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.Rectangle;
  99 import java.awt.event.ActionEvent;
 100 import java.awt.event.ActionListener;
 101 import java.awt.event.FocusEvent;
 102 import java.awt.event.FocusListener;
 103 import java.awt.event.ItemEvent;
 104 import java.awt.event.ItemListener;
 105 import java.awt.event.KeyEvent;
 106 import java.awt.event.KeyListener;
 107 import java.awt.event.WindowAdapter;
 108 import java.awt.event.WindowEvent;
 109 import java.io.IOException;
 110 import java.io.UnsupportedEncodingException;
 111 import java.net.URL;
 112 import java.net.URLEncoder;
 113 import java.util.Arrays;
 114 import java.util.Deque;
 115 import java.util.HashMap;
 116 import java.util.List;
 117 import java.util.Map;
 118 import java.util.StringTokenizer;
 119 import java.util.Vector;
 120
 121 import org.jmol.viewer.Viewer;
 122
 123 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 124         ItemListener, KeyListener, AlignViewControllerGuiI
 125 {
 126   public AlignViewControllerI avc;
 127
 128   public AlignmentPanel alignPanel;
 129
 130   public AlignViewport viewport;
 131
 132   // width and height may be overridden by applet parameters
 133   int frameWidth = 700;
 134
 135   int frameHeight = 500;
 136
 137   String jalviewServletURL;
 138
 139   /*
 140    * Flag for showing autocalculated consensus above or below other consensus
 141    * rows
 142    */
 143   private boolean showAutoCalculatedAbove;
 144
 145   private SequenceAnnotationOrder annotationSortOrder;
 146
 147   /**
 148    * Constructor that creates the frame and adds it to the display.
 149    *
 150    * @param al
 151    * @param applet
 152    * @param title
 153    * @param embedded
 154    */
 155   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 156           boolean embedded)
 157   {
 158     this(al, applet, title, embedded, true);
 159   }
 160
 161   /**
 162    * Constructor that optionally allows the frame to be displayed or only
 163    * created.
 164    *
 165    * @param al
 166    * @param applet
 167    * @param title
 168    * @param embedded
 169    * @param addToDisplay
 170    */
 171   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 172           boolean embedded, boolean addToDisplay)
 173   {
 174     this(al, null, null, applet, title, embedded, addToDisplay);
 175   }
 176
 177   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 178           HiddenColumns hidden, JalviewLite applet, String title,
 179           boolean embedded)
 180   {
 181     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 182   }
 183
 184   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 185           HiddenColumns hidden, JalviewLite applet, String title,
 186           boolean embedded, boolean addToDisplay)
 187   {
 188     if (applet != null)
 189     {
 190       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 191     }
 192
 193     try
 194     {
 195       jbInit();
 196     } catch (Exception ex)
 197     {
 198       ex.printStackTrace();
 199     }
 200     // need to get window geometry before we calculate alignment layout
 201     if (applet != null)
 202     {
 203       String param;
 204       try
 205       {
 206         param = applet.getParameter("windowWidth");
 207         if (param != null)
 208         {
 209           int width = Integer.parseInt(param);
 210           frameWidth = width;
 211         }
 212         param = applet.getParameter("windowHeight");
 213         if (param != null)
 214         {
 215           int height = Integer.parseInt(param);
 216           frameHeight = height;
 217         }
 218       } catch (Exception ex)
 219       {
 220       }
 221     }
 222     viewport = new AlignViewport(al, applet);
 223
 224     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 225     {
 226       viewport.hideSequence(hiddenSeqs);
 227     }
 228     if (hidden != null)
 229     {
 230       viewport.getAlignment().setHiddenColumns(hidden);
 231     }
 232     viewport.setScaleAboveWrapped(scaleAbove.getState());
 233
 234     alignPanel = new AlignmentPanel(this, viewport);
 235     avc = new jalview.controller.AlignViewController(this, viewport,
 236             alignPanel);
 237     viewport.updateConservation(alignPanel);
 238     viewport.updateConsensus(alignPanel);
 239
 240     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 241     followMouseOverFlag.setState(viewport.isFollowHighlight());
 242     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 243     showGroupConservation.setState(viewport.isShowGroupConservation());
 244     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 245     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 246     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 247     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 248     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 249     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 250     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 251     showAlignmentAnnotations.setState(true);
 252     showSequenceAnnotations.setState(false);
 253
 254     seqLimits.setState(viewport.getShowJVSuffix());
 255
 256     if (applet != null)
 257     {
 258       String param = applet.getParameter("sortBy");
 259       if (param != null)
 260       {
 261         if (param.equalsIgnoreCase("Id"))
 262         {
 263           sortIDMenuItem_actionPerformed();
 264         }
 265         else if (param.equalsIgnoreCase("Pairwise Identity"))
 266         {
 267           sortPairwiseMenuItem_actionPerformed();
 268         }
 269         else if (param.equalsIgnoreCase("Length"))
 270         {
 271           sortLengthMenuItem_actionPerformed();
 272         }
 273       }
 274
 275       param = applet.getParameter("wrap");
 276       if (param != null)
 277       {
 278         if (param.equalsIgnoreCase("true"))
 279         {
 280           wrapMenuItem.setState(true);
 281           wrapMenuItem_actionPerformed();
 282         }
 283       }
 284       param = applet.getParameter("centrecolumnlabels");
 285       if (param != null)
 286       {
 287         centreColumnLabelFlag.setState(true);
 288         centreColumnLabelFlag_stateChanged();
 289       }
 290
 291     }
 292     if (viewport.getAlignment().isNucleotide())
 293     {
 294       conservationMenuItem.setEnabled(false);
 295       clustalColour.setEnabled(false);
 296       BLOSUM62Colour.setEnabled(false);
 297       zappoColour.setEnabled(false);
 298       taylorColour.setEnabled(false);
 299       hydrophobicityColour.setEnabled(false);
 300       helixColour.setEnabled(false);
 301       strandColour.setEnabled(false);
 302       turnColour.setEnabled(false);
 303       buriedColour.setEnabled(false);
 304       viewport.updateStrucConsensus(alignPanel);
 305       if (viewport.getAlignment().hasRNAStructure())
 306       {
 307         RNAHelixColour.setEnabled(true);
 308       }
 309       else
 310       {
 311         RNAHelixColour.setEnabled(false);
 312       }
 313     }
 314     else
 315     {
 316       RNAHelixColour.setEnabled(false);
 317       purinePyrimidineColour.setEnabled(false);
 318       nucleotideColour.setEnabled(false);
 319     }
 320     // Some JVMS send keyevents to Top frame or lowest panel,
 321     // Havent worked out why yet. So add to both this frame and seqCanvas for
 322     // now
 323     this.addKeyListener(this);
 324     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 325     alignPanel.idPanel.idCanvas.addKeyListener(this);
 326     alignPanel.scalePanel.addKeyListener(this);
 327     alignPanel.annotationPanel.addKeyListener(this);
 328     alignPanel.annotationPanelHolder.addKeyListener(this);
 329     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 330     alignPanel.alabels.addKeyListener(this);
 331
 332     setAnnotationsVisibility();
 333
 334     if (addToDisplay)
 335     {
 336       addToDisplay(embedded);
 337     }
 338   }
 339
 340   /**
 341    * @param embedded
 342    */
 343   public void addToDisplay(boolean embedded)
 344   {
 345     createAlignFrameWindow(embedded);
 346     validate();
 347     alignPanel.adjustAnnotationHeight();
 348     alignPanel.paintAlignment(true, true);
 349   }
 350
 351   public AlignViewport getAlignViewport()
 352   {
 353     return viewport;
 354   }
 355
 356   public SeqCanvas getSeqcanvas()
 357   {
 358     return alignPanel.seqPanel.seqCanvas;
 359   }
 360
 361   /**
 362    * Load a features file onto the alignment
 363    *
 364    * @param file
 365    *          file URL, content, or other resolvable path
 366    * @param type
 367    *          is protocol for accessing data referred to by file
 368    */
 369
 370   public boolean parseFeaturesFile(String file, DataSourceType type)
 371   {
 372     return parseFeaturesFile(file, type, true);
 373   }
 374
 375   /**
 376    * Load a features file onto the alignment
 377    *
 378    * @param file
 379    *          file URL, content, or other resolvable path
 380    * @param sourceType
 381    *          is protocol for accessing data referred to by file
 382    * @param autoenabledisplay
 383    *          when true, display features flag will be automatically enabled if
 384    *          features are loaded
 385    * @return true if data parsed as a features file
 386    */
 387   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 388           boolean autoenabledisplay)
 389   {
 390     boolean featuresFile = false;
 391     try
 392     {
 393       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 394               .getFeatureRenderer().getFeatureColours();
 395       boolean relaxedIdMatching = viewport.applet
 396               .getDefaultParameter("relaxedidmatch", false);
 397       featuresFile = new FeaturesFile(file, sourceType).parse(
 398               viewport.getAlignment(), colours, true, relaxedIdMatching);
 399     } catch (Exception ex)
 400     {
 401       ex.printStackTrace();
 402     }
 403
 404     if (featuresFile)
 405     {
 406       if (autoenabledisplay)
 407       {
 408         viewport.setShowSequenceFeatures(true);
 409         sequenceFeatures.setState(true);
 410       }
 411       if (alignPanel.seqPanel.seqCanvas.fr != null)
 412       {
 413         // update the min/max ranges where necessary
 414         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 415       }
 416       if (viewport.featureSettings != null)
 417       {
 418         viewport.featureSettings.refreshTable();
 419       }
 420       alignPanel.paintAlignment(true, true);
 421       setStatus(MessageManager
 422               .getString("label.successfully_added_features_alignment"));
 423     }
 424     return featuresFile;
 425   }
 426
 427   @Override
 428   public void keyPressed(KeyEvent evt)
 429   {
 430     ViewportRanges ranges = viewport.getRanges();
 431
 432     if (viewport.cursorMode
 433             && ((evt.getKeyCode() >= KeyEvent.VK_0
 434                     && evt.getKeyCode() <= KeyEvent.VK_9)
 435                     || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 436                             && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 437             && Character.isDigit(evt.getKeyChar()))
 438     {
 439       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 440     }
 441
 442     switch (evt.getKeyCode())
 443     {
 444     case 27: // escape key
 445       deselectAllSequenceMenuItem_actionPerformed();
 446
 447       alignPanel.alabels.cancelDrag();
 448       break;
 449     case KeyEvent.VK_X:
 450       if (evt.isControlDown() || evt.isMetaDown())
 451       {
 452         cut_actionPerformed();
 453       }
 454       break;
 455     case KeyEvent.VK_C:
 456       if (viewport.cursorMode && !evt.isControlDown())
 457       {
 458         alignPanel.seqPanel.setCursorColumn();
 459       }
 460       if (evt.isControlDown() || evt.isMetaDown())
 461       {
 462         copy_actionPerformed();
 463       }
 464       break;
 465     case KeyEvent.VK_V:
 466       if (evt.isControlDown())
 467       {
 468         paste(evt.isShiftDown());
 469       }
 470       break;
 471     case KeyEvent.VK_A:
 472       if (evt.isControlDown() || evt.isMetaDown())
 473       {
 474         selectAllSequenceMenuItem_actionPerformed();
 475       }
 476       break;
 477     case KeyEvent.VK_DOWN:
 478       if (viewport.cursorMode)
 479       {
 480         alignPanel.seqPanel.moveCursor(0, 1);
 481       }
 482       else
 483       {
 484         moveSelectedSequences(false);
 485       }
 486       break;
 487
 488     case KeyEvent.VK_UP:
 489       if (viewport.cursorMode)
 490       {
 491         alignPanel.seqPanel.moveCursor(0, -1);
 492       }
 493       else
 494       {
 495         moveSelectedSequences(true);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_LEFT:
 500       if (evt.isAltDown() || !viewport.cursorMode)
 501       {
 502         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 503       }
 504       else
 505       {
 506         alignPanel.seqPanel.moveCursor(-1, 0);
 507       }
 508       break;
 509
 510     case KeyEvent.VK_RIGHT:
 511       if (evt.isAltDown() || !viewport.cursorMode)
 512       {
 513         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 514       }
 515       else
 516       {
 517         alignPanel.seqPanel.moveCursor(1, 0);
 518       }
 519       break;
 520
 521     case KeyEvent.VK_SPACE:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 525                 || evt.isShiftDown() || evt.isAltDown());
 526       }
 527       break;
 528
 529     case KeyEvent.VK_DELETE:
 530     case KeyEvent.VK_BACK_SPACE:
 531       if (viewport.cursorMode)
 532       {
 533         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 534                 || evt.isShiftDown() || evt.isAltDown());
 535       }
 536       else
 537       {
 538         cut_actionPerformed();
 539         alignPanel.seqPanel.seqCanvas.repaint();
 540       }
 541       break;
 542
 543     case KeyEvent.VK_S:
 544       if (viewport.cursorMode)
 545       {
 546         alignPanel.seqPanel.setCursorRow();
 547       }
 548       break;
 549     case KeyEvent.VK_P:
 550       if (viewport.cursorMode)
 551       {
 552         alignPanel.seqPanel.setCursorPosition();
 553       }
 554       break;
 555
 556     case KeyEvent.VK_ENTER:
 557     case KeyEvent.VK_COMMA:
 558       if (viewport.cursorMode)
 559       {
 560         alignPanel.seqPanel.setCursorRowAndColumn();
 561       }
 562       break;
 563
 564     case KeyEvent.VK_Q:
 565       if (viewport.cursorMode)
 566       {
 567         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 568       }
 569       break;
 570     case KeyEvent.VK_M:
 571       if (viewport.cursorMode)
 572       {
 573         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 574       }
 575       break;
 576
 577     case KeyEvent.VK_F2:
 578       viewport.cursorMode = !viewport.cursorMode;
 579       setStatus(MessageManager
 580               .formatMessage("label.keyboard_editing_mode", new String[]
 581               { (viewport.cursorMode ? "on" : "off") }));
 582       if (viewport.cursorMode)
 583       {
 584         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 585         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 586       }
 587       break;
 588
 589     case KeyEvent.VK_F:
 590       if (evt.isControlDown())
 591       {
 592         findMenuItem_actionPerformed();
 593       }
 594       break;
 595
 596     case KeyEvent.VK_H:
 597     {
 598       boolean toggleSeqs = !evt.isControlDown();
 599       boolean toggleCols = !evt.isShiftDown();
 600       toggleHiddenRegions(toggleSeqs, toggleCols);
 601       break;
 602     }
 603
 604     case KeyEvent.VK_PAGE_UP:
 605       ranges.pageUp();
 606       break;
 607
 608     case KeyEvent.VK_PAGE_DOWN:
 609       ranges.pageDown();
 610       break;
 611
 612     case KeyEvent.VK_Z:
 613       if (evt.isControlDown())
 614       {
 615         undoMenuItem_actionPerformed();
 616       }
 617       break;
 618
 619     case KeyEvent.VK_Y:
 620       if (evt.isControlDown())
 621       {
 622         redoMenuItem_actionPerformed();
 623       }
 624       break;
 625
 626     case KeyEvent.VK_L:
 627       if (evt.isControlDown())
 628       {
 629         trimAlignment(true);
 630       }
 631       break;
 632
 633     case KeyEvent.VK_R:
 634       if (evt.isControlDown())
 635       {
 636         trimAlignment(false);
 637       }
 638       break;
 639
 640     case KeyEvent.VK_E:
 641       if (evt.isControlDown())
 642       {
 643         if (evt.isShiftDown())
 644         {
 645           this.removeAllGapsMenuItem_actionPerformed();
 646         }
 647         else
 648         {
 649           removeGappedColumnMenuItem_actionPerformed();
 650         }
 651       }
 652       break;
 653     case KeyEvent.VK_I:
 654       if (evt.isControlDown())
 655       {
 656         if (evt.isAltDown())
 657         {
 658           invertColSel_actionPerformed();
 659         }
 660         else
 661         {
 662           invertSequenceMenuItem_actionPerformed();
 663         }
 664       }
 665       break;
 666
 667     case KeyEvent.VK_G:
 668       if (evt.isControlDown())
 669       {
 670         if (evt.isShiftDown())
 671         {
 672           this.unGroup_actionPerformed();
 673         }
 674         else
 675         {
 676           this.createGroup_actionPerformed();
 677         }
 678       }
 679       break;
 680
 681     case KeyEvent.VK_U:
 682       if (evt.isControlDown())
 683       {
 684         this.deleteGroups_actionPerformed();
 685       }
 686       break;
 687
 688     case KeyEvent.VK_T:
 689       if (evt.isControlDown())
 690       {
 691         newView(null);
 692       }
 693       break;
 694
 695     }
 696     // TODO: repaint flags set only if the keystroke warrants it
 697     alignPanel.paintAlignment(true, true);
 698   }
 699
 700   /**
 701    * called by key handler and the hide all/show all menu items
 702    *
 703    * @param toggleSeqs
 704    * @param toggleCols
 705    */
 706   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 707   {
 708     boolean hide = false;
 709     SequenceGroup sg = viewport.getSelectionGroup();
 710     if (!toggleSeqs && !toggleCols)
 711     {
 712       // Hide everything by the current selection - this is a hack - we do the
 713       // invert and then hide
 714       // first check that there will be visible columns after the invert.
