src/jalview/gui/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.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.GeneticCodeI;
  28 import jalview.analysis.ParseProperties;
  29 import jalview.analysis.SequenceIdMatcher;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.FeatureSettingsModelI;
  37 import jalview.api.SplitContainerI;
  38 import jalview.api.ViewStyleI;
  39 import jalview.api.analysis.SimilarityParamsI;
  40 import jalview.bin.Cache;
  41 import jalview.bin.Jalview;
  42 import jalview.commands.CommandI;
  43 import jalview.commands.EditCommand;
  44 import jalview.commands.EditCommand.Action;
  45 import jalview.commands.OrderCommand;
  46 import jalview.commands.RemoveGapColCommand;
  47 import jalview.commands.RemoveGapsCommand;
  48 import jalview.commands.SlideSequencesCommand;
  49 import jalview.commands.TrimRegionCommand;
  50 import jalview.datamodel.AlignedCodonFrame;
  51 import jalview.datamodel.Alignment;
  52 import jalview.datamodel.AlignmentAnnotation;
  53 import jalview.datamodel.AlignmentExportData;
  54 import jalview.datamodel.AlignmentI;
  55 import jalview.datamodel.AlignmentOrder;
  56 import jalview.datamodel.AlignmentView;
  57 import jalview.datamodel.ColumnSelection;
  58 import jalview.datamodel.HiddenColumns;
  59 import jalview.datamodel.HiddenSequences;
  60 import jalview.datamodel.PDBEntry;
  61 import jalview.datamodel.SeqCigar;
  62 import jalview.datamodel.Sequence;
  63 import jalview.datamodel.SequenceGroup;
  64 import jalview.datamodel.SequenceI;
  65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  67 import jalview.io.AlignmentProperties;
  68 import jalview.io.AnnotationFile;
  69 import jalview.io.BackupFiles;
  70 import jalview.io.BioJsHTMLOutput;
  71 import jalview.io.DataSourceType;
  72 import jalview.io.FileFormat;
  73 import jalview.io.FileFormatI;
  74 import jalview.io.FileFormats;
  75 import jalview.io.FileLoader;
  76 import jalview.io.FileParse;
  77 import jalview.io.FormatAdapter;
  78 import jalview.io.HtmlSvgOutput;
  79 import jalview.io.IdentifyFile;
  80 import jalview.io.JPredFile;
  81 import jalview.io.JalviewFileChooser;
  82 import jalview.io.JalviewFileView;
  83 import jalview.io.JnetAnnotationMaker;
  84 import jalview.io.NewickFile;
  85 import jalview.io.ScoreMatrixFile;
  86 import jalview.io.TCoffeeScoreFile;
  87 import jalview.io.vcf.VCFLoader;
  88 import jalview.jbgui.GAlignFrame;
  89 import jalview.schemes.ColourSchemeI;
  90 import jalview.schemes.ColourSchemes;
  91 import jalview.schemes.ResidueColourScheme;
  92 import jalview.schemes.TCoffeeColourScheme;
  93 import jalview.util.MessageManager;
  94 import jalview.viewmodel.AlignmentViewport;
  95 import jalview.viewmodel.ViewportRanges;
  96 import jalview.ws.DBRefFetcher;
  97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  98 import jalview.ws.jws1.Discoverer;
  99 import jalview.ws.jws2.Jws2Discoverer;
 100 import jalview.ws.jws2.jabaws2.Jws2Instance;
 101 import jalview.ws.seqfetcher.DbSourceProxy;
 102
 103 import java.awt.BorderLayout;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseEvent;
 125 import java.awt.print.PageFormat;
 126 import java.awt.print.PrinterJob;
 127 import java.beans.PropertyChangeEvent;
 128 import java.io.File;
 129 import java.io.FileWriter;
 130 import java.io.PrintWriter;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.ButtonGroup;
 141 import javax.swing.JCheckBoxMenuItem;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLayeredPane;
 145 import javax.swing.JMenu;
 146 import javax.swing.JMenuItem;
 147 import javax.swing.JScrollPane;
 148 import javax.swing.SwingUtilities;
 149
 150 /**
 151  * DOCUMENT ME!
 152  *
 153  * @author $author$
 154  * @version $Revision$
 155  */
 156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 157         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 158 {
 159
 160   public static final int DEFAULT_WIDTH = 700;
 161
 162   public static final int DEFAULT_HEIGHT = 500;
 163
 164   /*
 165    * The currently displayed panel (selected tabbed view if more than one)
 166    */
 167   public AlignmentPanel alignPanel;
 168
 169   AlignViewport viewport;
 170
 171   public AlignViewControllerI avc;
 172
 173   List<AlignmentPanel> alignPanels = new ArrayList<>();
 174
 175   /**
 176    * Last format used to load or save alignments in this window
 177    */
 178   FileFormatI currentFileFormat = null;
 179
 180   /**
 181    * Current filename for this alignment
 182    */
 183   String fileName = null;
 184
 185   /**
 186    * Creates a new AlignFrame object with specific width and height.
 187    *
 188    * @param al
 189    * @param width
 190    * @param height
 191    */
 192   public AlignFrame(AlignmentI al, int width, int height)
 193   {
 194     this(al, null, width, height);
 195   }
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width, height and
 199    * sequenceSetId
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    * @param sequenceSetId
 205    */
 206   public AlignFrame(AlignmentI al, int width, int height,
 207           String sequenceSetId)
 208   {
 209     this(al, null, width, height, sequenceSetId);
 210   }
 211
 212   /**
 213    * Creates a new AlignFrame object with specific width, height and
 214    * sequenceSetId
 215    *
 216    * @param al
 217    * @param width
 218    * @param height
 219    * @param sequenceSetId
 220    * @param viewId
 221    */
 222   public AlignFrame(AlignmentI al, int width, int height,
 223           String sequenceSetId, String viewId)
 224   {
 225     this(al, null, width, height, sequenceSetId, viewId);
 226   }
 227
 228   /**
 229    * new alignment window with hidden columns
 230    *
 231    * @param al
 232    *          AlignmentI
 233    * @param hiddenColumns
 234    *          ColumnSelection or null
 235    * @param width
 236    *          Width of alignment frame
 237    * @param height
 238    *          height of frame.
