = new MenuItem(
3074           MessageManager.getString("label.export_annotations"));
3075
3076   MenuItem closeMenuItem = new MenuItem(
3077           MessageManager.getString("action.close"));
3078
3079   MenuItem selectAllSequenceMenuItem = new MenuItem(
3080           MessageManager.getString("action.select_all"));
3081
3082   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3083           MessageManager.getString("action.deselect_all"));
3084
3085   MenuItem invertSequenceMenuItem = new MenuItem(
3086           MessageManager.getString("action.invert_selection"));
3087
3088   MenuItem remove2LeftMenuItem = new MenuItem();
3089
3090   MenuItem remove2RightMenuItem = new MenuItem();
3091
3092   MenuItem removeGappedColumnMenuItem = new MenuItem();
3093
3094   MenuItem removeAllGapsMenuItem = new MenuItem();
3095
3096   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3097
3098   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3099
3100   MenuItem sortPairwiseMenuItem = new MenuItem();
3101
3102   MenuItem sortIDMenuItem = new MenuItem();
3103
3104   MenuItem sortLengthMenuItem = new MenuItem();
3105
3106   MenuItem sortGroupMenuItem = new MenuItem();
3107
3108   MenuItem removeRedundancyMenuItem = new MenuItem();
3109
3110   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3111
3112   MenuItem PCAMenuItem = new MenuItem();
3113
3114   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3115
3116   MenuItem neighbourTreeMenuItem = new MenuItem();
3117
3118   BorderLayout borderLayout1 = new BorderLayout();
3119
3120   public Label statusBar = new Label();
3121
3122   MenuItem clustalColour = new MenuItem();
3123
3124   MenuItem zappoColour = new MenuItem();
3125
3126   MenuItem taylorColour = new MenuItem();
3127
3128   MenuItem hydrophobicityColour = new MenuItem();
3129
3130   MenuItem helixColour = new MenuItem();
3131
3132   MenuItem strandColour = new MenuItem();
3133
3134   MenuItem turnColour = new MenuItem();
3135
3136   MenuItem buriedColour = new MenuItem();
3137
3138   MenuItem purinePyrimidineColour = new MenuItem();
3139
3140   // MenuItem RNAInteractionColour = new MenuItem();
3141
3142   MenuItem RNAHelixColour = new MenuItem();
3143
3144   MenuItem userDefinedColour = new MenuItem();
3145
3146   MenuItem PIDColour = new MenuItem();
3147
3148   MenuItem BLOSUM62Colour = new MenuItem();
3149
3150   MenuItem tcoffeeColour = new MenuItem();
3151
3152   MenuItem njTreeBlosumMenuItem = new MenuItem();
3153
3154   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3155
3156   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3157
3158   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3159
3160   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3161
3162   MenuItem alProperties = new MenuItem(
3163           MessageManager.getString("label.alignment_props"));
3164
3165   MenuItem overviewMenuItem = new MenuItem();
3166
3167   MenuItem undoMenuItem = new MenuItem();
3168
3169   MenuItem redoMenuItem = new MenuItem();
3170
3171   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3172
3173   MenuItem noColourmenuItem = new MenuItem();
3174
3175   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3176
3177   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3178
3179   MenuItem findMenuItem = new MenuItem();
3180
3181   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3182
3183   MenuItem nucleotideColour = new MenuItem();
3184
3185   MenuItem deleteGroups = new MenuItem();
3186
3187   MenuItem grpsFromSelection = new MenuItem();
3188
3189   MenuItem createGroup = new MenuItem();
3190
3191   MenuItem unGroup = new MenuItem();
3192
3193   MenuItem delete = new MenuItem();
3194
3195   MenuItem copy = new MenuItem();
3196
3197   MenuItem cut = new MenuItem();
3198
3199   Menu pasteMenu = new Menu();
3200
3201   MenuItem pasteNew = new MenuItem();
3202
3203   MenuItem pasteThis = new MenuItem();
3204
3205   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3206
3207   MenuItem font = new MenuItem();
3208
3209   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3214
3215   MenuItem modifyPID = new MenuItem();
3216
3217   MenuItem modifyConservation = new MenuItem();
3218
3219   CheckboxMenuItem autoCalculate = null;
3220
3221   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3222           "Sort Alignment With New Tree", true);
3223
3224   Menu sortByTreeMenu = new Menu();
3225
3226   MenuItem inputText = new MenuItem();
3227
3228   MenuItem documentation = new MenuItem();
3229
3230   MenuItem about = new MenuItem();
3231
3232   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3233
3234   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3235
3236   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3237
3238   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3249
3250   /**
3251    * Initialise menus and other items
3252    *
3253    * @throws Exception
3254    */
3255   private void jbInit() throws Exception
3256   {
3257     setMenuBar(alignFrameMenuBar);
3258
3259     /*
3260      * Configure File menu items and actions
3261      */
3262     inputText
3263             .setLabel(MessageManager.getString("label.input_from_textbox"));
3264     inputText.addActionListener(this);
3265     Menu outputTextboxMenu = new Menu(
3266             MessageManager.getString("label.out_to_textbox"));
3267     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3268     {
3269       MenuItem item = new MenuItem(ff);
3270