 715       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 716               && sg.getStartRes() <= sg.getEndRes()))
 717       {
 718         // now invert the sequence set, if required - empty selection implies
 719         // that no hiding is required.
 720         if (sg != null)
 721         {
 722           invertSequenceMenuItem_actionPerformed();
 723           sg = viewport.getSelectionGroup();
 724           toggleSeqs = true;
 725
 726         }
 727         viewport.expandColSelection(sg, true);
 728         // finally invert the column selection and get the new sequence
 729         // selection and indicate it should be hidden.
 730         invertColSel_actionPerformed();
 731         toggleCols = true;
 732       }
 733     }
 734
 735     if (toggleSeqs)
 736     {
 737       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 738       {
 739         hide = true;
 740         viewport.hideAllSelectedSeqs();
 741       }
 742       else if (!(toggleCols && viewport.hasSelectedColumns()))
 743       {
 744         viewport.showAllHiddenSeqs();
 745       }
 746     }
 747
 748     if (toggleCols)
 749     {
 750       if (viewport.hasSelectedColumns())
 751       {
 752         viewport.hideSelectedColumns();
 753         if (!toggleSeqs)
 754         {
 755           viewport.setSelectionGroup(sg);
 756         }
 757       }
 758       else if (!hide)
 759       {
 760         viewport.showAllHiddenColumns();
 761       }
 762       viewport.sendSelection();
 763     }
 764   }
 765
 766   @Override
 767   public void keyReleased(KeyEvent evt)
 768   {
 769   }
 770
 771   @Override
 772   public void keyTyped(KeyEvent evt)
 773   {
 774   }
 775
 776   @Override
 777   public void itemStateChanged(ItemEvent evt)
 778   {
 779     final Object source = evt.getSource();
 780     if (source == displayNonconservedMenuItem)
 781     {
 782       displayNonconservedMenuItem_actionPerformed();
 783     }
 784     else if (source == colourTextMenuItem)
 785     {
 786       colourTextMenuItem_actionPerformed();
 787     }
 788     else if (source == wrapMenuItem)
 789     {
 790       wrapMenuItem_actionPerformed();
 791     }
 792     else if (source == scaleAbove)
 793     {
 794       viewport.setScaleAboveWrapped(scaleAbove.getState());
 795     }
 796     else if (source == scaleLeft)
 797     {
 798       viewport.setScaleLeftWrapped(scaleLeft.getState());
 799     }
 800     else if (source == scaleRight)
 801     {
 802       viewport.setScaleRightWrapped(scaleRight.getState());
 803     }
 804     else if (source == seqLimits)
 805     {
 806       seqLimits_itemStateChanged();
 807     }
 808     else if (source == viewBoxesMenuItem)
 809     {
 810       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 811     }
 812     else if (source == viewTextMenuItem)
 813     {
 814       viewport.setShowText(viewTextMenuItem.getState());
 815     }
 816     else if (source == renderGapsMenuItem)
 817     {
 818       viewport.setRenderGaps(renderGapsMenuItem.getState());
 819     }
 820     else if (source == annotationPanelMenuItem)
 821     {
 822       boolean showAnnotations = annotationPanelMenuItem.getState();
 823       showAlignmentAnnotations.setEnabled(showAnnotations);
 824       showSequenceAnnotations.setEnabled(showAnnotations);
 825       viewport.setShowAnnotation(showAnnotations);
 826       alignPanel.setAnnotationVisible(showAnnotations);
 827     }
 828     else if (source == sequenceFeatures)
 829     {
 830       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 831       alignPanel.seqPanel.seqCanvas.repaint();
 832     }
 833     else if (source == showAlignmentAnnotations)
 834     {
 835       setAnnotationsVisibility();
 836     }
 837     else if (source == showSequenceAnnotations)
 838     {
 839       setAnnotationsVisibility();
 840     }
 841     else if (source == sortAnnBySequence)
 842     {
 843       boolean newState = sortAnnBySequence.getState();
 844       sortAnnByLabel.setState(false);
 845       setAnnotationSortOrder(
 846               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 847                       : SequenceAnnotationOrder.NONE);
 848       setViewportAnnotationOrder();
 849     }
 850     else if (source == sortAnnByLabel)
 851     {
 852       boolean newState = sortAnnByLabel.getState();
 853       sortAnnBySequence.setState(false);
 854       setAnnotationSortOrder(
 855               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 856                       : SequenceAnnotationOrder.NONE);
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == showAutoFirst)
 860     {
 861       showAutoLast.setState(!showAutoFirst.getState());
 862       setShowAutoCalculatedAbove(showAutoFirst.getState());
 863       setViewportAnnotationOrder();
 864     }
 865     else if (source == showAutoLast)
 866     {
 867       showAutoFirst.setState(!showAutoLast.getState());
 868       setShowAutoCalculatedAbove(showAutoFirst.getState());
 869       setViewportAnnotationOrder();
 870     }
 871     else if (source == conservationMenuItem)
 872     {
 873       conservationMenuItem_actionPerformed();
 874     }
 875     else if (source == abovePIDThreshold)
 876     {
 877       abovePIDThreshold_actionPerformed();
 878     }
 879     else if (source == applyToAllGroups)
 880     {
 881       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 882     }
 883     else if (source == autoCalculate)
 884     {
 885       viewport.autoCalculateConsensus = autoCalculate.getState();
 886     }
 887     else if (source == sortByTree)
 888     {
 889       viewport.sortByTree = sortByTree.getState();
 890     }
 891     else if (source == this.centreColumnLabelFlag)
 892     {
 893       centreColumnLabelFlag_stateChanged();
 894     }
 895     else if (source == this.followMouseOverFlag)
 896     {
 897       mouseOverFlag_stateChanged();
 898     }
 899     else if (source == showGroupConsensus)
 900     {
 901       showGroupConsensus_actionPerformed();
 902     }
 903     else if (source == showGroupConservation)
 904     {
 905       showGroupConservation_actionPerformed();
 906     }
 907     else if (source == showSequenceLogo)
 908     {
 909       showSequenceLogo_actionPerformed();
 910     }
 911     else if (source == normSequenceLogo)
 912     {
 913       normSequenceLogo_actionPerformed();
 914     }
 915     else if (source == showConsensusHistogram)
 916     {
 917       showConsensusHistogram_actionPerformed();
 918     }
 919     else if (source == applyAutoAnnotationSettings)
 920     {
 921       applyAutoAnnotationSettings_actionPerformed();
 922     }
 923     // TODO: repaint flags set only if warranted
 924     alignPanel.paintAlignment(true, true);
 925   }
 926
 927   /**
 928    * Set the visibility state of sequence-related and/or alignment-related
 929    * annotations depending on checkbox selections, and repaint.
 930    *
 931    * @param visible
 932    */
 933   private void setAnnotationsVisibility()
 934   {
 935     boolean showForAlignment = showAlignmentAnnotations.getState();
 936     boolean showForSequences = showSequenceAnnotations.getState();
 937     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 938     {
 939       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 940               .getAlignmentAnnotation())
 941       {
 942         boolean visible = (aa.sequenceRef == null ? showForAlignment
 943                 : showForSequences);
 944         aa.visible = visible;
 945       }
 946     }
 947     alignPanel.validateAnnotationDimensions(true);
 948     validate();
 949     repaint();
 950   }
 951
 952   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 953   {
 954     this.annotationSortOrder = order;
 955   }
 956
 957   /**
 958    * Set flags on the viewport that control annotation ordering
 959    */
 960   private void setViewportAnnotationOrder()
 961   {
 962     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 963     this.alignPanel.av
 964             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 965   }
 966
 967   private void setShowAutoCalculatedAbove(boolean showAbove)
 968   {
 969     this.showAutoCalculatedAbove = showAbove;
 970   }
 971
 972   private void mouseOverFlag_stateChanged()
 973   {
 974     viewport.setFollowHighlight(followMouseOverFlag.getState());
 975     // TODO: could kick the scrollTo mechanism to reset view for current
 976     // searchresults.
 977   }
 978
 979   private void centreColumnLabelFlag_stateChanged()
 980   {
 981     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 982     this.alignPanel.annotationPanel.repaint();
 983   }
 984
 985   @Override
 986   public void actionPerformed(ActionEvent evt)
 987   {
 988     viewport.applet.currentAlignFrame = this;
 989
 990     Object source = evt.getSource();
 991
 992     if (source == inputText)
 993     {
 994       inputText_actionPerformed();
 995     }
 996     else if (source == loadTree)
 997     {
 998       loadTree_actionPerformed();
 999     }
1000     else if (source == loadApplication)
1001     {
1002       launchFullApplication();
1003     }
1004     else if (source == loadAnnotations)
1005     {
1006       loadAnnotations();
1007     }
1008     else if (source == outputAnnotations)
1009     {
1010       outputAnnotations(true);
1011     }
1012     else if (source == outputFeatures)
1013     {
1014       outputFeatures(true, "Jalview");
1015     }
1016     else if (source == closeMenuItem)
1017     {
1018       closeMenuItem_actionPerformed();
1019     }
1020     else if (source == copy)
1021     {
1022       copy_actionPerformed();
1023     }
1024     else if (source == undoMenuItem)
1025     {
1026       undoMenuItem_actionPerformed();
1027     }
1028     else if (source == redoMenuItem)
1029     {
1030       redoMenuItem_actionPerformed();
1031     }
1032     else if (source == inputText)
1033     {
1034       inputText_actionPerformed();
1035     }
1036     else if (source == closeMenuItem)
1037     {
1038       closeMenuItem_actionPerformed();
1039     }
1040     else if (source == undoMenuItem)
1041     {
1042       undoMenuItem_actionPerformed();
1043     }
1044     else if (source == redoMenuItem)
1045     {
1046       redoMenuItem_actionPerformed();
1047     }
1048     else if (source == copy)
1049     {
1050       copy_actionPerformed();
1051     }
1052     else if (source == pasteNew)
1053     {
1054       pasteNew_actionPerformed();
1055     }
1056     else if (source == pasteThis)
1057     {
1058       pasteThis_actionPerformed();
1059     }
1060     else if (source == cut)
1061     {
1062       cut_actionPerformed();
1063     }
1064     else if (source == delete)
1065     {
1066       delete_actionPerformed();
1067     }
1068     else if (source == createGroup)
1069     {
1070       createGroup_actionPerformed();
1071     }
1072     else if (source == unGroup)
1073     {
1074       unGroup_actionPerformed();
1075     }
1076     else if (source == grpsFromSelection)
1077     {
1078       makeGrpsFromSelection_actionPerformed();
1079     }
1080     else if (source == deleteGroups)
1081     {
1082       deleteGroups_actionPerformed();
1083     }
1084     else if (source == selectAllSequenceMenuItem)
1085     {
1086       selectAllSequenceMenuItem_actionPerformed();
1087     }
1088     else if (source == deselectAllSequenceMenuItem)
1089     {
1090       deselectAllSequenceMenuItem_actionPerformed();
1091     }
1092     else if (source == invertSequenceMenuItem)
1093     {
1094       invertSequenceMenuItem_actionPerformed();
1095       // uncomment to slave sequence selections in split frame
1096       // viewport.sendSelection();
1097     }
1098     else if (source == invertColSel)
1099     {
1100       viewport.invertColumnSelection();
1101       alignPanel.paintAlignment(false, false);
1102       viewport.sendSelection();
1103     }
1104     else if (source == remove2LeftMenuItem)
1105     {
1106       trimAlignment(true);
1107     }
1108     else if (source == remove2RightMenuItem)
1109     {
1110       trimAlignment(false);
1111     }
1112     else if (source == removeGappedColumnMenuItem)
1113     {
1114       removeGappedColumnMenuItem_actionPerformed();
1115     }
1116     else if (source == removeAllGapsMenuItem)
1117     {
1118       removeAllGapsMenuItem_actionPerformed();
1119     }
1120     else if (source == findMenuItem)
1121     {
1122       findMenuItem_actionPerformed();
1123     }
1124     else if (source == font)
1125     {
1126       new FontChooser(alignPanel);
1127     }
1128     else if (source == newView)
1129     {
1130       newView(null);
1131     }
1132     else if (source == showColumns)
1133     {
1134       viewport.showAllHiddenColumns();
1135       alignPanel.paintAlignment(true, true);
1136       viewport.sendSelection();
1137     }
1138     else if (source == showSeqs)
1139     {
1140       viewport.showAllHiddenSeqs();
1141       alignPanel.paintAlignment(true, true);
1142       // uncomment if we want to slave sequence selections in split frame
1143       // viewport.sendSelection();
1144     }
1145     else if (source == hideColumns)
1146     {
1147       viewport.hideSelectedColumns();
1148       alignPanel.paintAlignment(true, true);
1149       viewport.sendSelection();
1150     }
1151     else if (source == hideSequences
1152             && viewport.getSelectionGroup() != null)
1153     {
1154       viewport.hideAllSelectedSeqs();
1155       alignPanel.paintAlignment(true, true);
1156       // uncomment if we want to slave sequence selections in split frame
1157       // viewport.sendSelection();
1158     }
1159     else if (source == hideAllButSelection)
1160     {
1161       toggleHiddenRegions(false, false);
1162       alignPanel.paintAlignment(true, true);
1163       viewport.sendSelection();
1164     }
1165     else if (source == hideAllSelection)
1166     {
1167       SequenceGroup sg = viewport.getSelectionGroup();
1168       viewport.expandColSelection(sg, false);
1169       viewport.hideAllSelectedSeqs();
1170       viewport.hideSelectedColumns();
1171       alignPanel.paintAlignment(true, true);
1172       viewport.sendSelection();
1173     }
1174     else if (source == showAllHidden)
1175     {
1176       viewport.showAllHiddenColumns();
1177       viewport.showAllHiddenSeqs();
1178       alignPanel.paintAlignment(true, true);
1179       viewport.sendSelection();
1180     }
1181     else if (source == showGroupConsensus)
1182     {
1183       showGroupConsensus_actionPerformed();
1184     }
1185     else if (source == showGroupConservation)
1186     {
1187       showGroupConservation_actionPerformed();
1188     }
1189     else if (source == showSequenceLogo)
1190     {
1191       showSequenceLogo_actionPerformed();
1192     }
1193     else if (source == normSequenceLogo)
1194     {
1195       normSequenceLogo_actionPerformed();
1196     }
1197     else if (source == showConsensusHistogram)
1198     {
1199       showConsensusHistogram_actionPerformed();
1200     }
1201     else if (source == applyAutoAnnotationSettings)
1202     {
1203       applyAutoAnnotationSettings_actionPerformed();
1204     }
1205     else if (source == featureSettings)
1206     {
1207       showFeatureSettingsUI();
1208     }
1209     else if (source == alProperties)
1210     {
1211       StringBuffer contents = new jalview.io.AlignmentProperties(
1212               viewport.getAlignment()).formatAsString();
1213       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214       cap.setText(contents.toString());
1215       Frame frame = new Frame();