 239    */
 240   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 241           int height)
 242   {
 243     this(al, hiddenColumns, width, height, null);
 244   }
 245
 246   /**
 247    * Create alignment frame for al with hiddenColumns, a specific width and
 248    * height, and specific sequenceId
 249    *
 250    * @param al
 251    * @param hiddenColumns
 252    * @param width
 253    * @param height
 254    * @param sequenceSetId
 255    *          (may be null)
 256    */
 257   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 258           int height, String sequenceSetId)
 259   {
 260     this(al, hiddenColumns, width, height, sequenceSetId, null);
 261   }
 262
 263   /**
 264    * Create alignment frame for al with hiddenColumns, a specific width and
 265    * height, and specific sequenceId
 266    *
 267    * @param al
 268    * @param hiddenColumns
 269    * @param width
 270    * @param height
 271    * @param sequenceSetId
 272    *          (may be null)
 273    * @param viewId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 277           int height, String sequenceSetId, String viewId)
 278   {
 279     setSize(width, height);
 280
 281     if (al.getDataset() == null)
 282     {
 283       al.setDataset(null);
 284     }
 285
 286     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 287
 288     alignPanel = new AlignmentPanel(this, viewport);
 289
 290     addAlignmentPanel(alignPanel, true);
 291     init();
 292   }
 293
 294   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 295           HiddenColumns hiddenColumns, int width, int height)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns);
 305
 306     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 307     {
 308       viewport.hideSequence(hiddenSeqs);
 309     }
 310     alignPanel = new AlignmentPanel(this, viewport);
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   /**
 316    * Make a new AlignFrame from existing alignmentPanels
 317    *
 318    * @param ap
 319    *          AlignmentPanel
 320    * @param av
 321    *          AlignViewport
 322    */
 323   public AlignFrame(AlignmentPanel ap)
 324   {
 325     viewport = ap.av;
 326     alignPanel = ap;
 327     addAlignmentPanel(ap, false);
 328     init();
 329   }
 330
 331   /**
 332    * initalise the alignframe from the underlying viewport data and the
 333    * configurations
 334    */
 335   void init()
 336   {
 337     if (!Jalview.isHeadlessMode())
 338     {
 339       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 340     }
 341
 342     avc = new jalview.controller.AlignViewController(this, viewport,
 343             alignPanel);
 344     if (viewport.getAlignmentConservationAnnotation() == null)
 345     {
 346       // BLOSUM62Colour.setEnabled(false);
 347       conservationMenuItem.setEnabled(false);
 348       modifyConservation.setEnabled(false);
 349       // PIDColour.setEnabled(false);
 350       // abovePIDThreshold.setEnabled(false);
 351       // modifyPID.setEnabled(false);
 352     }
 353
 354     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 355             "No sort");
 356
 357     if (sortby.equals("Id"))
 358     {
 359       sortIDMenuItem_actionPerformed(null);
 360     }
 361     else if (sortby.equals("Pairwise Identity"))
 362     {
 363       sortPairwiseMenuItem_actionPerformed(null);
 364     }
 365
 366     this.alignPanel.av
 367             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 368
 369     setMenusFromViewport(viewport);
 370     buildSortByAnnotationScoresMenu();
 371     calculateTree.addActionListener(new ActionListener()
 372     {
 373
 374       @Override
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         openTreePcaDialog();
 378       }
 379     });
 380     buildColourMenu();
 381
 382     if (Desktop.desktop != null)
 383     {
 384       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 385       addServiceListeners();
 386       setGUINucleotide();
 387     }
 388
 389     if (viewport.getWrapAlignment())
 390     {
 391       wrapMenuItem_actionPerformed(null);
 392     }
 393
 394     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 395     {
 396       this.overviewMenuItem_actionPerformed(null);
 397     }
 398
 399     addKeyListener();
 400
 401     final List<AlignmentPanel> selviews = new ArrayList<>();
 402     final List<AlignmentPanel> origview = new ArrayList<>();
 403     final String menuLabel = MessageManager
 404             .getString("label.copy_format_from");
 405     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 406             new ViewSetProvider()
 407             {
 408
 409               @Override
 410               public AlignmentPanel[] getAllAlignmentPanels()
 411               {
 412                 origview.clear();
 413                 origview.add(alignPanel);
 414                 // make an array of all alignment panels except for this one
 415                 List<AlignmentPanel> aps = new ArrayList<>(
 416                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 417                 aps.remove(AlignFrame.this.alignPanel);
 418                 return aps.toArray(new AlignmentPanel[aps.size()]);
 419               }
 420             }, selviews, new ItemListener()
 421             {
 422
 423               @Override
 424               public void itemStateChanged(ItemEvent e)
 425               {
 426                 if (origview.size() > 0)
 427                 {
 428                   final AlignmentPanel ap = origview.get(0);
 429
 430                   /*
 431                    * Copy the ViewStyle of the selected panel to 'this one'.
 432                    * Don't change value of 'scaleProteinAsCdna' unless copying
 433                    * from a SplitFrame.
 434                    */
 435                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 436                           .getViewStyle();
 437                   boolean fromSplitFrame = selviews.get(0)
 438                           .getAlignViewport().getCodingComplement() != null;
 439                   if (!fromSplitFrame)
 440                   {
 441                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 442                             .getViewStyle().isScaleProteinAsCdna());
 443                   }
 444                   ap.getAlignViewport().setViewStyle(vs);
 445
 446                   /*
 447                    * Also rescale ViewStyle of SplitFrame complement if there is
 448                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 449                    * the whole ViewStyle (allow cDNA protein to have different
 450                    * fonts)
 451                    */
 452                   AlignViewportI complement = ap.getAlignViewport()
 453                           .getCodingComplement();
 454                   if (complement != null && vs.isScaleProteinAsCdna())
 455                   {
 456                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 457                     ((SplitFrame) af.getSplitViewContainer())
 458                             .adjustLayout();
 459                     af.setMenusForViewport();
 460                   }
 461
 462                   ap.updateLayout();
 463                   ap.setSelected(true);
 464                   ap.alignFrame.setMenusForViewport();
 465
 466                 }
 467               }
 468             });
 469     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 470             .indexOf("devel") > -1
 471             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 472                     .indexOf("test") > -1)
 473     {
 474       formatMenu.add(vsel);
 475     }
 476     addFocusListener(new FocusAdapter()
 477     {
 478       @Override
 479       public void focusGained(FocusEvent e)
 480       {
 481         Jalview.setCurrentAlignFrame(AlignFrame.this);
 482       }
 483     });
 484
 485   }
 486
 487   /**
 488    * Change the filename and format for the alignment, and enable the 'reload'
 489    * button functionality.
 490    *
 491    * @param file
 492    *          valid filename
 493    * @param format
 494    *          format of file
 495    */
 496   public void setFileName(String file, FileFormatI format)
 497   {
 498     fileName = file;
 499     setFileFormat(format);
 500     reload.setEnabled(true);
 501   }
 502
 503   /**
 504    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 505    * events
 506    */
 507   void addKeyListener()
 508   {
 509     addKeyListener(new KeyAdapter()
 510     {
 511       @Override
 512       public void keyPressed(KeyEvent evt)
 513       {
 514         if (viewport.cursorMode
 515                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 516                         && evt.getKeyCode() <= KeyEvent.VK_9)
 517                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 518                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 519                 && Character.isDigit(evt.getKeyChar()))
 520         {
 521           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 522         }
 523
 524         switch (evt.getKeyCode())
 525         {
 526
 527         case 27: // escape key
 528           deselectAllSequenceMenuItem_actionPerformed(null);
 529
 530           break;
 531
 532         case KeyEvent.VK_DOWN:
 533           if (evt.isAltDown() || !viewport.cursorMode)
 534           {
 535             moveSelectedSequences(false);
 536           }
 537           if (viewport.cursorMode)
 538           {
 539             alignPanel.getSeqPanel().moveCursor(0, 1);
 540           }
 541           break;
 542
 543         case KeyEvent.VK_UP:
 544           if (evt.isAltDown() || !viewport.cursorMode)
 545           {
 546             moveSelectedSequences(true);
 547           }
 548           if (viewport.cursorMode)
 549           {
 550             alignPanel.getSeqPanel().moveCursor(0, -1);
 551           }
 552
 553           break;
 554
 555         case KeyEvent.VK_LEFT:
