src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.analysis.TreeBuilder;
  26 import jalview.analysis.scoremodels.PIDModel;
  27 import jalview.analysis.scoremodels.ScoreModels;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.FeatureColourI;
  32 import jalview.api.FeatureRenderer;
  33 import jalview.api.FeatureSettingsControllerI;
  34 import jalview.api.SequenceStructureBinding;
  35 import jalview.bin.JalviewLite;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentAnnotation;
  46 import jalview.datamodel.AlignmentI;
  47 import jalview.datamodel.AlignmentOrder;
  48 import jalview.datamodel.ColumnSelection;
  49 import jalview.datamodel.HiddenColumns;
  50 import jalview.datamodel.PDBEntry;
  51 import jalview.datamodel.Sequence;
  52 import jalview.datamodel.SequenceGroup;
  53 import jalview.datamodel.SequenceI;
  54 import jalview.io.AnnotationFile;
  55 import jalview.io.AppletFormatAdapter;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FeaturesFile;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileFormatI;
  60 import jalview.io.FileFormats;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColour;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.ZappoColourScheme;
  77 import jalview.structure.StructureSelectionManager;
  78 import jalview.structures.models.AAStructureBindingModel;
  79 import jalview.util.MappingUtils;
  80 import jalview.util.MessageManager;
  81 import jalview.viewmodel.AlignmentViewport;
  82 import jalview.viewmodel.ViewportRanges;
  83
  84 import java.awt.BorderLayout;
  85 import java.awt.Canvas;
  86 import java.awt.CheckboxMenuItem;
  87 import java.awt.Color;
  88 import java.awt.FlowLayout;
  89 import java.awt.Font;
  90 import java.awt.FontMetrics;
  91 import java.awt.Frame;
  92 import java.awt.Graphics;
  93 import java.awt.Label;
  94 import java.awt.Menu;
  95 import java.awt.MenuBar;
  96 import java.awt.MenuItem;
  97 import java.awt.Panel;
  98 import java.awt.event.ActionEvent;
  99 import java.awt.event.ActionListener;
 100 import java.awt.event.FocusEvent;
 101 import java.awt.event.FocusListener;
 102 import java.awt.event.ItemEvent;
 103 import java.awt.event.ItemListener;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.KeyListener;
 106 import java.awt.event.WindowAdapter;
 107 import java.awt.event.WindowEvent;
 108 import java.io.IOException;
 109 import java.net.URL;
 110 import java.net.URLEncoder;
 111 import java.util.Arrays;
 112 import java.util.Deque;
 113 import java.util.HashMap;
 114 import java.util.List;
 115 import java.util.Map;
 116 import java.util.StringTokenizer;
 117 import java.util.Vector;
 118
 119 import org.jmol.viewer.Viewer;
 120
 121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 122         ItemListener, KeyListener, AlignViewControllerGuiI
 123 {
 124   public AlignViewControllerI avc;
 125
 126   public AlignmentPanel alignPanel;
 127
 128   public AlignViewport viewport;
 129
 130   // width and height may be overridden by applet parameters
 131   int frameWidth = 700;
 132
 133   int frameHeight = 500;
 134
 135   String jalviewServletURL;
 136
 137   /*
 138    * Flag for showing autocalculated consensus above or below other consensus
 139    * rows
 140    */
 141   private boolean showAutoCalculatedAbove;
 142
 143   private SequenceAnnotationOrder annotationSortOrder;
 144
 145   /**
 146    * Constructor that creates the frame and adds it to the display.
 147    *
 148    * @param al
 149    * @param applet
 150    * @param title
 151    * @param embedded
 152    */
 153   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 154           boolean embedded)
 155   {
 156     this(al, applet, title, embedded, true);
 157   }
 158
 159   /**
 160    * Constructor that optionally allows the frame to be displayed or only
 161    * created.
 162    *
 163    * @param al
 164    * @param applet
 165    * @param title
 166    * @param embedded
 167    * @param addToDisplay
 168    */
 169   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 170           boolean embedded, boolean addToDisplay)
 171   {
 172     this(al, null, null, applet, title, embedded, addToDisplay);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           HiddenColumns hidden, JalviewLite applet,
 177           String title, boolean embedded)
 178   {
 179     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 180   }
 181
 182   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 183           HiddenColumns hidden, JalviewLite applet,
 184           String title, boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237     viewport.updateInformation(alignPanel);
 238
 239     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 240     followMouseOverFlag.setState(viewport.isFollowHighlight());
 241     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 242     showGroupConservation.setState(viewport.isShowGroupConservation());
 243     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 244     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 245     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 246     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 247     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 248     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 250     showAlignmentAnnotations.setState(true);
 251     showSequenceAnnotations.setState(false);
 252
 253     seqLimits.setState(viewport.getShowJVSuffix());
 254
 255     if (applet != null)
 256     {
 257       String param = applet.getParameter("sortBy");
 258       if (param != null)
 259       {
 260         if (param.equalsIgnoreCase("Id"))
 261         {
 262           sortIDMenuItem_actionPerformed();
 263         }
 264         else if (param.equalsIgnoreCase("Pairwise Identity"))
 265         {
 266           sortPairwiseMenuItem_actionPerformed();
 267         }
 268         else if (param.equalsIgnoreCase("Length"))
 269         {
 270           sortLengthMenuItem_actionPerformed();
 271         }
 272       }
 273
 274       param = applet.getParameter("wrap");
 275       if (param != null)
 276       {
 277         if (param.equalsIgnoreCase("true"))
 278         {
 279           wrapMenuItem.setState(true);
 280           wrapMenuItem_actionPerformed();
 281         }
 282       }
 283       param = applet.getParameter("centrecolumnlabels");
 284       if (param != null)
 285       {
 286         centreColumnLabelFlag.setState(true);
 287         centreColumnLabelFlag_stateChanged();
 288       }
 289
 290     }
 291     if (viewport.getAlignment().isNucleotide())
 292     {
 293       conservationMenuItem.setEnabled(false);
 294       clustalColour.setEnabled(false);
 295       BLOSUM62Colour.setEnabled(false);
 296       zappoColour.setEnabled(false);
 297       taylorColour.setEnabled(false);
 298       hydrophobicityColour.setEnabled(false);
 299       helixColour.setEnabled(false);
 300       strandColour.setEnabled(false);
 301       turnColour.setEnabled(false);
 302       buriedColour.setEnabled(false);
 303       viewport.updateStrucConsensus(alignPanel);
 304       if (viewport.getAlignment().hasRNAStructure())
 305       {
 306         RNAHelixColour.setEnabled(true);
 307       }
 308       else
 309       {
 310         RNAHelixColour.setEnabled(false);
 311       }
 312     }
 313     else
 314     {
 315       RNAHelixColour.setEnabled(false);
 316       purinePyrimidineColour.setEnabled(false);
 317       nucleotideColour.setEnabled(false);
 318     }
 319     // Some JVMS send keyevents to Top frame or lowest panel,
 320     // Havent worked out why yet. So add to both this frame and seqCanvas for
 321     // now
 322     this.addKeyListener(this);
 323     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 324     alignPanel.idPanel.idCanvas.addKeyListener(this);
 325     alignPanel.scalePanel.addKeyListener(this);
 326     alignPanel.annotationPanel.addKeyListener(this);
 327     alignPanel.annotationPanelHolder.addKeyListener(this);
 328     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 329     alignPanel.alabels.addKeyListener(this);
 330
 331     setAnnotationsVisibility();
 332
 333     if (addToDisplay)
 334     {
 335       addToDisplay(embedded);
 336     }
 337   }
 338
 339   /**
 340    * @param embedded
 341    */
 342   public void addToDisplay(boolean embedded)
 343   {
 344     createAlignFrameWindow(embedded);
 345     validate();
 346     alignPanel.adjustAnnotationHeight();
 347     alignPanel.paintAlignment(true);
 348   }
 349
 350   public AlignViewport getAlignViewport()
 351   {
 352     return viewport;
 353   }
 354
 355   public SeqCanvas getSeqcanvas()
 356   {
 357     return alignPanel.seqPanel.seqCanvas;
 358   }
 359
 360   /**
 361    * Load a features file onto the alignment
 362    *
 363    * @param file
 364    *          file URL, content, or other resolvable path
 365    * @param type
 366    *          is protocol for accessing data referred to by file
 367    */
 368
 369   public boolean parseFeaturesFile(String file, DataSourceType type)
 370   {
 371     return parseFeaturesFile(file, type, true);
 372   }
 373
 374   /**
 375    * Load a features file onto the alignment
 376    *
 377    * @param file
 378    *          file URL, content, or other resolvable path
 379    * @param sourceType
 380    *          is protocol for accessing data referred to by file
 381    * @param autoenabledisplay
 382    *          when true, display features flag will be automatically enabled if
 383    *          features are loaded
 384    * @return true if data parsed as a features file
 385    */
 386   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 387           boolean autoenabledisplay)
 388   {
 389     boolean featuresFile = false;
 390     try
 391     {
 392       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 393               .getFeatureRenderer().getFeatureColours();
 394       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 395               "relaxedidmatch", false);
 396       featuresFile = new FeaturesFile(file, sourceType).parse(
 397               viewport.getAlignment(), colours, true, relaxedIdMatching);
 398     } catch (Exception ex)
 399     {
 400       ex.printStackTrace();
 401     }
 402
 403     if (featuresFile)
 404     {
 405       if (autoenabledisplay)
 406       {
 407         viewport.setShowSequenceFeatures(true);
 408         sequenceFeatures.setState(true);
 409       }
 410       if (alignPanel.seqPanel.seqCanvas.fr != null)
 411       {
 412         // update the min/max ranges where necessary
 413         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 414       }
 415       if (viewport.featureSettings != null)
 416       {
 417         viewport.featureSettings.refreshTable();
 418       }
 419       alignPanel.paintAlignment(true);
 420       statusBar.setText(MessageManager
 421               .getString("label.successfully_added_features_alignment"));
 422     }
 423     return featuresFile;
 424   }
 425
 426   @Override
 427   public void keyPressed(KeyEvent evt)
 428   {
 429     ViewportRanges ranges = viewport.getRanges();
 430
 431     if (viewport.cursorMode
 432             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 433                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 434                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 435             && Character.isDigit(evt.getKeyChar()))
 436     {
 437       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 438     }
 439
 440     switch (evt.getKeyCode())
 441     {
 442     case 27: // escape key
 443       deselectAllSequenceMenuItem_actionPerformed();
 444
 445       alignPanel.alabels.cancelDrag();
 446       break;
 447     case KeyEvent.VK_X:
 448       if (evt.isControlDown() || evt.isMetaDown())
 449       {
 450         cut_actionPerformed();
 451       }
 452       break;
 453     case KeyEvent.VK_C:
 454       if (viewport.cursorMode && !evt.isControlDown())
 455       {
 456         alignPanel.seqPanel.setCursorColumn();
 457       }
 458       if (evt.isControlDown() || evt.isMetaDown())
 459       {
 460         copy_actionPerformed();
 461       }
 462       break;
 463     case KeyEvent.VK_V:
 464       if (evt.isControlDown())
 465       {
 466         paste(evt.isShiftDown());
 467       }
 468       break;
 469     case KeyEvent.VK_A:
 470       if (evt.isControlDown() || evt.isMetaDown())
 471       {
 472         selectAllSequenceMenuItem_actionPerformed();
 473       }
 474       break;
 475     case KeyEvent.VK_DOWN:
 476       if (viewport.cursorMode)
 477       {
 478         alignPanel.seqPanel.moveCursor(0, 1);
 479       }
 480       else
 481       {
 482         moveSelectedSequences(false);
 483       }
 484       break;
 485
 486     case KeyEvent.VK_UP:
 487       if (viewport.cursorMode)
 488       {
 489         alignPanel.seqPanel.moveCursor(0, -1);
 490       }
 491       else
 492       {
 493         moveSelectedSequences(true);
 494       }
 495       break;
 496
 497     case KeyEvent.VK_LEFT:
 498       if (evt.isAltDown() || !viewport.cursorMode)
 499       {
 500         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 501       }
 502       else
 503       {
 504         alignPanel.seqPanel.moveCursor(-1, 0);
 505       }
 506       break;
 507
 508     case KeyEvent.VK_RIGHT:
 509       if (evt.isAltDown() || !viewport.cursorMode)
 510       {
 511         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 512       }
 513       else
 514       {
 515         alignPanel.seqPanel.moveCursor(1, 0);
 516       }
 517       break;
 518
 519     case KeyEvent.VK_SPACE:
 520       if (viewport.cursorMode)
 521       {
 522         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 523                 || evt.isShiftDown() || evt.isAltDown());
 524       }
 525       break;
 526
 527     case KeyEvent.VK_DELETE:
 528     case KeyEvent.VK_BACK_SPACE:
 529       if (viewport.cursorMode)
 530       {
 531         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 532                 || evt.isShiftDown() || evt.isAltDown());
 533       }
 534       else
 535       {
 536         cut_actionPerformed();
 537         alignPanel.seqPanel.seqCanvas.repaint();
 538       }
 539       break;
 540
 541     case KeyEvent.VK_S:
 542       if (viewport.cursorMode)
 543       {
 544         alignPanel.seqPanel.setCursorRow();
 545       }
 546       break;
 547     case KeyEvent.VK_P:
 548       if (viewport.cursorMode)
 549       {
 550         alignPanel.seqPanel.setCursorPosition();
 551       }
 552       break;
 553
 554     case KeyEvent.VK_ENTER:
 555     case KeyEvent.VK_COMMA:
 556       if (viewport.cursorMode)
 557       {
 558         alignPanel.seqPanel.setCursorRowAndColumn();
 559       }
 560       break;
 561
 562     case KeyEvent.VK_Q:
 563       if (viewport.cursorMode)
 564       {
 565         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 566       }
 567       break;
 568     case KeyEvent.VK_M:
 569       if (viewport.cursorMode)
 570       {
 571         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 572       }
 573       break;
 574
 575     case KeyEvent.VK_F2:
 576       viewport.cursorMode = !viewport.cursorMode;
 577       statusBar.setText(MessageManager.formatMessage(
 578               "label.keyboard_editing_mode",
 579               new String[] { (viewport.cursorMode ? "on" : "off") }));
 580       if (viewport.cursorMode)
 581       {
 582         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 583         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 584       }
 585       break;
 586
 587     case KeyEvent.VK_F:
 588       if (evt.isControlDown())
 589       {
 590         findMenuItem_actionPerformed();
 591       }
 592       break;
 593
 594     case KeyEvent.VK_H:
 595     {
 596       boolean toggleSeqs = !evt.isControlDown();
 597       boolean toggleCols = !evt.isShiftDown();
 598       toggleHiddenRegions(toggleSeqs, toggleCols);
 599       break;
 600     }
 601
 602     case KeyEvent.VK_PAGE_UP:
 603       if (viewport.getWrapAlignment())
 604       {
 605         ranges.scrollUp(true);
 606       }
 607       else
 608       {
 609         ranges.pageUp();
 610       }
 611       break;
 612
 613     case KeyEvent.VK_PAGE_DOWN:
 614       if (viewport.getWrapAlignment())
 615       {
 616         ranges.scrollUp(false);
 617       }
 618       else
 619       {
 620         ranges.pageDown();
 621       }
 622       break;
 623
 624     case KeyEvent.VK_Z:
 625       if (evt.isControlDown())
 626       {
 627         undoMenuItem_actionPerformed();
 628       }
 629       break;
 630
 631     case KeyEvent.VK_Y:
 632       if (evt.isControlDown())
 633       {
 634         redoMenuItem_actionPerformed();
 635       }
 636       break;
 637
 638     case KeyEvent.VK_L:
 639       if (evt.isControlDown())
 640       {
 641         trimAlignment(true);
 642       }
 643       break;
 644
 645     case KeyEvent.VK_R:
 646       if (evt.isControlDown())
 647       {
 648         trimAlignment(false);
 649       }
 650       break;
 651
 652     case KeyEvent.VK_E:
 653       if (evt.isControlDown())
 654       {
 655         if (evt.isShiftDown())
 656         {
 657           this.removeAllGapsMenuItem_actionPerformed();
 658         }
 659         else
 660         {
 661           removeGappedColumnMenuItem_actionPerformed();
 662         }
 663       }
 664       break;
 665     case KeyEvent.VK_I:
 666       if (evt.isControlDown())
 667       {
 668         if (evt.isAltDown())
 669         {
 670           invertColSel_actionPerformed();
 671         }
 672         else
 673         {
 674           invertSequenceMenuItem_actionPerformed();
 675         }
 676       }
 677       break;
 678
 679     case KeyEvent.VK_G:
 680       if (evt.isControlDown())
 681       {
 682         if (evt.isShiftDown())
 683         {
 684           this.unGroup_actionPerformed();
 685         }
 686         else
 687         {
 688           this.createGroup_actionPerformed();
 689         }
 690       }
 691       break;
 692
 693     case KeyEvent.VK_U:
 694       if (evt.isControlDown())
 695       {
 696         this.deleteGroups_actionPerformed();
 697       }
 698       break;
 699
 700     case KeyEvent.VK_T:
 701       if (evt.isControlDown())
 702       {
 703         newView(null);
 704       }
 705       break;
 706
 707     }
 708     alignPanel.paintAlignment(true);
 709   }
 710
 711   /**
 712    * called by key handler and the hide all/show all menu items
 713    *
 714    * @param toggleSeqs
 715    * @param toggleCols
 716    */
 717   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 718   {
 719     boolean hide = false;
 720     SequenceGroup sg = viewport.getSelectionGroup();
 721     if (!toggleSeqs && !toggleCols)
 722     {
 723       // Hide everything by the current selection - this is a hack - we do the
 724       // invert and then hide
 725       // first check that there will be visible columns after the invert.