1216       frame.add(cap);
1217       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1218               .formatMessage("label.alignment_properties", new String[]
1219               { getTitle() }), 400, 250);
1220     }
1221     else if (source == overviewMenuItem)
1222     {
1223       overviewMenuItem_actionPerformed();
1224     }
1225     else if (source == noColourmenuItem)
1226     {
1227       changeColour(null);
1228     }
1229     else if (source == clustalColour)
1230     {
1231       abovePIDThreshold.setState(false);
1232       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1233     }
1234     else if (source == zappoColour)
1235     {
1236       changeColour(new ZappoColourScheme());
1237     }
1238     else if (source == taylorColour)
1239     {
1240       changeColour(new TaylorColourScheme());
1241     }
1242     else if (source == hydrophobicityColour)
1243     {
1244       changeColour(new HydrophobicColourScheme());
1245     }
1246     else if (source == helixColour)
1247     {
1248       changeColour(new HelixColourScheme());
1249     }
1250     else if (source == strandColour)
1251     {
1252       changeColour(new StrandColourScheme());
1253     }
1254     else if (source == turnColour)
1255     {
1256       changeColour(new TurnColourScheme());
1257     }
1258     else if (source == buriedColour)
1259     {
1260       changeColour(new BuriedColourScheme());
1261     }
1262     else if (source == nucleotideColour)
1263     {
1264       changeColour(new NucleotideColourScheme());
1265     }
1266     else if (source == purinePyrimidineColour)
1267     {
1268       changeColour(new PurinePyrimidineColourScheme());
1269     }
1270     // else if (source == RNAInteractionColour)
1271     // {
1272     // changeColour(new RNAInteractionColourScheme());
1273     // }
1274     else if (source == RNAHelixColour)
1275     {
1276       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1277       // new RNAHelicesColourChooser(viewport, alignPanel);
1278     }
1279     else if (source == modifyPID)
1280     {
1281       modifyPID_actionPerformed();
1282     }
1283     else if (source == modifyConservation)
1284     {
1285       modifyConservation_actionPerformed();
1286     }
1287     else if (source == userDefinedColour)
1288     {
1289       new UserDefinedColours(alignPanel, null);
1290     }
1291     else if (source == PIDColour)
1292     {
1293       changeColour(new PIDColourScheme());
1294     }
1295     else if (source == BLOSUM62Colour)
1296     {
1297       changeColour(new Blosum62ColourScheme());
1298     }
1299     else if (source == tcoffeeColour)
1300     {
1301       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1302     }
1303     else if (source == annotationColour)
1304     {
1305       new AnnotationColourChooser(viewport, alignPanel);
1306     }
1307     else if (source == annotationColumnSelection)
1308     {
1309       new AnnotationColumnChooser(viewport, alignPanel);
1310     }
1311     else if (source == sortPairwiseMenuItem)
1312     {
1313       sortPairwiseMenuItem_actionPerformed();
1314     }
1315     else if (source == sortIDMenuItem)
1316     {
1317       sortIDMenuItem_actionPerformed();
1318     }
1319     else if (source == sortLengthMenuItem)
1320     {
1321       sortLengthMenuItem_actionPerformed();
1322     }
1323     else if (source == sortGroupMenuItem)
1324     {
1325       sortGroupMenuItem_actionPerformed();
1326     }
1327     else if (source == removeRedundancyMenuItem)
1328     {
1329       removeRedundancyMenuItem_actionPerformed();
1330     }
1331     else if (source == pairwiseAlignmentMenuItem)
1332     {
1333       pairwiseAlignmentMenuItem_actionPerformed();
1334     }
1335     else if (source == PCAMenuItem)
1336     {
1337       PCAMenuItem_actionPerformed();
1338     }
1339     else if (source == averageDistanceTreeMenuItem)
1340     {
1341       averageDistanceTreeMenuItem_actionPerformed();
1342     }
1343     else if (source == neighbourTreeMenuItem)
1344     {
1345       neighbourTreeMenuItem_actionPerformed();
1346     }
1347     else if (source == njTreeBlosumMenuItem)
1348     {
1349       njTreeBlosumMenuItem_actionPerformed();
1350     }
1351     else if (source == avDistanceTreeBlosumMenuItem)
1352     {
1353       avTreeBlosumMenuItem_actionPerformed();
1354     }
1355     else if (source == documentation)
1356     {
1357       documentation_actionPerformed();
1358     }
1359     else if (source == about)
1360     {
1361       about_actionPerformed();
1362     }
1363
1364   }
1365
1366   public void inputText_actionPerformed()
1367   {
1368     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1369     Frame frame = new Frame();
1370     frame.add(cap);
1371     jalview.bin.JalviewLite.addFrame(frame,
1372             MessageManager.getString("label.input_cut_paste"), 500, 500);
1373   }
1374
1375   protected void outputText_actionPerformed(ActionEvent e)
1376   {
1377     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378     Frame frame = new Frame();
1379     frame.add(cap);
1380     JalviewLite.addFrame(frame, MessageManager
1381             .formatMessage("label.alignment_output_command", new Object[]
1382             { e.getActionCommand() }), 600, 500);
1383
1384     FileFormatI fileFormat = FileFormats.getInstance()
1385             .forName(e.getActionCommand());
1386     cap.setText(
1387             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1388                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1389   }
1390
1391   public void loadAnnotations()
1392   {
1393     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1394     cap.setText(MessageManager
1395             .getString("label.paste_features_annotations_Tcoffee_here"));
1396     cap.setAnnotationImport();
1397     Frame frame = new Frame();
1398     frame.add(cap);
1399     jalview.bin.JalviewLite.addFrame(frame,
1400             MessageManager.getString("action.paste_annotations"), 400, 300);
1401
1402   }
1403
1404   public String outputAnnotations(boolean displayTextbox)
1405   {
1406     String annotation = new AnnotationFile()
1407             .printAnnotationsForView(viewport);
1408
1409     if (displayTextbox)
1410     {
1411       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1412       Frame frame = new Frame();
1413       frame.add(cap);
1414       jalview.bin.JalviewLite.addFrame(frame,
1415               MessageManager.getString("label.annotations"), 600, 500);
1416       cap.setText(annotation);
1417     }
1418
1419     return annotation;
1420   }
1421
1422   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1423   {
1424     if (alignPanel.getFeatureRenderer() != null
1425             && viewport.getFeaturesDisplayed() != null)
1426     {
1427       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1428
1429     }
1430     return null;
1431   }
1432
1433   private List<String> getDisplayedFeatureGroups()
1434   {
1435     if (alignPanel.getFeatureRenderer() != null
1436             && viewport.getFeaturesDisplayed() != null)
1437     {
1438       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1439
1440     }
1441     return null;
1442   }
1443
1444   public String outputFeatures(boolean displayTextbox, String format)
1445   {
1446     String features;
1447     FeaturesFile formatter = new FeaturesFile();
1448     if (format.equalsIgnoreCase("Jalview"))
1449     {
1450       features = formatter.printJalviewFormat(
1451               viewport.getAlignment().getSequencesArray(),
1452               alignPanel.getFeatureRenderer(), true, false);
1453     }
1454     else
1455     {
1456       features = formatter.printGffFormat(viewport.getAlignment()
1457               .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1458               false);
1459     }
1460
1461     if (displayTextbox)
1462     {
1463       boolean frimport = false;
1464       if (features == null || features.equals("No Features Visible"))
1465       {
1466         features = "# No features visible - paste some and import them here.";
1467         frimport = true;
1468       }
1469
1470       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1471       if (frimport)
1472       {
1473         cap.setAnnotationImport();
1474       }
1475       Frame frame = new Frame();
1476       frame.add(cap);
1477       jalview.bin.JalviewLite.addFrame(frame,
1478               MessageManager.getString("label.features"), 600, 500);
1479       cap.setText(features);
1480     }
1481     else
1482     {
1483       if (features == null)
1484       {
1485         features = "";
1486       }
1487     }
1488
1489     return features;
1490   }
1491
1492   void launchFullApplication()
1493   {
1494     StringBuffer url = new StringBuffer(jalviewServletURL);
1495
1496     // allow servlet parameters to be passed in applet parameter
1497     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1498             : "?";
1499     url.append(firstSep);
1500
1501     url.append(
1502             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1503
1504     if (viewport.applet.getParameter("features") != null)
1505     {
1506       url.append("&features=");
1507       url.append(appendProtocol(viewport.applet.getParameter("features")));
1508     }
1509
1510     if (viewport.applet.getParameter("annotations") != null)
1511     {
1512       url.append("&annotations=");
1513       url.append(
1514               appendProtocol(viewport.applet.getParameter("annotations")));
1515     }
1516
1517     if (viewport.applet.getParameter("jnetfile") != null
1518             || viewport.applet.getParameter("jpredfile") != null)
1519     {
1520       url.append("&annotations=");
1521       url.append(appendProtocol(
1522               viewport.applet.getParameter("jnetfile") != null
1523                       ? viewport.applet.getParameter("jnetfile")
1524                       : viewport.applet.getParameter("jpredfile")));
1525     }
1526
1527     if (viewport.applet.getParameter("defaultColour") != null)
1528     {
1529       url.append("&colour=" + removeWhiteSpace(
1530               viewport.applet.getParameter("defaultColour")));
1531     }
1532
1533     if (viewport.applet.getParameter("userDefinedColour") != null)
1534     {
1535       url.append("&colour=" + removeWhiteSpace(
1536               viewport.applet.getParameter("userDefinedColour")));
1537     }
1538     if (viewport.applet.getParameter("tree") != null)
1539     {
1540       url.append("&tree="
1541               + appendProtocol(viewport.applet.getParameter("tree")));
1542     }
1543     if (viewport.applet.getParameter("treeFile") != null)
1544     {
1545       url.append("&tree="
1546               + appendProtocol(viewport.applet.getParameter("treeFile")));
1547     }
1548
1549     showURL(url.toString(), "FULL_APP");
1550   }
1551
1552   String removeWhiteSpace(String colour)
1553   {
1554     StringBuffer sb = new StringBuffer();
1555     for (int i = 0; i < colour.length(); i++)
1556     {
1557       if (Character.isWhitespace(colour.charAt(i)))
1558       {
1559         sb.append("%20");
1560       }
1561       else
1562       {
1563         sb.append(colour.charAt(i));
1564       }
1565     }
1566
1567     return sb.toString();
1568   }
1569
1570   String appendProtocol(String url)
1571   {
1572     try
1573     {
1574       new URL(url);
1575       url = URLEncoder.encode(url, "UTF-8");
1576     }
1577     /*
1578      * When we finally deprecate 1.1 compatibility, we can start to use
1579      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1580      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1581      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1582      * ex.printStackTrace(); }
1583      */
1584     catch (java.net.MalformedURLException ex)
1585     {
1586       url = viewport.applet.getCodeBase() + url;
1587     }
1588     catch (UnsupportedEncodingException ex)
1589     {
1590       System.err.println(
1591               "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1592                       + url);
1593       ex.printStackTrace();
1594     }
1595     return url;
1596   }
1597
1598   public void closeMenuItem_actionPerformed()
1599   {
1600     PaintRefresher.RemoveComponent(alignPanel);
1601     if (alignPanel.seqPanel != null
1602             && alignPanel.seqPanel.seqCanvas != null)
1603     {
1604       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1605     }
1606     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1607     {
1608       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1609     }
1610
1611     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1612     {
1613       System.exit(0);
1614     }
1615
1616     viewport = null;
1617     if (alignPanel != null && alignPanel.overviewPanel != null)
1618     {
1619       alignPanel.overviewPanel.dispose();
1620     }
1621     alignPanel = null;
1622     this.dispose();
1623   }
1624
1625   /**
1626    * TODO: JAL-1104
1627    */
1628   void updateEditMenuBar()
1629   {
1630
1631     if (viewport.getHistoryList().size() > 0)
1632     {
1633       undoMenuItem.setEnabled(true);
1634       CommandI command = viewport.getHistoryList().peek();
1635       undoMenuItem.setLabel(MessageManager
1636               .formatMessage("label.undo_command", new Object[]
1637               { command.getDescription() }));
1638     }
1639     else
1640     {
1641       undoMenuItem.setEnabled(false);
1642       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1643     }
1644
1645     if (viewport.getRedoList().size() > 0)
1646     {
1647       redoMenuItem.setEnabled(true);
1648
1649       CommandI command = viewport.getRedoList().peek();
1650       redoMenuItem.setLabel(MessageManager
1651               .formatMessage("label.redo_command", new Object[]
1652               { command.getDescription() }));
1653     }
1654     else
1655     {
1656       redoMenuItem.setEnabled(false);
1657       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1658     }
1659   }
1660
1661   /**
1662    * TODO: JAL-1104
1663    */
1664   @Override
1665   public void addHistoryItem(CommandI command)
1666   {
1667     if (command.getSize() > 0)
1668     {
1669       viewport.addToHistoryList(command);
1670       viewport.clearRedoList();
1671       updateEditMenuBar();
1672       viewport.updateHiddenColumns();
1673     }
1674   }
1675
1676   /**
1677    * TODO: JAL-1104 DOCUMENT ME!
1678    *
1679    * @param e
1680    *          DOCUMENT ME!
1681    */
1682   protected void undoMenuItem_actionPerformed()
1683   {
1684     if (viewport.getHistoryList().isEmpty())
1685     {
1686       return;
1687     }
1688
1689     CommandI command = viewport.getHistoryList().pop();
1690     viewport.addToRedoList(command);
1691     command.undoCommand(null);
1692
1693     AlignmentViewport originalSource = getOriginatingSource(command);
1694     // JBPNote Test
1695     if (originalSource != viewport)
1696     {
1697       System.err
1698               .println("Warning: Viewport object mismatch whilst undoing");
1699     }
1700     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1701                                           // viewport.getColumnSelection().getHiddenColumns()
1702                                           // != null;
1703     updateEditMenuBar();
1704     originalSource.firePropertyChange("alignment", null,
1705             originalSource.getAlignment().getSequences());
1706   }
1707
1708   /**
1709    * TODO: JAL-1104 DOCUMENT ME!
1710    *
1711    * @param e
1712    *          DOCUMENT ME!