3271       item.addActionListener(new java.awt.event.ActionListener()
3272       {
3273         @Override
3274         public void actionPerformed(ActionEvent e)
3275         {
3276           outputText_actionPerformed(e);
3277         }
3278       });
3279
3280       outputTextboxMenu.add(item);
3281     }
3282     closeMenuItem.addActionListener(this);
3283     loadApplication.addActionListener(this);
3284     loadTree.addActionListener(this);
3285     loadAnnotations.addActionListener(this);
3286     outputFeatures.addActionListener(this);
3287     outputAnnotations.addActionListener(this);
3288
3289     /*
3290      * Configure Edit menu items and actions
3291      */
3292     undoMenuItem.setEnabled(false);
3293     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3294     undoMenuItem.addActionListener(this);
3295     redoMenuItem.setEnabled(false);
3296     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3297     redoMenuItem.addActionListener(this);
3298     copy.setLabel(MessageManager.getString("action.copy"));
3299     copy.addActionListener(this);
3300     cut.setLabel(MessageManager.getString("action.cut"));
3301     cut.addActionListener(this);
3302     delete.setLabel(MessageManager.getString("action.delete"));
3303     delete.addActionListener(this);
3304     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3305     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3306     pasteNew.addActionListener(this);
3307     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3308     pasteThis.addActionListener(this);
3309     remove2LeftMenuItem.setLabel(MessageManager
3310             .getString("action.remove_left"));
3311     remove2LeftMenuItem.addActionListener(this);
3312     remove2RightMenuItem.setLabel(MessageManager
3313             .getString("action.remove_right"));
3314     remove2RightMenuItem.addActionListener(this);
3315     removeGappedColumnMenuItem.setLabel(MessageManager
3316             .getString("action.remove_empty_columns"));
3317     removeGappedColumnMenuItem.addActionListener(this);
3318     removeAllGapsMenuItem.setLabel(MessageManager
3319             .getString("action.remove_all_gaps"));
3320     removeAllGapsMenuItem.addActionListener(this);
3321     removeRedundancyMenuItem.setLabel(MessageManager
3322             .getString("action.remove_redundancy"));
3323     removeRedundancyMenuItem.addActionListener(this);
3324
3325     /*
3326      * Configure Select menu items and actions
3327      */
3328     findMenuItem.setLabel(MessageManager.getString("action.find"));
3329     findMenuItem.addActionListener(this);
3330     selectAllSequenceMenuItem.addActionListener(this);
3331     deselectAllSequenceMenuItem.addActionListener(this);
3332     invertSequenceMenuItem.setLabel(MessageManager
3333             .getString("action.invert_sequence_selection"));
3334     invertSequenceMenuItem.addActionListener(this);
3335     invertColSel.setLabel(MessageManager
3336             .getString("action.invert_column_selection"));
3337     invertColSel.addActionListener(this);
3338     deleteGroups.setLabel(MessageManager
3339             .getString("action.undefine_groups"));
3340     deleteGroups.addActionListener(this);
3341     grpsFromSelection.setLabel(MessageManager
3342             .getString("action.make_groups_selection"));
3343     grpsFromSelection.addActionListener(this);
3344     createGroup.setLabel(MessageManager.getString("action.create_group"));
3345     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3346     annotationColumnSelection.setLabel(MessageManager
3347             .getString("action.select_by_annotation"));
3348     annotationColumnSelection.addActionListener(this);
3349
3350     /*
3351      * Configure View menu items and actions
3352      */
3353     newView.setLabel(MessageManager.getString("action.new_view"));
3354     newView.addActionListener(this);
3355     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3356     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3357     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3358     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3359     hideColumns
3360             .setLabel(MessageManager.getString("label.selected_columns"));
3361     hideSequences.setLabel(MessageManager
3362             .getString("label.selected_sequences"));
3363     hideAllButSelection.setLabel(MessageManager
3364             .getString("label.all_but_selected_region"));
3365     hideAllSelection.setLabel(MessageManager
3366             .getString("label.selected_region"));
3367     showAllHidden.setLabel(MessageManager
3368             .getString("label.all_sequences_columns"));
3369     showColumns.addActionListener(this);
3370     showSeqs.addActionListener(this);
3371     hideColumns.addActionListener(this);
3372     hideSequences.addActionListener(this);
3373     hideAllButSelection.addActionListener(this);
3374     hideAllSelection.addActionListener(this);
3375     showAllHidden.addActionListener(this);
3376     featureSettings.setLabel(MessageManager
3377             .getString("action.feature_settings"));
3378     featureSettings.addActionListener(this);
3379     sequenceFeatures.setLabel(MessageManager
3380             .getString("label.show_sequence_features"));
3381     sequenceFeatures.addItemListener(this);
3382     sequenceFeatures.setState(false);
3383     followMouseOverFlag.setLabel(MessageManager
3384             .getString("label.automatic_scrolling"));
3385     followMouseOverFlag.addItemListener(this);