 726       if (viewport.hasSelectedColumns()
 727               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 728                       .getEndRes()))
 729       {
 730         // now invert the sequence set, if required - empty selection implies
 731         // that no hiding is required.
 732         if (sg != null)
 733         {
 734           invertSequenceMenuItem_actionPerformed();
 735           sg = viewport.getSelectionGroup();
 736           toggleSeqs = true;
 737
 738         }
 739         viewport.expandColSelection(sg, true);
 740         // finally invert the column selection and get the new sequence
 741         // selection and indicate it should be hidden.
 742         invertColSel_actionPerformed();
 743         toggleCols = true;
 744       }
 745     }
 746
 747     if (toggleSeqs)
 748     {
 749       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 750       {
 751         hide = true;
 752         viewport.hideAllSelectedSeqs();
 753       }
 754       else if (!(toggleCols && viewport.hasSelectedColumns()))
 755       {
 756         viewport.showAllHiddenSeqs();
 757       }
 758     }
 759
 760     if (toggleCols)
 761     {
 762       if (viewport.hasSelectedColumns())
 763       {
 764         viewport.hideSelectedColumns();
 765         if (!toggleSeqs)
 766         {
 767           viewport.setSelectionGroup(sg);
 768         }
 769       }
 770       else if (!hide)
 771       {
 772         viewport.showAllHiddenColumns();
 773       }
 774       viewport.sendSelection();
 775     }
 776   }
 777
 778   @Override
 779   public void keyReleased(KeyEvent evt)
 780   {
 781   }
 782
 783   @Override
 784   public void keyTyped(KeyEvent evt)
 785   {
 786   }
 787
 788   @Override
 789   public void itemStateChanged(ItemEvent evt)
 790   {
 791     final Object source = evt.getSource();
 792     if (source == displayNonconservedMenuItem)
 793     {
 794       displayNonconservedMenuItem_actionPerformed();
 795     }
 796     else if (source == colourTextMenuItem)
 797     {
 798       colourTextMenuItem_actionPerformed();
 799     }
 800     else if (source == wrapMenuItem)
 801     {
 802       wrapMenuItem_actionPerformed();
 803     }
 804     else if (source == scaleAbove)
 805     {
 806       viewport.setScaleAboveWrapped(scaleAbove.getState());
 807     }
 808     else if (source == scaleLeft)
 809     {
 810       viewport.setScaleLeftWrapped(scaleLeft.getState());
 811     }
 812     else if (source == scaleRight)
 813     {
 814       viewport.setScaleRightWrapped(scaleRight.getState());
 815     }
 816     else if (source == seqLimits)
 817     {
 818       seqLimits_itemStateChanged();
 819     }
 820     else if (source == viewBoxesMenuItem)
 821     {
 822       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 823     }
 824     else if (source == viewTextMenuItem)
 825     {
 826       viewport.setShowText(viewTextMenuItem.getState());
 827     }
 828     else if (source == renderGapsMenuItem)
 829     {
 830       viewport.setRenderGaps(renderGapsMenuItem.getState());
 831     }
 832     else if (source == annotationPanelMenuItem)
 833     {
 834       boolean showAnnotations = annotationPanelMenuItem.getState();
 835       showAlignmentAnnotations.setEnabled(showAnnotations);
 836       showSequenceAnnotations.setEnabled(showAnnotations);
 837       viewport.setShowAnnotation(showAnnotations);
 838       alignPanel.setAnnotationVisible(showAnnotations);
 839     }
 840     else if (source == sequenceFeatures)
 841     {
 842       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 843       alignPanel.seqPanel.seqCanvas.repaint();
 844     }
 845     else if (source == showAlignmentAnnotations)
 846     {
 847       setAnnotationsVisibility();
 848     }
 849     else if (source == showSequenceAnnotations)
 850     {
 851       setAnnotationsVisibility();
 852     }
 853     else if (source == sortAnnBySequence)
 854     {
 855       boolean newState = sortAnnBySequence.getState();
 856       sortAnnByLabel.setState(false);
 857       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 858               : SequenceAnnotationOrder.NONE);
 859       setViewportAnnotationOrder();
 860     }
 861     else if (source == sortAnnByLabel)
 862     {
 863       boolean newState = sortAnnByLabel.getState();
 864       sortAnnBySequence.setState(false);
 865       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 866               : SequenceAnnotationOrder.NONE);
 867       setViewportAnnotationOrder();
 868     }
 869     else if (source == showAutoFirst)
 870     {
 871       showAutoLast.setState(!showAutoFirst.getState());
 872       setShowAutoCalculatedAbove(showAutoFirst.getState());
 873       setViewportAnnotationOrder();
 874     }
 875     else if (source == showAutoLast)
 876     {
 877       showAutoFirst.setState(!showAutoLast.getState());
 878       setShowAutoCalculatedAbove(showAutoFirst.getState());
 879       setViewportAnnotationOrder();
 880     }
 881     else if (source == conservationMenuItem)
 882     {
 883       conservationMenuItem_actionPerformed();
 884     }
 885     else if (source == abovePIDThreshold)
 886     {
 887       abovePIDThreshold_actionPerformed();
 888     }
 889     else if (source == applyToAllGroups)
 890     {
 891       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 892     }
 893     else if (source == autoCalculate)
 894     {
 895       viewport.autoCalculateConsensus = autoCalculate.getState();
 896     }
 897     else if (source == sortByTree)
 898     {
 899       viewport.sortByTree = sortByTree.getState();
 900     }
 901     else if (source == this.centreColumnLabelFlag)
 902     {
 903       centreColumnLabelFlag_stateChanged();
 904     }
 905     else if (source == this.followMouseOverFlag)
 906     {
 907       mouseOverFlag_stateChanged();
 908     }
 909     else if (source == showGroupConsensus)
 910     {
 911       showGroupConsensus_actionPerformed();
 912     }
 913     else if (source == showGroupConservation)
 914     {
 915       showGroupConservation_actionPerformed();
 916     }
 917     else if (source == showSequenceLogo)
 918     {
 919       showSequenceLogo_actionPerformed();
 920     }
 921     else if (source == normSequenceLogo)
 922     {
 923       normSequenceLogo_actionPerformed();
 924     }
 925     else if (source == showConsensusHistogram)
 926     {
 927       showConsensusHistogram_actionPerformed();
 928     }
 929     else if (source == applyAutoAnnotationSettings)
 930     {
 931       applyAutoAnnotationSettings_actionPerformed();
 932     }
 933     alignPanel.paintAlignment(true);
 934   }
 935
 936   /**
 937    * Set the visibility state of sequence-related and/or alignment-related
 938    * annotations depending on checkbox selections, and repaint.
 939    *
 940    * @param visible
 941    */
 942   private void setAnnotationsVisibility()
 943   {
 944     boolean showForAlignment = showAlignmentAnnotations.getState();
 945     boolean showForSequences = showSequenceAnnotations.getState();
 946     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 947     {
 948       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 949               .getAlignmentAnnotation())
 950       {
 951         boolean visible = (aa.sequenceRef == null ? showForAlignment
 952                 : showForSequences);
 953         aa.visible = visible;
 954       }
 955     }
 956     alignPanel.validateAnnotationDimensions(true);
 957     validate();
 958     repaint();
 959   }
 960
 961   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 962   {
 963     this.annotationSortOrder = order;
 964   }
 965
 966   /**
 967    * Set flags on the viewport that control annotation ordering
 968    */
 969   private void setViewportAnnotationOrder()
 970   {
 971     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 972     this.alignPanel.av
 973             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 974   }
 975
 976   private void setShowAutoCalculatedAbove(boolean showAbove)
 977   {
 978     this.showAutoCalculatedAbove = showAbove;
 979   }
 980
 981   private void mouseOverFlag_stateChanged()
 982   {
 983     viewport.setFollowHighlight(followMouseOverFlag.getState());
 984     // TODO: could kick the scrollTo mechanism to reset view for current
 985     // searchresults.
 986   }
 987
 988   private void centreColumnLabelFlag_stateChanged()
 989   {
 990     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 991     this.alignPanel.annotationPanel.repaint();
 992   }
 993
 994   @Override
 995   public void actionPerformed(ActionEvent evt)
 996   {
 997     viewport.applet.currentAlignFrame = this;
 998
 999     Object source = evt.getSource();
1000
1001     if (source == inputText)
1002     {
1003       inputText_actionPerformed();
1004     }
1005     else if (source == loadTree)
1006     {
1007       loadTree_actionPerformed();
1008     }
1009     else if (source == loadApplication)
1010     {
1011       launchFullApplication();
1012     }
1013     else if (source == loadAnnotations)
1014     {
1015       loadAnnotations();
1016     }
1017     else if (source == outputAnnotations)
1018     {
1019       outputAnnotations(true);
1020     }
1021     else if (source == outputFeatures)
1022     {
1023       outputFeatures(true, "Jalview");
1024     }
1025     else if (source == closeMenuItem)
1026     {
1027       closeMenuItem_actionPerformed();
1028     }
1029     else if (source == copy)
1030     {
1031       copy_actionPerformed();
1032     }
1033     else if (source == undoMenuItem)
1034     {
1035       undoMenuItem_actionPerformed();
1036     }
1037     else if (source == redoMenuItem)
1038     {
1039       redoMenuItem_actionPerformed();
1040     }
1041     else if (source == inputText)
1042     {
1043       inputText_actionPerformed();
1044     }
1045     else if (source == closeMenuItem)
1046     {
1047       closeMenuItem_actionPerformed();
1048     }
1049     else if (source == undoMenuItem)
1050     {
1051       undoMenuItem_actionPerformed();
1052     }
1053     else if (source == redoMenuItem)
1054     {
1055       redoMenuItem_actionPerformed();
1056     }
1057     else if (source == copy)
1058     {
1059       copy_actionPerformed();
1060     }
1061     else if (source == pasteNew)
1062     {
1063       pasteNew_actionPerformed();
1064     }
1065     else if (source == pasteThis)
1066     {
1067       pasteThis_actionPerformed();
1068     }
1069     else if (source == cut)
1070     {
1071       cut_actionPerformed();
1072     }
1073     else if (source == delete)
1074     {
1075       delete_actionPerformed();
1076     }
1077     else if (source == createGroup)
1078     {
1079       createGroup_actionPerformed();
1080     }
1081     else if (source == unGroup)
1082     {
1083       unGroup_actionPerformed();
1084     }
1085     else if (source == grpsFromSelection)
1086     {
1087       makeGrpsFromSelection_actionPerformed();
1088     }
1089     else if (source == deleteGroups)
1090     {
1091       deleteGroups_actionPerformed();
1092     }
1093     else if (source == selectAllSequenceMenuItem)
1094     {
1095       selectAllSequenceMenuItem_actionPerformed();
1096     }
1097     else if (source == deselectAllSequenceMenuItem)
1098     {
1099       deselectAllSequenceMenuItem_actionPerformed();
1100     }
1101     else if (source == invertSequenceMenuItem)
1102     {
1103       invertSequenceMenuItem_actionPerformed();
1104       // uncomment to slave sequence selections in split frame
1105       // viewport.sendSelection();
1106     }
1107     else if (source == invertColSel)
1108     {
1109       viewport.invertColumnSelection();
1110       alignPanel.paintAlignment(true);
1111       viewport.sendSelection();
1112     }
1113     else if (source == remove2LeftMenuItem)
1114     {
1115       trimAlignment(true);
1116     }
1117     else if (source == remove2RightMenuItem)
1118     {
1119       trimAlignment(false);
1120     }
1121     else if (source == removeGappedColumnMenuItem)
1122     {
1123       removeGappedColumnMenuItem_actionPerformed();
1124     }
1125     else if (source == removeAllGapsMenuItem)
1126     {
1127       removeAllGapsMenuItem_actionPerformed();
1128     }
1129     else if (source == findMenuItem)
1130     {
1131       findMenuItem_actionPerformed();
1132     }
1133     else if (source == font)
1134     {
1135       new FontChooser(alignPanel);
1136     }
1137     else if (source == newView)
1138     {
1139       newView(null);
1140     }
1141     else if (source == showColumns)
1142     {
1143       viewport.showAllHiddenColumns();
1144       alignPanel.paintAlignment(true);
1145       viewport.sendSelection();
1146     }
1147     else if (source == showSeqs)
1148     {
1149       viewport.showAllHiddenSeqs();
1150       alignPanel.paintAlignment(true);
1151       // uncomment if we want to slave sequence selections in split frame
1152       // viewport.sendSelection();
1153     }
1154     else if (source == hideColumns)
1155     {
1156       viewport.hideSelectedColumns();
1157       alignPanel.paintAlignment(true);
1158       viewport.sendSelection();
1159     }
1160     else if (source == hideSequences
1161             && viewport.getSelectionGroup() != null)
1162     {
1163       viewport.hideAllSelectedSeqs();
1164       alignPanel.paintAlignment(true);
1165       // uncomment if we want to slave sequence selections in split frame
1166       // viewport.sendSelection();
1167     }
1168     else if (source == hideAllButSelection)
1169     {
1170       toggleHiddenRegions(false, false);
1171       alignPanel.paintAlignment(true);
1172       viewport.sendSelection();
1173     }
1174     else if (source == hideAllSelection)
1175     {
1176       SequenceGroup sg = viewport.getSelectionGroup();
1177       viewport.expandColSelection(sg, false);
1178       viewport.hideAllSelectedSeqs();
1179       viewport.hideSelectedColumns();
1180       alignPanel.paintAlignment(true);
1181       viewport.sendSelection();
1182     }
1183     else if (source == showAllHidden)
1184     {
1185       viewport.showAllHiddenColumns();
1186       viewport.showAllHiddenSeqs();
1187       alignPanel.paintAlignment(true);
1188       viewport.sendSelection();
1189     }
1190     else if (source == showGroupConsensus)
1191     {
1192       showGroupConsensus_actionPerformed();
1193     }
1194     else if (source == showGroupConservation)
1195     {
1196       showGroupConservation_actionPerformed();
1197     }
1198     else if (source == showSequenceLogo)
1199     {
1200       showSequenceLogo_actionPerformed();
1201     }
1202     else if (source == normSequenceLogo)
1203     {
1204       normSequenceLogo_actionPerformed();
1205     }
1206     else if (source == showConsensusHistogram)
1207     {
1208       showConsensusHistogram_actionPerformed();
1209     }
1210     else if (source == applyAutoAnnotationSettings)
1211     {
1212       applyAutoAnnotationSettings_actionPerformed();
1213     }
1214     else if (source == featureSettings)
1215     {
1216       new FeatureSettings(alignPanel);