 556           if (evt.isAltDown() || !viewport.cursorMode)
 557           {
 558             slideSequences(false,
 559                     alignPanel.getSeqPanel().getKeyboardNo1());
 560           }
 561           else
 562           {
 563             alignPanel.getSeqPanel().moveCursor(-1, 0);
 564           }
 565
 566           break;
 567
 568         case KeyEvent.VK_RIGHT:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 572           }
 573           else
 574           {
 575             alignPanel.getSeqPanel().moveCursor(1, 0);
 576           }
 577           break;
 578
 579         case KeyEvent.VK_SPACE:
 580           if (viewport.cursorMode)
 581           {
 582             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 583                     || evt.isShiftDown() || evt.isAltDown());
 584           }
 585           break;
 586
 587         // case KeyEvent.VK_A:
 588         // if (viewport.cursorMode)
 589         // {
 590         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 591         // //System.out.println("A");
 592         // }
 593         // break;
 594         /*
 595          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 596          * System.out.println("closing bracket"); } break;
 597          */
 598         case KeyEvent.VK_DELETE:
 599         case KeyEvent.VK_BACK_SPACE:
 600           if (!viewport.cursorMode)
 601           {
 602             cut_actionPerformed(null);
 603           }
 604           else
 605           {
 606             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 607                     || evt.isShiftDown() || evt.isAltDown());
 608           }
 609
 610           break;
 611
 612         case KeyEvent.VK_S:
 613           if (viewport.cursorMode)
 614           {
 615             alignPanel.getSeqPanel().setCursorRow();
 616           }
 617           break;
 618         case KeyEvent.VK_C:
 619           if (viewport.cursorMode && !evt.isControlDown())
 620           {
 621             alignPanel.getSeqPanel().setCursorColumn();
 622           }
 623           break;
 624         case KeyEvent.VK_P:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setCursorPosition();
 628           }
 629           break;
 630
 631         case KeyEvent.VK_ENTER:
 632         case KeyEvent.VK_COMMA:
 633           if (viewport.cursorMode)
 634           {
 635             alignPanel.getSeqPanel().setCursorRowAndColumn();
 636           }
 637           break;
 638
 639         case KeyEvent.VK_Q:
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 643           }
 644           break;
 645         case KeyEvent.VK_M:
 646           if (viewport.cursorMode)
 647           {
 648             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 649           }
 650           break;
 651
 652         case KeyEvent.VK_F2:
 653           viewport.cursorMode = !viewport.cursorMode;
 654           statusBar.setText(MessageManager
 655                   .formatMessage("label.keyboard_editing_mode", new String[]
 656                   { (viewport.cursorMode ? "on" : "off") }));
 657           if (viewport.cursorMode)
 658           {
 659             ViewportRanges ranges = viewport.getRanges();
 660             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 661                     .getStartRes();
 662             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 663                     .getStartSeq();
 664           }
 665           alignPanel.getSeqPanel().seqCanvas.repaint();
 666           break;
 667
 668         case KeyEvent.VK_F1:
 669           try
 670           {
 671             Help.showHelpWindow();
 672           } catch (Exception ex)
 673           {
 674             ex.printStackTrace();
 675           }
 676           break;
 677         case KeyEvent.VK_H:
 678         {
 679           boolean toggleSeqs = !evt.isControlDown();
 680           boolean toggleCols = !evt.isShiftDown();
 681           toggleHiddenRegions(toggleSeqs, toggleCols);
 682           break;
 683         }
 684         case KeyEvent.VK_B:
 685         {
 686           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 687           boolean modifyExisting = true; // always modify, don't clear
 688                                          // evt.isShiftDown();
 689           boolean invertHighlighted = evt.isAltDown();
 690           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 691                   toggleSel);
 692           break;
 693         }
 694         case KeyEvent.VK_PAGE_UP:
 695           viewport.getRanges().pageUp();
 696           break;
 697         case KeyEvent.VK_PAGE_DOWN:
 698           viewport.getRanges().pageDown();
 699           break;
 700         }
 701       }
 702
 703       @Override
 704       public void keyReleased(KeyEvent evt)
 705       {
 706         switch (evt.getKeyCode())
 707         {
 708         case KeyEvent.VK_LEFT:
 709           if (evt.isAltDown() || !viewport.cursorMode)
 710           {
 711             viewport.firePropertyChange("alignment", null,
 712                     viewport.getAlignment().getSequences());
 713           }
 714           break;
 715
 716         case KeyEvent.VK_RIGHT:
 717           if (evt.isAltDown() || !viewport.cursorMode)
 718           {
 719             viewport.firePropertyChange("alignment", null,
 720                     viewport.getAlignment().getSequences());
 721           }
 722           break;
 723         }
 724       }
 725     });
 726   }
 727
 728   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 729   {
 730     ap.alignFrame = this;
 731     avc = new jalview.controller.AlignViewController(this, viewport,
 732             alignPanel);
 733
 734     alignPanels.add(ap);
 735
 736     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 737
 738     int aSize = alignPanels.size();
 739
 740     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 741
 742     if (aSize == 1 && ap.av.getViewName() == null)
 743     {
 744       this.getContentPane().add(ap, BorderLayout.CENTER);
 745     }
 746     else
 747     {
 748       if (aSize == 2)
 749       {
 750         setInitialTabVisible();
 751       }
 752
 753       expandViews.setEnabled(true);
 754       gatherViews.setEnabled(true);
 755       tabbedPane.addTab(ap.av.getViewName(), ap);
 756
 757       ap.setVisible(false);
 758     }
 759
 760     if (newPanel)
 761     {
 762       if (ap.av.isPadGaps())
 763       {
 764         ap.av.getAlignment().padGaps();
 765       }
 766       ap.av.updateConservation(ap);
 767       ap.av.updateConsensus(ap);
 768       ap.av.updateStrucConsensus(ap);
 769     }
 770   }
 771
 772   public void setInitialTabVisible()
 773   {
 774     expandViews.setEnabled(true);
 775     gatherViews.setEnabled(true);
 776     tabbedPane.setVisible(true);
 777     AlignmentPanel first = alignPanels.get(0);
 778     tabbedPane.addTab(first.av.getViewName(), first);
 779     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 780   }
 781
 782   public AlignViewport getViewport()
 783   {
 784     return viewport;
 785   }
 786
 787   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 788   private void addServiceListeners()
 789   {
 790     final java.beans.PropertyChangeListener thisListener;
 791     Desktop.instance.addJalviewPropertyChangeListener("services",
 792             thisListener = new java.beans.PropertyChangeListener()
 793             {
 794               @Override
 795               public void propertyChange(PropertyChangeEvent evt)
 796               {
 797                 // // System.out.println("Discoverer property change.");
 798                 // if (evt.getPropertyName().equals("services"))
 799                 {
 800                   SwingUtilities.invokeLater(new Runnable()
 801                   {
 802
 803                     @Override
 804                     public void run()
 805                     {
 806                       System.err.println(
 807                               "Rebuild WS Menu for service change");
 808                       BuildWebServiceMenu();
 809                     }
 810
 811                   });
 812                 }
 813               }
 814             });
 815     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 816     {
 817       @Override
 818       public void internalFrameClosed(
 819               javax.swing.event.InternalFrameEvent evt)
 820       {
 821         // System.out.println("deregistering discoverer listener");
 822         Desktop.instance.removeJalviewPropertyChangeListener("services",
 823                 thisListener);
 824         closeMenuItem_actionPerformed(true);
 825       };
 826     });
 827     // Finally, build the menu once to get current service state
 828     new Thread(new Runnable()
 829     {
 830       @Override
 831       public void run()
 832       {
 833         BuildWebServiceMenu();
 834       }
 835     }).start();
 836   }
 837
 838   /**
 839    * Configure menu items that vary according to whether the alignment is
 840    * nucleotide or protein
 841    */
 842   public void setGUINucleotide()
 843   {
 844     AlignmentI al = getViewport().getAlignment();
 845     boolean nucleotide = al.isNucleotide();
 846
 847     loadVcf.setVisible(nucleotide);
 848     showTranslation.setVisible(nucleotide);
 849     showReverse.setVisible(nucleotide);
 850     showReverseComplement.setVisible(nucleotide);
 851     conservationMenuItem.setEnabled(!nucleotide);
 852     modifyConservation
 853             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 854     showGroupConservation.setEnabled(!nucleotide);
 855
 856     showComplementMenuItem
 857             .setText(nucleotide ? MessageManager.getString("label.protein")
 858                     : MessageManager.getString("label.nucleotide"));
 859   }
 860
 861   /**
 862    * set up menus for the current viewport. This may be called after any
 863    * operation that affects the data in the current view (selection changed,
 864    * etc) to update the menus to reflect the new state.