3386     alProperties.addActionListener(this);
3387     overviewMenuItem.setLabel(MessageManager
3388             .getString("label.overview_window"));
3389     overviewMenuItem.addActionListener(this);
3390
3391     /*
3392      * Configure Annotations menu items and actions
3393      */
3394     annotationPanelMenuItem.setLabel(MessageManager
3395             .getString("label.show_annotations"));
3396     annotationPanelMenuItem.addItemListener(this);
3397     showGroupConsensus.setLabel(MessageManager
3398             .getString("label.group_consensus"));
3399     showGroupConservation.setLabel(MessageManager
3400             .getString("label.group_conservation"));
3401     showConsensusHistogram.setLabel(MessageManager
3402             .getString("label.show_consensus_histogram"));
3403     showSequenceLogo.setLabel(MessageManager
3404             .getString("label.show_consensus_logo"));
3405     normSequenceLogo.setLabel(MessageManager
3406             .getString("label.norm_consensus_logo"));
3407     applyAutoAnnotationSettings.setLabel(MessageManager
3408             .getString("label.apply_all_groups"));
3409     applyAutoAnnotationSettings.setState(true);
3410     Menu autoAnnMenu = new Menu(
3411             MessageManager.getString("label.autocalculated_annotation"));
3412     showGroupConsensus.addItemListener(this);
3413     showGroupConservation.addItemListener(this);
3414     showConsensusHistogram.addItemListener(this);
3415     showSequenceLogo.addItemListener(this);
3416     normSequenceLogo.addItemListener(this);
3417     applyAutoAnnotationSettings.addItemListener(this);
3418     showAlignmentAnnotations = new CheckboxMenuItem(
3419             MessageManager.getString("label.show_all_al_annotations"));
3420     showSequenceAnnotations = new CheckboxMenuItem(
3421             MessageManager.getString("label.show_all_seq_annotations"));
3422     sortAnnBySequence = new CheckboxMenuItem(
3423             MessageManager.getString("label.sort_annotations_by_sequence"));
3424     sortAnnByLabel = new CheckboxMenuItem(
3425             MessageManager.getString("label.sort_annotations_by_label"));
3426     showAutoFirst = new CheckboxMenuItem(
3427             MessageManager.getString("label.show_first"));
3428     showAutoFirst.setState(false); // pending applet parameter
3429     setShowAutoCalculatedAbove(showAutoFirst.getState());
3430     showAutoLast = new CheckboxMenuItem(
3431             MessageManager.getString("label.show_last"));
3432     showAutoLast.setState(!showAutoFirst.getState());
3433     showAlignmentAnnotations.addItemListener(this);
3434     showSequenceAnnotations.addItemListener(this);
3435     sortAnnBySequence.addItemListener(this);
3436     sortAnnByLabel.addItemListener(this);
3437     showAutoFirst.addItemListener(this);
3438     showAutoLast.addItemListener(this);
3439
3440     /*
3441      * Configure Format menu items and actions
3442      */
3443     font.setLabel(MessageManager.getString("action.font"));
3444     font.addActionListener(this);
3445     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3446     scaleAbove.setState(true);
3447     scaleAbove.setEnabled(false);
3448     scaleAbove.addItemListener(this);
3449     scaleLeft.setEnabled(false);
3450     scaleLeft.setState(true);
3451     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3452     scaleLeft.addItemListener(this);
3453     scaleRight.setEnabled(false);
3454     scaleRight.setState(true);
3455     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3456     scaleRight.addItemListener(this);
3457     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3458     viewBoxesMenuItem.setState(true);
3459     viewBoxesMenuItem.addItemListener(this);
3460     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3461     viewTextMenuItem.setState(true);
3462     viewTextMenuItem.addItemListener(this);
3463     colourTextMenuItem.setLabel(MessageManager
3464             .getString("label.colour_text"));
3465     colourTextMenuItem.addItemListener(this);
3466     displayNonconservedMenuItem.setLabel(MessageManager
3467             .getString("label.show_non_conserved"));
3468     displayNonconservedMenuItem.addItemListener(this);
3469     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3470     wrapMenuItem.addItemListener(this);
3471     renderGapsMenuItem.setLabel(MessageManager
3472             .getString("action.show_gaps"));
3473     renderGapsMenuItem.setState(true);
3474     renderGapsMenuItem.addItemListener(this);
3475     centreColumnLabelFlag.setLabel(MessageManager
3476             .getString("label.centre_column_labels"));
3477     centreColumnLabelFlag.addItemListener(this);
3478     seqLimits.setState(true);
3479     seqLimits.setLabel(MessageManager
3480             .getString("label.show_sequence_limits"));
3481     seqLimits.addItemListener(this);
3482
3483     /*
3484      * Configure Colour menu items and actions
3485      */
3486     applyToAllGroups.setLabel(MessageManager
3487             .getString("label.apply_colour_to_all_groups"));
3488     applyToAllGroups.setState(true);
3489     applyToAllGroups.addItemListener(this);
3490     clustalColour.setLabel(MessageManager
3491             .getString("label.colourScheme_clustal"));
3492     clustalColour.addActionListener(this);
3493     zappoColour.setLabel(MessageManager
3494             .getString("label.colourScheme_zappo"));
3495     zappoColour.addActionListener(this);