1217     }
1218     else if (source == alProperties)
1219     {
1220       StringBuffer contents = new jalview.io.AlignmentProperties(
1221               viewport.getAlignment()).formatAsString();
1222       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1223       cap.setText(contents.toString());
1224       Frame frame = new Frame();
1225       frame.add(cap);
1226       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1227               "label.alignment_properties", new String[] { getTitle() }),
1228               400, 250);
1229     }
1230     else if (source == overviewMenuItem)
1231     {
1232       overviewMenuItem_actionPerformed();
1233     }
1234     else if (source == noColourmenuItem)
1235     {
1236       changeColour(null);
1237     }
1238     else if (source == clustalColour)
1239     {
1240       abovePIDThreshold.setState(false);
1241       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1242     }
1243     else if (source == zappoColour)
1244     {
1245       changeColour(new ZappoColourScheme());
1246     }
1247     else if (source == taylorColour)
1248     {
1249       changeColour(new TaylorColourScheme());
1250     }
1251     else if (source == hydrophobicityColour)
1252     {
1253       changeColour(new HydrophobicColourScheme());
1254     }
1255     else if (source == helixColour)
1256     {
1257       changeColour(new HelixColourScheme());
1258     }
1259     else if (source == strandColour)
1260     {
1261       changeColour(new StrandColourScheme());
1262     }
1263     else if (source == turnColour)
1264     {
1265       changeColour(new TurnColourScheme());
1266     }
1267     else if (source == buriedColour)
1268     {
1269       changeColour(new BuriedColourScheme());
1270     }
1271     else if (source == nucleotideColour)
1272     {
1273       changeColour(new NucleotideColourScheme());
1274     }
1275     else if (source == purinePyrimidineColour)
1276     {
1277       changeColour(new PurinePyrimidineColourScheme());
1278     }
1279     // else if (source == RNAInteractionColour)
1280     // {
1281     // changeColour(new RNAInteractionColourScheme());
1282     // }
1283     else if (source == RNAHelixColour)
1284     {
1285       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1286       // new RNAHelicesColourChooser(viewport, alignPanel);
1287     }
1288     else if (source == modifyPID)
1289     {
1290       modifyPID_actionPerformed();
1291     }
1292     else if (source == modifyConservation)
1293     {
1294       modifyConservation_actionPerformed();
1295     }
1296     else if (source == userDefinedColour)
1297     {
1298       new UserDefinedColours(alignPanel, null);
1299     }
1300     else if (source == PIDColour)
1301     {
1302       changeColour(new PIDColourScheme());
1303     }
1304     else if (source == BLOSUM62Colour)
1305     {
1306       changeColour(new Blosum62ColourScheme());
1307     }
1308     else if (source == tcoffeeColour)
1309     {
1310       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1311     }
1312     else if (source == annotationColour)
1313     {
1314       new AnnotationColourChooser(viewport, alignPanel);
1315     }
1316     else if (source == annotationColumnSelection)
1317     {
1318       new AnnotationColumnChooser(viewport, alignPanel);
1319     }
1320     else if (source == sortPairwiseMenuItem)
1321     {
1322       sortPairwiseMenuItem_actionPerformed();
1323     }
1324     else if (source == sortIDMenuItem)
1325     {
1326       sortIDMenuItem_actionPerformed();
1327     }
1328     else if (source == sortLengthMenuItem)
1329     {
1330       sortLengthMenuItem_actionPerformed();
1331     }
1332     else if (source == sortGroupMenuItem)
1333     {
1334       sortGroupMenuItem_actionPerformed();
1335     }
1336     else if (source == removeRedundancyMenuItem)
1337     {
1338       removeRedundancyMenuItem_actionPerformed();
1339     }
1340     else if (source == pairwiseAlignmentMenuItem)
1341     {
1342       pairwiseAlignmentMenuItem_actionPerformed();
1343     }
1344     else if (source == PCAMenuItem)
1345     {
1346       PCAMenuItem_actionPerformed();
1347     }
1348     else if (source == averageDistanceTreeMenuItem)
1349     {
1350       averageDistanceTreeMenuItem_actionPerformed();
1351     }
1352     else if (source == neighbourTreeMenuItem)
1353     {
1354       neighbourTreeMenuItem_actionPerformed();
1355     }
1356     else if (source == njTreeBlosumMenuItem)
1357     {
1358       njTreeBlosumMenuItem_actionPerformed();
1359     }
1360     else if (source == avDistanceTreeBlosumMenuItem)
1361     {
1362       avTreeBlosumMenuItem_actionPerformed();
1363     }
1364     else if (source == documentation)
1365     {
1366       documentation_actionPerformed();
1367     }
1368     else if (source == about)
1369     {
1370       about_actionPerformed();
1371     }
1372
1373   }
1374
1375   public void inputText_actionPerformed()
1376   {
1377     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378     Frame frame = new Frame();
1379     frame.add(cap);
1380     jalview.bin.JalviewLite.addFrame(frame,
1381             MessageManager.getString("label.input_cut_paste"), 500, 500);
1382   }
1383
1384   protected void outputText_actionPerformed(ActionEvent e)
1385   {
1386     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1387     Frame frame = new Frame();
1388     frame.add(cap);
1389     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1390             "label.alignment_output_command",
1391             new Object[] { e.getActionCommand() }), 600, 500);
1392
1393     FileFormatI fileFormat = FileFormats.getInstance().forName(
1394             e.getActionCommand());
1395     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1396             fileFormat, viewport.getAlignment(),
1397             viewport.getShowJVSuffix()));
1398   }
1399
1400   public void loadAnnotations()
1401   {
1402     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1403     cap.setText(MessageManager
1404             .getString("label.paste_features_annotations_Tcoffee_here"));
1405     cap.setAnnotationImport();
1406     Frame frame = new Frame();
1407     frame.add(cap);
1408     jalview.bin.JalviewLite.addFrame(frame,
1409             MessageManager.getString("action.paste_annotations"), 400, 300);
1410
1411   }
1412
1413   public String outputAnnotations(boolean displayTextbox)
1414   {
1415     String annotation = new AnnotationFile()
1416             .printAnnotationsForView(viewport);
1417
1418     if (displayTextbox)
1419     {
1420       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1421       Frame frame = new Frame();
1422       frame.add(cap);
1423       jalview.bin.JalviewLite.addFrame(frame,
1424               MessageManager.getString("label.annotations"), 600, 500);
1425       cap.setText(annotation);
1426     }
1427
1428     return annotation;
1429   }
1430
1431   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1432   {
1433     if (alignPanel.getFeatureRenderer() != null
1434             && viewport.getFeaturesDisplayed() != null)
1435     {
1436       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1437
1438     }
1439     return null;
1440   }
1441
1442   public String outputFeatures(boolean displayTextbox, String format)
1443   {
1444     String features;
1445     FeaturesFile formatter = new FeaturesFile();
1446     if (format.equalsIgnoreCase("Jalview"))
1447     {
1448       features = formatter.printJalviewFormat(viewport.getAlignment()
1449               .getSequencesArray(), getDisplayedFeatureCols());
1450     }
1451     else
1452     {
1453       features = formatter.printGffFormat(viewport.getAlignment()
1454               .getSequencesArray(), getDisplayedFeatureCols());
1455     }
1456
1457     if (displayTextbox)
1458     {
1459       boolean frimport = false;
1460       if (features == null || features.equals("No Features Visible"))
1461       {
1462         features = "# No features visible - paste some and import them here.";
1463         frimport = true;
1464       }
1465
1466       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1467       if (frimport)
1468       {
1469         cap.setAnnotationImport();
1470       }
1471       Frame frame = new Frame();
1472       frame.add(cap);
1473       jalview.bin.JalviewLite.addFrame(frame,
1474               MessageManager.getString("label.features"), 600, 500);
1475       cap.setText(features);
1476     }
1477     else
1478     {
1479       if (features == null)
1480       {
1481         features = "";
1482       }
1483     }
1484
1485     return features;
1486   }
1487
1488   void launchFullApplication()
1489   {
1490     StringBuffer url = new StringBuffer(jalviewServletURL);
1491
1492     // allow servlet parameters to be passed in applet parameter
1493     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1494             : "?";
1495     url.append(firstSep);
1496
1497     url.append("open="
1498             + appendProtocol(viewport.applet.getParameter("file")));
1499
1500     if (viewport.applet.getParameter("features") != null)
1501     {
1502       url.append("&features=");
1503       url.append(appendProtocol(viewport.applet.getParameter("features")));
1504     }
1505
1506     if (viewport.applet.getParameter("annotations") != null)
1507     {
1508       url.append("&annotations=");
1509       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1510     }
1511
1512     if (viewport.applet.getParameter("jnetfile") != null
1513             || viewport.applet.getParameter("jpredfile") != null)
1514     {
1515       url.append("&annotations=");
1516       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1517               .getParameter("jnetfile") : viewport.applet
1518               .getParameter("jpredfile")));
1519     }
1520
1521     if (viewport.applet.getParameter("defaultColour") != null)
1522     {
1523       url.append("&colour="
1524               + removeWhiteSpace(viewport.applet
1525                       .getParameter("defaultColour")));
1526     }
1527
1528     if (viewport.applet.getParameter("userDefinedColour") != null)
1529     {
1530       url.append("&colour="
1531               + removeWhiteSpace(viewport.applet
1532                       .getParameter("userDefinedColour")));
1533     }
1534     if (viewport.applet.getParameter("tree") != null)
1535     {
1536       url.append("&tree="
1537               + appendProtocol(viewport.applet.getParameter("tree")));
1538     }
1539     if (viewport.applet.getParameter("treeFile") != null)
1540     {
1541       url.append("&tree="
1542               + appendProtocol(viewport.applet.getParameter("treeFile")));
1543     }
1544
1545     showURL(url.toString(), "FULL_APP");
1546   }
1547
1548   String removeWhiteSpace(String colour)
1549   {
1550     StringBuffer sb = new StringBuffer();
1551     for (int i = 0; i < colour.length(); i++)
1552     {
1553       if (Character.isWhitespace(colour.charAt(i)))
1554       {
1555         sb.append("%20");
1556       }
1557       else
1558       {
1559         sb.append(colour.charAt(i));
1560       }
1561     }
1562
1563     return sb.toString();
1564   }
1565
1566   String appendProtocol(String url)
1567   {
1568     try
1569     {
1570       new URL(url);
1571       url = URLEncoder.encode(url);
1572     }
1573     /*
1574      * When we finally deprecate 1.1 compatibility, we can start to use
1575      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1576      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1577      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1578      * ex.printStackTrace(); }
1579      */
1580     catch (java.net.MalformedURLException ex)
1581     {
1582       url = viewport.applet.getCodeBase() + url;
1583     }
1584     return url;
1585   }
1586
1587   public void closeMenuItem_actionPerformed()
1588   {
1589     PaintRefresher.RemoveComponent(alignPanel);
1590     if (alignPanel.seqPanel != null
1591             && alignPanel.seqPanel.seqCanvas != null)
1592     {
1593       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1594     }
1595     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1596     {
1597       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1598     }
1599
1600     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1601     {
1602       System.exit(0);
1603     }
1604     else
1605     {
1606     }
1607     viewport = null;
1608     alignPanel = null;
1609     this.dispose();
1610   }
1611
1612   /**
1613    * TODO: JAL-1104
1614    */
1615   void updateEditMenuBar()
1616   {
1617
1618     if (viewport.getHistoryList().size() > 0)
1619     {
1620       undoMenuItem.setEnabled(true);
1621       CommandI command = viewport.getHistoryList().peek();
1622       undoMenuItem.setLabel(MessageManager.formatMessage(
1623               "label.undo_command",
1624               new Object[] { command.getDescription() }));
1625     }
1626     else
1627     {
1628       undoMenuItem.setEnabled(false);
1629       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1630     }
1631
1632     if (viewport.getRedoList().size() > 0)
1633     {
1634       redoMenuItem.setEnabled(true);
1635
1636       CommandI command = viewport.getRedoList().peek();
1637       redoMenuItem.setLabel(MessageManager.formatMessage(
1638               "label.redo_command",
1639               new Object[] { command.getDescription() }));
1640     }
1641     else
1642     {
1643       redoMenuItem.setEnabled(false);
1644       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1645     }
1646   }
1647
1648   /**
1649    * TODO: JAL-1104
1650    */
1651   @Override
1652   public void addHistoryItem(CommandI command)
1653   {
1654     if (command.getSize() > 0)
1655     {
1656       viewport.addToHistoryList(command);
1657       viewport.clearRedoList();
1658       updateEditMenuBar();
1659       viewport.updateHiddenColumns();
1660     }
1661   }
1662
1663   /**
1664    * TODO: JAL-1104 DOCUMENT ME!
1665    *
1666    * @param e
1667    *          DOCUMENT ME!
1668    */
1669   protected void undoMenuItem_actionPerformed()
1670   {
1671     if (viewport.getHistoryList().isEmpty())
1672     {
1673       return;
1674     }
1675
1676     CommandI command = viewport.getHistoryList().pop();
1677     viewport.addToRedoList(command);
1678     command.undoCommand(null);
1679
1680     AlignmentViewport originalSource = getOriginatingSource(command);
1681     // JBPNote Test
1682     if (originalSource != viewport)
1683     {
1684       System.err
1685               .println("Warning: Viewport object mismatch whilst undoing");
1686     }
1687     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1688                                           // viewport.getColumnSelection().getHiddenColumns()
1689                                           // != null;
1690     updateEditMenuBar();
1691     originalSource.firePropertyChange("alignment", null, originalSource
1692             .getAlignment().getSequences());
1693   }
1694
1695   /**
1696    * TODO: JAL-1104 DOCUMENT ME!
1697    *
1698    * @param e
1699    *          DOCUMENT ME!