 865    */
 866   @Override
 867   public void setMenusForViewport()
 868   {
 869     setMenusFromViewport(viewport);
 870   }
 871
 872   /**
 873    * Need to call this method when tabs are selected for multiple views, or when
 874    * loading from Jalview2XML.java
 875    *
 876    * @param av
 877    *          AlignViewport
 878    */
 879   public void setMenusFromViewport(AlignViewport av)
 880   {
 881     padGapsMenuitem.setSelected(av.isPadGaps());
 882     colourTextMenuItem.setSelected(av.isShowColourText());
 883     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 884     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 885     conservationMenuItem.setSelected(av.getConservationSelected());
 886     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 887     seqLimits.setSelected(av.getShowJVSuffix());
 888     idRightAlign.setSelected(av.isRightAlignIds());
 889     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 890     renderGapsMenuItem.setSelected(av.isRenderGaps());
 891     wrapMenuItem.setSelected(av.getWrapAlignment());
 892     scaleAbove.setVisible(av.getWrapAlignment());
 893     scaleLeft.setVisible(av.getWrapAlignment());
 894     scaleRight.setVisible(av.getWrapAlignment());
 895     annotationPanelMenuItem.setState(av.isShowAnnotation());
 896     /*
 897      * Show/hide annotations only enabled if annotation panel is shown
 898      */
 899     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 902     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 904     viewTextMenuItem.setSelected(av.getShowText());
 905     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 906     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 907     showGroupConservation.setSelected(av.isShowGroupConservation());
 908     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 909     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 910     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 911
 912     ColourMenuHelper.setColourSelected(colourMenu,
 913             av.getGlobalColourScheme());
 914
 915     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 916     hiddenMarkers.setState(av.getShowHiddenMarkers());
 917     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 918     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 919     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 920     autoCalculate.setSelected(av.autoCalculateConsensus);
 921     sortByTree.setSelected(av.sortByTree);
 922     listenToViewSelections.setSelected(av.followSelection);
 923
 924     showProducts.setEnabled(canShowProducts());
 925     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 926
 927     updateEditMenuBar();
 928   }
 929
 930   /**
 931    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 932    *
 933    * @param b
 934    */
 935   public void setGroovyEnabled(boolean b)
 936   {
 937     runGroovy.setEnabled(b);
 938   }
 939
 940   private IProgressIndicator progressBar;
 941
 942   /*
 943    * (non-Javadoc)
 944    *
 945    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 946    */
 947   @Override
 948   public void setProgressBar(String message, long id)
 949   {
 950     progressBar.setProgressBar(message, id);
 951   }
 952
 953   @Override
 954   public void registerHandler(final long id,
 955           final IProgressIndicatorHandler handler)
 956   {
 957     progressBar.registerHandler(id, handler);
 958   }
 959
 960   /**
 961    *
 962    * @return true if any progress bars are still active
 963    */
 964   @Override
 965   public boolean operationInProgress()
 966   {
 967     return progressBar.operationInProgress();
 968   }
 969
 970   /**
 971    * Sets the text of the status bar. Note that setting a null or empty value
 972    * will cause the status bar to be hidden, with possibly undesirable flicker
 973    * of the screen layout.
 974    */
 975   @Override
 976   public void setStatus(String text)
 977   {
 978     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 979   }
 980
 981   /*
 982    * Added so Castor Mapping file can obtain Jalview Version
 983    */
 984   public String getVersion()
 985   {
 986     return jalview.bin.Cache.getProperty("VERSION");
 987   }
 988
 989   public FeatureRenderer getFeatureRenderer()
 990   {
 991     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 992   }
 993
 994   @Override
 995   public void fetchSequence_actionPerformed(ActionEvent e)
 996   {
 997     new jalview.gui.SequenceFetcher(this);
 998   }
 999
1000   @Override
1001   public void addFromFile_actionPerformed(ActionEvent e)
1002   {
1003     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1004   }
1005
1006   @Override
1007   public void reload_actionPerformed(ActionEvent e)
1008   {
1009     if (fileName != null)
1010     {
1011       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1012       // originating file's format
1013       // TODO: work out how to recover feature settings for correct view(s) when
1014       // file is reloaded.
1015       if (FileFormat.Jalview.equals(currentFileFormat))
1016       {
1017         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1018         for (int i = 0; i < frames.length; i++)
1019         {
1020           if (frames[i] instanceof AlignFrame && frames[i] != this
1021                   && ((AlignFrame) frames[i]).fileName != null
1022                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1023           {
1024             try
1025             {
1026               frames[i].setSelected(true);
1027               Desktop.instance.closeAssociatedWindows();
1028             } catch (java.beans.PropertyVetoException ex)
1029             {
1030             }
1031           }
1032
1033         }
1034         Desktop.instance.closeAssociatedWindows();
1035
1036         FileLoader loader = new FileLoader();
1037         DataSourceType protocol = fileName.startsWith("http:")
1038                 ? DataSourceType.URL
1039                 : DataSourceType.FILE;
1040         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1041       }
1042       else
1043       {
1044         Rectangle bounds = this.getBounds();
1045
1046         FileLoader loader = new FileLoader();
1047         DataSourceType protocol = fileName.startsWith("http:")
1048                 ? DataSourceType.URL
1049                 : DataSourceType.FILE;
1050         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1051                 protocol, currentFileFormat);
1052
1053         newframe.setBounds(bounds);
1054         if (featureSettings != null && featureSettings.isShowing())
1055         {
1056           final Rectangle fspos = featureSettings.frame.getBounds();
1057           // TODO: need a 'show feature settings' function that takes bounds -
1058           // need to refactor Desktop.addFrame
1059           newframe.featureSettings_actionPerformed(null);
1060           final FeatureSettings nfs = newframe.featureSettings;
1061           SwingUtilities.invokeLater(new Runnable()
1062           {
1063             @Override
1064             public void run()
1065             {
1066               nfs.frame.setBounds(fspos);
1067             }
1068           });
1069           this.featureSettings.close();
1070           this.featureSettings = null;
1071         }
1072         this.closeMenuItem_actionPerformed(true);
1073       }
1074     }
1075   }
1076
1077   @Override
1078   public void addFromText_actionPerformed(ActionEvent e)
1079   {
1080     Desktop.instance
1081             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1082   }
1083
1084   @Override
1085   public void addFromURL_actionPerformed(ActionEvent e)
1086   {
1087     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1088   }
1089
1090   @Override
1091   public void save_actionPerformed(ActionEvent e)
1092   {
1093     if (fileName == null || (currentFileFormat == null)
1094             || fileName.startsWith("http"))
1095     {
1096       saveAs_actionPerformed(null);
1097     }
1098     else
1099     {
1100       saveAlignment(fileName, currentFileFormat);
1101     }
1102   }
1103
1104   /**
1105    * DOCUMENT ME!
1106    *
1107    * @param e
1108    *          DOCUMENT ME!