3496     taylorColour.setLabel(MessageManager
3497             .getString("label.colourScheme_taylor"));
3498     taylorColour.addActionListener(this);
3499     hydrophobicityColour.setLabel(MessageManager
3500             .getString("label.colourScheme_hydrophobic"));
3501     hydrophobicityColour.addActionListener(this);
3502     helixColour.setLabel(MessageManager
3503             .getString("label.colourScheme_helix_propensity"));
3504     helixColour.addActionListener(this);
3505     strandColour.setLabel(MessageManager
3506             .getString("label.colourScheme_strand_propensity"));
3507     strandColour.addActionListener(this);
3508     turnColour.setLabel(MessageManager
3509             .getString("label.colourScheme_turn_propensity"));
3510     turnColour.addActionListener(this);
3511     buriedColour.setLabel(MessageManager
3512             .getString("label.colourScheme_buried_index"));
3513     buriedColour.addActionListener(this);
3514     purinePyrimidineColour.setLabel(MessageManager
3515             .getString("label.colourScheme_purine/pyrimidine"));
3516     purinePyrimidineColour.addActionListener(this);
3517     // RNAInteractionColour.setLabel(MessageManager
3518     // .getString("label.rna_interaction"));
3519     // RNAInteractionColour.addActionListener(this);
3520     RNAHelixColour.setLabel(MessageManager
3521             .getString("label.colourScheme_rna_helices"));
3522     RNAHelixColour.addActionListener(this);
3523     userDefinedColour.setLabel(MessageManager
3524             .getString("action.user_defined"));
3525     userDefinedColour.addActionListener(this);
3526     PIDColour.setLabel(MessageManager
3527             .getString("label.colourScheme_%_identity"));
3528     PIDColour.addActionListener(this);
3529     BLOSUM62Colour.setLabel(MessageManager
3530             .getString("label.colourScheme_blosum62"));
3531     BLOSUM62Colour.addActionListener(this);
3532     tcoffeeColour.setLabel(MessageManager
3533             .getString("label.colourScheme_t-coffee_scores"));
3534     // it will be enabled only if a score file is provided
3535     tcoffeeColour.setEnabled(false);
3536     tcoffeeColour.addActionListener(this);
3537     conservationMenuItem.setLabel(MessageManager
3538             .getString("action.by_conservation"));
3539     conservationMenuItem.addItemListener(this);
3540     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3541     noColourmenuItem.addActionListener(this);
3542     abovePIDThreshold.setLabel(MessageManager
3543             .getString("label.above_identity_threshold"));
3544     abovePIDThreshold.addItemListener(this);
3545     nucleotideColour.setLabel(MessageManager
3546             .getString("label.colourScheme_nucleotide"));
3547     nucleotideColour.addActionListener(this);
3548     modifyPID.setLabel(MessageManager
3549             .getString("label.modify_identity_threshold"));
3550     modifyPID.setEnabled(abovePIDThreshold.getState());
3551     modifyPID.addActionListener(this);
3552     modifyConservation.setLabel(MessageManager
3553             .getString("label.modify_conservation_threshold"));
3554     modifyConservation.setEnabled(conservationMenuItem.getState());
3555     modifyConservation.addActionListener(this);
3556     annotationColour.setLabel(MessageManager
3557             .getString("action.by_annotation"));
3558     annotationColour.addActionListener(this);
3559
3560     /*
3561      * Configure Calculate menu items and actions
3562      */
3563     sortPairwiseMenuItem.setLabel(MessageManager
3564             .getString("action.by_pairwise_id"));
3565     sortPairwiseMenuItem.addActionListener(this);
3566     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3567     sortIDMenuItem.addActionListener(this);
3568     sortLengthMenuItem.setLabel(MessageManager
3569             .getString("action.by_length"));
3570     sortLengthMenuItem.addActionListener(this);
3571     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3572     sortGroupMenuItem.addActionListener(this);
3573     pairwiseAlignmentMenuItem.setLabel(MessageManager
3574             .getString("action.pairwise_alignment"));
3575     pairwiseAlignmentMenuItem.addActionListener(this);
3576     PCAMenuItem.setLabel(MessageManager
3577             .getString("label.principal_component_analysis"));
3578     PCAMenuItem.addActionListener(this);
3579     autoCalculate = new CheckboxMenuItem(
3580             MessageManager.getString("label.autocalculate_consensus"), true);
3581     averageDistanceTreeMenuItem.setLabel(MessageManager
3582             .getString("label.average_distance_identity"));
3583     averageDistanceTreeMenuItem.addActionListener(this);
3584     neighbourTreeMenuItem.setLabel(MessageManager
3585             .getString("label.neighbour_joining_identity"));
3586     neighbourTreeMenuItem.addActionListener(this);
3587     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3588             .getString("label.average_distance_blosum62"));
3589     avDistanceTreeBlosumMenuItem.addActionListener(this);
3590     njTreeBlosumMenuItem.setLabel(MessageManager
3591             .getString("label.neighbour_blosum62"));
3592     njTreeBlosumMenuItem.addActionListener(this);
3593     sortByTreeMenu.setLabel(MessageManager
3594             .getString("action.by_tree_order"));
3595     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3596     Menu calculateTreeMenu = new Menu(
3597             MessageManager.getString("action.calculate_tree"));
