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