1109    */
1110   @Override
1111   public void saveAs_actionPerformed(ActionEvent e)
1112   {
1113     String format = currentFileFormat == null ? null
1114             : currentFileFormat.getName();
1115     JalviewFileChooser chooser = JalviewFileChooser
1116             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1117
1118     chooser.setFileView(new JalviewFileView());
1119     chooser.setDialogTitle(
1120             MessageManager.getString("label.save_alignment_to_file"));
1121     chooser.setToolTipText(MessageManager.getString("action.save"));
1122
1123     int value = chooser.showSaveDialog(this);
1124
1125     if (value == JalviewFileChooser.APPROVE_OPTION)
1126     {
1127       currentFileFormat = chooser.getSelectedFormat();
1128       while (currentFileFormat == null)
1129       {
1130         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1131                 MessageManager.getString(
1132                         "label.select_file_format_before_saving"),
1133                 MessageManager.getString("label.file_format_not_specified"),
1134                 JvOptionPane.WARNING_MESSAGE);
1135         currentFileFormat = chooser.getSelectedFormat();
1136         value = chooser.showSaveDialog(this);
1137         if (value != JalviewFileChooser.APPROVE_OPTION)
1138         {
1139           return;
1140         }
1141       }
1142
1143       fileName = chooser.getSelectedFile().getPath();
1144
1145       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1146
1147       Cache.setProperty("LAST_DIRECTORY", fileName);
1148       saveAlignment(fileName, currentFileFormat);
1149     }
1150   }
1151
1152   public boolean saveAlignment(String file, FileFormatI format)
1153   {
1154     boolean success = true;
1155
1156     if (FileFormat.Jalview.equals(format))
1157     {
1158       String shortName = title;
1159
1160       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161       {
1162         shortName = shortName.substring(
1163                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1164       }
1165
1166       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1167               shortName);
1168
1169       statusBar.setText(MessageManager.formatMessage(
1170               "label.successfully_saved_to_file_in_format", new Object[]
1171               { fileName, format }));
1172
1173     }
1174     else
1175     {
1176       AlignmentExportData exportData = getAlignmentForExport(format,
1177               viewport, null);
1178       if (exportData.getSettings().isCancelled())
1179       {
1180         return false;
1181       }
1182       FormatAdapter f = new FormatAdapter(alignPanel,
1183               exportData.getSettings());
1184       String output = f.formatSequences(format, exportData.getAlignment(), // class
1185                                                                            // cast
1186                                                                            // exceptions
1187                                                                            // will
1188               // occur in the distant future
1189               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1190               f.getCacheSuffixDefault(format),
1191               viewport.getAlignment().getHiddenColumns());
1192
1193       if (output == null)
1194       {
1195         success = false;
1196       }
1197       else
1198       {
1199         // create backupfiles object and get new temp filename destination
1200         BackupFiles backupfiles = new BackupFiles(file);
1201
1202         try
1203         {
1204           PrintWriter out = new PrintWriter(
1205                   new FileWriter(backupfiles.getTempFilePath()));
1206
1207           out.print(output);
1208           out.close();
1209           this.setTitle(file);
1210           statusBar.setText(MessageManager.formatMessage(
1211                   "label.successfully_saved_to_file_in_format", new Object[]
1212                   { fileName, format.getName() }));
1213         } catch (Exception ex)
1214         {
1215           success = false;
1216           ex.printStackTrace();
1217         }
1218
1219         backupfiles.setWriteSuccess(success);
1220         // do the backup file roll and rename the temp file to actual file
1221         success = backupfiles.rollBackupsAndRenameTempFile();
1222
1223       }
1224     }
1225
1226     if (!success)
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, MessageManager
1229               .formatMessage("label.couldnt_save_file", new Object[]
1230               { fileName }),
1231               MessageManager.getString("label.error_saving_file"),
1232               JvOptionPane.WARNING_MESSAGE);
1233     }
1234
1235     return success;
1236   }
1237
1238   private void warningMessage(String warning, String title)
1239   {
1240     if (new jalview.util.Platform().isHeadless())
1241     {
1242       System.err.println("Warning: " + title + "\nWarning: " + warning);
1243
1244     }
1245     else
1246     {
1247       JvOptionPane.showInternalMessageDialog(this, warning, title,
1248               JvOptionPane.WARNING_MESSAGE);
1249     }
1250     return;
1251   }
1252
1253   /**
1254    * DOCUMENT ME!
1255    *
1256    * @param e
1257    *          DOCUMENT ME!
1258    */
1259   @Override
1260   protected void outputText_actionPerformed(ActionEvent e)
1261   {
1262     FileFormatI fileFormat = FileFormats.getInstance()
1263             .forName(e.getActionCommand());
1264     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1265             viewport, null);
1266     if (exportData.getSettings().isCancelled())
1267     {
1268       return;
1269     }
1270     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1271     cap.setForInput(null);
1272     try
1273     {
1274       FileFormatI format = fileFormat;
1275       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1276               .formatSequences(format, exportData.getAlignment(),
1277                       exportData.getOmitHidden(),
1278                       exportData.getStartEndPostions(),
1279                       viewport.getAlignment().getHiddenColumns()));
1280       Desktop.addInternalFrame(cap, MessageManager
1281               .formatMessage("label.alignment_output_command", new Object[]
1282               { e.getActionCommand() }), 600, 500);
1283     } catch (OutOfMemoryError oom)
1284     {
1285       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1286               oom);
1287       cap.dispose();
1288     }
1289
1290   }
1291
1292   public static AlignmentExportData getAlignmentForExport(
1293           FileFormatI format, AlignViewportI viewport,
1294           AlignExportSettingI exportSettings)
1295   {
1296     AlignmentI alignmentToExport = null;
1297     AlignExportSettingI settings = exportSettings;
1298     String[] omitHidden = null;
1299
1300     HiddenSequences hiddenSeqs = viewport.getAlignment()
1301             .getHiddenSequences();
1302
1303     alignmentToExport = viewport.getAlignment();
1304
1305     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1306     if (settings == null)
1307     {
1308       settings = new AlignExportSettings(hasHiddenSeqs,
1309               viewport.hasHiddenColumns(), format);
1310     }
1311     // settings.isExportAnnotations();
1312
1313     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1314     {
1315       omitHidden = viewport.getViewAsString(false,
1316               settings.isExportHiddenSequences());
1317     }
1318
1319     int[] alignmentStartEnd = new int[2];
1320     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1321     {
1322       alignmentToExport = hiddenSeqs.getFullAlignment();
1323     }
1324     else
1325     {
1326       alignmentToExport = viewport.getAlignment();
1327     }
1328     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1329             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1330     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1331             omitHidden, alignmentStartEnd, settings);
1332     return ed;
1333   }
1334
1335   /**
1336    * DOCUMENT ME!
1337    *
1338    * @param e
1339    *          DOCUMENT ME!
1340    */
1341   @Override
1342   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343   {
1344     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1345     htmlSVG.exportHTML(null);
1346   }
1347
1348   @Override
1349   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350   {
1351     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1352     bjs.exportHTML(null);
1353   }
1354
1355   public void createImageMap(File file, String image)
1356   {
1357     alignPanel.makePNGImageMap(file, image);
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   @Override
1367   public void createPNG(File f)
1368   {
1369     alignPanel.makePNG(f);
1370   }
1371
1372   /**
1373    * DOCUMENT ME!
1374    *
1375    * @param e
1376    *          DOCUMENT ME!
1377    */
1378   @Override
1379   public void createEPS(File f)
1380   {
1381     alignPanel.makeEPS(f);
1382   }
1383
1384   @Override
1385   public void createSVG(File f)
1386   {
1387     alignPanel.makeSVG(f);
1388   }
1389
1390   @Override
1391   public void pageSetup_actionPerformed(ActionEvent e)
1392   {
1393     PrinterJob printJob = PrinterJob.getPrinterJob();
1394     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1395   }
1396
1397   /**
1398    * DOCUMENT ME!
1399    *
1400    * @param e
1401    *          DOCUMENT ME!
1402    */
1403   @Override
1404   public void printMenuItem_actionPerformed(ActionEvent e)
1405   {
1406     // Putting in a thread avoids Swing painting problems
1407     PrintThread thread = new PrintThread(alignPanel);
1408     thread.start();
1409   }
1410
1411   @Override
1412   public void exportFeatures_actionPerformed(ActionEvent e)
1413   {
1414     new AnnotationExporter(alignPanel).exportFeatures();
1415   }
1416
1417   @Override
1418   public void exportAnnotations_actionPerformed(ActionEvent e)
1419   {
1420     new AnnotationExporter(alignPanel).exportAnnotations();
1421   }
1422
1423   @Override
1424   public void associatedData_actionPerformed(ActionEvent e)
1425   {
1426     // Pick the tree file
1427     JalviewFileChooser chooser = new JalviewFileChooser(
1428             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429     chooser.setFileView(new JalviewFileView());
1430     chooser.setDialogTitle(
1431             MessageManager.getString("label.load_jalview_annotations"));
1432     chooser.setToolTipText(
1433             MessageManager.getString("label.load_jalview_annotations"));
1434
1435     int value = chooser.showOpenDialog(null);
1436
1437     if (value == JalviewFileChooser.APPROVE_OPTION)
1438     {
1439       String choice = chooser.getSelectedFile().getPath();
1440       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441       loadJalviewDataFile(choice, null, null, null);
1442     }
1443
1444   }
1445
1446   /**
1447    * Close the current view or all views in the alignment frame. If the frame
1448    * only contains one view then the alignment will be removed from memory.