3598     autoCalculate.addItemListener(this);
3599     sortByTree.addItemListener(this);
3600
3601     /*
3602      * Configure Help menu items and actions
3603      */
3604     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3605     documentation.setLabel(MessageManager.getString("label.documentation"));
3606     documentation.addActionListener(this);
3607     about.setLabel(MessageManager.getString("label.about"));
3608     about.addActionListener(this);
3609
3610     /*
3611      * Add top level menus to frame
3612      */
3613     alignFrameMenuBar.add(fileMenu);
3614     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3615     alignFrameMenuBar.add(editMenu);
3616     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3617     alignFrameMenuBar.add(selectMenu);
3618     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3619     alignFrameMenuBar.add(viewMenu);
3620     Menu annotationsMenu = new Menu(
3621             MessageManager.getString("action.annotations"));
3622     alignFrameMenuBar.add(annotationsMenu);
3623     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3624     alignFrameMenuBar.add(formatMenu);
3625     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3626     alignFrameMenuBar.add(colourMenu);
3627     Menu calculateMenu = new Menu(
3628             MessageManager.getString("action.calculate"));
3629     alignFrameMenuBar.add(calculateMenu);
3630     alignFrameMenuBar.add(helpMenu);
3631
3632     /*
3633      * File menu
3634      */
3635     fileMenu.add(inputText);
3636     fileMenu.add(loadTree);
3637     fileMenu.add(loadAnnotations);
3638     fileMenu.addSeparator();
3639     fileMenu.add(outputTextboxMenu);
3640     fileMenu.add(outputFeatures);
3641     fileMenu.add(outputAnnotations);
3642     if (jalviewServletURL != null)
3643     {
3644       fileMenu.add(loadApplication);
3645     }
3646     fileMenu.addSeparator();
3647     fileMenu.add(closeMenuItem);
3648
3649     /*
3650      * Edit menu
3651      */
3652     editMenu.add(undoMenuItem);
3653     editMenu.add(redoMenuItem);
3654     editMenu.add(cut);
3655     editMenu.add(copy);
3656     pasteMenu.add(pasteNew);
3657     pasteMenu.add(pasteThis);
3658     editMenu.add(pasteMenu);
3659     editMenu.add(delete);
3660     editMenu.addSeparator();
3661     editMenu.add(remove2LeftMenuItem);
3662     editMenu.add(remove2RightMenuItem);
3663     editMenu.add(removeGappedColumnMenuItem);
3664     editMenu.add(removeAllGapsMenuItem);
3665     editMenu.add(removeRedundancyMenuItem);
3666
3667     /*
3668      * Select menu
3669      */
3670     selectMenu.add(findMenuItem);
3671     selectMenu.addSeparator();
3672     selectMenu.add(selectAllSequenceMenuItem);
3673     selectMenu.add(deselectAllSequenceMenuItem);
3674     selectMenu.add(invertSequenceMenuItem);
3675     selectMenu.add(invertColSel);
3676     selectMenu.add(createGroup);
3677     selectMenu.add(unGroup);
3678     selectMenu.add(grpsFromSelection);
3679     selectMenu.add(deleteGroups);
3680     selectMenu.add(annotationColumnSelection);
3681
3682     /*
3683      * View menu
3684      */
3685     viewMenu.add(newView);
3686     viewMenu.addSeparator();
3687     showMenu.add(showColumns);
3688     showMenu.add(showSeqs);
3689     showMenu.add(showAllHidden);
3690     viewMenu.add(showMenu);
3691     hideMenu.add(hideColumns);
3692     hideMenu.add(hideSequences);
3693     hideMenu.add(hideAllSelection);
3694     hideMenu.add(hideAllButSelection);
3695     viewMenu.add(hideMenu);
3696     viewMenu.addSeparator();
3697     viewMenu.add(followMouseOverFlag);
3698     viewMenu.addSeparator();
3699     viewMenu.add(sequenceFeatures);
3700     viewMenu.add(featureSettings);
3701     viewMenu.addSeparator();
3702     viewMenu.add(alProperties);
3703     viewMenu.addSeparator();
3704     viewMenu.add(overviewMenuItem);
3705
3706     /*
3707      * Annotations menu
3708      */
3709     annotationsMenu.add(annotationPanelMenuItem);
3710     annotationsMenu.addSeparator();
3711     annotationsMenu.add(showAlignmentAnnotations);
3712     annotationsMenu.add(showSequenceAnnotations);
3713     annotationsMenu.add(sortAnnBySequence);
3714     annotationsMenu.add(sortAnnByLabel);
3715     annotationsMenu.addSeparator();
3716     autoAnnMenu.add(showAutoFirst);
3717     autoAnnMenu.add(showAutoLast);
3718     autoAnnMenu.addSeparator();
3719     autoAnnMenu.add(applyAutoAnnotationSettings);
3720     autoAnnMenu.add(showConsensusHistogram);
3721     autoAnnMenu.add(showSequenceLogo);
3722     autoAnnMenu.add(normSequenceLogo);
3723     autoAnnMenu.addSeparator();
3724     autoAnnMenu.add(showGroupConservation);
3725     autoAnnMenu.add(showGroupConsensus);
3726     annotationsMenu.add(autoAnnMenu);
3727
3728     /*
3729      * Format menu
3730      */
3731     formatMenu.add(font);
3732     formatMenu.add(seqLimits);
3733     formatMenu.add(wrapMenuItem);
3734     formatMenu.add(scaleAbove);
3735     formatMenu.add(scaleLeft);
3736     formatMenu.add(scaleRight);
3737     formatMenu.add(viewBoxesMenuItem);
3738     formatMenu.add(viewTextMenuItem);
3739     formatMenu.add(colourTextMenuItem);
3740     formatMenu.add(displayNonconservedMenuItem);
3741     formatMenu.add(renderGapsMenuItem);
3742     formatMenu.add(centreColumnLabelFlag);
3743
3744     /*
3745      * Colour menu
3746      */
3747     colourMenu.add(applyToAllGroups);
3748     colourMenu.addSeparator();
3749     colourMenu.add(noColourmenuItem);
3750     colourMenu.add(clustalColour);