1713    */
1714   protected void redoMenuItem_actionPerformed()
1715   {
1716     if (viewport.getRedoList().isEmpty())
1717     {
1718       return;
1719     }
1720
1721     CommandI command = viewport.getRedoList().pop();
1722     viewport.addToHistoryList(command);
1723     command.doCommand(null);
1724
1725     AlignmentViewport originalSource = getOriginatingSource(command);
1726     // JBPNote Test
1727     if (originalSource != viewport)
1728     {
1729       System.err
1730               .println("Warning: Viewport object mismatch whilst re-doing");
1731     }
1732     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1733                                           // viewport.getColumnSelection().getHiddenColumns()
1734                                           // != null;
1735
1736     updateEditMenuBar();
1737     originalSource.firePropertyChange("alignment", null,
1738             originalSource.getAlignment().getSequences());
1739   }
1740
1741   AlignmentViewport getOriginatingSource(CommandI command)
1742   {
1743     AlignmentViewport originalSource = null;
1744     // For sequence removal and addition, we need to fire
1745     // the property change event FROM the viewport where the
1746     // original alignment was altered
1747     AlignmentI al = null;
1748     if (command instanceof EditCommand)
1749     {
1750       EditCommand editCommand = (EditCommand) command;
1751       al = editCommand.getAlignment();
1752       Vector comps = PaintRefresher.components
1753               .get(viewport.getSequenceSetId());
1754       for (int i = 0; i < comps.size(); i++)
1755       {
1756         if (comps.elementAt(i) instanceof AlignmentPanel)
1757         {
1758           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1759           {
1760             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1761             break;
1762           }
1763         }
1764       }
1765     }
1766
1767     if (originalSource == null)
1768     {
1769       // The original view is closed, we must validate
1770       // the current view against the closed view first
1771       if (al != null)
1772       {
1773         PaintRefresher.validateSequences(al, viewport.getAlignment());
1774       }
1775
1776       originalSource = viewport;
1777     }
1778
1779     return originalSource;
1780   }
1781
1782   /**
1783    * Move the currently selected sequences up or down one position in the
1784    * alignment
1785    *
1786    * @param up
1787    */
1788   public void moveSelectedSequences(boolean up)
1789   {
1790     SequenceGroup sg = viewport.getSelectionGroup();
1791     if (sg == null)
1792     {
1793       return;
1794     }
1795     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1796             up ? null : viewport.getHiddenRepSequences(), up);
1797     alignPanel.paintAlignment(true, false);
1798
1799     /*
1800      * Also move cDNA/protein complement sequences
1801      */
1802     AlignViewportI complement = viewport.getCodingComplement();
1803     if (complement != null)
1804     {
1805       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1806               viewport, complement);
1807       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1808               up ? null : complement.getHiddenRepSequences(), up);
1809       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1810               false);
1811     }
1812   }
1813
1814   synchronized void slideSequences(boolean right, int size)
1815   {
1816     List<SequenceI> sg = new Vector<>();
1817     if (viewport.cursorMode)
1818     {
1819       sg.add(viewport.getAlignment()
1820               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1821     }
1822     else if (viewport.getSelectionGroup() != null
1823             && viewport.getSelectionGroup().getSize() != viewport
1824                     .getAlignment().getHeight())
1825     {
1826       sg = viewport.getSelectionGroup()
1827               .getSequences(viewport.getHiddenRepSequences());
1828     }
1829
1830     if (sg.size() < 1)
1831     {
1832       return;
1833     }
1834
1835     Vector<SequenceI> invertGroup = new Vector();
1836
1837     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1838     {
1839       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1840       {
1841         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1842       }
1843     }
1844
1845     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1846
1847     SequenceI[] seqs2 = invertGroup
1848             .toArray(new SequenceI[invertGroup.size()]);
1849     for (int i = 0; i < invertGroup.size(); i++)
1850     {
1851       seqs2[i] = invertGroup.elementAt(i);
1852     }
1853
1854     SlideSequencesCommand ssc;
1855     if (right)
1856     {
1857       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1858               viewport.getGapCharacter());
1859     }
1860     else
1861     {
1862       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1863               viewport.getGapCharacter());
1864     }
1865
1866     int groupAdjustment = 0;
1867     if (ssc.getGapsInsertedBegin() && right)
1868     {
1869       if (viewport.cursorMode)
1870       {
1871         alignPanel.seqPanel.moveCursor(size, 0);
1872       }
1873       else
1874       {
1875         groupAdjustment = size;
1876       }
1877     }
1878     else if (!ssc.getGapsInsertedBegin() && !right)
1879     {
1880       if (viewport.cursorMode)
1881       {
1882         alignPanel.seqPanel.moveCursor(-size, 0);
1883       }
1884       else
1885       {
1886         groupAdjustment = -size;
1887       }
1888     }
1889
1890     if (groupAdjustment != 0)
1891     {
1892       viewport.getSelectionGroup().setStartRes(
1893               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1894       viewport.getSelectionGroup().setEndRes(
1895               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1896     }
1897
1898     boolean appendHistoryItem = false;
1899     Deque<CommandI> historyList = viewport.getHistoryList();
1900     if (historyList != null && historyList.size() > 0
1901             && historyList.peek() instanceof SlideSequencesCommand)
1902     {
1903       appendHistoryItem = ssc.appendSlideCommand(
1904               (SlideSequencesCommand) historyList.peek());
1905     }
1906
1907     if (!appendHistoryItem)
1908     {
1909       addHistoryItem(ssc);
1910     }
1911
1912     repaint();
1913   }
1914
1915   static StringBuffer copiedSequences;
1916
1917   static HiddenColumns copiedHiddenColumns;
1918
1919   protected void copy_actionPerformed()
1920   {
1921     if (viewport.getSelectionGroup() == null)
1922     {
1923       return;
1924     }
1925
1926     SequenceGroup sg = viewport.getSelectionGroup();
1927     copiedSequences = new StringBuffer();
1928     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1929     for (int i = 0; i < sg.getSize(); i++)
1930     {
1931       SequenceI seq = sg.getSequenceAt(i);
1932       int index = viewport.getAlignment().findIndex(seq);
1933       orderedSeqs.put(index, seq);
1934     }
1935
1936     int index = 0, startRes, endRes;
1937     char ch;
1938
1939     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1940     {
1941       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1942       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1943
1944       // create new HiddenColumns object with copy of hidden regions
1945       // between startRes and endRes, offset by startRes
1946       copiedHiddenColumns = new HiddenColumns(
1947               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1948               hiddenCutoff, hiddenOffset);
1949     }
1950     else
1951     {
1952       copiedHiddenColumns = null;
1953     }
1954
1955     for (int i = 0; i < sg.getSize(); i++)
1956     {
1957       SequenceI seq = null;
1958
1959       while (seq == null)
1960       {
1961         if (orderedSeqs.containsKey(index))
1962         {
1963           seq = orderedSeqs.get(index);
1964           index++;
1965           break;
1966         }
1967         else
1968         {
1969           index++;
1970         }
1971       }
1972
1973       // FIND START RES
1974       // Returns residue following index if gap
1975       startRes = seq.findPosition(sg.getStartRes());
1976
1977       // FIND END RES
1978       // Need to find the residue preceeding index if gap
1979       endRes = 0;
1980
1981       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1982       {
1983         ch = seq.getCharAt(j);
1984         if (!jalview.util.Comparison.isGap((ch)))
1985         {
1986           endRes++;
1987         }
1988       }
1989
1990       if (endRes > 0)
1991       {
1992         endRes += seq.getStart() - 1;
1993       }
1994
1995       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1996               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1997                       sg.getEndRes() + 1)
1998               + "\n");
1999     }
2000
2001   }
2002
2003   protected void pasteNew_actionPerformed()
2004   {
2005     paste(true);
2006   }
2007
2008   protected void pasteThis_actionPerformed()
2009   {
2010     paste(false);
2011   }
2012
2013   void paste(boolean newAlignment)
2014   {
2015     try
2016     {
2017       if (copiedSequences == null)
2018       {
2019         return;
2020       }
2021
2022       StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2023               "\t");
2024       Vector seqs = new Vector();
2025       while (st.hasMoreElements())
2026       {
2027         String name = st.nextToken();
2028         int start = Integer.parseInt(st.nextToken());
2029         int end = Integer.parseInt(st.nextToken());
2030         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2031       }
2032       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2033       for (int i = 0; i < seqs.size(); i++)
2034       {
2035         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2036       }
2037
2038       if (newAlignment)
2039       {
2040         String newtitle = MessageManager
2041                 .getString("label.copied_sequences");
2042         if (getTitle().startsWith(
2043                 MessageManager.getString("label.copied_sequences")))
2044         {
2045           newtitle = getTitle();
2046         }
2047         else
2048         {
2049           newtitle = newtitle.concat(MessageManager
2050                   .formatMessage("label.from_msname", new String[]
2051                   { getTitle() }));
2052         }
2053         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2054                 viewport.applet, newtitle, false);
2055         af.viewport.setHiddenColumns(copiedHiddenColumns);
2056
2057         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2058                 frameHeight);
2059       }
2060       else
2061       {
2062         addSequences(newSeqs);
2063       }
2064
2065     } catch (Exception ex)
2066     {
2067     } // could be anything being pasted in here
2068
2069   }
2070
2071   void addSequences(SequenceI[] seqs)
2072   {
2073     for (int i = 0; i < seqs.length; i++)
2074     {
2075       viewport.getAlignment().addSequence(seqs[i]);
2076     }
2077
2078     // !newAlignment
2079     addHistoryItem(new EditCommand(
2080             MessageManager.getString("label.add_sequences"), Action.PASTE,
2081             seqs, 0, viewport.getAlignment().getWidth(),
2082             viewport.getAlignment()));
2083
2084     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2085                                                                              // 2019.04.18
2086     viewport.getAlignment().getWidth();
2087     viewport.firePropertyChange("alignment", null,
2088             viewport.getAlignment().getSequences());
2089
2090   }
2091
2092   protected void cut_actionPerformed()
2093   {
2094     copy_actionPerformed();
2095     delete_actionPerformed();
2096   }
2097
2098   protected void delete_actionPerformed()
2099   {
2100
2101     SequenceGroup sg = viewport.getSelectionGroup();
2102     if (sg == null)
2103     {
2104       return;
2105     }
2106
2107     Vector seqs = new Vector();
2108     SequenceI seq;
2109     for (int i = 0; i < sg.getSize(); i++)
2110     {
2111       seq = sg.getSequenceAt(i);
2112       seqs.addElement(seq);
2113     }
2114
2115     /*
2116      * If the cut affects all sequences, warn, remove highlighted columns
2117      */
2118     if (sg.getSize() == viewport.getAlignment().getHeight())
2119     {
2120       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2121               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2122       if (isEntireAlignWidth)
2123       {
2124         String title = MessageManager.getString("label.delete_all");
2125         Panel infoPanel = new Panel();
2126         infoPanel.setLayout(new FlowLayout());
2127         infoPanel.add(
2128                 new Label(MessageManager.getString("warn.delete_all")));
2129
2130         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2131         dialog.setMainPanel(infoPanel);
2132         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2133         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2134         dialog.setVisible(true);
2135
2136         if (!dialog.accept)
2137         {
2138           return;
2139         }
2140       }
2141       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2142               sg.getEndRes() + 1);
2143     }
2144
2145     SequenceI[] cut = new SequenceI[seqs.size()];
2146     for (int i = 0; i < seqs.size(); i++)
2147     {
2148       cut[i] = (SequenceI) seqs.elementAt(i);
2149     }
2150
2151     /*
2152      * //ADD HISTORY ITEM
2153      */
2154     addHistoryItem(new EditCommand(
2155             MessageManager.getString("label.cut_sequences"), Action.CUT,
2156             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2157             viewport.getAlignment()));
2158
2159     viewport.setSelectionGroup(null);
2160     viewport.getAlignment().deleteGroup(sg);
2161
2162     viewport.firePropertyChange("alignment", null,
2163             viewport.getAlignment().getSequences());
2164
2165     if (viewport.getAlignment().getHeight() < 1)
2166     {
2167       this.setVisible(false);
2168     }
2169     viewport.sendSelection();
2170   }
2171
2172   /**
2173    * group consensus toggled
2174    *
2175    */
2176   protected void showGroupConsensus_actionPerformed()
2177   {
2178     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2179     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180
2181   }
2182
2183   /**
2184    * group conservation toggled.
2185    */
2186   protected void showGroupConservation_actionPerformed()
2187   {
2188     viewport.setShowGroupConservation(showGroupConservation.getState());
2189     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190   }
2191
2192   /*
2193    * (non-Javadoc)
2194    *
2195    * @see
2196    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2197    * .event.ActionEvent)
2198    */
2199   protected void showConsensusHistogram_actionPerformed()
2200   {
2201     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2202     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2203   }
2204
2205   /*
2206    * (non-Javadoc)
2207    *
2208    * @see
2209    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2210    * .event.ActionEvent)
2211    */
2212   protected void showSequenceLogo_actionPerformed()
2213   {
2214     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2215     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2216   }
2217
2218   protected void normSequenceLogo_actionPerformed()
2219   {
2220     showSequenceLogo.setState(true);
2221     viewport.setShowSequenceLogo(true);
2222     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2223     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2224   }
2225
2226   protected void applyAutoAnnotationSettings_actionPerformed()
2227   {
2228     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2229   }
2230
2231   protected void makeGrpsFromSelection_actionPerformed()
2232   {
2233     if (avc.makeGroupsFromSelection())
2234     {
2235       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2236       alignPanel.updateAnnotation();
2237       alignPanel.paintAlignment(true, true);
2238     }
2239   }
2240
2241   protected void createGroup_actionPerformed()
2242   {
2243     avc.createGroup();
2244   }
2245
2246   protected void unGroup_actionPerformed()
2247   {
2248     if (avc.unGroup())
2249     {
2250       alignPanel.alignmentChanged();
2251     }
2252   }
2253
2254   protected void deleteGroups_actionPerformed()
2255   {
2256     if (avc.deleteGroups())
2257     {
2258       alignPanel.alignmentChanged();
2259     }
2260   }
2261
2262   public void selectAllSequenceMenuItem_actionPerformed()
2263   {
2264     SequenceGroup sg = new SequenceGroup();
2265     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2266     {
2267       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2268     }
2269     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2270     viewport.setSelectionGroup(sg);
2271     // JAL-2034 - should delegate to
2272     // alignPanel to decide if overview needs
2273     // updating.
2274     alignPanel.paintAlignment(false, false);
2275     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2276     viewport.sendSelection();
2277   }
2278
2279   public void deselectAllSequenceMenuItem_actionPerformed()
2280   {
2281     if (viewport.cursorMode)
2282     {
2283       alignPanel.seqPanel.keyboardNo1 = null;
2284       alignPanel.seqPanel.keyboardNo2 = null;
2285     }
2286     viewport.setSelectionGroup(null);
2287     viewport.getColumnSelection().clear();
2288     viewport.setSelectionGroup(null);
2289     alignPanel.idPanel.idCanvas.searchResults = null;
2290     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2291     // JAL-2034 - should delegate to
2292     // alignPanel to decide if overview needs
2293     // updating.
