src/jalview/appletgui/AlignFrame.java

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