1700    */
1701   protected void redoMenuItem_actionPerformed()
1702   {
1703     if (viewport.getRedoList().isEmpty())
1704     {
1705       return;
1706     }
1707
1708     CommandI command = viewport.getRedoList().pop();
1709     viewport.addToHistoryList(command);
1710     command.doCommand(null);
1711
1712     AlignmentViewport originalSource = getOriginatingSource(command);
1713     // JBPNote Test
1714     if (originalSource != viewport)
1715     {
1716       System.err
1717               .println("Warning: Viewport object mismatch whilst re-doing");
1718     }
1719     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1720                                           // viewport.getColumnSelection().getHiddenColumns()
1721                                           // != null;
1722
1723     updateEditMenuBar();
1724     originalSource.firePropertyChange("alignment", null, originalSource
1725             .getAlignment().getSequences());
1726   }
1727
1728   AlignmentViewport getOriginatingSource(CommandI command)
1729   {
1730     AlignmentViewport originalSource = null;
1731     // For sequence removal and addition, we need to fire
1732     // the property change event FROM the viewport where the
1733     // original alignment was altered
1734     AlignmentI al = null;
1735     if (command instanceof EditCommand)
1736     {
1737       EditCommand editCommand = (EditCommand) command;
1738       al = editCommand.getAlignment();
1739       Vector comps = (Vector) PaintRefresher.components.get(viewport
1740               .getSequenceSetId());
1741       for (int i = 0; i < comps.size(); i++)
1742       {
1743         if (comps.elementAt(i) instanceof AlignmentPanel)
1744         {
1745           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1746           {
1747             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1748             break;
1749           }
1750         }
1751       }
1752     }
1753
1754     if (originalSource == null)
1755     {
1756       // The original view is closed, we must validate
1757       // the current view against the closed view first
1758       if (al != null)
1759       {
1760         PaintRefresher.validateSequences(al, viewport.getAlignment());
1761       }
1762
1763       originalSource = viewport;
1764     }
1765
1766     return originalSource;
1767   }
1768
1769   /**
1770    * Move the currently selected sequences up or down one position in the
1771    * alignment
1772    *
1773    * @param up
1774    */
1775   public void moveSelectedSequences(boolean up)
1776   {
1777     SequenceGroup sg = viewport.getSelectionGroup();
1778     if (sg == null)
1779     {
1780       return;
1781     }
1782     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1783             up ? null : viewport.getHiddenRepSequences(), up);
1784     alignPanel.paintAlignment(true);
1785
1786     /*
1787      * Also move cDNA/protein complement sequences
1788      */
1789     AlignViewportI complement = viewport.getCodingComplement();
1790     if (complement != null)
1791     {
1792       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1793               viewport, complement);
1794       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1795               up ? null : complement.getHiddenRepSequences(), up);
1796       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1797     }
1798   }
1799
1800   synchronized void slideSequences(boolean right, int size)
1801   {
1802     List<SequenceI> sg = new Vector<>();
1803     if (viewport.cursorMode)
1804     {
1805       sg.add(viewport.getAlignment().getSequenceAt(
1806               alignPanel.seqPanel.seqCanvas.cursorY));
1807     }
1808     else if (viewport.getSelectionGroup() != null
1809             && viewport.getSelectionGroup().getSize() != viewport
1810                     .getAlignment().getHeight())
1811     {
1812       sg = viewport.getSelectionGroup().getSequences(
1813               viewport.getHiddenRepSequences());
1814     }
1815
1816     if (sg.size() < 1)
1817     {
1818       return;
1819     }
1820
1821     Vector<SequenceI> invertGroup = new Vector();
1822
1823     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1824     {
1825       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1826       {
1827         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1828       }
1829     }
1830
1831     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1832
1833     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1834             .size()]);
1835     for (int i = 0; i < invertGroup.size(); i++)
1836     {
1837       seqs2[i] = invertGroup.elementAt(i);
1838     }
1839
1840     SlideSequencesCommand ssc;
1841     if (right)
1842     {
1843       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1844               size, viewport.getGapCharacter());
1845     }
1846     else
1847     {
1848       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1849               size, viewport.getGapCharacter());
1850     }
1851
1852     int groupAdjustment = 0;
1853     if (ssc.getGapsInsertedBegin() && right)
1854     {
1855       if (viewport.cursorMode)
1856       {
1857         alignPanel.seqPanel.moveCursor(size, 0);
1858       }
1859       else
1860       {
1861         groupAdjustment = size;
1862       }
1863     }
1864     else if (!ssc.getGapsInsertedBegin() && !right)
1865     {
1866       if (viewport.cursorMode)
1867       {
1868         alignPanel.seqPanel.moveCursor(-size, 0);
1869       }
1870       else
1871       {
1872         groupAdjustment = -size;
1873       }
1874     }
1875
1876     if (groupAdjustment != 0)
1877     {
1878       viewport.getSelectionGroup().setStartRes(
1879               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1880       viewport.getSelectionGroup().setEndRes(
1881               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1882     }
1883
1884     boolean appendHistoryItem = false;
1885     Deque<CommandI> historyList = viewport.getHistoryList();
1886     if (historyList != null && historyList.size() > 0
1887             && historyList.peek() instanceof SlideSequencesCommand)
1888     {
1889       appendHistoryItem = ssc
1890               .appendSlideCommand((SlideSequencesCommand) historyList
1891                       .peek());
1892     }
1893
1894     if (!appendHistoryItem)
1895     {
1896       addHistoryItem(ssc);
1897     }
1898
1899     repaint();
1900   }
1901
1902   static StringBuffer copiedSequences;
1903
1904   static Vector copiedHiddenColumns;
1905
1906   protected void copy_actionPerformed()
1907   {
1908     if (viewport.getSelectionGroup() == null)
1909     {
1910       return;
1911     }
1912
1913     SequenceGroup sg = viewport.getSelectionGroup();
1914     copiedSequences = new StringBuffer();
1915     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1916     for (int i = 0; i < sg.getSize(); i++)
1917     {
1918       SequenceI seq = sg.getSequenceAt(i);
1919       int index = viewport.getAlignment().findIndex(seq);
1920       orderedSeqs.put(index, seq);
1921     }
1922
1923     int index = 0, startRes, endRes;
1924     char ch;
1925
1926     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1927     {
1928       copiedHiddenColumns = new Vector();
1929       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1930       for (int[] region : viewport.getAlignment().getHiddenColumns()
1931               .getHiddenRegions())
1932       {
1933         copiedHiddenColumns.addElement(new int[] {
1934             region[0] - hiddenOffset, region[1] - hiddenOffset });
1935       }
1936     }
1937     else
1938     {
1939       copiedHiddenColumns = null;
1940     }
1941
1942     for (int i = 0; i < sg.getSize(); i++)
1943     {
1944       SequenceI seq = null;
1945
1946       while (seq == null)
1947       {
1948         if (orderedSeqs.containsKey(index))
1949         {
1950           seq = orderedSeqs.get(index);
1951           index++;
1952           break;
1953         }
1954         else
1955         {
1956           index++;
1957         }
1958       }
1959
1960       // FIND START RES
1961       // Returns residue following index if gap
1962       startRes = seq.findPosition(sg.getStartRes());
1963
1964       // FIND END RES
1965       // Need to find the residue preceeding index if gap
1966       endRes = 0;
1967
1968       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1969       {
1970         ch = seq.getCharAt(j);
1971         if (!jalview.util.Comparison.isGap((ch)))
1972         {
1973           endRes++;
1974         }
1975       }
1976
1977       if (endRes > 0)
1978       {
1979         endRes += seq.getStart() - 1;
1980       }
1981
1982       copiedSequences.append(seq.getName()
1983               + "\t"
1984               + startRes
1985               + "\t"
1986               + endRes
1987               + "\t"
1988               + seq.getSequenceAsString(sg.getStartRes(),
1989                       sg.getEndRes() + 1) + "\n");
1990     }
1991
1992   }
1993
1994   protected void pasteNew_actionPerformed()
1995   {
1996     paste(true);
1997   }
1998
1999   protected void pasteThis_actionPerformed()
2000   {
2001     paste(false);
2002   }
2003
2004   void paste(boolean newAlignment)
2005   {
2006     try
2007     {
2008
2009       if (copiedSequences == null)
2010       {
2011         return;
2012       }
2013
2014       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2015       Vector seqs = new Vector();
2016       while (st.hasMoreElements())
2017       {
2018         String name = st.nextToken();
2019         int start = Integer.parseInt(st.nextToken());
2020         int end = Integer.parseInt(st.nextToken());
2021         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2022       }
2023       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2024       for (int i = 0; i < seqs.size(); i++)
2025       {
2026         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2027       }
2028
2029       if (newAlignment)
2030       {
2031         String newtitle = MessageManager
2032                 .getString("label.copied_sequences");
2033         if (getTitle().startsWith(
2034                 MessageManager.getString("label.copied_sequences")))
2035         {
2036           newtitle = getTitle();
2037         }
2038         else
2039         {
2040           newtitle = newtitle.concat(MessageManager.formatMessage(
2041                   "label.from_msname", new String[] { getTitle() }));
2042         }
2043         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2044                 viewport.applet, newtitle, false);
2045         if (copiedHiddenColumns != null)
2046         {
2047           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2048           {
2049             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2050             af.viewport.hideColumns(region[0], region[1]);
2051           }
2052         }
2053
2054         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2055                 frameHeight);
2056       }
2057       else
2058       {
2059         addSequences(newSeqs);
2060       }
2061
2062     } catch (Exception ex)
2063     {
2064     } // could be anything being pasted in here
2065
2066   }
2067
2068   void addSequences(SequenceI[] seqs)
2069   {
2070     for (int i = 0; i < seqs.length; i++)
2071     {
2072       viewport.getAlignment().addSequence(seqs[i]);
2073     }
2074
2075     // !newAlignment
2076     addHistoryItem(new EditCommand(
2077             MessageManager.getString("label.add_sequences"), Action.PASTE,
2078             seqs, 0, viewport.getAlignment().getWidth(),
2079             viewport.getAlignment()));
2080
2081     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2082     viewport.getAlignment().getWidth();
2083     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2084             .getSequences());
2085
2086   }
2087
2088   protected void cut_actionPerformed()
2089   {
2090     copy_actionPerformed();
2091     delete_actionPerformed();
2092   }
2093
2094   protected void delete_actionPerformed()
2095   {
2096
2097     SequenceGroup sg = viewport.getSelectionGroup();
2098     if (sg == null)
2099     {
2100       return;
2101     }
2102
2103     Vector seqs = new Vector();
2104     SequenceI seq;
2105     for (int i = 0; i < sg.getSize(); i++)
2106     {
2107       seq = sg.getSequenceAt(i);
2108       seqs.addElement(seq);
2109     }
2110
2111     /*
2112      * If the cut affects all sequences, warn, remove highlighted columns
2113      */
2114     if (sg.getSize() == viewport.getAlignment().getHeight())
2115     {
2116       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2117               .getAlignment().getWidth()) ? true : false;
2118       if (isEntireAlignWidth)
2119       {
2120         String title = MessageManager.getString("label.delete_all");
2121         Panel infoPanel = new Panel();
2122         infoPanel.setLayout(new FlowLayout());
2123         infoPanel
2124                 .add(new Label(MessageManager.getString("warn.delete_all")));
2125
2126         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2127         dialog.setMainPanel(infoPanel);
2128         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2129         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2130         dialog.setVisible(true);
2131
2132         if (!dialog.accept)
2133         {
2134           return;
2135         }
2136       }
2137       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2138               sg.getEndRes() + 1);
2139     }
2140
2141     SequenceI[] cut = new SequenceI[seqs.size()];
2142     for (int i = 0; i < seqs.size(); i++)
2143     {
2144       cut[i] = (SequenceI) seqs.elementAt(i);
2145     }
2146
2147     /*
2148      * //ADD HISTORY ITEM
2149      */
2150     addHistoryItem(new EditCommand(
2151             MessageManager.getString("label.cut_sequences"), Action.CUT,
2152             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2153             viewport.getAlignment()));
2154
2155     viewport.setSelectionGroup(null);
2156     viewport.getAlignment().deleteGroup(sg);
2157
2158     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2159             .getSequences());
2160
2161     if (viewport.getAlignment().getHeight() < 1)
2162     {
2163       this.setVisible(false);
2164     }
2165     viewport.sendSelection();
2166   }
2167
2168   /**
2169    * group consensus toggled
2170    *
2171    */
2172   protected void showGroupConsensus_actionPerformed()
2173   {
2174     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2175     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2176
2177   }
2178
2179   /**
2180    * group conservation toggled.
2181    */
2182   protected void showGroupConservation_actionPerformed()
2183   {
2184     viewport.setShowGroupConservation(showGroupConservation.getState());
2185     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2186   }
2187
2188   /*
2189    * (non-Javadoc)
2190    *
2191    * @see
2192    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2193    * .event.ActionEvent)
2194    */
2195   protected void showConsensusHistogram_actionPerformed()
2196   {
2197     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2198     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2199   }
2200
2201   /*
2202    * (non-Javadoc)
2203    *
2204    * @see
2205    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2206    * .event.ActionEvent)
2207    */
2208   protected void showSequenceLogo_actionPerformed()
2209   {
2210     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2211     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2212   }
2213
2214   protected void normSequenceLogo_actionPerformed()
2215   {
2216     showSequenceLogo.setState(true);
2217     viewport.setShowSequenceLogo(true);
2218     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2219     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2220   }
2221
2222   protected void applyAutoAnnotationSettings_actionPerformed()
2223   {
2224     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2225   }
2226
2227   protected void makeGrpsFromSelection_actionPerformed()
2228   {
2229     if (avc.makeGroupsFromSelection())
2230     {
2231       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2232       alignPanel.updateAnnotation();
2233       alignPanel.paintAlignment(true);
2234     }
2235   }
2236
2237   protected void createGroup_actionPerformed()
2238   {
2239     avc.createGroup();
2240   }
2241
2242   protected void unGroup_actionPerformed()
2243   {
2244     if (avc.unGroup())
2245     {
2246       alignPanel.alignmentChanged();
2247     }
2248   }
2249
2250   protected void deleteGroups_actionPerformed()
2251   {
2252     if (avc.deleteGroups())
2253     {
2254       alignPanel.alignmentChanged();
2255     }
2256   }
2257
2258   public void selectAllSequenceMenuItem_actionPerformed()
2259   {
2260     SequenceGroup sg = new SequenceGroup();
2261     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2262     {
2263       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2264     }
2265     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2266     viewport.setSelectionGroup(sg);
2267     // JAL-2034 - should delegate to
2268     // alignPanel to decide if overview needs
2269     // updating.
2270     alignPanel.paintAlignment(false);
2271     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2272     viewport.sendSelection();
2273   }
2274
2275   public void deselectAllSequenceMenuItem_actionPerformed()
2276   {
2277     if (viewport.cursorMode)
2278     {
2279       alignPanel.seqPanel.keyboardNo1 = null;
2280       alignPanel.seqPanel.keyboardNo2 = null;
2281     }
2282     viewport.setSelectionGroup(null);
2283     viewport.getColumnSelection().clear();
2284     viewport.setSelectionGroup(null);
2285     alignPanel.idPanel.idCanvas.searchResults = null;
2286     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2287     // JAL-2034 - should delegate to
2288     // alignPanel to decide if overview needs
2289     // updating.