2294     alignPanel.paintAlignment(false, false);
2295     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2296     viewport.sendSelection();
2297   }
2298
2299   public void invertSequenceMenuItem_actionPerformed()
2300   {
2301     SequenceGroup sg = viewport.getSelectionGroup();
2302     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2303     {
2304       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2305     }
2306
2307     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2308     viewport.sendSelection();
2309   }
2310
2311   public void invertColSel_actionPerformed()
2312   {
2313     viewport.invertColumnSelection();
2314     alignPanel.paintAlignment(true, false);
2315     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2316     viewport.sendSelection();
2317   }
2318
2319   void trimAlignment(boolean trimLeft)
2320   {
2321     AlignmentI al = viewport.getAlignment();
2322     ViewportRanges ranges = viewport.getRanges();
2323     ColumnSelection colSel = viewport.getColumnSelection();
2324     int column;
2325
2326     if (!colSel.isEmpty())
2327     {
2328       if (trimLeft)
2329       {
2330         column = colSel.getMin();
2331       }
2332       else
2333       {
2334         column = colSel.getMax();
2335       }
2336
2337       SequenceI[] seqs;
2338       if (viewport.getSelectionGroup() != null)
2339       {
2340         seqs = viewport.getSelectionGroup()
2341                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2342       }
2343       else
2344       {
2345         seqs = al.getSequencesArray();
2346       }
2347
2348       TrimRegionCommand trimRegion;
2349       if (trimLeft)
2350       {
2351         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2352                 column, al);
2353         ranges.setStartRes(0);
2354       }
2355       else
2356       {
2357         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2358                 column, al);
2359       }
2360
2361       setStatus(MessageManager
2362               .formatMessage("label.removed_columns", new String[]
2363               { Integer.valueOf(trimRegion.getSize()).toString() }));
2364       addHistoryItem(trimRegion);
2365
2366       for (SequenceGroup sg : al.getGroups())
2367       {
2368         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2369                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2370         {
2371           al.deleteGroup(sg);
2372         }
2373       }
2374
2375       viewport.firePropertyChange("alignment", null, al.getSequences());
2376     }
2377   }
2378
2379   public void removeGappedColumnMenuItem_actionPerformed()
2380   {
2381     AlignmentI al = viewport.getAlignment();
2382     ViewportRanges ranges = viewport.getRanges();
2383     int start = 0;
2384     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2385
2386     SequenceI[] seqs;
2387     if (viewport.getSelectionGroup() != null)
2388     {
2389       seqs = viewport.getSelectionGroup()
2390               .getSequencesAsArray(viewport.getHiddenRepSequences());
2391       start = viewport.getSelectionGroup().getStartRes();
2392       end = viewport.getSelectionGroup().getEndRes();
2393     }
2394     else
2395     {
2396       seqs = viewport.getAlignment().getSequencesArray();
2397     }
2398
2399     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2400             "Remove Gapped Columns", seqs, start, end,
2401             viewport.getAlignment());
2402
2403     addHistoryItem(removeGapCols);
2404
2405     setStatus(MessageManager
2406             .formatMessage("label.removed_empty_columns", new String[]
2407             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2408
2409     // This is to maintain viewport position on first residue
2410     // of first sequence
2411     SequenceI seq = al.getSequenceAt(0);
2412     int startRes = seq.findPosition(ranges.getStartRes());
2413     // ShiftList shifts;
2414     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2415     // edit.alColumnChanges=shifts.getInverse();
2416     // if (viewport.hasHiddenColumns)
2417     // viewport.getColumnSelection().compensateForEdits(shifts);
2418     ranges.setStartRes(seq.findIndex(startRes) - 1);
2419     viewport.firePropertyChange("alignment", null, al.getSequences());
2420
2421   }
2422
2423   public void removeAllGapsMenuItem_actionPerformed()
2424   {
2425     AlignmentI al = viewport.getAlignment();
2426     ViewportRanges ranges = viewport.getRanges();
2427     int start = 0;
2428     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2429
2430     SequenceI[] seqs;
2431     if (viewport.getSelectionGroup() != null)
2432     {
2433       seqs = viewport.getSelectionGroup()
2434               .getSequencesAsArray(viewport.getHiddenRepSequences());
2435       start = viewport.getSelectionGroup().getStartRes();
2436       end = viewport.getSelectionGroup().getEndRes();
2437     }
2438     else
2439     {
2440       seqs = viewport.getAlignment().getSequencesArray();
2441     }
2442
2443     // This is to maintain viewport position on first residue
2444     // of first sequence
2445     SequenceI seq = al.getSequenceAt(0);
2446     int startRes = seq.findPosition(ranges.getStartRes());
2447
2448     addHistoryItem(
2449             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2450
2451     ranges.setStartRes(seq.findIndex(startRes) - 1);
2452
2453     viewport.firePropertyChange("alignment", null, al.getSequences());
2454
2455   }
2456
2457   public void findMenuItem_actionPerformed()
2458   {
2459     new Finder(alignPanel);
2460   }
2461
2462   /**
2463    * create a new view derived from the current view
2464    *
2465    * @param viewtitle
2466    * @return frame for the new view
2467    */
2468   public AlignFrame newView(String viewtitle)
2469   {
2470     AlignmentI newal;
2471     if (viewport.hasHiddenRows())
2472     {
2473       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2474               .getFullAlignment().getSequencesArray());
2475     }
2476     else
2477     {
2478       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2479     }
2480
2481     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2482     {
2483       for (int i = 0; i < viewport.getAlignment()
2484               .getAlignmentAnnotation().length; i++)
2485       {
2486         if (!viewport.getAlignment()
2487                 .getAlignmentAnnotation()[i].autoCalculated)
2488         {
2489           newal.addAnnotation(
2490                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2491         }
2492       }
2493     }
2494
2495     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2496
2497     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2498     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2499     PaintRefresher.Register(newaf.alignPanel,
2500             newaf.alignPanel.av.getSequenceSetId());
2501
2502     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2503             newaf.alignPanel.av.getSequenceSetId());
2504     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2505             newaf.alignPanel.av.getSequenceSetId());
2506
2507     Vector comps = PaintRefresher.components
2508             .get(viewport.getSequenceSetId());
2509     int viewSize = -1;
2510     for (int i = 0; i < comps.size(); i++)
2511     {
2512       if (comps.elementAt(i) instanceof AlignmentPanel)
2513       {
2514         viewSize++;
2515       }
2516     }
2517
2518     String title = new String(this.getTitle());
2519     if (viewtitle != null)
2520     {
2521       title = viewtitle + " ( " + title + ")";
2522     }
2523     else
2524     {
2525       if (title.indexOf("(View") > -1)
2526       {
2527         title = title.substring(0, title.indexOf("(View"));
2528       }
2529       title += "(View " + viewSize + ")";
2530     }
2531
2532     newaf.setTitle(title.toString());
2533
2534     newaf.viewport.setHistoryList(viewport.getHistoryList());
2535     newaf.viewport.setRedoList(viewport.getRedoList());
2536     return newaf;
2537   }
2538
2539   /**
2540    *
2541    * @return list of feature groups on the view
2542    */
2543   public String[] getFeatureGroups()
2544   {
2545     FeatureRenderer fr = null;
2546     if (alignPanel != null
2547             && (fr = alignPanel.getFeatureRenderer()) != null)
2548     {
2549       List<String> gps = fr.getFeatureGroups();
2550       String[] _gps = gps.toArray(new String[gps.size()]);
2551       return _gps;
2552     }
2553     return null;
2554   }
2555
2556   /**
2557    * get sequence feature groups that are hidden or shown
2558    *
2559    * @param visible
2560    *          true is visible
2561    * @return list
2562    */
2563   public String[] getFeatureGroupsOfState(boolean visible)
2564   {
2565     FeatureRenderer fr = null;
2566     if (alignPanel != null
2567             && (fr = alignPanel.getFeatureRenderer()) != null)
2568     {
2569       List<String> gps = fr.getGroups(visible);
2570       String[] _gps = gps.toArray(new String[gps.size()]);
2571       return _gps;
2572     }
2573     return null;
2574   }
2575
2576   /**
2577    * Change the display state for the given feature groups
2578    *
2579    * @param groups
2580    *          list of group strings
2581    * @param state
2582    *          visible or invisible
2583    */
2584   public void setFeatureGroupState(String[] groups, boolean state)
2585   {
2586     FeatureRenderer fr = null;
2587     this.sequenceFeatures.setState(true);
2588     viewport.setShowSequenceFeatures(true);
2589     if (alignPanel != null
2590             && (fr = alignPanel.getFeatureRenderer()) != null)
2591     {
2592
2593       fr.setGroupVisibility(Arrays.asList(groups), state);
2594       alignPanel.seqPanel.seqCanvas.repaint();
2595       if (alignPanel.overviewPanel != null)
2596       {
2597         alignPanel.overviewPanel.updateOverviewImage();
2598       }
2599     }
2600   }
2601
2602   public void seqLimits_itemStateChanged()
2603   {
2604     viewport.setShowJVSuffix(seqLimits.getState());
2605     alignPanel.fontChanged();
2606     alignPanel.paintAlignment(true, false);
2607   }
2608
2609   protected void colourTextMenuItem_actionPerformed()
2610   {
2611     viewport.setColourText(colourTextMenuItem.getState());
2612     alignPanel.paintAlignment(false, false);
2613   }
2614
2615   protected void displayNonconservedMenuItem_actionPerformed()
2616   {
2617     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2618     alignPanel.paintAlignment(false, false);
2619   }
2620
2621   protected void wrapMenuItem_actionPerformed()
2622   {
2623     viewport.setWrapAlignment(wrapMenuItem.getState());
2624     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2625     scaleAbove.setEnabled(wrapMenuItem.getState());
2626     scaleLeft.setEnabled(wrapMenuItem.getState());
2627     scaleRight.setEnabled(wrapMenuItem.getState());
2628     alignPanel.paintAlignment(true, false);
2629   }
2630
2631   public void overviewMenuItem_actionPerformed()
2632   {
2633     if (alignPanel.overviewPanel != null)
2634     {
2635       return;
2636     }
2637
2638     Frame frame = new Frame();
2639     final OverviewPanel overview = new OverviewPanel(alignPanel);
2640     frame.add(overview);
2641     // +50 must allow for applet frame window
2642     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2643             .formatMessage("label.overview_params", new String[]
2644             { this.getTitle() }), overview.getPreferredSize().width,
2645             overview.getPreferredSize().height + 50);
2646
2647     frame.pack();
2648     final AlignmentPanel ap = alignPanel;
2649     frame.addWindowListener(new WindowAdapter()
2650     {
2651       @Override
2652       public void windowClosing(WindowEvent e)
2653       {
2654         overview.dispose();
2655         if (ap != null)
2656         {
2657           ap.setOverviewPanel(null);
2658         }
2659       };
2660     });
2661
2662     alignPanel.setOverviewPanel(overview);
2663
2664   }
2665
2666   @Override
2667   public void changeColour(ColourSchemeI cs)
2668   {
2669     viewport.setGlobalColourScheme(cs);
2670
2671     alignPanel.paintAlignment(true, true);
2672   }
2673
2674   protected void modifyPID_actionPerformed()
2675   {
2676     if (viewport.getAbovePIDThreshold()
2677             && viewport.getGlobalColourScheme() != null)
2678     {
2679       SliderPanel.setPIDSliderSource(alignPanel,
2680               viewport.getResidueShading(), alignPanel.getViewName());
2681       SliderPanel.showPIDSlider();
2682     }
2683   }
2684
2685   protected void modifyConservation_actionPerformed()
2686   {
2687     if (viewport.getConservationSelected()
2688             && viewport.getGlobalColourScheme() != null)
2689     {
2690       SliderPanel.setConservationSlider(alignPanel,
2691               viewport.getResidueShading(), alignPanel.getViewName());
2692       SliderPanel.showConservationSlider();
2693     }
2694   }
2695
2696   protected void conservationMenuItem_actionPerformed()
2697   {
2698     boolean selected = conservationMenuItem.getState();
2699     modifyConservation.setEnabled(selected);
2700     viewport.setConservationSelected(selected);
2701     viewport.getResidueShading().setConservationApplied(selected);
2702
2703     changeColour(viewport.getGlobalColourScheme());
2704
2705     if (selected)
2706     {
2707       modifyConservation_actionPerformed();
2708     }
2709     else
2710     {
2711       SliderPanel.hideConservationSlider();
2712     }
2713   }
2714
2715   public void abovePIDThreshold_actionPerformed()
2716   {
2717     boolean selected = abovePIDThreshold.getState();
2718     modifyPID.setEnabled(selected);
2719     viewport.setAbovePIDThreshold(selected);
2720     if (!selected)
2721     {
2722       viewport.getResidueShading().setThreshold(0,
2723               viewport.isIgnoreGapsConsensus());
2724     }
2725
2726     changeColour(viewport.getGlobalColourScheme());
2727
2728     if (selected)
2729     {
2730       modifyPID_actionPerformed();
2731     }
2732     else
2733     {
2734       SliderPanel.hidePIDSlider();
2735     }
2736   }
2737
2738   public void sortPairwiseMenuItem_actionPerformed()
2739   {
2740     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741     AlignmentSorter.sortByPID(viewport.getAlignment(),
2742             viewport.getAlignment().getSequenceAt(0));
2743
2744     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2745             viewport.getAlignment()));
2746     alignPanel.paintAlignment(true, false);
2747   }
2748
2749   public void sortIDMenuItem_actionPerformed()
2750   {
2751     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752     AlignmentSorter.sortByID(viewport.getAlignment());
2753     addHistoryItem(
2754             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2755     alignPanel.paintAlignment(true, false);
2756   }
2757
2758   public void sortLengthMenuItem_actionPerformed()
2759   {
2760     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2761     AlignmentSorter.sortByLength(viewport.getAlignment());
2762     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2763             viewport.getAlignment()));
2764     alignPanel.paintAlignment(true, false);
2765   }
2766
2767   public void sortGroupMenuItem_actionPerformed()
2768   {
2769     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2770     AlignmentSorter.sortByGroup(viewport.getAlignment());
2771     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2772             viewport.getAlignment()));
2773     alignPanel.paintAlignment(true, false);
2774
2775   }
2776
2777   public void removeRedundancyMenuItem_actionPerformed()
2778   {
2779     new RedundancyPanel(alignPanel);
2780   }
2781
2782   public void pairwiseAlignmentMenuItem_actionPerformed()
2783   {
2784     if (viewport.getSelectionGroup() != null
2785             && viewport.getSelectionGroup().getSize() > 1)
2786     {
2787       Frame frame = new Frame();
2788       frame.add(new PairwiseAlignPanel(alignPanel));
2789       jalview.bin.JalviewLite.addFrame(frame,
2790               MessageManager.getString("action.pairwise_alignment"), 600,
2791               500);
2792     }
2793   }
2794
2795   public void PCAMenuItem_actionPerformed()
2796   {
2797     // are the sequences aligned?
2798     if (!viewport.getAlignment().isAligned(false))
2799     {
2800       SequenceI current;
2801       int Width = viewport.getAlignment().getWidth();
2802
2803       for (int i = 0; i < viewport.getAlignment().getSequences()
2804               .size(); i++)
2805       {
2806         current = viewport.getAlignment().getSequenceAt(i);
2807
2808         if (current.getLength() < Width)
2809         {
2810           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2811         }
2812       }
2813       alignPanel.paintAlignment(false, false);
2814     }
2815
2816     if ((viewport.getSelectionGroup() != null
2817             && viewport.getSelectionGroup().getSize() < 4
2818             && viewport.getSelectionGroup().getSize() > 0)
2819             || viewport.getAlignment().getHeight() < 4)
2820     {
2821       return;
2822     }
2823
2824     try
2825     {
2826       new PCAPanel(viewport);
2827     } catch (java.lang.OutOfMemoryError ex)
2828     {
2829     }
2830
2831   }
2832
2833   public void averageDistanceTreeMenuItem_actionPerformed()
2834   {
2835     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2836             "Average distance tree using PID");
2837   }
2838
2839   public void neighbourTreeMenuItem_actionPerformed()
2840   {
2841     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2842             "Neighbour joining tree using PID");
2843   }
2844
2845   protected void njTreeBlosumMenuItem_actionPerformed()
2846   {
2847     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2848             ScoreModels.getInstance().getBlosum62().getName(),
2849             "Neighbour joining tree using BLOSUM62");
2850   }
2851
2852   protected void avTreeBlosumMenuItem_actionPerformed()
2853   {
2854     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2855             ScoreModels.getInstance().getBlosum62().getName(),
2856             "Average distance tree using BLOSUM62");
2857   }
2858
2859   void newTreePanel(String type, String pwType, String title)
2860   {
2861     // are the sequences aligned?