3751     colourMenu.add(BLOSUM62Colour);
3752     colourMenu.add(PIDColour);
3753     colourMenu.add(zappoColour);
3754     colourMenu.add(taylorColour);
3755     colourMenu.add(hydrophobicityColour);
3756     colourMenu.add(helixColour);
3757     colourMenu.add(strandColour);
3758     colourMenu.add(turnColour);
3759     colourMenu.add(buriedColour);
3760     colourMenu.add(nucleotideColour);
3761     colourMenu.add(purinePyrimidineColour);
3762     // colourMenu.add(RNAInteractionColour);
3763     colourMenu.add(tcoffeeColour);
3764     colourMenu.add(userDefinedColour);
3765     colourMenu.addSeparator();
3766     colourMenu.add(conservationMenuItem);
3767     colourMenu.add(modifyConservation);
3768     colourMenu.add(abovePIDThreshold);
3769     colourMenu.add(modifyPID);
3770     colourMenu.add(annotationColour);
3771     colourMenu.add(RNAHelixColour);
3772
3773     /*
3774      * Calculate menu
3775      */
3776     sortMenu.add(sortIDMenuItem);
3777     sortMenu.add(sortLengthMenuItem);
3778     sortMenu.add(sortByTreeMenu);
3779     sortMenu.add(sortGroupMenuItem);
3780     sortMenu.add(sortPairwiseMenuItem);
3781     calculateMenu.add(sortMenu);
3782     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3783     calculateTreeMenu.add(neighbourTreeMenuItem);
3784     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3785     calculateTreeMenu.add(njTreeBlosumMenuItem);
3786     calculateMenu.add(calculateTreeMenu);
3787     calculateMenu.addSeparator();
3788     calculateMenu.add(pairwiseAlignmentMenuItem);
3789     calculateMenu.add(PCAMenuItem);
3790     calculateMenu.add(autoCalculate);
3791     calculateMenu.add(sortByTree);
3792
3793     /*
3794      * Help menu
3795      */
3796     helpMenu.add(documentation);
3797     helpMenu.add(about);
3798
3799     /*
3800      * Status bar
3801      */
3802     statusBar.setBackground(Color.white);
3803     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3804     statusBar.setText(MessageManager.getString("label.status_bar"));
3805     this.add(statusBar, BorderLayout.SOUTH);
3806   }
3807
3808   @Override
3809   public void setStatus(String string)
3810   {
3811     statusBar.setText(string);
3812   };
3813
3814   MenuItem featureSettings = new MenuItem();
3815
3816   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3817
3818   MenuItem annotationColour = new MenuItem();
3819
3820   MenuItem annotationColumnSelection = new MenuItem();
3821
3822   MenuItem invertColSel = new MenuItem();
3823
3824   MenuItem showColumns = new MenuItem();
3825
3826   MenuItem showSeqs = new MenuItem();
3827
3828   MenuItem hideColumns = new MenuItem();
3829
3830   MenuItem hideSequences = new MenuItem();
3831
3832   MenuItem hideAllButSelection = new MenuItem();
3833
3834   MenuItem hideAllSelection = new MenuItem();
3835
3836   MenuItem showAllHidden = new MenuItem();
3837
3838   MenuItem newView = new MenuItem();
3839
3840   private CheckboxMenuItem showAlignmentAnnotations;
3841
3842   private CheckboxMenuItem showSequenceAnnotations;
3843
3844   private CheckboxMenuItem sortAnnBySequence;
3845
3846   private CheckboxMenuItem sortAnnByLabel;
3847
3848   private CheckboxMenuItem showAutoFirst;
3849
3850   private CheckboxMenuItem showAutoLast;
3851
3852   private SplitFrame splitFrame;
3853
3854   /**
3855    * Attach the alignFrame panels after embedding menus, if necessary. This used
3856    * to be called setEmbedded, but is now creates the dropdown menus in a
3857    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3858    *
3859    * @param reallyEmbedded
3860    *          true to attach the view to the applet area on the page rather than
3861    *          in a new window
3862    */
3863   public void createAlignFrameWindow(boolean reallyEmbedded)
3864   {
3865     if (reallyEmbedded)
3866     {
3867       embedAlignFrameInApplet(viewport.applet);
3868     }
3869     else
3870     {
3871       // //////
3872       // test and embed menu bar if necessary.
3873       //
3874       if (embedMenuIfNeeded(alignPanel))
3875       {
3876         /*
3877          * adjust for status bar height too. ? pointless as overridden by layout
3878          * manager
3879          */
3880         alignPanel.setSize(getSize().width,
3881                 getSize().height - statusBar.getHeight());
3882       }
3883       add(statusBar, BorderLayout.SOUTH);
3884       add(alignPanel, BorderLayout.CENTER);
3885       // and register with the applet so it can pass external API calls to us
3886       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3887               frameHeight);
3888     }
3889   }
3890
3891   /**
3892    * Add the components of this AlignFrame to the applet container.
3893    *
3894    * @param theApplet
3895    */
3896   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3897   {
3898     // ////
3899     // Explicitly build the embedded menu panel for the on-page applet
3900     //
3901     // view cannot be closed if its actually on the page
3902     fileMenu.remove(closeMenuItem);
3903     fileMenu.remove(3); // Remove Separator
3904     // construct embedded menu, using default font
3905     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3906     // and actually add the components to the applet area
3907     theApplet.setLayout(new BorderLayout());
3908     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3909     theApplet.add(statusBar, BorderLayout.SOUTH);
3910     // TODO should size be left to the layout manager?