2290     alignPanel.paintAlignment(false);
2291     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2292     viewport.sendSelection();
2293   }
2294
2295   public void invertSequenceMenuItem_actionPerformed()
2296   {
2297     SequenceGroup sg = viewport.getSelectionGroup();
2298     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2299     {
2300       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2301     }
2302
2303     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2304     viewport.sendSelection();
2305   }
2306
2307   public void invertColSel_actionPerformed()
2308   {
2309     viewport.invertColumnSelection();
2310     alignPanel.paintAlignment(true);
2311     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2312     viewport.sendSelection();
2313   }
2314
2315   void trimAlignment(boolean trimLeft)
2316   {
2317     AlignmentI al = viewport.getAlignment();
2318     ViewportRanges ranges = viewport.getRanges();
2319     ColumnSelection colSel = viewport.getColumnSelection();
2320     int column;
2321
2322     if (!colSel.isEmpty())
2323     {
2324       if (trimLeft)
2325       {
2326         column = colSel.getMin();
2327       }
2328       else
2329       {
2330         column = colSel.getMax();
2331       }
2332
2333       SequenceI[] seqs;
2334       if (viewport.getSelectionGroup() != null)
2335       {
2336         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2337                 viewport.getHiddenRepSequences());
2338       }
2339       else
2340       {
2341         seqs = al.getSequencesArray();
2342       }
2343
2344       TrimRegionCommand trimRegion;
2345       if (trimLeft)
2346       {
2347         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2348                 column, al);
2349         ranges.setStartRes(0);
2350       }
2351       else
2352       {
2353         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2354                 column, al);
2355       }
2356
2357       statusBar.setText(MessageManager.formatMessage(
2358               "label.removed_columns",
2359               new String[] { Integer.valueOf(trimRegion.getSize())
2360                       .toString() }));
2361       addHistoryItem(trimRegion);
2362
2363       for (SequenceGroup sg : al.getGroups())
2364       {
2365         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2366                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2367         {
2368           al.deleteGroup(sg);
2369         }
2370       }
2371
2372       viewport.firePropertyChange("alignment", null, al.getSequences());
2373     }
2374   }
2375
2376   public void removeGappedColumnMenuItem_actionPerformed()
2377   {
2378     AlignmentI al = viewport.getAlignment();
2379     ViewportRanges ranges = viewport.getRanges();
2380     int start = 0;
2381     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2382
2383     SequenceI[] seqs;
2384     if (viewport.getSelectionGroup() != null)
2385     {
2386       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2387               viewport.getHiddenRepSequences());
2388       start = viewport.getSelectionGroup().getStartRes();
2389       end = viewport.getSelectionGroup().getEndRes();
2390     }
2391     else
2392     {
2393       seqs = viewport.getAlignment().getSequencesArray();
2394     }
2395
2396     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2397             "Remove Gapped Columns", seqs, start, end,
2398             viewport.getAlignment());
2399
2400     addHistoryItem(removeGapCols);
2401
2402     statusBar.setText(MessageManager.formatMessage(
2403             "label.removed_empty_columns",
2404             new String[] { Integer.valueOf(removeGapCols.getSize())
2405                     .toString() }));
2406
2407     // This is to maintain viewport position on first residue
2408     // of first sequence
2409     SequenceI seq = al.getSequenceAt(0);
2410     int startRes = seq.findPosition(ranges.getStartRes());
2411     // ShiftList shifts;
2412     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2413     // edit.alColumnChanges=shifts.getInverse();
2414     // if (viewport.hasHiddenColumns)
2415     // viewport.getColumnSelection().compensateForEdits(shifts);
2416     ranges.setStartRes(seq.findIndex(startRes) - 1);
2417     viewport.firePropertyChange("alignment", null, al.getSequences());
2418
2419   }
2420
2421   public void removeAllGapsMenuItem_actionPerformed()
2422   {
2423     AlignmentI al = viewport.getAlignment();
2424     ViewportRanges ranges = viewport.getRanges();
2425     int start = 0;
2426     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2427
2428     SequenceI[] seqs;
2429     if (viewport.getSelectionGroup() != null)
2430     {
2431       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2432               viewport.getHiddenRepSequences());
2433       start = viewport.getSelectionGroup().getStartRes();
2434       end = viewport.getSelectionGroup().getEndRes();
2435     }
2436     else
2437     {
2438       seqs = viewport.getAlignment().getSequencesArray();
2439     }
2440
2441     // This is to maintain viewport position on first residue
2442     // of first sequence
2443     SequenceI seq = al.getSequenceAt(0);
2444     int startRes = seq.findPosition(ranges.getStartRes());
2445
2446     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2447             al));
2448
2449     ranges.setStartRes(seq.findIndex(startRes) - 1);
2450
2451     viewport.firePropertyChange("alignment", null, al.getSequences());
2452
2453   }
2454
2455   public void findMenuItem_actionPerformed()
2456   {
2457     new Finder(alignPanel);
2458   }
2459
2460   /**
2461    * create a new view derived from the current view
2462    *
2463    * @param viewtitle
2464    * @return frame for the new view
2465    */
2466   public AlignFrame newView(String viewtitle)
2467   {
2468     AlignmentI newal;
2469     if (viewport.hasHiddenRows())
2470     {
2471       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2472               .getFullAlignment().getSequencesArray());
2473     }
2474     else
2475     {
2476       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2477     }
2478
2479     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2480     {
2481       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2482       {
2483         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2484         {
2485           newal.addAnnotation(viewport.getAlignment()
2486                   .getAlignmentAnnotation()[i]);
2487         }
2488       }
2489     }
2490
2491     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2492
2493     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2494     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2495     PaintRefresher.Register(newaf.alignPanel,
2496             newaf.alignPanel.av.getSequenceSetId());
2497
2498     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2499             newaf.alignPanel.av.getSequenceSetId());
2500     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2501             newaf.alignPanel.av.getSequenceSetId());
2502
2503     Vector comps = (Vector) PaintRefresher.components.get(viewport
2504             .getSequenceSetId());
2505     int viewSize = -1;
2506     for (int i = 0; i < comps.size(); i++)
2507     {
2508       if (comps.elementAt(i) instanceof AlignmentPanel)
2509       {
2510         viewSize++;
2511       }
2512     }
2513
2514     String title = new String(this.getTitle());
2515     if (viewtitle != null)
2516     {
2517       title = viewtitle + " ( " + title + ")";
2518     }
2519     else
2520     {
2521       if (title.indexOf("(View") > -1)
2522       {
2523         title = title.substring(0, title.indexOf("(View"));
2524       }
2525       title += "(View " + viewSize + ")";
2526     }
2527
2528     newaf.setTitle(title.toString());
2529
2530     newaf.viewport.setHistoryList(viewport.getHistoryList());
2531     newaf.viewport.setRedoList(viewport.getRedoList());
2532     return newaf;
2533   }
2534
2535   /**
2536    *
2537    * @return list of feature groups on the view
2538    */
2539   public String[] getFeatureGroups()
2540   {
2541     FeatureRenderer fr = null;
2542     if (alignPanel != null
2543             && (fr = alignPanel.getFeatureRenderer()) != null)
2544     {
2545       List<String> gps = fr.getFeatureGroups();
2546       String[] _gps = gps.toArray(new String[gps.size()]);
2547       return _gps;
2548     }
2549     return null;
2550   }
2551
2552   /**
2553    * get sequence feature groups that are hidden or shown
2554    *
2555    * @param visible
2556    *          true is visible
2557    * @return list
2558    */
2559   public String[] getFeatureGroupsOfState(boolean visible)
2560   {
2561     FeatureRenderer fr = null;
2562     if (alignPanel != null
2563             && (fr = alignPanel.getFeatureRenderer()) != null)
2564     {
2565       List<String> gps = fr.getGroups(visible);
2566       String[] _gps = gps.toArray(new String[gps.size()]);
2567       return _gps;
2568     }
2569     return null;
2570   }
2571
2572   /**
2573    * Change the display state for the given feature groups
2574    *
2575    * @param groups
2576    *          list of group strings
2577    * @param state
2578    *          visible or invisible
2579    */
2580   public void setFeatureGroupState(String[] groups, boolean state)
2581   {
2582     FeatureRenderer fr = null;
2583     this.sequenceFeatures.setState(true);
2584     viewport.setShowSequenceFeatures(true);
2585     if (alignPanel != null
2586             && (fr = alignPanel.getFeatureRenderer()) != null)
2587     {
2588
2589       fr.setGroupVisibility(Arrays.asList(groups), state);
2590       alignPanel.seqPanel.seqCanvas.repaint();
2591       if (alignPanel.overviewPanel != null)
2592       {
2593         alignPanel.overviewPanel.updateOverviewImage();
2594       }
2595     }
2596   }
2597
2598   public void seqLimits_itemStateChanged()
2599   {
2600     viewport.setShowJVSuffix(seqLimits.getState());
2601     alignPanel.fontChanged();
2602     alignPanel.paintAlignment(true);
2603   }
2604
2605   protected void colourTextMenuItem_actionPerformed()
2606   {
2607     viewport.setColourText(colourTextMenuItem.getState());
2608     alignPanel.paintAlignment(true);
2609   }
2610
2611   protected void displayNonconservedMenuItem_actionPerformed()
2612   {
2613     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2614     alignPanel.paintAlignment(true);
2615   }
2616
2617   protected void wrapMenuItem_actionPerformed()
2618   {
2619     viewport.setWrapAlignment(wrapMenuItem.getState());
2620     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2621     scaleAbove.setEnabled(wrapMenuItem.getState());
2622     scaleLeft.setEnabled(wrapMenuItem.getState());
2623     scaleRight.setEnabled(wrapMenuItem.getState());
2624     alignPanel.paintAlignment(true);
2625   }
2626
2627   public void overviewMenuItem_actionPerformed()
2628   {
2629     if (alignPanel.overviewPanel != null)
2630     {
2631       return;
2632     }
2633
2634     Frame frame = new Frame();
2635     OverviewPanel overview = new OverviewPanel(alignPanel);
2636     frame.add(overview);
2637     // +50 must allow for applet frame window
2638     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2639             "label.overview_params", new String[] { this.getTitle() }),
2640             overview.getPreferredSize().width,
2641             overview.getPreferredSize().height + 50);
2642
2643     frame.pack();
2644     final AlignmentPanel ap = alignPanel;
2645     frame.addWindowListener(new WindowAdapter()
2646     {
2647       @Override
2648       public void windowClosing(WindowEvent e)
2649       {
2650         if (ap != null)
2651         {
2652           ap.setOverviewPanel(null);
2653         }
2654       };
2655     });
2656
2657     alignPanel.setOverviewPanel(overview);
2658
2659   }
2660
2661   @Override
2662   public void changeColour(ColourSchemeI cs)
2663   {
2664     viewport.setGlobalColourScheme(cs);
2665
2666     alignPanel.paintAlignment(true);
2667   }
2668
2669   protected void modifyPID_actionPerformed()
2670   {
2671     if (viewport.getAbovePIDThreshold()
2672             && viewport.getGlobalColourScheme() != null)
2673     {
2674       SliderPanel.setPIDSliderSource(alignPanel,
2675               viewport.getResidueShading(), alignPanel.getViewName());
2676       SliderPanel.showPIDSlider();
2677     }
2678   }
2679
2680   protected void modifyConservation_actionPerformed()
2681   {
2682     if (viewport.getConservationSelected()
2683             && viewport.getGlobalColourScheme() != null)
2684     {
2685       SliderPanel.setConservationSlider(alignPanel,
2686               viewport.getResidueShading(), alignPanel.getViewName());
2687       SliderPanel.showConservationSlider();
2688     }
2689   }
2690
2691   protected void conservationMenuItem_actionPerformed()
2692   {
2693     boolean selected = conservationMenuItem.getState();
2694     modifyConservation.setEnabled(selected);
2695     viewport.setConservationSelected(selected);
2696     viewport.getResidueShading().setConservationApplied(selected);
2697
2698     changeColour(viewport.getGlobalColourScheme());
2699
2700     if (selected)
2701     {
2702       modifyConservation_actionPerformed();
2703     }
2704     else
2705     {
2706       SliderPanel.hideConservationSlider();
2707     }
2708   }
2709
2710   public void abovePIDThreshold_actionPerformed()
2711   {
2712     boolean selected = abovePIDThreshold.getState();
2713     modifyPID.setEnabled(selected);
2714     viewport.setAbovePIDThreshold(selected);
2715     if (!selected)
2716     {
2717       viewport.getResidueShading().setThreshold(0,
2718               viewport.isIgnoreGapsConsensus());
2719     }
2720
2721     changeColour(viewport.getGlobalColourScheme());
2722
2723     if (selected)
2724     {
2725       modifyPID_actionPerformed();
2726     }
2727     else
2728     {
2729       SliderPanel.hidePIDSlider();
2730     }
2731   }
2732
2733   public void sortPairwiseMenuItem_actionPerformed()
2734   {
2735     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2736     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2737             .getAlignment().getSequenceAt(0));
2738
2739     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2740             viewport.getAlignment()));
2741     alignPanel.paintAlignment(true);
2742   }
2743
2744   public void sortIDMenuItem_actionPerformed()
2745   {
2746     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2747     AlignmentSorter.sortByID(viewport.getAlignment());
2748     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2749             viewport.getAlignment()));
2750     alignPanel.paintAlignment(true);
2751   }
2752
2753   public void sortLengthMenuItem_actionPerformed()
2754   {
2755     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2756     AlignmentSorter.sortByLength(viewport.getAlignment());
2757     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2758             viewport.getAlignment()));
2759     alignPanel.paintAlignment(true);
2760   }
2761
2762   public void sortGroupMenuItem_actionPerformed()
2763   {
2764     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2765     AlignmentSorter.sortByGroup(viewport.getAlignment());
2766     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2767             viewport.getAlignment()));
2768     alignPanel.paintAlignment(true);
2769
2770   }
2771
2772   public void removeRedundancyMenuItem_actionPerformed()
2773   {
2774     new RedundancyPanel(alignPanel);
2775   }
2776
2777   public void pairwiseAlignmentMenuItem_actionPerformed()
2778   {
2779     if (viewport.getSelectionGroup() != null
2780             && viewport.getSelectionGroup().getSize() > 1)
2781     {
2782       Frame frame = new Frame();
2783       frame.add(new PairwiseAlignPanel(alignPanel));
2784       jalview.bin.JalviewLite.addFrame(frame,
2785               MessageManager.getString("action.pairwise_alignment"), 600,
2786               500);
2787     }
2788   }
2789
2790   public void PCAMenuItem_actionPerformed()
2791   {
2792     // are the sequences aligned?
2793     if (!viewport.getAlignment().isAligned(false))
2794     {
2795       SequenceI current;
2796       int Width = viewport.getAlignment().getWidth();
2797
2798       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2799       {
2800         current = viewport.getAlignment().getSequenceAt(i);
2801
2802         if (current.getLength() < Width)
2803         {
2804           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2805         }
2806       }
2807       alignPanel.paintAlignment(true);
2808     }
2809
2810     if ((viewport.getSelectionGroup() != null
2811             && viewport.getSelectionGroup().getSize() < 4 && viewport
2812             .getSelectionGroup().getSize() > 0)
2813             || viewport.getAlignment().getHeight() < 4)
2814     {
2815       return;
2816     }
2817
2818     try
2819     {
2820       new PCAPanel(viewport);
2821     } catch (java.lang.OutOfMemoryError ex)
2822     {
2823     }
2824
2825   }
2826
2827   public void averageDistanceTreeMenuItem_actionPerformed()
2828   {
2829     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2830             "Average distance tree using PID");
2831   }
2832
2833   public void neighbourTreeMenuItem_actionPerformed()
2834   {
2835     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2836             "Neighbour joining tree using PID");
2837   }
2838
2839   protected void njTreeBlosumMenuItem_actionPerformed()
2840   {
2841     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2842             .getBlosum62().getName(),
2843             "Neighbour joining tree using BLOSUM62");
2844   }
2845
2846   protected void avTreeBlosumMenuItem_actionPerformed()
2847   {
2848     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2849             .getBlosum62().getName(),
2850             "Average distance tree using BLOSUM62");
2851   }
2852
2853   void newTreePanel(String type, String pwType, String title)
2854   {
2855     // are the sequences aligned?