2862     if (!viewport.getAlignment().isAligned(false))
2863     {
2864       SequenceI current;
2865       int Width = viewport.getAlignment().getWidth();
2866
2867       for (int i = 0; i < viewport.getAlignment().getSequences()
2868               .size(); i++)
2869       {
2870         current = viewport.getAlignment().getSequenceAt(i);
2871
2872         if (current.getLength() < Width)
2873         {
2874           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2875         }
2876       }
2877       alignPanel.paintAlignment(false, false);
2878
2879     }
2880
2881     if ((viewport.getSelectionGroup() != null
2882             && viewport.getSelectionGroup().getSize() > 1)
2883             || (viewport.getAlignment().getHeight() > 1))
2884     {
2885       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2886
2887       addTreeMenuItem(tp, title);
2888
2889       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2890     }
2891   }
2892
2893   void loadTree_actionPerformed()
2894   {
2895     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2896     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2897     cap.setTreeImport();
2898     Frame frame = new Frame();
2899     frame.add(cap);
2900     jalview.bin.JalviewLite.addFrame(frame,
2901             MessageManager.getString("label.paste_newick_file"), 400, 300);
2902   }
2903
2904   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2905   {
2906     TreePanel tp = new TreePanel(alignPanel, treeFile,
2907             MessageManager.getString("label.load_tree_from_file"), tree);
2908     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2909     addTreeMenuItem(tp, treeFile);
2910   }
2911
2912   /**
2913    * sort the alignment using the given treePanel
2914    *
2915    * @param treePanel
2916    *          tree used to sort view
2917    * @param title
2918    *          string used for undo event name
2919    */
2920   public void sortByTree(TreePanel treePanel, String title)
2921   {
2922     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2923     AlignmentSorter.sortByTree(viewport.getAlignment(),
2924             treePanel.getTree());
2925     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2926     // HistoryItem.SORT));
2927     addHistoryItem(new OrderCommand(MessageManager
2928             .formatMessage("label.order_by_params", new String[]
2929             { title }), oldOrder, viewport.getAlignment()));
2930     alignPanel.paintAlignment(true, false);
2931   }
2932
2933   /**
2934    * Do any automatic reordering of the alignment and add the necessary bits to
2935    * the menu structure for the new tree
2936    *
2937    * @param treePanel
2938    * @param title
2939    */
2940   protected void addTreeMenuItem(final TreePanel treePanel,
2941           final String title)
2942   {
2943     final MenuItem item = new MenuItem(title);
2944     sortByTreeMenu.add(item);
2945     item.addActionListener(new java.awt.event.ActionListener()
2946     {
2947       @Override
2948       public void actionPerformed(ActionEvent evt)
2949       {
2950         sortByTree(treePanel, title); // treePanel.getTitle());
2951       }
2952     });
2953
2954     treePanel.addWindowListener(new WindowAdapter()
2955     {
2956       @Override
2957       public void windowOpened(WindowEvent e)
2958       {
2959         if (viewport.sortByTree)
2960         {
2961           sortByTree(treePanel, title);
2962         }
2963         super.windowOpened(e);
2964       }
2965
2966       @Override
2967       public void windowClosing(WindowEvent e)
2968       {
2969         sortByTreeMenu.remove(item);
2970       };
2971     });
2972   }
2973
2974   public boolean sortBy(AlignmentOrder alorder, String undoname)
2975   {
2976     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2977     if (viewport.applet.debug)
2978     {
2979       System.err.println("Sorting " + alorder.getOrder().size()
2980               + " in alignment '" + getTitle() + "'");
2981     }
2982     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2983     if (undoname != null)
2984     {
2985       addHistoryItem(new OrderCommand(undoname, oldOrder,
2986               viewport.getAlignment()));
2987     }
2988     alignPanel.paintAlignment(true, false);
2989     return true;
2990   }
2991
2992   protected void documentation_actionPerformed()
2993   {
2994     alignPanel.av.applet.openJalviewHelpUrl();
2995   }
2996
2997   protected void about_actionPerformed()
2998   {
2999
3000     class AboutPanel extends Canvas
3001     {
3002       String version;
3003
3004       String builddate;
3005
3006       public AboutPanel(String version, String builddate)
3007       {
3008         this.version = version;
3009         this.builddate = builddate;
3010       }
3011
3012       @Override
3013       public void paint(Graphics g)
3014       {
3015         g.setColor(Color.white);
3016         g.fillRect(0, 0, getSize().width, getSize().height);
3017         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3018         FontMetrics fm = g.getFontMetrics();
3019         int fh = fm.getHeight();
3020         int y = 5, x = 7;
3021         g.setColor(Color.black);
3022         // TODO: update this text for each release or centrally store it for
3023         // lite and application
3024         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3025         g.drawString(MessageManager
3026                 .formatMessage("label.jalviewLite_release", new String[]
3027                 { version }), x, y += fh);
3028         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3029         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3030                 new String[]
3031                 { builddate }), x, y += fh);
3032         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3033         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3034                 y += fh * 1.5);
3035         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3036                 x + 50, y += fh + 8);
3037         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3038                 x, y += fh);
3039         g.drawString(MessageManager
3040                 .getString("label.jalview_distribution_lists"), x, y += fh);
3041         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3042                 x, y += fh + 8);
3043         g.drawString(
3044                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3045                 y += fh);
3046         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3047                 x, y += fh);
3048         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3049                 x, y += fh);
3050       }
3051     }
3052
3053     Frame frame = new Frame();
3054     frame.add(new AboutPanel(JalviewLite.getVersion(),
3055             JalviewLite.getBuildDate()));
3056     jalview.bin.JalviewLite.addFrame(frame,
3057             MessageManager.getString("label.jalview"), 580, 220);
3058
3059   }
3060
3061   public void showURL(String url, String target)
3062   {
3063     if (viewport.applet == null)
3064     {
3065       System.out.println("Not running as applet - no browser available.");
3066     }
3067     else
3068     {
3069       viewport.applet.showURL(url, target);
3070     }
3071   }
3072
3073   // ////////////////////////////////////////////////////////////////////////////////
3074   // JBuilder Graphics here
3075
3076   MenuBar alignFrameMenuBar = new MenuBar();
3077
3078   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3079
3080   MenuItem loadApplication = new MenuItem(
3081           MessageManager.getString("label.view_full_application"));
3082
3083   MenuItem loadTree = new MenuItem(
3084           MessageManager.getString("label.load_associated_tree"));
3085
3086   MenuItem loadAnnotations = new MenuItem(
3087           MessageManager.getString("label.load_features_annotations"));
3088
3089   MenuItem outputFeatures = new MenuItem(
3090           MessageManager.getString("label.export_features"));
3091
3092   MenuItem outputAnnotations = new MenuItem(
3093           MessageManager.getString("label.export_annotations"));
3094
3095   MenuItem closeMenuItem = new MenuItem(
3096           MessageManager.getString("action.close"));
3097
3098   MenuItem selectAllSequenceMenuItem = new MenuItem(
3099           MessageManager.getString("action.select_all"));
3100
3101   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3102           MessageManager.getString("action.deselect_all"));
3103
3104   MenuItem invertSequenceMenuItem = new MenuItem(
3105           MessageManager.getString("action.invert_selection"));
3106
3107   MenuItem remove2LeftMenuItem = new MenuItem();
3108
3109   MenuItem remove2RightMenuItem = new MenuItem();
3110
3111   MenuItem removeGappedColumnMenuItem = new MenuItem();
3112
3113   MenuItem removeAllGapsMenuItem = new MenuItem();
3114
3115   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3116
3117   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3118
3119   MenuItem sortPairwiseMenuItem = new MenuItem();
3120
3121   MenuItem sortIDMenuItem = new MenuItem();
3122
3123   MenuItem sortLengthMenuItem = new MenuItem();
3124
3125   MenuItem sortGroupMenuItem = new MenuItem();
3126
3127   MenuItem removeRedundancyMenuItem = new MenuItem();
3128
3129   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3130
3131   MenuItem PCAMenuItem = new MenuItem();
3132
3133   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3134
3135   MenuItem neighbourTreeMenuItem = new MenuItem();
3136
3137   BorderLayout borderLayout1 = new BorderLayout();
3138
3139   public Label statusBar = new Label();
3140
3141   MenuItem clustalColour = new MenuItem();
3142
3143   MenuItem zappoColour = new MenuItem();
3144
3145   MenuItem taylorColour = new MenuItem();
3146
3147   MenuItem hydrophobicityColour = new MenuItem();
3148
3149   MenuItem helixColour = new MenuItem();
3150
3151   MenuItem strandColour = new MenuItem();
3152
3153   MenuItem turnColour = new MenuItem();
3154
3155   MenuItem buriedColour = new MenuItem();
3156
3157   MenuItem purinePyrimidineColour = new MenuItem();
3158
3159   // MenuItem RNAInteractionColour = new MenuItem();
3160
3161   MenuItem RNAHelixColour = new MenuItem();
3162
3163   MenuItem userDefinedColour = new MenuItem();
3164
3165   MenuItem PIDColour = new MenuItem();
3166
3167   MenuItem BLOSUM62Colour = new MenuItem();
3168
3169   MenuItem tcoffeeColour = new MenuItem();
3170
3171   MenuItem njTreeBlosumMenuItem = new MenuItem();
3172
3173   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3174
3175   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3176
3177   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3178
3179   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3180
3181   MenuItem alProperties = new MenuItem(
3182           MessageManager.getString("label.alignment_props"));
3183
3184   MenuItem overviewMenuItem = new MenuItem();
3185
3186   MenuItem undoMenuItem = new MenuItem();
3187
3188   MenuItem redoMenuItem = new MenuItem();
3189
3190   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3191
3192   MenuItem noColourmenuItem = new MenuItem();
3193
3194   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3195
3196   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3197
3198   MenuItem findMenuItem = new MenuItem();
3199
3200   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3201
3202   MenuItem nucleotideColour = new MenuItem();
3203
3204   MenuItem deleteGroups = new MenuItem();
3205
3206   MenuItem grpsFromSelection = new MenuItem();
3207
3208   MenuItem createGroup = new MenuItem();
3209
3210   MenuItem unGroup = new MenuItem();
3211
3212   MenuItem delete = new MenuItem();
3213
3214   MenuItem copy = new MenuItem();
3215
3216   MenuItem cut = new MenuItem();
3217
3218   Menu pasteMenu = new Menu();
3219
3220   MenuItem pasteNew = new MenuItem();
3221
3222   MenuItem pasteThis = new MenuItem();
3223
3224   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3225
3226   MenuItem font = new MenuItem();
3227
3228   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3229
3230   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3231
3232   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3233
3234   MenuItem modifyPID = new MenuItem();
3235
3236   MenuItem modifyConservation = new MenuItem();
3237
3238   CheckboxMenuItem autoCalculate = null;
3239
3240   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3241           "Sort Alignment With New Tree", true);
3242
3243   Menu sortByTreeMenu = new Menu();
3244
3245   MenuItem inputText = new MenuItem();
3246
3247   MenuItem documentation = new MenuItem();
3248
3249   MenuItem about = new MenuItem();
3250
3251   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3252
3253   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3254
3255   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3256
3257   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3258
3259   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3260
3261   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3262
3263   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3264
3265   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3266
3267   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3268
3269   /**
3270    * Initialise menus and other items
3271    *
3272    * @throws Exception
3273    */
3274   private void jbInit() throws Exception
3275   {
3276     setMenuBar(alignFrameMenuBar);
3277
3278     /*
3279      * Configure File menu items and actions
3280      */
3281     inputText
3282             .setLabel(MessageManager.getString("label.input_from_textbox"));
3283     inputText.addActionListener(this);
3284     Menu outputTextboxMenu = new Menu(
3285             MessageManager.getString("label.out_to_textbox"));
3286     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3287     {
3288       MenuItem item = new MenuItem(ff);
3289
3290       item.addActionListener(new java.awt.event.ActionListener()
3291       {
3292         @Override
3293         public void actionPerformed(ActionEvent e)
3294         {
3295           outputText_actionPerformed(e);
3296         }
3297       });
3298
3299       outputTextboxMenu.add(item);
3300     }
3301     closeMenuItem.addActionListener(this);
3302     loadApplication.addActionListener(this);
3303     loadTree.addActionListener(this);
3304     loadAnnotations.addActionListener(this);
3305     outputFeatures.addActionListener(this);
3306     outputAnnotations.addActionListener(this);
3307
3308     /*
3309      * Configure Edit menu items and actions
3310      */
3311     undoMenuItem.setEnabled(false);
3312     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3313     undoMenuItem.addActionListener(this);
3314     redoMenuItem.setEnabled(false);
3315     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3316     redoMenuItem.addActionListener(this);
3317     copy.setLabel(MessageManager.getString("action.copy"));
3318     copy.addActionListener(this);
3319     cut.setLabel(MessageManager.getString("action.cut"));
3320     cut.addActionListener(this);
3321     delete.setLabel(MessageManager.getString("action.delete"));
3322     delete.addActionListener(this);
3323     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3324     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3325     pasteNew.addActionListener(this);
3326     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3327     pasteThis.addActionListener(this);
3328     remove2LeftMenuItem
3329             .setLabel(MessageManager.getString("action.remove_left"));
3330     remove2LeftMenuItem.addActionListener(this);
3331     remove2RightMenuItem
3332             .setLabel(MessageManager.getString("action.remove_right"));
3333     remove2RightMenuItem.addActionListener(this);
3334     removeGappedColumnMenuItem.setLabel(
3335             MessageManager.getString("action.remove_empty_columns"));
3336     removeGappedColumnMenuItem.addActionListener(this);
3337     removeAllGapsMenuItem
3338             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3339     removeAllGapsMenuItem.addActionListener(this);
3340     removeRedundancyMenuItem
3341             .setLabel(MessageManager.getString("action.remove_redundancy"));
3342     removeRedundancyMenuItem.addActionListener(this);
3343
3344     /*
3345      * Configure Select menu items and actions
3346      */
3347     findMenuItem.setLabel(MessageManager.getString("action.find"));
3348     findMenuItem.addActionListener(this);
3349     selectAllSequenceMenuItem.addActionListener(this);
3350     deselectAllSequenceMenuItem.addActionListener(this);
3351     invertSequenceMenuItem.setLabel(
3352             MessageManager.getString("action.invert_sequence_selection"));
3353     invertSequenceMenuItem.addActionListener(this);
3354     invertColSel.setLabel(
3355             MessageManager.getString("action.invert_column_selection"));
3356     invertColSel.addActionListener(this);
3357     deleteGroups
3358             .setLabel(MessageManager.getString("action.undefine_groups"));
3359     deleteGroups.addActionListener(this);
3360     grpsFromSelection.setLabel(
3361             MessageManager.getString("action.make_groups_selection"));
3362     grpsFromSelection.addActionListener(this);
3363     createGroup.setLabel(MessageManager.getString("action.create_group"));
3364     createGroup.addActionListener(this);
3365     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3366     unGroup.addActionListener(this);
3367
3368     annotationColumnSelection.setLabel(
3369             MessageManager.getString("action.select_by_annotation"));
3370     annotationColumnSelection.addActionListener(this);
3371
3372     /*
3373      * Configure View menu items and actions
3374      */
3375     newView.setLabel(MessageManager.getString("action.new_view"));
3376     newView.addActionListener(this);
3377     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3378     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3379     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3380     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3381     hideColumns
3382             .setLabel(MessageManager.getString("label.selected_columns"));
3383     hideSequences
3384             .setLabel(MessageManager.getString("label.selected_sequences"));
3385     hideAllButSelection.setLabel(
3386             MessageManager.getString("label.all_but_selected_region"));
3387     hideAllSelection
3388             .setLabel(MessageManager.getString("label.selected_region"));
3389     showAllHidden.setLabel(
3390             MessageManager.getString("label.all_sequences_columns"));
3391     showColumns.addActionListener(this);
3392     showSeqs.addActionListener(this);
3393     hideColumns.addActionListener(this);
3394     hideSequences.addActionListener(this);
3395     hideAllButSelection.addActionListener(this);
3396     hideAllSelection.addActionListener(this);
3397     showAllHidden.addActionListener(this);
3398     featureSettings
3399             .setLabel(MessageManager.getString("action.feature_settings"));
3400     featureSettings.addActionListener(this);
3401     sequenceFeatures.setLabel(
3402             MessageManager.getString("label.show_sequence_features"));
3403     sequenceFeatures.addItemListener(this);
3404     sequenceFeatures.setState(false);
3405     followMouseOverFlag.setLabel(
3406             MessageManager.getString("label.automatic_scrolling"));
3407     followMouseOverFlag.addItemListener(this);
3408     alProperties.addActionListener(this);
3409     overviewMenuItem
3410             .setLabel(MessageManager.getString("label.overview_window"));
3411     overviewMenuItem.addActionListener(this);
3412
3413     /*
3414      * Configure Annotations menu items and actions
3415      */
3416     annotationPanelMenuItem
3417             .setLabel(MessageManager.getString("label.show_annotations"));