3911     alignPanel.setSize(theApplet.getSize().width,
3912             theApplet.getSize().height - embeddedMenu.getHeight()
3913                     - statusBar.getHeight());
3914     theApplet.add(alignPanel, BorderLayout.CENTER);
3915     final AlignFrame me = this;
3916     theApplet.addFocusListener(new FocusListener()
3917     {
3918
3919       @Override
3920       public void focusLost(FocusEvent e)
3921       {
3922         if (theApplet.currentAlignFrame == me)
3923         {
3924           theApplet.currentAlignFrame = null;
3925         }
3926       }
3927
3928       @Override
3929       public void focusGained(FocusEvent e)
3930       {
3931         theApplet.currentAlignFrame = me;
3932       }
3933     });
3934     theApplet.validate();
3935   }
3936
3937   /**
3938    * create a new binding between structures in an existing jmol viewer instance
3939    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3940    * this does not open a new Jmol window, or modify the display of the
3941    * structures in the original jmol window. Note This method doesn't work
3942    * without an additional javascript library to exchange messages between the
3943    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3944    *
3945    * @param viewer
3946    *          JmolViewer instance
3947    * @param sequenceIds
3948    *          - sequence Ids to search for associations
3949    */
3950   public SequenceStructureBinding addStructureViewInstance(
3951           Object jmolviewer, String[] sequenceIds)
3952   {
3953     Viewer viewer = null;
3954     try
3955     {
3956       viewer = (Viewer) jmolviewer;
3957     } catch (ClassCastException ex)
3958     {
3959       System.err.println("Unsupported viewer object :"
3960               + jmolviewer.getClass());
3961     }
3962     if (viewer == null)
3963     {
3964       System.err.println("Can't use this object as a structure viewer:"
3965               + jmolviewer.getClass());
3966       return null;
3967     }
3968     SequenceI[] seqs = null;
3969     if (sequenceIds == null || sequenceIds.length == 0)
3970     {
3971       seqs = viewport.getAlignment().getSequencesArray();
3972     }
3973     else
3974     {
3975       Vector sqi = new Vector();
3976       AlignmentI al = viewport.getAlignment();
3977       for (int sid = 0; sid < sequenceIds.length; sid++)
3978       {
3979         SequenceI sq = al.findName(sequenceIds[sid]);
3980         if (sq != null)
3981         {
3982           sqi.addElement(sq);
3983         }
3984       }
3985       if (sqi.size() > 0)
3986       {
3987         seqs = new SequenceI[sqi.size()];
3988         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3989         {
3990           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3991         }
3992       }
3993       else
3994       {
3995         return null;
3996       }
3997     }
3998     AAStructureBindingModel jmv = null;
3999     // TODO: search for a jmv that involves viewer
4000     if (jmv == null)
4001     { // create a new viewer/jalview binding.
4002       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4003     }
4004     return jmv;
4005
4006   }
4007
4008   /**
4009    * bind a pdb file to a sequence in the current view
4010    *
4011    * @param sequenceId
4012    *          - sequenceId within the dataset.
4013    * @param pdbEntryString
4014    *          - the short name for the PDB file
4015    * @param pdbFile
4016    *          - pdb file - either a URL or a valid PDB file.
4017    * @return true if binding was as success TODO: consider making an exception
4018    *         structure for indicating when PDB parsing or sequenceId location
4019    *         fails.
4020    */
4021   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4022           String pdbFile)
4023   {
4024     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4025     boolean needtoadd = false;
4026     if (toaddpdb != null)
4027     {
4028       Vector pdbe = toaddpdb.getAllPDBEntries();
4029       PDBEntry pdbentry = null;
4030       if (pdbe != null && pdbe.size() > 0)
4031       {
4032         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4033         {
4034           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4035           if (!pdbentry.getId().equals(pdbEntryString)
4036                   && !pdbentry.getFile().equals(pdbFile))
4037           {
4038             pdbentry = null;
4039           }
4040           else
4041           {
4042             continue;
4043           }
4044         }
4045       }
4046       if (pdbentry == null)
4047       {
4048         pdbentry = new PDBEntry();
4049         pdbentry.setId(pdbEntryString);
4050         pdbentry.setFile(pdbFile);
4051         needtoadd = true; // add this new entry to sequence.
4052       }
4053       // resolve data source
4054       // TODO: this code should be a refactored to an io package
4055       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4056               pdbFile, FileFormat.PDB);
4057       if (protocol == null)
4058       {
4059         return false;
4060       }
4061       if (needtoadd)
4062       {
4063         pdbentry.setProperty("protocol", protocol);
4064         toaddpdb.addPDBId(pdbentry);
4065         alignPanel.getStructureSelectionManager()
4066                 .registerPDBEntry(pdbentry);
4067       }
4068     }
4069     return true;
4070   }
4071
4072   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4073   {
4074     if (seqs != null)
4075     {
4076       Vector sequences = new Vector();
4077       for (int i = 0; i < seqs.length; i++)
4078       {
4079         if (seqs[i] != null)
4080         {
4081           sequences.addElement(new Object[] { seqs[i],
4082               (chains != null) ? chains[i] : null });
4083         }
4084       }
4085       seqs = new SequenceI[sequences.size()];
4086       chains = new String[sequences.size()];
4087       for (int i = 0, isize = sequences.size(); i < isize; i++)
4088       {
4089         Object[] oj = (Object[]) sequences.elementAt(i);
4090
4091         seqs[i] = (SequenceI) oj[0];
4092         chains[i] = (String) oj[1];
4093       }
4094     }
4095     return new Object[] { seqs, chains };
4096
4097   }
4098
4099   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4100           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4101   {
4102     // Scrub any null sequences from the array
4103     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4104     seqs = (SequenceI[]) sqch[0];
4105     chains = (String[]) sqch[1];
4106     if (seqs == null || seqs.length == 0)
4107     {
4108       System.err
4109               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4110     }
4111     if (protocol == null)
4112     {
4113       String sourceType = (String) pdb.getProperty("protocol");
4114       try
4115       {
4116         protocol = DataSourceType.valueOf(sourceType);
4117       } catch (IllegalArgumentException e)
4118       {
4119         // ignore
4120       }
4121       if (protocol == null)
4122       {
4123         System.err.println("Couldn't work out protocol to open structure: "
4124                 + pdb.getId());
4125         return;
4126       }
4127     }
4128     if (applet.useXtrnalSviewer)
4129     {
4130       // register the association(s) and quit, don't create any windows.