2856     if (!viewport.getAlignment().isAligned(false))
2857     {
2858       SequenceI current;
2859       int Width = viewport.getAlignment().getWidth();
2860
2861       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2862       {
2863         current = viewport.getAlignment().getSequenceAt(i);
2864
2865         if (current.getLength() < Width)
2866         {
2867           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2868         }
2869       }
2870       alignPanel.paintAlignment(true);
2871
2872     }
2873
2874     if ((viewport.getSelectionGroup() != null && viewport
2875             .getSelectionGroup().getSize() > 1)
2876             || (viewport.getAlignment().getHeight() > 1))
2877     {
2878       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2879
2880       addTreeMenuItem(tp, title);
2881
2882       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2883     }
2884   }
2885
2886   void loadTree_actionPerformed()
2887   {
2888     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2889     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2890     cap.setTreeImport();
2891     Frame frame = new Frame();
2892     frame.add(cap);
2893     jalview.bin.JalviewLite.addFrame(frame,
2894             MessageManager.getString("label.paste_newick_file"), 400, 300);
2895   }
2896
2897   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2898   {
2899     TreePanel tp = new TreePanel(alignPanel, treeFile,
2900             MessageManager.getString("label.load_tree_from_file"), tree);
2901     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2902     addTreeMenuItem(tp, treeFile);
2903   }
2904
2905   /**
2906    * sort the alignment using the given treePanel
2907    *
2908    * @param treePanel
2909    *          tree used to sort view
2910    * @param title
2911    *          string used for undo event name
2912    */
2913   public void sortByTree(TreePanel treePanel, String title)
2914   {
2915     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2916     AlignmentSorter
2917             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2918     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2919     // HistoryItem.SORT));
2920     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2921             "label.order_by_params", new String[] { title }), oldOrder,
2922             viewport.getAlignment()));
2923     alignPanel.paintAlignment(true);
2924   }
2925
2926   /**
2927    * Do any automatic reordering of the alignment and add the necessary bits to
2928    * the menu structure for the new tree
2929    *
2930    * @param treePanel
2931    * @param title
2932    */
2933   protected void addTreeMenuItem(final TreePanel treePanel,
2934           final String title)
2935   {
2936     final MenuItem item = new MenuItem(title);
2937     sortByTreeMenu.add(item);
2938     item.addActionListener(new java.awt.event.ActionListener()
2939     {
2940       @Override
2941       public void actionPerformed(ActionEvent evt)
2942       {
2943         sortByTree(treePanel, title); // treePanel.getTitle());
2944       }
2945     });
2946
2947     treePanel.addWindowListener(new WindowAdapter()
2948     {
2949       @Override
2950       public void windowOpened(WindowEvent e)
2951       {
2952         if (viewport.sortByTree)
2953         {
2954           sortByTree(treePanel, title);
2955         }
2956         super.windowOpened(e);
2957       }
2958
2959       @Override
2960       public void windowClosing(WindowEvent e)
2961       {
2962         sortByTreeMenu.remove(item);
2963       };
2964     });
2965   }
2966
2967   public boolean sortBy(AlignmentOrder alorder, String undoname)
2968   {
2969     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2970     if (viewport.applet.debug)
2971     {
2972       System.err.println("Sorting " + alorder.getOrder().size()
2973               + " in alignment '" + getTitle() + "'");
2974     }
2975     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2976     if (undoname != null)
2977     {
2978       addHistoryItem(new OrderCommand(undoname, oldOrder,
2979               viewport.getAlignment()));
2980     }
2981     alignPanel.paintAlignment(true);
2982     return true;
2983   }
2984
2985   protected void documentation_actionPerformed()
2986   {
2987     alignPanel.av.applet.openJalviewHelpUrl();
2988   }
2989
2990   protected void about_actionPerformed()
2991   {
2992
2993     class AboutPanel extends Canvas
2994     {
2995       String version;
2996
2997       String builddate;
2998
2999       public AboutPanel(String version, String builddate)
3000       {
3001         this.version = version;
3002         this.builddate = builddate;
3003       }
3004
3005       @Override
3006       public void paint(Graphics g)
3007       {
3008         g.setColor(Color.white);
3009         g.fillRect(0, 0, getSize().width, getSize().height);
3010         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3011         FontMetrics fm = g.getFontMetrics();
3012         int fh = fm.getHeight();
3013         int y = 5, x = 7;
3014         g.setColor(Color.black);
3015         // TODO: update this text for each release or centrally store it for
3016         // lite and application
3017         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3018         g.drawString(MessageManager.formatMessage(
3019                 "label.jalviewLite_release", new String[] { version }), x,
3020                 y += fh);
3021         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3022         g.drawString(MessageManager.formatMessage(
3023                 "label.jaview_build_date", new String[] { builddate }), x,
3024                 y += fh);
3025         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3026         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3027                 x, y += fh * 1.5);
3028         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3029                 x + 50, y += fh + 8);
3030         g.drawString(
3031                 MessageManager.getString("label.jalview_dev_managers"), x,
3032                 y += fh);
3033         g.drawString(MessageManager
3034                 .getString("label.jalview_distribution_lists"), x, y += fh);
3035         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3036                 x, y += fh + 8);
3037         g.drawString(
3038                 MessageManager.getString("label.jalview_cite_1_authors"),
3039                 x, y += fh);
3040         g.drawString(
3041                 MessageManager.getString("label.jalview_cite_1_title"), x,
3042                 y += fh);
3043         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3044                 x, y += fh);
3045       }
3046     }
3047
3048     Frame frame = new Frame();
3049     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3050             .getBuildDate()));
3051     jalview.bin.JalviewLite.addFrame(frame,
3052             MessageManager.getString("label.jalview"), 580, 220);
3053
3054   }
3055
3056   public void showURL(String url, String target)
3057   {
3058     if (viewport.applet == null)
3059     {
3060       System.out.println("Not running as applet - no browser available.");
3061     }
3062     else
3063     {
3064       viewport.applet.showURL(url, target);
3065     }
3066   }
3067
3068   // ////////////////////////////////////////////////////////////////////////////////
3069   // JBuilder Graphics here
3070
3071   MenuBar alignFrameMenuBar = new MenuBar();
3072
3073   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3074
3075   MenuItem loadApplication = new MenuItem(
3076           MessageManager.getString("label.view_full_application"));
3077
3078   MenuItem loadTree = new MenuItem(
3079           MessageManager.getString("label.load_associated_tree"));
3080
3081   MenuItem loadAnnotations = new MenuItem(
3082           MessageManager.getString("label.load_features_annotations"));
3083
3084   MenuItem outputFeatures = new MenuItem(
3085           MessageManager.getString("label.export_features"));
3086
3087   MenuItem outputAnnotations = new MenuItem(
3088           MessageManager.getString("label.export_annotations"));
3089
3090   MenuItem closeMenuItem = new MenuItem(
3091           MessageManager.getString("action.close"));
3092
3093   MenuItem selectAllSequenceMenuItem = new MenuItem(
3094           MessageManager.getString("action.select_all"));
3095
3096   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3097           MessageManager.getString("action.deselect_all"));
3098
3099   MenuItem invertSequenceMenuItem = new MenuItem(
3100           MessageManager.getString("action.invert_selection"));
3101
3102   MenuItem remove2LeftMenuItem = new MenuItem();
3103
3104   MenuItem remove2RightMenuItem = new MenuItem();
3105
3106   MenuItem removeGappedColumnMenuItem = new MenuItem();
3107
3108   MenuItem removeAllGapsMenuItem = new MenuItem();
3109
3110   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3111
3112   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3113
3114   MenuItem sortPairwiseMenuItem = new MenuItem();
3115
3116   MenuItem sortIDMenuItem = new MenuItem();
3117
3118   MenuItem sortLengthMenuItem = new MenuItem();
3119
3120   MenuItem sortGroupMenuItem = new MenuItem();
3121
3122   MenuItem removeRedundancyMenuItem = new MenuItem();
3123
3124   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3125
3126   MenuItem PCAMenuItem = new MenuItem();
3127
3128   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3129
3130   MenuItem neighbourTreeMenuItem = new MenuItem();
3131
3132   BorderLayout borderLayout1 = new BorderLayout();
3133
3134   public Label statusBar = new Label();
3135
3136   MenuItem clustalColour = new MenuItem();
3137
3138   MenuItem zappoColour = new MenuItem();
3139
3140   MenuItem taylorColour = new MenuItem();
3141
3142   MenuItem hydrophobicityColour = new MenuItem();
3143
3144   MenuItem helixColour = new MenuItem();
3145
3146   MenuItem strandColour = new MenuItem();
3147
3148   MenuItem turnColour = new MenuItem();
3149
3150   MenuItem buriedColour = new MenuItem();
3151
3152   MenuItem purinePyrimidineColour = new MenuItem();
3153
3154   // MenuItem RNAInteractionColour = new MenuItem();
3155
3156   MenuItem RNAHelixColour = new MenuItem();
3157
3158   MenuItem userDefinedColour = new MenuItem();
3159
3160   MenuItem PIDColour = new MenuItem();
3161
3162   MenuItem BLOSUM62Colour = new MenuItem();
3163
3164   MenuItem tcoffeeColour = new MenuItem();
3165
3166   MenuItem njTreeBlosumMenuItem = new MenuItem();
3167
3168   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3169
3170   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3171
3172   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3173
3174   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3175
3176   MenuItem alProperties = new MenuItem(
3177           MessageManager.getString("label.alignment_props"));
3178
3179   MenuItem overviewMenuItem = new MenuItem();
3180
3181   MenuItem undoMenuItem = new MenuItem();
3182
3183   MenuItem redoMenuItem = new MenuItem();
3184
3185   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3186
3187   MenuItem noColourmenuItem = new MenuItem();
3188
3189   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3190
3191   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3192
3193   MenuItem findMenuItem = new MenuItem();
3194
3195   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3196
3197   MenuItem nucleotideColour = new MenuItem();
3198
3199   MenuItem deleteGroups = new MenuItem();
3200
3201   MenuItem grpsFromSelection = new MenuItem();
3202
3203   MenuItem createGroup = new MenuItem();
3204
3205   MenuItem unGroup = new MenuItem();
3206
3207   MenuItem delete = new MenuItem();
3208
3209   MenuItem copy = new MenuItem();
3210
3211   MenuItem cut = new MenuItem();
3212
3213   Menu pasteMenu = new Menu();
3214
3215   MenuItem pasteNew = new MenuItem();
3216
3217   MenuItem pasteThis = new MenuItem();
3218
3219   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3220
3221   MenuItem font = new MenuItem();
3222
3223   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3224
3225   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3226
3227   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3228
3229   MenuItem modifyPID = new MenuItem();
3230
3231   MenuItem modifyConservation = new MenuItem();
3232
3233   CheckboxMenuItem autoCalculate = null;
3234
3235   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3236           "Sort Alignment With New Tree", true);
3237
3238   Menu sortByTreeMenu = new Menu();
3239
3240   MenuItem inputText = new MenuItem();
3241
3242   MenuItem documentation = new MenuItem();
3243
3244   MenuItem about = new MenuItem();
3245
3246   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3253
3254   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3255
3256   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3257
3258   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3259
3260   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3261
3262   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3263
3264   /**
3265    * Initialise menus and other items
3266    *
3267    * @throws Exception
3268    */
3269   private void jbInit() throws Exception
3270   {
3271     setMenuBar(alignFrameMenuBar);
3272
3273     /*
3274      * Configure File menu items and actions
3275      */
3276     inputText
3277             .setLabel(MessageManager.getString("label.input_from_textbox"));
3278     inputText.addActionListener(this);
3279     Menu outputTextboxMenu = new Menu(
3280             MessageManager.getString("label.out_to_textbox"));
3281     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3282     {
3283       MenuItem item = new MenuItem(ff);
3284
3285       item.addActionListener(new java.awt.event.ActionListener()
3286       {
3287         @Override
3288         public void actionPerformed(ActionEvent e)
3289         {
3290           outputText_actionPerformed(e);
3291         }
3292       });
3293
3294       outputTextboxMenu.add(item);
3295     }
3296     closeMenuItem.addActionListener(this);
3297     loadApplication.addActionListener(this);
3298     loadTree.addActionListener(this);
3299     loadAnnotations.addActionListener(this);
3300     outputFeatures.addActionListener(this);
3301     outputAnnotations.addActionListener(this);
3302
3303     /*
3304      * Configure Edit menu items and actions
3305      */
3306     undoMenuItem.setEnabled(false);
3307     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3308     undoMenuItem.addActionListener(this);
3309     redoMenuItem.setEnabled(false);
3310     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3311     redoMenuItem.addActionListener(this);
3312     copy.setLabel(MessageManager.getString("action.copy"));
3313     copy.addActionListener(this);
3314     cut.setLabel(MessageManager.getString("action.cut"));
3315     cut.addActionListener(this);
3316     delete.setLabel(MessageManager.getString("action.delete"));
3317     delete.addActionListener(this);
3318     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3319     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3320     pasteNew.addActionListener(this);
3321     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3322     pasteThis.addActionListener(this);
3323     remove2LeftMenuItem.setLabel(MessageManager
3324             .getString("action.remove_left"));
3325     remove2LeftMenuItem.addActionListener(this);
3326     remove2RightMenuItem.setLabel(MessageManager
3327             .getString("action.remove_right"));
3328     remove2RightMenuItem.addActionListener(this);
3329     removeGappedColumnMenuItem.setLabel(MessageManager
3330             .getString("action.remove_empty_columns"));
3331     removeGappedColumnMenuItem.addActionListener(this);
3332     removeAllGapsMenuItem.setLabel(MessageManager
3333             .getString("action.remove_all_gaps"));
3334     removeAllGapsMenuItem.addActionListener(this);
3335     removeRedundancyMenuItem.setLabel(MessageManager
3336             .getString("action.remove_redundancy"));
3337     removeRedundancyMenuItem.addActionListener(this);
3338
3339     /*
3340      * Configure Select menu items and actions
3341      */
3342     findMenuItem.setLabel(MessageManager.getString("action.find"));
3343     findMenuItem.addActionListener(this);
3344     selectAllSequenceMenuItem.addActionListener(this);
3345     deselectAllSequenceMenuItem.addActionListener(this);
3346     invertSequenceMenuItem.setLabel(MessageManager
3347             .getString("action.invert_sequence_selection"));
3348     invertSequenceMenuItem.addActionListener(this);
3349     invertColSel.setLabel(MessageManager
3350             .getString("action.invert_column_selection"));
3351     invertColSel.addActionListener(this);
3352     deleteGroups.setLabel(MessageManager
3353             .getString("action.undefine_groups"));
3354     deleteGroups.addActionListener(this);
3355     grpsFromSelection.setLabel(MessageManager
3356             .getString("action.make_groups_selection"));
3357     grpsFromSelection.addActionListener(this);
3358     createGroup.setLabel(MessageManager.getString("action.create_group"));
3359     createGroup.addActionListener(this);
3360     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3361     unGroup.addActionListener(this);
3362
3363     annotationColumnSelection.setLabel(MessageManager
3364             .getString("action.select_by_annotation"));
3365     annotationColumnSelection.addActionListener(this);
3366
3367     /*
3368      * Configure View menu items and actions
3369      */
3370     newView.setLabel(MessageManager.getString("action.new_view"));
3371     newView.addActionListener(this);
3372     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3373     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3374     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3375     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3376     hideColumns
3377             .setLabel(MessageManager.getString("label.selected_columns"));
3378     hideSequences.setLabel(MessageManager
3379             .getString("label.selected_sequences"));
3380     hideAllButSelection.setLabel(MessageManager
3381             .getString("label.all_but_selected_region"));
3382     hideAllSelection.setLabel(MessageManager
3383             .getString("label.selected_region"));
3384     showAllHidden.setLabel(MessageManager
3385             .getString("label.all_sequences_columns"));
3386     showColumns.addActionListener(this);
3387     showSeqs.addActionListener(this);
3388     hideColumns.addActionListener(this);
3389     hideSequences.addActionListener(this);
3390     hideAllButSelection.addActionListener(this);
3391     hideAllSelection.addActionListener(this);
3392     showAllHidden.addActionListener(this);
3393     featureSettings.setLabel(MessageManager
3394             .getString("action.feature_settings"));
3395     featureSettings.addActionListener(this);
3396     sequenceFeatures.setLabel(MessageManager
3397             .getString("label.show_sequence_features"));
3398     sequenceFeatures.addItemListener(this);
3399     sequenceFeatures.setState(false);
3400     followMouseOverFlag.setLabel(MessageManager
3401             .getString("label.automatic_scrolling"));
3402     followMouseOverFlag.addItemListener(this);
3403     alProperties.addActionListener(this);
3404     overviewMenuItem.setLabel(MessageManager
3405             .getString("label.overview_window"));
3406     overviewMenuItem.addActionListener(this);
3407
3408     /*
3409      * Configure Annotations menu items and actions
3410      */
3411     annotationPanelMenuItem.setLabel(MessageManager
3412             .getString("label.show_annotations"));
3413     annotationPanelMenuItem.addItemListener(this);
3414     showGroupConsensus.setLabel(MessageManager