1449    *
1450    * @param closeAllTabs
1451    */
1452   @Override
1453   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454   {
1455     if (alignPanels != null && alignPanels.size() < 2)
1456     {
1457       closeAllTabs = true;
1458     }
1459
1460     try
1461     {
1462       if (alignPanels != null)
1463       {
1464         if (closeAllTabs)
1465         {
1466           if (this.isClosed())
1467           {
1468             // really close all the windows - otherwise wait till
1469             // setClosed(true) is called
1470             for (int i = 0; i < alignPanels.size(); i++)
1471             {
1472               AlignmentPanel ap = alignPanels.get(i);
1473               ap.closePanel();
1474             }
1475           }
1476         }
1477         else
1478         {
1479           closeView(alignPanel);
1480         }
1481       }
1482
1483       if (closeAllTabs)
1484       {
1485         /*
1486          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1487          * be called recursively, with the frame now in 'closed' state
1488          */
1489         this.setClosed(true);
1490       }
1491     } catch (Exception ex)
1492     {
1493       ex.printStackTrace();
1494     }
1495   }
1496
1497   /**
1498    * Close the specified panel and close up tabs appropriately.
1499    *
1500    * @param panelToClose
1501    */
1502   public void closeView(AlignmentPanel panelToClose)
1503   {
1504     int index = tabbedPane.getSelectedIndex();
1505     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1506     alignPanels.remove(panelToClose);
1507     panelToClose.closePanel();
1508     panelToClose = null;
1509
1510     tabbedPane.removeTabAt(closedindex);
1511     tabbedPane.validate();
1512
1513     if (index > closedindex || index == tabbedPane.getTabCount())
1514     {
1515       // modify currently selected tab index if necessary.
1516       index--;
1517     }
1518
1519     this.tabSelectionChanged(index);
1520   }
1521
1522   /**
1523    * DOCUMENT ME!
1524    */
1525   void updateEditMenuBar()
1526   {
1527
1528     if (viewport.getHistoryList().size() > 0)
1529     {
1530       undoMenuItem.setEnabled(true);
1531       CommandI command = viewport.getHistoryList().peek();
1532       undoMenuItem.setText(MessageManager
1533               .formatMessage("label.undo_command", new Object[]
1534               { command.getDescription() }));
1535     }
1536     else
1537     {
1538       undoMenuItem.setEnabled(false);
1539       undoMenuItem.setText(MessageManager.getString("action.undo"));
1540     }
1541
1542     if (viewport.getRedoList().size() > 0)
1543     {
1544       redoMenuItem.setEnabled(true);
1545
1546       CommandI command = viewport.getRedoList().peek();
1547       redoMenuItem.setText(MessageManager
1548               .formatMessage("label.redo_command", new Object[]
1549               { command.getDescription() }));
1550     }
1551     else
1552     {
1553       redoMenuItem.setEnabled(false);
1554       redoMenuItem.setText(MessageManager.getString("action.redo"));
1555     }
1556   }
1557
1558   @Override
1559   public void addHistoryItem(CommandI command)
1560   {
1561     if (command.getSize() > 0)
1562     {
1563       viewport.addToHistoryList(command);
1564       viewport.clearRedoList();
1565       updateEditMenuBar();
1566       viewport.updateHiddenColumns();
1567       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1568       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1569       // viewport.getColumnSelection()
1570       // .getHiddenColumns().size() > 0);
1571     }
1572   }
1573
1574   /**
1575    *
1576    * @return alignment objects for all views
1577    */
1578   AlignmentI[] getViewAlignments()
1579   {
1580     if (alignPanels != null)
1581     {
1582       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1583       int i = 0;
1584       for (AlignmentPanel ap : alignPanels)
1585       {
1586         als[i++] = ap.av.getAlignment();
1587       }
1588       return als;
1589     }
1590     if (viewport != null)
1591     {
1592       return new AlignmentI[] { viewport.getAlignment() };
1593     }
1594     return null;
1595   }
1596
1597   /**
1598    * DOCUMENT ME!
1599    *
1600    * @param e
1601    *          DOCUMENT ME!
1602    */
1603   @Override
1604   protected void undoMenuItem_actionPerformed(ActionEvent e)
1605   {
1606     if (viewport.getHistoryList().isEmpty())
1607     {
1608       return;
1609     }
1610     CommandI command = viewport.getHistoryList().pop();
1611     viewport.addToRedoList(command);
1612     command.undoCommand(getViewAlignments());
1613
1614     AlignmentViewport originalSource = getOriginatingSource(command);
1615     updateEditMenuBar();
1616
1617     if (originalSource != null)
1618     {
1619       if (originalSource != viewport)
1620       {
1621         Cache.log.warn(
1622                 "Implementation worry: mismatch of viewport origin for undo");
1623       }
1624       originalSource.updateHiddenColumns();
1625       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1626       // null
1627       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1628       // viewport.getColumnSelection()
1629       // .getHiddenColumns().size() > 0);
1630       originalSource.firePropertyChange("alignment", null,
1631               originalSource.getAlignment().getSequences());
1632     }
1633   }
1634
1635   /**
1636    * DOCUMENT ME!
1637    *
1638    * @param e
1639    *          DOCUMENT ME!
1640    */
1641   @Override
1642   protected void redoMenuItem_actionPerformed(ActionEvent e)
1643   {
1644     if (viewport.getRedoList().size() < 1)
1645     {
1646       return;
1647     }
1648
1649     CommandI command = viewport.getRedoList().pop();
1650     viewport.addToHistoryList(command);
1651     command.doCommand(getViewAlignments());
1652
1653     AlignmentViewport originalSource = getOriginatingSource(command);
1654     updateEditMenuBar();
1655
1656     if (originalSource != null)
1657     {
1658
1659       if (originalSource != viewport)
1660       {
1661         Cache.log.warn(
1662                 "Implementation worry: mismatch of viewport origin for redo");
1663       }
1664       originalSource.updateHiddenColumns();
1665       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666       // null
1667       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1668       // viewport.getColumnSelection()
1669       // .getHiddenColumns().size() > 0);
1670       originalSource.firePropertyChange("alignment", null,
1671               originalSource.getAlignment().getSequences());
1672     }
1673   }
1674
1675   AlignmentViewport getOriginatingSource(CommandI command)
1676   {
1677     AlignmentViewport originalSource = null;
1678     // For sequence removal and addition, we need to fire
1679     // the property change event FROM the viewport where the
1680     // original alignment was altered
1681     AlignmentI al = null;
1682     if (command instanceof EditCommand)
1683     {
1684       EditCommand editCommand = (EditCommand) command;
1685       al = editCommand.getAlignment();
1686       List<Component> comps = PaintRefresher.components
1687               .get(viewport.getSequenceSetId());
1688
1689       for (Component comp : comps)
1690       {
1691         if (comp instanceof AlignmentPanel)
1692         {
1693           if (al == ((AlignmentPanel) comp).av.getAlignment())
1694           {
1695             originalSource = ((AlignmentPanel) comp).av;
1696             break;
1697           }
1698         }
1699       }
1700     }
1701
1702     if (originalSource == null)
1703     {
1704       // The original view is closed, we must validate
1705       // the current view against the closed view first
1706       if (al != null)
1707       {
1708         PaintRefresher.validateSequences(al, viewport.getAlignment());
1709       }
1710
1711       originalSource = viewport;
1712     }
1713
1714     return originalSource;
1715   }
1716
1717   /**
1718    * DOCUMENT ME!
1719    *
1720    * @param up
1721    *          DOCUMENT ME!