4131       if (StructureSelectionManager.getStructureSelectionManager(applet)
4132               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4133       {
4134         System.err.println("Failed to map " + pdb.getFile() + " ("
4135                 + protocol + ") to any sequences");
4136       }
4137       return;
4138     }
4139     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4140     {
4141       // can only do alignments with Jmol
4142       // find the last jmol window assigned to this alignment
4143       AppletJmol ajm = null, tajm;
4144       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4145       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4146       {
4147         tajm = (AppletJmol) jmols.elementAt(i);
4148         if (tajm.ap.alignFrame == this)
4149         {
4150           ajm = tajm;
4151           break;
4152         }
4153       }
4154       if (ajm != null)
4155       {
4156         System.err
4157                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4158         // try and add the pdb structure
4159         // ajm.addS
4160         ajm = null;
4161       }
4162     }
4163     // otherwise, create a new window
4164     if (applet.jmolAvailable)
4165     {
4166       new AppletJmol(pdb, seqs, chains, alignPanel,
4167               protocol);
4168       applet.lastFrameX += 40;
4169       applet.lastFrameY += 40;
4170     }
4171     else
4172     {
4173       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4174     }
4175
4176   }
4177
4178   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4179           SequenceI[][] seqs, String[][] chains, String[] protocols)
4180   {
4181     // TODO Auto-generated method stub
4182     System.err.println("Aligned Structure View: Not yet implemented.");
4183   }
4184
4185   /**
4186    * modify the current selection, providing the user has not made a selection
4187    * already.
4188    *
4189    * @param sel
4190    *          - sequences from this alignment
4191    * @param csel
4192    *          - columns to be selected on the alignment
4193    */
4194   public void select(SequenceGroup sel, ColumnSelection csel)
4195   {
4196     alignPanel.seqPanel.selection(sel, csel, null);
4197   }
4198
4199   public void scrollTo(int row, int column)
4200   {
4201     alignPanel.seqPanel.scrollTo(row, column);
4202   }
4203
4204   public void scrollToRow(int row)
4205   {
4206     alignPanel.seqPanel.scrollToRow(row);
4207   }
4208
4209   public void scrollToColumn(int column)
4210   {
4211     alignPanel.seqPanel.scrollToColumn(column);
4212   }
4213
4214   /**
4215    * @return the alignments unique ID.
4216    */
4217   public String getSequenceSetId()
4218   {
4219     return viewport.getSequenceSetId();
4220   }
4221
4222   /**
4223    * Load the (T-Coffee) score file from the specified url
4224    *
4225    * @param source
4226    *          File/URL/T-COFFEE score file contents
4227    * @throws IOException
4228    * @return true if alignment was annotated with data from source
4229    */
4230   public boolean loadScoreFile(String source) throws IOException
4231   {
4232
4233     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4234             AppletFormatAdapter.checkProtocol(source));
4235     if (!file.isValid())
4236     {
4237       // TODO: raise dialog for gui
4238       System.err.println("Problems parsing T-Coffee scores: "
4239               + file.getWarningMessage());
4240       System.err.println("Origin was:\n" + source);
4241       return false;
4242     }
4243
4244     /*
4245      * check that the score matrix matches the alignment dimensions
4246      */
4247     AlignmentI aln;
4248     if ((aln = viewport.getAlignment()) != null
4249             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4250                     .getWidth()))
4251     {
4252       // TODO: raise a dialog box here rather than bomb out.
4253       System.err
4254               .println("The scores matrix does not match the alignment dimensions");
4255
4256     }
4257
4258     // TODO add parameter to indicate if matching should be done
4259     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4260     {
4261       alignPanel.fontChanged();
4262       tcoffeeColour.setEnabled(true);
4263       // switch to this color
4264       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4265       return true;
4266     }
4267     else
4268     {
4269       System.err.println("Problems resolving T-Coffee scores:");
4270       if (file.getWarningMessage() != null)
4271       {
4272         System.err.println(file.getWarningMessage());
4273       }
4274     }
4275     return false;
4276   }
4277
4278   public SplitFrame getSplitFrame()
4279   {
4280     return this.splitFrame;
4281   }
4282
4283   public void setSplitFrame(SplitFrame sf)
4284   {
4285     this.splitFrame = sf;
4286   }
4287
4288   // may not need this
4289   @Override
4290   public void setShowSeqFeatures(boolean b)
4291   {
4292     // showSeqFeatures.setSelected(b);
4293     viewport.setShowSequenceFeatures(b);
4294
4295   }
4296
4297   @Override
4298   public void setMenusForViewport()
4299   {
4300     // setMenusFromViewport(viewport);
4301
4302   }
4303
4304   @Override
4305   public void refreshFeatureUI(boolean enableIfNecessary)
4306   {
4307     if (enableIfNecessary)
4308     {
4309       sequenceFeatures.setState(true);
4310       alignPanel.av.setShowSequenceFeatures(true);
4311     }
4312   }
4313
4314   @Override
4315   public FeatureSettingsControllerI getFeatureSettingsUI()
4316   {
4317     return alignPanel.av.featureSettings;
4318   }
4319
4320 }