3415             .getString("label.group_consensus"));
3416     showGroupConservation.setLabel(MessageManager
3417             .getString("label.group_conservation"));
3418     showConsensusHistogram.setLabel(MessageManager
3419             .getString("label.show_consensus_histogram"));
3420     showSequenceLogo.setLabel(MessageManager
3421             .getString("label.show_consensus_logo"));
3422     normSequenceLogo.setLabel(MessageManager
3423             .getString("label.norm_consensus_logo"));
3424     applyAutoAnnotationSettings.setLabel(MessageManager
3425             .getString("label.apply_all_groups"));
3426     applyAutoAnnotationSettings.setState(true);
3427     Menu autoAnnMenu = new Menu(
3428             MessageManager.getString("label.autocalculated_annotation"));
3429     showGroupConsensus.addItemListener(this);
3430     showGroupConservation.addItemListener(this);
3431     showConsensusHistogram.addItemListener(this);
3432     showSequenceLogo.addItemListener(this);
3433     normSequenceLogo.addItemListener(this);
3434     applyAutoAnnotationSettings.addItemListener(this);
3435     showAlignmentAnnotations = new CheckboxMenuItem(
3436             MessageManager.getString("label.show_all_al_annotations"));
3437     showSequenceAnnotations = new CheckboxMenuItem(
3438             MessageManager.getString("label.show_all_seq_annotations"));
3439     sortAnnBySequence = new CheckboxMenuItem(
3440             MessageManager.getString("label.sort_annotations_by_sequence"));
3441     sortAnnByLabel = new CheckboxMenuItem(
3442             MessageManager.getString("label.sort_annotations_by_label"));
3443     showAutoFirst = new CheckboxMenuItem(
3444             MessageManager.getString("label.show_first"));
3445     showAutoFirst.setState(false); // pending applet parameter
3446     setShowAutoCalculatedAbove(showAutoFirst.getState());
3447     showAutoLast = new CheckboxMenuItem(
3448             MessageManager.getString("label.show_last"));
3449     showAutoLast.setState(!showAutoFirst.getState());
3450     showAlignmentAnnotations.addItemListener(this);
3451     showSequenceAnnotations.addItemListener(this);
3452     sortAnnBySequence.addItemListener(this);
3453     sortAnnByLabel.addItemListener(this);
3454     showAutoFirst.addItemListener(this);
3455     showAutoLast.addItemListener(this);
3456
3457     /*
3458      * Configure Format menu items and actions
3459      */
3460     font.setLabel(MessageManager.getString("action.font"));
3461     font.addActionListener(this);
3462     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3463     scaleAbove.setState(true);
3464     scaleAbove.setEnabled(false);
3465     scaleAbove.addItemListener(this);
3466     scaleLeft.setEnabled(false);
3467     scaleLeft.setState(true);
3468     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3469     scaleLeft.addItemListener(this);
3470     scaleRight.setEnabled(false);
3471     scaleRight.setState(true);
3472     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3473     scaleRight.addItemListener(this);
3474     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3475     viewBoxesMenuItem.setState(true);
3476     viewBoxesMenuItem.addItemListener(this);
3477     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3478     viewTextMenuItem.setState(true);
3479     viewTextMenuItem.addItemListener(this);
3480     colourTextMenuItem.setLabel(MessageManager
3481             .getString("label.colour_text"));
3482     colourTextMenuItem.addItemListener(this);
3483     displayNonconservedMenuItem.setLabel(MessageManager
3484             .getString("label.show_non_conserved"));
3485     displayNonconservedMenuItem.addItemListener(this);
3486     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3487     wrapMenuItem.addItemListener(this);
3488     renderGapsMenuItem.setLabel(MessageManager
3489             .getString("action.show_gaps"));
3490     renderGapsMenuItem.setState(true);
3491     renderGapsMenuItem.addItemListener(this);
3492     centreColumnLabelFlag.setLabel(MessageManager
3493             .getString("label.centre_column_labels"));
3494     centreColumnLabelFlag.addItemListener(this);
3495     seqLimits.setState(true);
3496     seqLimits.setLabel(MessageManager
3497             .getString("label.show_sequence_limits"));
3498     seqLimits.addItemListener(this);
3499
3500     /*
3501      * Configure Colour menu items and actions
3502      */
3503     applyToAllGroups.setLabel(MessageManager
3504             .getString("label.apply_colour_to_all_groups"));
3505     applyToAllGroups.setState(true);
3506     applyToAllGroups.addItemListener(this);
3507     clustalColour.setLabel(MessageManager
3508             .getString("label.colourScheme_clustal"));
3509     clustalColour.addActionListener(this);
3510     zappoColour.setLabel(MessageManager
3511             .getString("label.colourScheme_zappo"));
3512     zappoColour.addActionListener(this);
3513     taylorColour.setLabel(MessageManager
3514             .getString("label.colourScheme_taylor"));
3515     taylorColour.addActionListener(this);
3516     hydrophobicityColour.setLabel(MessageManager
3517             .getString("label.colourScheme_hydrophobic"));
3518     hydrophobicityColour.addActionListener(this);
3519     helixColour.setLabel(MessageManager
3520             .getString("label.colourScheme_helix_propensity"));
3521     helixColour.addActionListener(this);
3522     strandColour.setLabel(MessageManager
3523             .getString("label.colourScheme_strand_propensity"));
3524     strandColour.addActionListener(this);
3525     turnColour.setLabel(MessageManager
3526             .getString("label.colourScheme_turn_propensity"));
3527     turnColour.addActionListener(this);
3528     buriedColour.setLabel(MessageManager
3529             .getString("label.colourScheme_buried_index"));
3530     buriedColour.addActionListener(this);
3531     purinePyrimidineColour.setLabel(MessageManager
3532             .getString("label.colourScheme_purine/pyrimidine"));
3533     purinePyrimidineColour.addActionListener(this);
3534     // RNAInteractionColour.setLabel(MessageManager
3535     // .getString("label.rna_interaction"));
3536     // RNAInteractionColour.addActionListener(this);
3537     RNAHelixColour.setLabel(MessageManager
3538             .getString("label.colourScheme_rna_helices"));
3539     RNAHelixColour.addActionListener(this);
3540     userDefinedColour.setLabel(MessageManager
3541             .getString("action.user_defined"));
3542     userDefinedColour.addActionListener(this);
3543     PIDColour.setLabel(MessageManager
3544             .getString("label.colourScheme_%_identity"));
3545     PIDColour.addActionListener(this);
3546     BLOSUM62Colour.setLabel(MessageManager
3547             .getString("label.colourScheme_blosum62"));
3548     BLOSUM62Colour.addActionListener(this);
3549     tcoffeeColour.setLabel(MessageManager
3550             .getString("label.colourScheme_t-coffee_scores"));
3551     // it will be enabled only if a score file is provided
3552     tcoffeeColour.setEnabled(false);
3553     tcoffeeColour.addActionListener(this);
3554     conservationMenuItem.setLabel(MessageManager
3555             .getString("action.by_conservation"));
3556     conservationMenuItem.addItemListener(this);
3557     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3558     noColourmenuItem.addActionListener(this);
3559     abovePIDThreshold.setLabel(MessageManager
3560             .getString("label.above_identity_threshold"));
3561     abovePIDThreshold.addItemListener(this);
3562     nucleotideColour.setLabel(MessageManager
3563             .getString("label.colourScheme_nucleotide"));
3564     nucleotideColour.addActionListener(this);
3565     modifyPID.setLabel(MessageManager
3566             .getString("label.modify_identity_threshold"));
3567     modifyPID.setEnabled(abovePIDThreshold.getState());
3568     modifyPID.addActionListener(this);
3569     modifyConservation.setLabel(MessageManager
3570             .getString("label.modify_conservation_threshold"));
3571     modifyConservation.setEnabled(conservationMenuItem.getState());
3572     modifyConservation.addActionListener(this);
3573     annotationColour.setLabel(MessageManager
3574             .getString("action.by_annotation"));
3575     annotationColour.addActionListener(this);
3576
3577     /*
3578      * Configure Calculate menu items and actions
3579      */
3580     sortPairwiseMenuItem.setLabel(MessageManager
3581             .getString("action.by_pairwise_id"));
3582     sortPairwiseMenuItem.addActionListener(this);
3583     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3584     sortIDMenuItem.addActionListener(this);
3585     sortLengthMenuItem.setLabel(MessageManager
3586             .getString("action.by_length"));
3587     sortLengthMenuItem.addActionListener(this);
3588     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3589     sortGroupMenuItem.addActionListener(this);
3590     pairwiseAlignmentMenuItem.setLabel(MessageManager
3591             .getString("action.pairwise_alignment"));
3592     pairwiseAlignmentMenuItem.addActionListener(this);
3593     PCAMenuItem.setLabel(MessageManager
3594             .getString("label.principal_component_analysis"));
3595     PCAMenuItem.addActionListener(this);
3596     autoCalculate = new CheckboxMenuItem(
3597             MessageManager.getString("label.autocalculate_consensus"), true);
3598     averageDistanceTreeMenuItem.setLabel(MessageManager
3599             .getString("label.average_distance_identity"));
3600     averageDistanceTreeMenuItem.addActionListener(this);
3601     neighbourTreeMenuItem.setLabel(MessageManager
3602             .getString("label.neighbour_joining_identity"));
3603     neighbourTreeMenuItem.addActionListener(this);
3604     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3605             .getString("label.average_distance_blosum62"));
3606     avDistanceTreeBlosumMenuItem.addActionListener(this);
3607     njTreeBlosumMenuItem.setLabel(MessageManager
3608             .getString("label.neighbour_blosum62"));
3609     njTreeBlosumMenuItem.addActionListener(this);
3610     sortByTreeMenu.setLabel(MessageManager
3611             .getString("action.by_tree_order"));
3612     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3613     Menu calculateTreeMenu = new Menu(
3614             MessageManager.getString("action.calculate_tree"));
3615     autoCalculate.addItemListener(this);
3616     sortByTree.addItemListener(this);
3617
3618     /*
3619      * Configure Help menu items and actions
3620      */
3621     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3622     documentation.setLabel(MessageManager.getString("label.documentation"));
3623     documentation.addActionListener(this);
3624     about.setLabel(MessageManager.getString("label.about"));
3625     about.addActionListener(this);
3626
3627     /*
3628      * Add top level menus to frame
3629      */
3630     alignFrameMenuBar.add(fileMenu);
3631     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3632     alignFrameMenuBar.add(editMenu);
3633     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3634     alignFrameMenuBar.add(selectMenu);
3635     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3636     alignFrameMenuBar.add(viewMenu);
3637     Menu annotationsMenu = new Menu(
3638             MessageManager.getString("action.annotations"));
3639     alignFrameMenuBar.add(annotationsMenu);
3640     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3641     alignFrameMenuBar.add(formatMenu);
3642     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3643     alignFrameMenuBar.add(colourMenu);
3644     Menu calculateMenu = new Menu(
3645             MessageManager.getString("action.calculate"));
3646     alignFrameMenuBar.add(calculateMenu);
3647     alignFrameMenuBar.add(helpMenu);
3648
3649     /*
3650      * File menu
3651      */
3652     fileMenu.add(inputText);
3653     fileMenu.add(loadTree);
3654     fileMenu.add(loadAnnotations);
3655     fileMenu.addSeparator();
3656     fileMenu.add(outputTextboxMenu);
3657     fileMenu.add(outputFeatures);
3658     fileMenu.add(outputAnnotations);
3659     if (jalviewServletURL != null)
3660     {
3661       fileMenu.add(loadApplication);
3662     }
3663     fileMenu.addSeparator();
3664     fileMenu.add(closeMenuItem);
3665
3666     /*
3667      * Edit menu
3668      */
3669     editMenu.add(undoMenuItem);
3670     editMenu.add(redoMenuItem);
3671     editMenu.add(cut);
3672     editMenu.add(copy);
3673     pasteMenu.add(pasteNew);
3674     pasteMenu.add(pasteThis);
3675     editMenu.add(pasteMenu);
3676     editMenu.add(delete);
3677     editMenu.addSeparator();
3678     editMenu.add(remove2LeftMenuItem);
3679     editMenu.add(remove2RightMenuItem);
3680     editMenu.add(removeGappedColumnMenuItem);
3681     editMenu.add(removeAllGapsMenuItem);
3682     editMenu.add(removeRedundancyMenuItem);
3683
3684     /*
3685      * Select menu
3686      */
3687     selectMenu.add(findMenuItem);
3688     selectMenu.addSeparator();
3689     selectMenu.add(selectAllSequenceMenuItem);
3690     selectMenu.add(deselectAllSequenceMenuItem);
3691     selectMenu.add(invertSequenceMenuItem);
3692     selectMenu.add(invertColSel);
3693     selectMenu.add(createGroup);
3694     selectMenu.add(unGroup);
3695     selectMenu.add(grpsFromSelection);
3696     selectMenu.add(deleteGroups);
3697     selectMenu.add(annotationColumnSelection);
3698
3699     /*
3700      * View menu
3701      */
3702     viewMenu.add(newView);
3703     viewMenu.addSeparator();
3704     showMenu.add(showColumns);
3705     showMenu.add(showSeqs);
3706     showMenu.add(showAllHidden);
3707     viewMenu.add(showMenu);
3708     hideMenu.add(hideColumns);
3709     hideMenu.add(hideSequences);
3710     hideMenu.add(hideAllSelection);
3711     hideMenu.add(hideAllButSelection);
3712     viewMenu.add(hideMenu);
3713     viewMenu.addSeparator();
3714     viewMenu.add(followMouseOverFlag);
3715     viewMenu.addSeparator();
3716     viewMenu.add(sequenceFeatures);
3717     viewMenu.add(featureSettings);
3718     viewMenu.addSeparator();
3719     viewMenu.add(alProperties);
3720     viewMenu.addSeparator();
3721     viewMenu.add(overviewMenuItem);
3722
3723     /*
3724      * Annotations menu
3725      */
3726     annotationsMenu.add(annotationPanelMenuItem);
3727     annotationsMenu.addSeparator();
3728     annotationsMenu.add(showAlignmentAnnotations);
3729     annotationsMenu.add(showSequenceAnnotations);
3730     annotationsMenu.add(sortAnnBySequence);
3731     annotationsMenu.add(sortAnnByLabel);
3732     annotationsMenu.addSeparator();
3733     autoAnnMenu.add(showAutoFirst);
3734     autoAnnMenu.add(showAutoLast);
3735     autoAnnMenu.addSeparator();
3736     autoAnnMenu.add(applyAutoAnnotationSettings);
3737     autoAnnMenu.add(showConsensusHistogram);
3738     autoAnnMenu.add(showSequenceLogo);
3739     autoAnnMenu.add(normSequenceLogo);
3740     autoAnnMenu.addSeparator();
3741     autoAnnMenu.add(showGroupConservation);
3742     autoAnnMenu.add(showGroupConsensus);
3743     annotationsMenu.add(autoAnnMenu);
3744
3745     /*
3746      * Format menu
3747      */
3748     formatMenu.add(font);
3749     formatMenu.add(seqLimits);
3750     formatMenu.add(wrapMenuItem);
3751     formatMenu.add(scaleAbove);
3752     formatMenu.add(scaleLeft);
3753     formatMenu.add(scaleRight);
3754     formatMenu.add(viewBoxesMenuItem);
3755     formatMenu.add(viewTextMenuItem);
3756     formatMenu.add(colourTextMenuItem);
3757     formatMenu.add(displayNonconservedMenuItem);
3758     formatMenu.add(renderGapsMenuItem);
3759     formatMenu.add(centreColumnLabelFlag);
3760
3761     /*
3762      * Colour menu
3763      */
3764     colourMenu.add(applyToAllGroups);
3765     colourMenu.addSeparator();
3766     colourMenu.add(noColourmenuItem);
3767     colourMenu.add(clustalColour);
3768     colourMenu.add(BLOSUM62Colour);
3769     colourMenu.add(PIDColour);
3770     colourMenu.add(zappoColour);
3771     colourMenu.add(taylorColour);
3772     colourMenu.add(hydrophobicityColour);
3773     colourMenu.add(helixColour);
3774     colourMenu.add(strandColour);
3775     colourMenu.add(turnColour);
3776     colourMenu.add(buriedColour);
3777     colourMenu.add(nucleotideColour);
3778     colourMenu.add(purinePyrimidineColour);
3779     // colourMenu.add(RNAInteractionColour);
3780     colourMenu.add(tcoffeeColour);
3781     colourMenu.add(userDefinedColour);
3782     colourMenu.addSeparator();
3783     colourMenu.add(conservationMenuItem);
3784     colourMenu.add(modifyConservation);
3785     colourMenu.add(abovePIDThreshold);
3786     colourMenu.add(modifyPID);
3787     colourMenu.add(annotationColour);
3788     colourMenu.add(RNAHelixColour);
3789
3790     /*
3791      * Calculate menu
3792      */
3793     sortMenu.add(sortIDMenuItem);
3794     sortMenu.add(sortLengthMenuItem);
3795     sortMenu.add(sortByTreeMenu);
3796     sortMenu.add(sortGroupMenuItem);
3797     sortMenu.add(sortPairwiseMenuItem);
3798     calculateMenu.add(sortMenu);
3799     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3800     calculateTreeMenu.add(neighbourTreeMenuItem);
3801     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3802     calculateTreeMenu.add(njTreeBlosumMenuItem);
3803     calculateMenu.add(calculateTreeMenu);
3804     calculateMenu.addSeparator();
3805     calculateMenu.add(pairwiseAlignmentMenuItem);
3806     calculateMenu.add(PCAMenuItem);
3807     calculateMenu.add(autoCalculate);
3808     calculateMenu.add(sortByTree);
3809
3810     /*
3811      * Help menu
3812      */
3813     helpMenu.add(documentation);
3814     helpMenu.add(about);
3815
3816     /*
3817      * Status bar
3818      */
3819     statusBar.setBackground(Color.white);
3820     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3821     statusBar.setText(MessageManager.getString("label.status_bar"));
3822     this.add(statusBar, BorderLayout.SOUTH);
3823   }
3824
3825   @Override
3826   public void setStatus(String string)
3827   {
3828     statusBar.setText(string);
3829   };
3830
3831   MenuItem featureSettings = new MenuItem();
3832
3833   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3834
3835   MenuItem annotationColour = new MenuItem();
3836
3837   MenuItem annotationColumnSelection = new MenuItem();
3838
3839   MenuItem invertColSel = new MenuItem();
3840
3841   MenuItem showColumns = new MenuItem();
3842
3843   MenuItem showSeqs = new MenuItem();
3844
3845   MenuItem hideColumns = new MenuItem();
3846
3847   MenuItem hideSequences = new MenuItem();
3848
3849   MenuItem hideAllButSelection = new MenuItem();
3850
3851   MenuItem hideAllSelection = new MenuItem();
3852
3853   MenuItem showAllHidden = new MenuItem();
3854
3855   MenuItem newView = new MenuItem();
3856
3857   private CheckboxMenuItem showAlignmentAnnotations;
3858
3859   private CheckboxMenuItem showSequenceAnnotations;
3860
3861   private CheckboxMenuItem sortAnnBySequence;
3862
3863   private CheckboxMenuItem sortAnnByLabel;
3864
3865   private CheckboxMenuItem showAutoFirst;
3866
3867   private CheckboxMenuItem showAutoLast;
3868
3869   private SplitFrame splitFrame;
3870
3871   /**
3872    * Attach the alignFrame panels after embedding menus, if necessary. This used
3873    * to be called setEmbedded, but is now creates the dropdown menus in a
3874    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3875    *
3876    * @param reallyEmbedded
3877    *          true to attach the view to the applet area on the page rather than
3878    *          in a new window
3879    */
3880   public void createAlignFrameWindow(boolean reallyEmbedded)
3881   {
3882     if (reallyEmbedded)
3883     {
3884       embedAlignFrameInApplet(viewport.applet);
3885     }
3886     else
3887     {
3888       // //////
3889       // test and embed menu bar if necessary.