3418     annotationPanelMenuItem.addItemListener(this);
3419     showGroupConsensus
3420             .setLabel(MessageManager.getString("label.group_consensus"));
3421     showGroupConservation
3422             .setLabel(MessageManager.getString("label.group_conservation"));
3423     showConsensusHistogram.setLabel(
3424             MessageManager.getString("label.show_consensus_histogram"));
3425     showSequenceLogo.setLabel(
3426             MessageManager.getString("label.show_consensus_logo"));
3427     normSequenceLogo.setLabel(
3428             MessageManager.getString("label.norm_consensus_logo"));
3429     applyAutoAnnotationSettings
3430             .setLabel(MessageManager.getString("label.apply_all_groups"));
3431     applyAutoAnnotationSettings.setState(true);
3432     Menu autoAnnMenu = new Menu(
3433             MessageManager.getString("label.autocalculated_annotation"));
3434     showGroupConsensus.addItemListener(this);
3435     showGroupConservation.addItemListener(this);
3436     showConsensusHistogram.addItemListener(this);
3437     showSequenceLogo.addItemListener(this);
3438     normSequenceLogo.addItemListener(this);
3439     applyAutoAnnotationSettings.addItemListener(this);
3440     showAlignmentAnnotations = new CheckboxMenuItem(
3441             MessageManager.getString("label.show_all_al_annotations"));
3442     showSequenceAnnotations = new CheckboxMenuItem(
3443             MessageManager.getString("label.show_all_seq_annotations"));
3444     sortAnnBySequence = new CheckboxMenuItem(
3445             MessageManager.getString("label.sort_annotations_by_sequence"));
3446     sortAnnByLabel = new CheckboxMenuItem(
3447             MessageManager.getString("label.sort_annotations_by_label"));
3448     showAutoFirst = new CheckboxMenuItem(
3449             MessageManager.getString("label.show_first"));
3450     showAutoFirst.setState(false); // pending applet parameter
3451     setShowAutoCalculatedAbove(showAutoFirst.getState());
3452     showAutoLast = new CheckboxMenuItem(
3453             MessageManager.getString("label.show_last"));
3454     showAutoLast.setState(!showAutoFirst.getState());
3455     showAlignmentAnnotations.addItemListener(this);
3456     showSequenceAnnotations.addItemListener(this);
3457     sortAnnBySequence.addItemListener(this);
3458     sortAnnByLabel.addItemListener(this);
3459     showAutoFirst.addItemListener(this);
3460     showAutoLast.addItemListener(this);
3461
3462     /*
3463      * Configure Format menu items and actions
3464      */
3465     font.setLabel(MessageManager.getString("action.font"));
3466     font.addActionListener(this);
3467     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3468     scaleAbove.setState(true);
3469     scaleAbove.setEnabled(false);
3470     scaleAbove.addItemListener(this);
3471     scaleLeft.setEnabled(false);
3472     scaleLeft.setState(true);
3473     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3474     scaleLeft.addItemListener(this);
3475     scaleRight.setEnabled(false);
3476     scaleRight.setState(true);
3477     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3478     scaleRight.addItemListener(this);
3479     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3480     viewBoxesMenuItem.setState(true);
3481     viewBoxesMenuItem.addItemListener(this);
3482     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3483     viewTextMenuItem.setState(true);
3484     viewTextMenuItem.addItemListener(this);
3485     colourTextMenuItem
3486             .setLabel(MessageManager.getString("label.colour_text"));
3487     colourTextMenuItem.addItemListener(this);
3488     displayNonconservedMenuItem
3489             .setLabel(MessageManager.getString("label.show_non_conserved"));
3490     displayNonconservedMenuItem.addItemListener(this);
3491     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3492     wrapMenuItem.addItemListener(this);
3493     renderGapsMenuItem
3494             .setLabel(MessageManager.getString("action.show_gaps"));
3495     renderGapsMenuItem.setState(true);
3496     renderGapsMenuItem.addItemListener(this);
3497     centreColumnLabelFlag.setLabel(
3498             MessageManager.getString("label.centre_column_labels"));
3499     centreColumnLabelFlag.addItemListener(this);
3500     seqLimits.setState(true);
3501     seqLimits.setLabel(
3502             MessageManager.getString("label.show_sequence_limits"));
3503     seqLimits.addItemListener(this);
3504
3505     /*
3506      * Configure Colour menu items and actions
3507      */
3508     applyToAllGroups.setLabel(
3509             MessageManager.getString("label.apply_colour_to_all_groups"));
3510     applyToAllGroups.setState(true);
3511     applyToAllGroups.addItemListener(this);
3512     clustalColour.setLabel(
3513             MessageManager.getString("label.colourScheme_clustal"));
3514     clustalColour.addActionListener(this);
3515     zappoColour
3516             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3517     zappoColour.addActionListener(this);
3518     taylorColour.setLabel(
3519             MessageManager.getString("label.colourScheme_taylor"));
3520     taylorColour.addActionListener(this);
3521     hydrophobicityColour.setLabel(
3522             MessageManager.getString("label.colourScheme_hydrophobic"));
3523     hydrophobicityColour.addActionListener(this);
3524     helixColour.setLabel(MessageManager
3525             .getString("label.colourScheme_helixpropensity"));
3526     helixColour.addActionListener(this);
3527     strandColour.setLabel(MessageManager
3528             .getString("label.colourScheme_strandpropensity"));
3529     strandColour.addActionListener(this);
3530     turnColour.setLabel(
3531             MessageManager.getString("label.colourScheme_turnpropensity"));
3532     turnColour.addActionListener(this);
3533     buriedColour.setLabel(
3534             MessageManager.getString("label.colourScheme_buriedindex"));
3535     buriedColour.addActionListener(this);
3536     purinePyrimidineColour.setLabel(MessageManager
3537             .getString("label.colourScheme_purine/pyrimidine"));
3538     purinePyrimidineColour.addActionListener(this);
3539     // RNAInteractionColour.setLabel(MessageManager
3540     // .getString("label.rna_interaction"));
3541     // RNAInteractionColour.addActionListener(this);
3542     RNAHelixColour.setLabel(
3543             MessageManager.getString("label.colourScheme_rnahelices"));
3544     RNAHelixColour.addActionListener(this);
3545     userDefinedColour
3546             .setLabel(MessageManager.getString("action.user_defined"));
3547     userDefinedColour.addActionListener(this);
3548     PIDColour.setLabel(
3549             MessageManager.getString("label.colourScheme_%identity"));
3550     PIDColour.addActionListener(this);
3551     BLOSUM62Colour.setLabel(
3552             MessageManager.getString("label.colourScheme_blosum62"));
3553     BLOSUM62Colour.addActionListener(this);
3554     tcoffeeColour.setLabel(
3555             MessageManager.getString("label.colourScheme_t-coffeescores"));
3556     // it will be enabled only if a score file is provided
3557     tcoffeeColour.setEnabled(false);
3558     tcoffeeColour.addActionListener(this);
3559     conservationMenuItem
3560             .setLabel(MessageManager.getString("action.by_conservation"));
3561     conservationMenuItem.addItemListener(this);
3562     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3563     noColourmenuItem.addActionListener(this);
3564     abovePIDThreshold.setLabel(
3565             MessageManager.getString("label.above_identity_threshold"));
3566     abovePIDThreshold.addItemListener(this);
3567     nucleotideColour.setLabel(
3568             MessageManager.getString("label.colourScheme_nucleotide"));
3569     nucleotideColour.addActionListener(this);
3570     modifyPID.setLabel(
3571             MessageManager.getString("label.modify_identity_threshold"));
3572     modifyPID.setEnabled(abovePIDThreshold.getState());
3573     modifyPID.addActionListener(this);
3574     modifyConservation.setLabel(MessageManager
3575             .getString("label.modify_conservation_threshold"));
3576     modifyConservation.setEnabled(conservationMenuItem.getState());
3577     modifyConservation.addActionListener(this);
3578     annotationColour
3579             .setLabel(MessageManager.getString("action.by_annotation"));
3580     annotationColour.addActionListener(this);
3581
3582     /*
3583      * Configure Calculate menu items and actions
3584      */
3585     sortPairwiseMenuItem
3586             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3587     sortPairwiseMenuItem.addActionListener(this);
3588     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3589     sortIDMenuItem.addActionListener(this);
3590     sortLengthMenuItem
3591             .setLabel(MessageManager.getString("action.by_length"));
3592     sortLengthMenuItem.addActionListener(this);
3593     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3594     sortGroupMenuItem.addActionListener(this);
3595     pairwiseAlignmentMenuItem.setLabel(
3596             MessageManager.getString("action.pairwise_alignment"));
3597     pairwiseAlignmentMenuItem.addActionListener(this);
3598     PCAMenuItem.setLabel(
3599             MessageManager.getString("label.principal_component_analysis"));
3600     PCAMenuItem.addActionListener(this);
3601     autoCalculate = new CheckboxMenuItem(
3602             MessageManager.getString("label.autocalculate_consensus"),
3603             true);
3604     averageDistanceTreeMenuItem.setLabel(
3605             MessageManager.getString("label.average_distance_identity"));
3606     averageDistanceTreeMenuItem.addActionListener(this);
3607     neighbourTreeMenuItem.setLabel(
3608             MessageManager.getString("label.neighbour_joining_identity"));
3609     neighbourTreeMenuItem.addActionListener(this);
3610     avDistanceTreeBlosumMenuItem.setLabel(
3611             MessageManager.getString("label.average_distance_blosum62"));
3612     avDistanceTreeBlosumMenuItem.addActionListener(this);
3613     njTreeBlosumMenuItem
3614             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3615     njTreeBlosumMenuItem.addActionListener(this);
3616     sortByTreeMenu
3617             .setLabel(MessageManager.getString("action.by_tree_order"));
3618     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3619     Menu calculateTreeMenu = new Menu(
3620             MessageManager.getString("action.calculate_tree"));
3621     autoCalculate.addItemListener(this);
3622     sortByTree.addItemListener(this);
3623
3624     /*
3625      * Configure Help menu items and actions
3626      */
3627     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3628     documentation.setLabel(MessageManager.getString("label.documentation"));
3629     documentation.addActionListener(this);
3630     about.setLabel(MessageManager.getString("label.about"));
3631     about.addActionListener(this);
3632
3633     /*
3634      * Add top level menus to frame
3635      */
3636     alignFrameMenuBar.add(fileMenu);
3637     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3638     alignFrameMenuBar.add(editMenu);
3639     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3640     alignFrameMenuBar.add(selectMenu);
3641     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3642     alignFrameMenuBar.add(viewMenu);
3643     Menu annotationsMenu = new Menu(
3644             MessageManager.getString("action.annotations"));
3645     alignFrameMenuBar.add(annotationsMenu);
3646     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3647     alignFrameMenuBar.add(formatMenu);
3648     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3649     alignFrameMenuBar.add(colourMenu);
3650     Menu calculateMenu = new Menu(
3651             MessageManager.getString("action.calculate"));
3652     alignFrameMenuBar.add(calculateMenu);
3653     alignFrameMenuBar.add(helpMenu);
3654
3655     /*
3656      * File menu
3657      */
3658     fileMenu.add(inputText);
3659     fileMenu.add(loadTree);
3660     fileMenu.add(loadAnnotations);
3661     fileMenu.addSeparator();
3662     fileMenu.add(outputTextboxMenu);
3663     fileMenu.add(outputFeatures);
3664     fileMenu.add(outputAnnotations);
3665     if (jalviewServletURL != null)
3666     {
3667       fileMenu.add(loadApplication);
3668     }
3669     fileMenu.addSeparator();
3670     fileMenu.add(closeMenuItem);
3671
3672     /*
3673      * Edit menu
3674      */
3675     editMenu.add(undoMenuItem);
3676     editMenu.add(redoMenuItem);
3677     editMenu.add(cut);
3678     editMenu.add(copy);
3679     pasteMenu.add(pasteNew);
3680     pasteMenu.add(pasteThis);
3681     editMenu.add(pasteMenu);
3682     editMenu.add(delete);
3683     editMenu.addSeparator();
3684     editMenu.add(remove2LeftMenuItem);
3685     editMenu.add(remove2RightMenuItem);
3686     editMenu.add(removeGappedColumnMenuItem);
3687     editMenu.add(removeAllGapsMenuItem);
3688     editMenu.add(removeRedundancyMenuItem);
3689
3690     /*
3691      * Select menu
3692      */
3693     selectMenu.add(findMenuItem);
3694     selectMenu.addSeparator();
3695     selectMenu.add(selectAllSequenceMenuItem);
3696     selectMenu.add(deselectAllSequenceMenuItem);
3697     selectMenu.add(invertSequenceMenuItem);
3698     selectMenu.add(invertColSel);
3699     selectMenu.add(createGroup);
3700     selectMenu.add(unGroup);
3701     selectMenu.add(grpsFromSelection);
3702     selectMenu.add(deleteGroups);
3703     selectMenu.add(annotationColumnSelection);
3704
3705     /*
3706      * View menu
3707      */
3708     viewMenu.add(newView);
3709     viewMenu.addSeparator();
3710     showMenu.add(showColumns);
3711     showMenu.add(showSeqs);
3712     showMenu.add(showAllHidden);
3713     viewMenu.add(showMenu);
3714     hideMenu.add(hideColumns);
3715     hideMenu.add(hideSequences);
3716     hideMenu.add(hideAllSelection);
3717     hideMenu.add(hideAllButSelection);
3718     viewMenu.add(hideMenu);
3719     viewMenu.addSeparator();
3720     viewMenu.add(followMouseOverFlag);
3721     viewMenu.addSeparator();
3722     viewMenu.add(sequenceFeatures);
3723     viewMenu.add(featureSettings);
3724     viewMenu.addSeparator();
3725     viewMenu.add(alProperties);
3726     viewMenu.addSeparator();
3727     viewMenu.add(overviewMenuItem);
3728
3729     /*
3730      * Annotations menu
3731      */
3732     annotationsMenu.add(annotationPanelMenuItem);
3733     annotationsMenu.addSeparator();
3734     annotationsMenu.add(showAlignmentAnnotations);
3735     annotationsMenu.add(showSequenceAnnotations);
3736     annotationsMenu.add(sortAnnBySequence);
3737     annotationsMenu.add(sortAnnByLabel);
3738     annotationsMenu.addSeparator();
3739     autoAnnMenu.add(showAutoFirst);
3740     autoAnnMenu.add(showAutoLast);
3741     autoAnnMenu.addSeparator();
3742     autoAnnMenu.add(applyAutoAnnotationSettings);
3743     autoAnnMenu.add(showConsensusHistogram);
3744     autoAnnMenu.add(showSequenceLogo);
3745     autoAnnMenu.add(normSequenceLogo);
3746     autoAnnMenu.addSeparator();
3747     autoAnnMenu.add(showGroupConservation);
3748     autoAnnMenu.add(showGroupConsensus);
3749     annotationsMenu.add(autoAnnMenu);
3750
3751     /*
3752      * Format menu
3753      */
3754     formatMenu.add(font);
3755     formatMenu.add(seqLimits);
3756     formatMenu.add(wrapMenuItem);
3757     formatMenu.add(scaleAbove);
3758     formatMenu.add(scaleLeft);
3759     formatMenu.add(scaleRight);
3760     formatMenu.add(viewBoxesMenuItem);
3761     formatMenu.add(viewTextMenuItem);
3762     formatMenu.add(colourTextMenuItem);
3763     formatMenu.add(displayNonconservedMenuItem);
3764     formatMenu.add(renderGapsMenuItem);
3765     formatMenu.add(centreColumnLabelFlag);
3766
3767     /*
3768      * Colour menu
3769      */
3770     colourMenu.add(applyToAllGroups);
3771     colourMenu.addSeparator();
3772     colourMenu.add(noColourmenuItem);
3773     colourMenu.add(clustalColour);
3774     colourMenu.add(BLOSUM62Colour);
3775     colourMenu.add(PIDColour);
3776     colourMenu.add(zappoColour);
3777     colourMenu.add(taylorColour);
3778     colourMenu.add(hydrophobicityColour);
3779     colourMenu.add(helixColour);
3780     colourMenu.add(strandColour);
3781     colourMenu.add(turnColour);
3782     colourMenu.add(buriedColour);
3783     colourMenu.add(nucleotideColour);
3784     colourMenu.add(purinePyrimidineColour);
3785     // colourMenu.add(RNAInteractionColour);
3786     colourMenu.add(tcoffeeColour);
3787     colourMenu.add(userDefinedColour);
3788     colourMenu.addSeparator();
3789     colourMenu.add(conservationMenuItem);
3790     colourMenu.add(modifyConservation);
3791     colourMenu.add(abovePIDThreshold);
3792     colourMenu.add(modifyPID);
3793     colourMenu.add(annotationColour);
3794     colourMenu.add(RNAHelixColour);
3795
3796     /*
3797      * Calculate menu
3798      */
3799     sortMenu.add(sortIDMenuItem);
3800     sortMenu.add(sortLengthMenuItem);
3801     sortMenu.add(sortByTreeMenu);
3802     sortMenu.add(sortGroupMenuItem);
3803     sortMenu.add(sortPairwiseMenuItem);
3804     calculateMenu.add(sortMenu);
3805     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3806     calculateTreeMenu.add(neighbourTreeMenuItem);
3807     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3808     calculateTreeMenu.add(njTreeBlosumMenuItem);
3809     calculateMenu.add(calculateTreeMenu);
3810     calculateMenu.addSeparator();
3811     calculateMenu.add(pairwiseAlignmentMenuItem);
3812     calculateMenu.add(PCAMenuItem);
3813     calculateMenu.add(autoCalculate);
3814     calculateMenu.add(sortByTree);
3815
3816     /*
3817      * Help menu
3818      */
3819     helpMenu.add(documentation);
3820     helpMenu.add(about);
3821
3822     /*
3823      * Status bar
3824      */
3825     statusBar.setBackground(Color.white);
3826     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3827     setStatus(MessageManager.getString("label.status_bar"));
3828     this.add(statusBar, BorderLayout.SOUTH);
3829   }
3830
3831   @Override
3832   public void setStatus(String string)
3833   {
3834     statusBar.setText(string);
3835   };
3836
3837   MenuItem featureSettings = new MenuItem();
3838
3839   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3840
3841   MenuItem annotationColour = new MenuItem();
3842
3843   MenuItem annotationColumnSelection = new MenuItem();
3844
3845   MenuItem invertColSel = new MenuItem();
3846
3847   MenuItem showColumns = new MenuItem();
3848
3849   MenuItem showSeqs = new MenuItem();
3850
3851   MenuItem hideColumns = new MenuItem();
3852
3853   MenuItem hideSequences = new MenuItem();
3854
3855   MenuItem hideAllButSelection = new MenuItem();
3856
3857   MenuItem hideAllSelection = new MenuItem();
3858
3859   MenuItem showAllHidden = new MenuItem();
3860
3861   MenuItem newView = new MenuItem();
3862
3863   private CheckboxMenuItem showAlignmentAnnotations;
3864
3865   private CheckboxMenuItem showSequenceAnnotations;
3866
3867   private CheckboxMenuItem sortAnnBySequence;
3868
3869   private CheckboxMenuItem sortAnnByLabel;
3870
3871   private CheckboxMenuItem showAutoFirst;
3872
3873   private CheckboxMenuItem showAutoLast;
3874
3875   private SplitFrame splitFrame;
3876
3877   /**
3878    * Attach the alignFrame panels after embedding menus, if necessary. This used
3879    * to be called setEmbedded, but is now creates the dropdown menus in a
3880    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3881    *
3882    * @param reallyEmbedded
3883    *          true to attach the view to the applet area on the page rather than
3884    *          in a new window
3885    */
3886   public void createAlignFrameWindow(boolean reallyEmbedded)
3887   {
3888     if (reallyEmbedded)
3889     {
3890       embedAlignFrameInApplet(viewport.applet);
3891     }
3892     else
3893     {
3894       // //////
3895       // test and embed menu bar if necessary.