1722    */
1723   public void moveSelectedSequences(boolean up)
1724   {
1725     SequenceGroup sg = viewport.getSelectionGroup();
1726
1727     if (sg == null)
1728     {
1729       return;
1730     }
1731     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1732             viewport.getHiddenRepSequences(), up);
1733     alignPanel.paintAlignment(true, false);
1734   }
1735
1736   synchronized void slideSequences(boolean right, int size)
1737   {
1738     List<SequenceI> sg = new ArrayList<>();
1739     if (viewport.cursorMode)
1740     {
1741       sg.add(viewport.getAlignment()
1742               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1743     }
1744     else if (viewport.getSelectionGroup() != null
1745             && viewport.getSelectionGroup().getSize() != viewport
1746                     .getAlignment().getHeight())
1747     {
1748       sg = viewport.getSelectionGroup()
1749               .getSequences(viewport.getHiddenRepSequences());
1750     }
1751
1752     if (sg.size() < 1)
1753     {
1754       return;
1755     }
1756
1757     List<SequenceI> invertGroup = new ArrayList<>();
1758
1759     for (SequenceI seq : viewport.getAlignment().getSequences())
1760     {
1761       if (!sg.contains(seq))
1762       {
1763         invertGroup.add(seq);
1764       }
1765     }
1766
1767     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1768
1769     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1770     for (int i = 0; i < invertGroup.size(); i++)
1771     {
1772       seqs2[i] = invertGroup.get(i);
1773     }
1774
1775     SlideSequencesCommand ssc;
1776     if (right)
1777     {
1778       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1779               viewport.getGapCharacter());
1780     }
1781     else
1782     {
1783       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1784               viewport.getGapCharacter());
1785     }
1786
1787     int groupAdjustment = 0;
1788     if (ssc.getGapsInsertedBegin() && right)
1789     {
1790       if (viewport.cursorMode)
1791       {
1792         alignPanel.getSeqPanel().moveCursor(size, 0);
1793       }
1794       else
1795       {
1796         groupAdjustment = size;
1797       }
1798     }
1799     else if (!ssc.getGapsInsertedBegin() && !right)
1800     {
1801       if (viewport.cursorMode)
1802       {
1803         alignPanel.getSeqPanel().moveCursor(-size, 0);
1804       }
1805       else
1806       {
1807         groupAdjustment = -size;
1808       }
1809     }
1810
1811     if (groupAdjustment != 0)
1812     {
1813       viewport.getSelectionGroup().setStartRes(
1814               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1815       viewport.getSelectionGroup().setEndRes(
1816               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817     }
1818
1819     /*
1820      * just extend the last slide command if compatible; but not if in
1821      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1822      */
1823     boolean appendHistoryItem = false;
1824     Deque<CommandI> historyList = viewport.getHistoryList();
1825     boolean inSplitFrame = getSplitViewContainer() != null;
1826     if (!inSplitFrame && historyList != null && historyList.size() > 0
1827             && historyList.peek() instanceof SlideSequencesCommand)
1828     {
1829       appendHistoryItem = ssc.appendSlideCommand(
1830               (SlideSequencesCommand) historyList.peek());
1831     }
1832
1833     if (!appendHistoryItem)
1834     {
1835       addHistoryItem(ssc);
1836     }
1837
1838     repaint();
1839   }
1840
1841   /**
1842    * DOCUMENT ME!
1843    *
1844    * @param e
1845    *          DOCUMENT ME!
1846    */
1847   @Override
1848   protected void copy_actionPerformed(ActionEvent e)
1849   {
1850     if (viewport.getSelectionGroup() == null)
1851     {
1852       return;
1853     }
1854     // TODO: preserve the ordering of displayed alignment annotation in any
1855     // internal paste (particularly sequence associated annotation)
1856     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1857     String[] omitHidden = null;
1858
1859     if (viewport.hasHiddenColumns())
1860     {
1861       omitHidden = viewport.getViewAsString(true);
1862     }
1863
1864     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1865             seqs, omitHidden, null);
1866
1867     StringSelection ss = new StringSelection(output);
1868
1869     try
1870     {
1871       jalview.gui.Desktop.internalCopy = true;
1872       // Its really worth setting the clipboard contents
1873       // to empty before setting the large StringSelection!!
1874       Toolkit.getDefaultToolkit().getSystemClipboard()
1875               .setContents(new StringSelection(""), null);
1876
1877       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1878               Desktop.instance);
1879     } catch (OutOfMemoryError er)
1880     {
1881       new OOMWarning("copying region", er);
1882       return;
1883     }
1884
1885     HiddenColumns hiddenColumns = null;
1886     if (viewport.hasHiddenColumns())
1887     {
1888       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1889       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1890
1891       // create new HiddenColumns object with copy of hidden regions
1892       // between startRes and endRes, offset by startRes
1893       hiddenColumns = new HiddenColumns(
1894               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1895               hiddenCutoff, hiddenOffset);
1896     }
1897
1898     Desktop.jalviewClipboard = new Object[] { seqs,
1899         viewport.getAlignment().getDataset(), hiddenColumns };
1900     statusBar.setText(MessageManager.formatMessage(
1901             "label.copied_sequences_to_clipboard", new Object[]
1902             { Integer.valueOf(seqs.length).toString() }));
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void pasteNew_actionPerformed(ActionEvent e)
1913   {
1914     paste(true);
1915   }
1916
1917   /**
1918    * DOCUMENT ME!
1919    *
1920    * @param e
1921    *          DOCUMENT ME!
1922    */
1923   @Override
1924   protected void pasteThis_actionPerformed(ActionEvent e)
1925   {
1926     paste(false);
1927   }
1928
1929   /**
1930    * Paste contents of Jalview clipboard
1931    *
1932    * @param newAlignment
1933    *          true to paste to a new alignment, otherwise add to this.
1934    */
1935   void paste(boolean newAlignment)
1936   {
1937     boolean externalPaste = true;
1938     try
1939     {
1940       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1941       Transferable contents = c.getContents(this);
1942
1943       if (contents == null)
1944       {
1945         return;
1946       }
1947
1948       String str;
1949       FileFormatI format;
1950       try
1951       {
1952         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1953         if (str.length() < 1)
1954         {
1955           return;
1956         }
1957
1958         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1959
1960       } catch (OutOfMemoryError er)
1961       {
1962         new OOMWarning("Out of memory pasting sequences!!", er);
1963         return;
1964       }
1965
1966       SequenceI[] sequences;
1967       boolean annotationAdded = false;
1968       AlignmentI alignment = null;
1969
1970       if (Desktop.jalviewClipboard != null)
1971       {
1972         // The clipboard was filled from within Jalview, we must use the
1973         // sequences
1974         // And dataset from the copied alignment
1975         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1976         // be doubly sure that we create *new* sequence objects.
1977         sequences = new SequenceI[newseq.length];
1978         for (int i = 0; i < newseq.length; i++)
1979         {
1980           sequences[i] = new Sequence(newseq[i]);
1981         }
1982         alignment = new Alignment(sequences);
1983         externalPaste = false;
1984       }
1985       else
1986       {
1987         // parse the clipboard as an alignment.
1988         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1989                 format);
1990         sequences = alignment.getSequencesArray();
1991       }
1992
1993       int alwidth = 0;
1994       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1995       int fgroup = -1;
1996
1997       if (newAlignment)
1998       {
1999
2000         if (Desktop.jalviewClipboard != null)
2001         {
2002           // dataset is inherited
2003           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2004         }
2005         else
2006         {
2007           // new dataset is constructed
2008           alignment.setDataset(null);
2009         }
2010         alwidth = alignment.getWidth() + 1;
2011       }
2012       else
2013       {
2014         AlignmentI pastedal = alignment; // preserve pasted alignment object
2015         // Add pasted sequences and dataset into existing alignment.
2016         alignment = viewport.getAlignment();
2017         alwidth = alignment.getWidth() + 1;
2018         // decide if we need to import sequences from an existing dataset
2019         boolean importDs = Desktop.jalviewClipboard != null
2020                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2021         // importDs==true instructs us to copy over new dataset sequences from
2022         // an existing alignment
2023         Vector newDs = (importDs) ? new Vector() : null; // used to create
2024         // minimum dataset set
2025
2026         for (int i = 0; i < sequences.length; i++)
2027         {
2028           if (importDs)
2029           {
2030             newDs.addElement(null);
2031           }
2032           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2033           // paste
2034           if (importDs && ds != null)
2035           {
2036             if (!newDs.contains(ds))
2037             {
2038               newDs.setElementAt(ds, i);
2039               ds = new Sequence(ds);
2040               // update with new dataset sequence
2041               sequences[i].setDatasetSequence(ds);
2042             }
2043             else
2044             {
2045               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2046             }
2047           }
2048           else
2049           {
2050             // copy and derive new dataset sequence
2051             sequences[i] = sequences[i].deriveSequence();
2052             alignment.getDataset()
2053                     .addSequence(sequences[i].getDatasetSequence());
2054             // TODO: avoid creation of duplicate dataset sequences with a
2055             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2056           }
2057           alignment.addSequence(sequences[i]); // merges dataset
2058         }
2059         if (newDs != null)
2060         {
2061           newDs.clear(); // tidy up
2062         }
2063         if (alignment.getAlignmentAnnotation() != null)
2064         {
2065           for (AlignmentAnnotation alan : alignment
2066                   .getAlignmentAnnotation())
2067           {
2068             if (alan.graphGroup > fgroup)
2069             {
2070               fgroup = alan.graphGroup;
2071             }
2072           }
2073         }
2074         if (pastedal.getAlignmentAnnotation() != null)
2075         {
2076           // Add any annotation attached to alignment.