3890       //
3891       if (embedMenuIfNeeded(alignPanel))
3892       {
3893         /*
3894          * adjust for status bar height too. ? pointless as overridden by layout
3895          * manager
3896          */
3897         alignPanel.setSize(getSize().width,
3898                 getSize().height - statusBar.getHeight());
3899       }
3900       add(statusBar, BorderLayout.SOUTH);
3901       add(alignPanel, BorderLayout.CENTER);
3902       // and register with the applet so it can pass external API calls to us
3903       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3904               frameHeight);
3905     }
3906   }
3907
3908   /**
3909    * Add the components of this AlignFrame to the applet container.
3910    *
3911    * @param theApplet
3912    */
3913   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3914   {
3915     // ////
3916     // Explicitly build the embedded menu panel for the on-page applet
3917     //
3918     // view cannot be closed if its actually on the page
3919     fileMenu.remove(closeMenuItem);
3920     fileMenu.remove(3); // Remove Separator
3921     // construct embedded menu, using default font
3922     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3923     // and actually add the components to the applet area
3924     theApplet.setLayout(new BorderLayout());
3925     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3926     theApplet.add(statusBar, BorderLayout.SOUTH);
3927     // TODO should size be left to the layout manager?
3928     alignPanel.setSize(theApplet.getSize().width,
3929             theApplet.getSize().height - embeddedMenu.getHeight()
3930                     - statusBar.getHeight());
3931     theApplet.add(alignPanel, BorderLayout.CENTER);
3932     final AlignFrame me = this;
3933     theApplet.addFocusListener(new FocusListener()
3934     {
3935
3936       @Override
3937       public void focusLost(FocusEvent e)
3938       {
3939         if (theApplet.currentAlignFrame == me)
3940         {
3941           theApplet.currentAlignFrame = null;
3942         }
3943       }
3944
3945       @Override
3946       public void focusGained(FocusEvent e)
3947       {
3948         theApplet.currentAlignFrame = me;
3949       }
3950     });
3951     theApplet.validate();
3952   }
3953
3954   /**
3955    * create a new binding between structures in an existing jmol viewer instance
3956    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3957    * this does not open a new Jmol window, or modify the display of the
3958    * structures in the original jmol window. Note This method doesn't work
3959    * without an additional javascript library to exchange messages between the
3960    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3961    *
3962    * @param viewer
3963    *          JmolViewer instance
3964    * @param sequenceIds
3965    *          - sequence Ids to search for associations
3966    */
3967   public SequenceStructureBinding addStructureViewInstance(
3968           Object jmolviewer, String[] sequenceIds)
3969   {
3970     Viewer viewer = null;
3971     try
3972     {
3973       viewer = (Viewer) jmolviewer;
3974     } catch (ClassCastException ex)
3975     {
3976       System.err.println("Unsupported viewer object :"
3977               + jmolviewer.getClass());
3978     }
3979     if (viewer == null)
3980     {
3981       System.err.println("Can't use this object as a structure viewer:"
3982               + jmolviewer.getClass());
3983       return null;
3984     }
3985     SequenceI[] seqs = null;
3986     if (sequenceIds == null || sequenceIds.length == 0)
3987     {
3988       seqs = viewport.getAlignment().getSequencesArray();
3989     }
3990     else
3991     {
3992       Vector sqi = new Vector();
3993       AlignmentI al = viewport.getAlignment();
3994       for (int sid = 0; sid < sequenceIds.length; sid++)
3995       {
3996         SequenceI sq = al.findName(sequenceIds[sid]);
3997         if (sq != null)
3998         {
3999           sqi.addElement(sq);
4000         }
4001       }
4002       if (sqi.size() > 0)
4003       {
4004         seqs = new SequenceI[sqi.size()];
4005         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4006         {
4007           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4008         }
4009       }
4010       else
4011       {
4012         return null;
4013       }
4014     }
4015     AAStructureBindingModel jmv = null;
4016     // TODO: search for a jmv that involves viewer
4017     if (jmv == null)
4018     { // create a new viewer/jalview binding.
4019       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4020     }
4021     return jmv;
4022
4023   }
4024
4025   /**
4026    * bind a pdb file to a sequence in the current view
4027    *
4028    * @param sequenceId
4029    *          - sequenceId within the dataset.
4030    * @param pdbEntryString
4031    *          - the short name for the PDB file
4032    * @param pdbFile
4033    *          - pdb file - either a URL or a valid PDB file.
4034    * @return true if binding was as success TODO: consider making an exception
4035    *         structure for indicating when PDB parsing or sequenceId location
4036    *         fails.
4037    */
4038   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4039           String pdbFile)
4040   {
4041     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4042     boolean needtoadd = false;
4043     if (toaddpdb != null)
4044     {
4045       Vector pdbe = toaddpdb.getAllPDBEntries();
4046       PDBEntry pdbentry = null;
4047       if (pdbe != null && pdbe.size() > 0)
4048       {
4049         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4050         {
4051           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4052           if (!pdbentry.getId().equals(pdbEntryString)
4053                   && !pdbentry.getFile().equals(pdbFile))
4054           {
4055             pdbentry = null;
4056           }
4057           else
4058           {
4059             continue;
4060           }
4061         }
4062       }
4063       if (pdbentry == null)
4064       {
4065         pdbentry = new PDBEntry();
4066         pdbentry.setId(pdbEntryString);
4067         pdbentry.setFile(pdbFile);
4068         needtoadd = true; // add this new entry to sequence.
4069       }
4070       // resolve data source
4071       // TODO: this code should be a refactored to an io package
4072       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4073               pdbFile, FileFormat.PDB);
4074       if (protocol == null)
4075       {
4076         return false;
4077       }
4078       if (needtoadd)
4079       {
4080         pdbentry.setProperty("protocol", protocol);
4081         toaddpdb.addPDBId(pdbentry);
4082         alignPanel.getStructureSelectionManager()
4083                 .registerPDBEntry(pdbentry);
4084       }
4085     }
4086     return true;
4087   }
4088
4089   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4090   {
4091     if (seqs != null)
4092     {
4093       Vector sequences = new Vector();
4094       for (int i = 0; i < seqs.length; i++)
4095       {
4096         if (seqs[i] != null)
4097         {
4098           sequences.addElement(new Object[] { seqs[i],
4099               (chains != null) ? chains[i] : null });
4100         }
4101       }
4102       seqs = new SequenceI[sequences.size()];
4103       chains = new String[sequences.size()];
4104       for (int i = 0, isize = sequences.size(); i < isize; i++)
4105       {
4106         Object[] oj = (Object[]) sequences.elementAt(i);
4107
4108         seqs[i] = (SequenceI) oj[0];
4109         chains[i] = (String) oj[1];
4110       }
4111     }
4112     return new Object[] { seqs, chains };
4113
4114   }
4115
4116   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4117           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4118   {
4119     // Scrub any null sequences from the array
4120     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4121     seqs = (SequenceI[]) sqch[0];
4122     chains = (String[]) sqch[1];
4123     if (seqs == null || seqs.length == 0)
4124     {
4125       System.err
4126               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4127     }
4128     if (protocol == null)
4129     {
4130       String sourceType = (String) pdb.getProperty("protocol");
4131       try
4132       {
4133         protocol = DataSourceType.valueOf(sourceType);
4134       } catch (IllegalArgumentException e)
4135       {
4136         // ignore
4137       }
4138       if (protocol == null)
4139       {
4140         System.err.println("Couldn't work out protocol to open structure: "
4141                 + pdb.getId());
4142         return;
4143       }
4144     }
4145     if (applet.useXtrnalSviewer)
4146     {
4147       // register the association(s) and quit, don't create any windows.
4148       if (StructureSelectionManager.getStructureSelectionManager(applet)
4149               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4150       {
4151         System.err.println("Failed to map " + pdb.getFile() + " ("
4152                 + protocol + ") to any sequences");
4153       }
4154       return;
4155     }
4156     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4157     {
4158       // can only do alignments with Jmol
4159       // find the last jmol window assigned to this alignment
4160       AppletJmol ajm = null, tajm;
4161       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4162       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4163       {
4164         tajm = (AppletJmol) jmols.elementAt(i);
4165         if (tajm.ap.alignFrame == this)
4166         {
4167           ajm = tajm;
4168           break;
4169         }
4170       }
4171       if (ajm != null)
4172       {
4173         System.err
4174                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4175         // try and add the pdb structure
4176         // ajm.addS
4177         ajm = null;
4178       }
4179     }
4180     // otherwise, create a new window
4181     if (applet.jmolAvailable)
4182     {
4183       new AppletJmol(pdb, seqs, chains, alignPanel,
4184               protocol);
4185       applet.lastFrameX += 40;
4186       applet.lastFrameY += 40;
4187     }
4188     else
4189     {
4190       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4191     }
4192
4193   }
4194
4195   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4196           SequenceI[][] seqs, String[][] chains, String[] protocols)
4197   {
4198     // TODO Auto-generated method stub
4199     System.err.println("Aligned Structure View: Not yet implemented.");
4200   }
4201
4202   /**
4203    * modify the current selection, providing the user has not made a selection
4204    * already.
4205    *
4206    * @param sel
4207    *          - sequences from this alignment
4208    * @param csel
4209    *          - columns to be selected on the alignment
4210    */
4211   public void select(SequenceGroup sel, ColumnSelection csel,
4212           HiddenColumns hidden)
4213   {
4214     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4215   }
4216
4217   public void scrollTo(int row, int column)
4218   {
4219     alignPanel.seqPanel.scrollTo(row, column);
4220   }
4221
4222   public void scrollToRow(int row)
4223   {
4224     alignPanel.seqPanel.scrollToRow(row);
4225   }
4226
4227   public void scrollToColumn(int column)
4228   {
4229     alignPanel.seqPanel.scrollToColumn(column);
4230   }
4231
4232   /**
4233    * @return the alignments unique ID.
4234    */
4235   public String getSequenceSetId()
4236   {
4237     return viewport.getSequenceSetId();
4238   }
4239
4240   /**
4241    * Load the (T-Coffee) score file from the specified url
4242    *
4243    * @param source
4244    *          File/URL/T-COFFEE score file contents
4245    * @throws IOException
4246    * @return true if alignment was annotated with data from source
4247    */
4248   public boolean loadScoreFile(String source) throws IOException
4249   {
4250
4251     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4252             AppletFormatAdapter.checkProtocol(source));
4253     if (!file.isValid())
4254     {
4255       // TODO: raise dialog for gui
4256       System.err.println("Problems parsing T-Coffee scores: "
4257               + file.getWarningMessage());
4258       System.err.println("Origin was:\n" + source);
4259       return false;
4260     }
4261
4262     /*
4263      * check that the score matrix matches the alignment dimensions
4264      */
4265     AlignmentI aln;
4266     if ((aln = viewport.getAlignment()) != null
4267             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4268                     .getWidth()))
4269     {
4270       // TODO: raise a dialog box here rather than bomb out.
4271       System.err
4272               .println("The scores matrix does not match the alignment dimensions");
4273
4274     }
4275
4276     // TODO add parameter to indicate if matching should be done
4277     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4278     {
4279       alignPanel.fontChanged();
4280       tcoffeeColour.setEnabled(true);
4281       // switch to this color
4282       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4283       return true;
4284     }
4285     else
4286     {
4287       System.err.println("Problems resolving T-Coffee scores:");
4288       if (file.getWarningMessage() != null)
4289       {
4290         System.err.println(file.getWarningMessage());
4291       }
4292     }
4293     return false;
4294   }
4295
4296   public SplitFrame getSplitFrame()
4297   {
4298     return this.splitFrame;
4299   }
4300
4301   public void setSplitFrame(SplitFrame sf)
4302   {
4303     this.splitFrame = sf;
4304   }
4305
4306   // may not need this
4307   @Override
4308   public void setShowSeqFeatures(boolean b)
4309   {
4310     // showSeqFeatures.setSelected(b);
4311     viewport.setShowSequenceFeatures(b);
4312
4313   }
4314
4315   @Override
4316   public void setMenusForViewport()
4317   {
4318     // setMenusFromViewport(viewport);
4319
4320   }
4321
4322   @Override
4323   public void refreshFeatureUI(boolean enableIfNecessary)
4324   {
4325     if (enableIfNecessary)
4326     {
4327       sequenceFeatures.setState(true);
4328       alignPanel.av.setShowSequenceFeatures(true);
4329     }
4330   }
4331
4332   @Override
4333   public FeatureSettingsControllerI getFeatureSettingsUI()
4334   {
4335     return alignPanel.av.featureSettings;
4336   }
4337
4338 }