3896       //
3897       if (embedMenuIfNeeded(alignPanel))
3898       {
3899         /*
3900          * adjust for status bar height too. ? pointless as overridden by layout
3901          * manager
3902          */
3903         alignPanel.setSize(getSize().width,
3904                 getSize().height - statusBar.getHeight());
3905       }
3906       add(statusBar, BorderLayout.SOUTH);
3907       add(alignPanel, BorderLayout.CENTER);
3908       // and register with the applet so it can pass external API calls to us
3909       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3910               frameHeight);
3911     }
3912   }
3913
3914   /**
3915    * Add the components of this AlignFrame to the applet container.
3916    *
3917    * @param theApplet
3918    */
3919   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3920   {
3921     // ////
3922     // Explicitly build the embedded menu panel for the on-page applet
3923     //
3924     // view cannot be closed if its actually on the page
3925     fileMenu.remove(closeMenuItem);
3926     fileMenu.remove(3); // Remove Separator
3927     // construct embedded menu, using default font
3928     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3929     // and actually add the components to the applet area
3930     theApplet.setLayout(new BorderLayout());
3931     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3932     theApplet.add(statusBar, BorderLayout.SOUTH);
3933     // TODO should size be left to the layout manager?
3934     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3935             - embeddedMenu.getHeight() - statusBar.getHeight());
3936     theApplet.add(alignPanel, BorderLayout.CENTER);
3937     final AlignFrame me = this;
3938     theApplet.addFocusListener(new FocusListener()
3939     {
3940
3941       @Override
3942       public void focusLost(FocusEvent e)
3943       {
3944         if (theApplet.currentAlignFrame == me)
3945         {
3946           theApplet.currentAlignFrame = null;
3947         }
3948       }
3949
3950       @Override
3951       public void focusGained(FocusEvent e)
3952       {
3953         theApplet.currentAlignFrame = me;
3954       }
3955     });
3956     theApplet.validate();
3957   }
3958
3959   /**
3960    * create a new binding between structures in an existing jmol viewer instance
3961    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3962    * this does not open a new Jmol window, or modify the display of the
3963    * structures in the original jmol window. Note This method doesn't work
3964    * without an additional javascript library to exchange messages between the
3965    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3966    *
3967    * @param jmolViewer
3968    *          JmolViewer instance
3969    * @param sequenceIds
3970    *          - sequence Ids to search for associations
3971    */
3972   public SequenceStructureBinding addStructureViewInstance(
3973           Object jmolviewer, String[] sequenceIds)
3974   {
3975     Viewer viewer = null;
3976     try
3977     {
3978       viewer = (Viewer) jmolviewer;
3979     } catch (ClassCastException ex)
3980     {
3981       System.err.println(
3982               "Unsupported viewer object :" + jmolviewer.getClass());
3983     }
3984     if (viewer == null)
3985     {
3986       System.err.println("Can't use this object as a structure viewer:"
3987               + jmolviewer.getClass());
3988       return null;
3989     }
3990     SequenceI[] seqs = null;
3991     if (sequenceIds == null || sequenceIds.length == 0)
3992     {
3993       seqs = viewport.getAlignment().getSequencesArray();
3994     }
3995     else
3996     {
3997       Vector sqi = new Vector();
3998       AlignmentI al = viewport.getAlignment();
3999       for (int sid = 0; sid < sequenceIds.length; sid++)
4000       {
4001         SequenceI sq = al.findName(sequenceIds[sid]);
4002         if (sq != null)
4003         {
4004           sqi.addElement(sq);
4005         }
4006       }
4007       if (sqi.size() > 0)
4008       {
4009         seqs = new SequenceI[sqi.size()];
4010         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4011         {
4012           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4013         }
4014       }
4015       else
4016       {
4017         return null;
4018       }
4019     }
4020     AAStructureBindingModel jmv = null;
4021     // TODO: search for a jmv that involves viewer
4022     if (jmv == null)
4023     { // create a new viewer/jalview binding.
4024       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4025     }
4026     return jmv;
4027
4028   }
4029
4030   /**
4031    * bind a pdb file to a sequence in the current view
4032    *
4033    * @param sequenceId
4034    *          - sequenceId within the dataset.
4035    * @param pdbEntryString
4036    *          - the short name for the PDB file
4037    * @param pdbFile
4038    *          - pdb file - either a URL or a valid PDB file.
4039    * @return true if binding was as success TODO: consider making an exception
4040    *         structure for indicating when PDB parsing or sequenceId location
4041    *         fails.
4042    */
4043   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4044           String pdbFile)
4045   {
4046     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4047     boolean needtoadd = false;
4048     if (toaddpdb != null)
4049     {
4050       Vector pdbe = toaddpdb.getAllPDBEntries();
4051       PDBEntry pdbentry = null;
4052       if (pdbe != null && pdbe.size() > 0)
4053       {
4054         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4055         {
4056           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4057           if (!pdbentry.getId().equals(pdbEntryString)
4058                   && !pdbentry.getFile().equals(pdbFile))
4059           {
4060             pdbentry = null;
4061           }
4062           else
4063           {
4064             continue;
4065           }
4066         }
4067       }
4068       if (pdbentry == null)
4069       {
4070         pdbentry = new PDBEntry();
4071         pdbentry.setId(pdbEntryString);
4072         pdbentry.setFile(pdbFile);
4073         needtoadd = true; // add this new entry to sequence.
4074       }
4075       // resolve data source
4076       // TODO: this code should be a refactored to an io package
4077       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4078               FileFormat.PDB);
4079       if (protocol == null)
4080       {
4081         return false;
4082       }
4083       if (needtoadd)
4084       {
4085         pdbentry.setProperty("protocol", protocol);
4086         toaddpdb.addPDBId(pdbentry);
4087         alignPanel.getStructureSelectionManager()
4088                 .registerPDBEntry(pdbentry);
4089       }
4090     }
4091     return true;
4092   }
4093
4094   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4095   {
4096     if (seqs != null)
4097     {
4098       Vector sequences = new Vector();
4099       for (int i = 0; i < seqs.length; i++)
4100       {
4101         if (seqs[i] != null)
4102         {
4103           sequences
4104                   .addElement(new Object[]
4105                   { seqs[i], (chains != null) ? chains[i] : null });
4106         }
4107       }
4108       seqs = new SequenceI[sequences.size()];
4109       chains = new String[sequences.size()];
4110       for (int i = 0, isize = sequences.size(); i < isize; i++)
4111       {
4112         Object[] oj = (Object[]) sequences.elementAt(i);
4113
4114         seqs[i] = (SequenceI) oj[0];
4115         chains[i] = (String) oj[1];
4116       }
4117     }
4118     return new Object[] { seqs, chains };
4119
4120   }
4121
4122   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4123           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4124   {
4125     // Scrub any null sequences from the array
4126     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4127     seqs = (SequenceI[]) sqch[0];
4128     chains = (String[]) sqch[1];
4129     if (seqs == null || seqs.length == 0)
4130     {
4131       System.err.println(
4132               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4133     }
4134     if (protocol == null)
4135     {
4136       String sourceType = (String) pdb.getProperty("protocol");
4137       try
4138       {
4139         protocol = DataSourceType.valueOf(sourceType);
4140       } catch (IllegalArgumentException e)
4141       {
4142         // ignore
4143       }
4144       if (protocol == null)
4145       {
4146         System.err.println("Couldn't work out protocol to open structure: "
4147                 + pdb.getId());
4148         return;
4149       }
4150     }
4151     if (applet.useXtrnalSviewer)
4152     {
4153       // register the association(s) and quit, don't create any windows.
4154       if (StructureSelectionManager.getStructureSelectionManager(applet)
4155               .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4156       {
4157         System.err.println("Failed to map " + pdb.getFile() + " ("
4158                 + protocol + ") to any sequences");
4159       }
4160       return;
4161     }
4162     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4163     {
4164       // can only do alignments with Jmol
4165       // find the last jmol window assigned to this alignment
4166       AppletJmol ajm = null, tajm;
4167       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4168       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4169       {
4170         tajm = (AppletJmol) jmols.elementAt(i);
4171         if (tajm.ap.alignFrame == this)
4172         {
4173           ajm = tajm;
4174           break;
4175         }
4176       }
4177       if (ajm != null)
4178       {
4179         System.err.println(
4180                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4181         // try and add the pdb structure
4182         // ajm.addS
4183         ajm = null;
4184       }
4185     }
4186     // otherwise, create a new window
4187     if (applet.jmolAvailable)
4188     {
4189       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4190       applet.lastFrameX += 40;
4191       applet.lastFrameY += 40;
4192     }
4193     else
4194     {
4195       new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4196     }
4197
4198   }
4199
4200   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4201           SequenceI[][] seqs, String[][] chains, String[] protocols)
4202   {
4203     // TODO Auto-generated method stub
4204     System.err.println("Aligned Structure View: Not yet implemented.");
4205   }
4206
4207   /**
4208    * modify the current selection, providing the user has not made a selection
4209    * already.
4210    *
4211    * @param sel
4212    *          - sequences from this alignment
4213    * @param csel
4214    *          - columns to be selected on the alignment
4215    */
4216   public void select(SequenceGroup sel, ColumnSelection csel,
4217           HiddenColumns hidden)
4218   {
4219     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4220   }
4221
4222   public void scrollTo(int row, int column)
4223   {
4224     alignPanel.seqPanel.scrollTo(row, column);
4225   }
4226
4227   public void scrollToRow(int row)
4228   {
4229     alignPanel.seqPanel.scrollToRow(row);
4230   }
4231
4232   public void scrollToColumn(int column)
4233   {
4234     alignPanel.seqPanel.scrollToColumn(column);
4235   }
4236
4237   /**
4238    * @return the alignments unique ID.
4239    */
4240   public String getSequenceSetId()
4241   {
4242     return viewport.getSequenceSetId();
4243   }
4244
4245   /**
4246    * Load the (T-Coffee) score file from the specified url
4247    *
4248    * @param source
4249    *          File/URL/T-COFFEE score file contents
4250    * @throws IOException
4251    * @return true if alignment was annotated with data from source
4252    */
4253   public boolean loadScoreFile(String source) throws IOException
4254   {
4255
4256     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4257             AppletFormatAdapter.checkProtocol(source));
4258     if (!file.isValid())
4259     {
4260       // TODO: raise dialog for gui
4261       System.err.println("Problems parsing T-Coffee scores: "
4262               + file.getWarningMessage());
4263       System.err.println("Origin was:\n" + source);
4264       return false;
4265     }
4266
4267     /*
4268      * check that the score matrix matches the alignment dimensions
4269      */
4270     AlignmentI aln;
4271     if ((aln = viewport.getAlignment()) != null
4272             && (aln.getHeight() != file.getHeight()
4273                     || aln.getWidth() != file.getWidth()))
4274     {
4275       // TODO: raise a dialog box here rather than bomb out.
4276       System.err.println(
4277               "The scores matrix does not match the alignment dimensions");
4278
4279     }
4280
4281     // TODO add parameter to indicate if matching should be done
4282     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4283     {
4284       alignPanel.fontChanged();
4285       tcoffeeColour.setEnabled(true);
4286       // switch to this color
4287       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4288       return true;
4289     }
4290     else
4291     {
4292       System.err.println("Problems resolving T-Coffee scores:");
4293       if (file.getWarningMessage() != null)
4294       {
4295         System.err.println(file.getWarningMessage());
4296       }
4297     }
4298     return false;
4299   }
4300
4301   public SplitFrame getSplitFrame()
4302   {
4303     return this.splitFrame;
4304   }
4305
4306   public void setSplitFrame(SplitFrame sf)
4307   {
4308     this.splitFrame = sf;
4309   }
4310
4311   // may not need this
4312   @Override
4313   public void setShowSeqFeatures(boolean b)
4314   {
4315     // showSeqFeatures.setSelected(b);
4316     viewport.setShowSequenceFeatures(b);
4317
4318   }
4319
4320   @Override
4321   public void setMenusForViewport()
4322   {
4323     // setMenusFromViewport(viewport);
4324
4325   }
4326
4327   @Override
4328   public void refreshFeatureUI(boolean enableIfNecessary)
4329   {
4330     if (enableIfNecessary)
4331     {
4332       sequenceFeatures.setState(true);
4333       alignPanel.av.setShowSequenceFeatures(true);
4334     }
4335   }
4336
4337   @Override
4338   public FeatureSettingsControllerI getFeatureSettingsUI()
4339   {
4340     return alignPanel.av.featureSettings;
4341   }
4342
4343   @Override
4344   public FeatureSettingsControllerI showFeatureSettingsUI()
4345   {
4346     return new FeatureSettings(alignPanel);
4347   }
4348
4349   private Rectangle fs_bounds = null;
4350
4351   @Override
4352   public void setFeatureSettingsGeometry(Rectangle bounds)
4353   {
4354     fs_bounds = bounds;
4355   }
4356
4357   @Override
4358   public Rectangle getFeatureSettingsGeometry()
4359   {
4360     return fs_bounds;
4361   }
4362
4363 }