2077           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2078           for (int i = 0; i < alann.length; i++)
2079           {
2080             annotationAdded = true;
2081             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2082             {
2083               AlignmentAnnotation newann = new AlignmentAnnotation(
2084                       alann[i]);
2085               if (newann.graphGroup > -1)
2086               {
2087                 if (newGraphGroups.size() <= newann.graphGroup
2088                         || newGraphGroups.get(newann.graphGroup) == null)
2089                 {
2090                   for (int q = newGraphGroups
2091                           .size(); q <= newann.graphGroup; q++)
2092                   {
2093                     newGraphGroups.add(q, null);
2094                   }
2095                   newGraphGroups.set(newann.graphGroup,
2096                           Integer.valueOf(++fgroup));
2097                 }
2098                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2099                         .intValue();
2100               }
2101
2102               newann.padAnnotation(alwidth);
2103               alignment.addAnnotation(newann);
2104             }
2105           }
2106         }
2107       }
2108       if (!newAlignment)
2109       {
2110         // /////
2111         // ADD HISTORY ITEM
2112         //
2113         addHistoryItem(new EditCommand(
2114                 MessageManager.getString("label.add_sequences"),
2115                 Action.PASTE, sequences, 0, alignment.getWidth(),
2116                 alignment));
2117       }
2118       // Add any annotations attached to sequences
2119       for (int i = 0; i < sequences.length; i++)
2120       {
2121         if (sequences[i].getAnnotation() != null)
2122         {
2123           AlignmentAnnotation newann;
2124           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125           {
2126             annotationAdded = true;
2127             newann = sequences[i].getAnnotation()[a];
2128             newann.adjustForAlignment();
2129             newann.padAnnotation(alwidth);
2130             if (newann.graphGroup > -1)
2131             {
2132               if (newann.graphGroup > -1)
2133               {
2134                 if (newGraphGroups.size() <= newann.graphGroup
2135                         || newGraphGroups.get(newann.graphGroup) == null)
2136                 {
2137                   for (int q = newGraphGroups
2138                           .size(); q <= newann.graphGroup; q++)
2139                   {
2140                     newGraphGroups.add(q, null);
2141                   }
2142                   newGraphGroups.set(newann.graphGroup,
2143                           Integer.valueOf(++fgroup));
2144                 }
2145                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2146                         .intValue();
2147               }
2148             }
2149             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2150             // was
2151             // duplicated
2152             // earlier
2153             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2154                     a);
2155           }
2156         }
2157       }
2158       if (!newAlignment)
2159       {
2160
2161         // propagate alignment changed.
2162         viewport.getRanges().setEndSeq(alignment.getHeight());
2163         if (annotationAdded)
2164         {
2165           // Duplicate sequence annotation in all views.
2166           AlignmentI[] alview = this.getViewAlignments();
2167           for (int i = 0; i < sequences.length; i++)
2168           {
2169             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2170             if (sann == null)
2171             {
2172               continue;
2173             }
2174             for (int avnum = 0; avnum < alview.length; avnum++)
2175             {
2176               if (alview[avnum] != alignment)
2177               {
2178                 // duplicate in a view other than the one with input focus
2179                 int avwidth = alview[avnum].getWidth() + 1;
2180                 // this relies on sann being preserved after we
2181                 // modify the sequence's annotation array for each duplication
2182                 for (int a = 0; a < sann.length; a++)
2183                 {
2184                   AlignmentAnnotation newann = new AlignmentAnnotation(
2185                           sann[a]);
2186                   sequences[i].addAlignmentAnnotation(newann);
2187                   newann.padAnnotation(avwidth);
2188                   alview[avnum].addAnnotation(newann); // annotation was
2189                   // duplicated earlier
2190                   // TODO JAL-1145 graphGroups are not updated for sequence
2191                   // annotation added to several views. This may cause
2192                   // strangeness
2193                   alview[avnum].setAnnotationIndex(newann, a);
2194                 }
2195               }
2196             }
2197           }
2198           buildSortByAnnotationScoresMenu();
2199         }
2200         viewport.firePropertyChange("alignment", null,
2201                 alignment.getSequences());
2202         if (alignPanels != null)
2203         {
2204           for (AlignmentPanel ap : alignPanels)
2205           {
2206             ap.validateAnnotationDimensions(false);
2207           }
2208         }
2209         else
2210         {
2211           alignPanel.validateAnnotationDimensions(false);
2212         }
2213
2214       }
2215       else
2216       {
2217         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2218                 DEFAULT_HEIGHT);
2219         String newtitle = new String("Copied sequences");
2220
2221         if (Desktop.jalviewClipboard != null
2222                 && Desktop.jalviewClipboard[2] != null)
2223         {
2224           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2225           af.viewport.setHiddenColumns(hc);
2226         }
2227
2228         // >>>This is a fix for the moment, until a better solution is
2229         // found!!<<<
2230         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2231                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2232                         .getFeatureRenderer());
2233
2234         // TODO: maintain provenance of an alignment, rather than just make the
2235         // title a concatenation of operations.
2236         if (!externalPaste)
2237         {
2238           if (title.startsWith("Copied sequences"))
2239           {
2240             newtitle = title;
2241           }
2242           else
2243           {
2244             newtitle = newtitle.concat("- from " + title);
2245           }
2246         }
2247         else
2248         {
2249           newtitle = new String("Pasted sequences");
2250         }
2251
2252         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2253                 DEFAULT_HEIGHT);
2254
2255       }
2256
2257     } catch (Exception ex)
2258     {
2259       ex.printStackTrace();
2260       System.out.println("Exception whilst pasting: " + ex);
2261       // could be anything being pasted in here
2262     }
2263
2264   }
2265
2266   @Override
2267   protected void expand_newalign(ActionEvent e)
2268   {
2269     try
2270     {
2271       AlignmentI alignment = AlignmentUtils
2272               .expandContext(getViewport().getAlignment(), -1);
2273       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2274               DEFAULT_HEIGHT);
2275       String newtitle = new String("Flanking alignment");
2276
2277       if (Desktop.jalviewClipboard != null
2278               && Desktop.jalviewClipboard[2] != null)
2279       {
2280         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2281         af.viewport.setHiddenColumns(hc);
2282       }
2283
2284       // >>>This is a fix for the moment, until a better solution is
2285       // found!!<<<
2286       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2287               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2288                       .getFeatureRenderer());
2289
2290       // TODO: maintain provenance of an alignment, rather than just make the
2291       // title a concatenation of operations.
2292       {
2293         if (title.startsWith("Copied sequences"))
2294         {
2295           newtitle = title;
2296         }
2297         else
2298         {
2299           newtitle = newtitle.concat("- from " + title);
2300         }
2301       }
2302
2303       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2304
2305     } catch (Exception ex)
2306     {
2307       ex.printStackTrace();
2308       System.out.println("Exception whilst pasting: " + ex);
2309       // could be anything being pasted in here
2310     } catch (OutOfMemoryError oom)
2311     {
2312       new OOMWarning("Viewing flanking region of alignment", oom);
2313     }
2314   }
2315
2316   /**
2317    * DOCUMENT ME!
2318    *
2319    * @param e
2320    *          DOCUMENT ME!
2321    */
2322   @Override
2323   protected void cut_actionPerformed(ActionEvent e)
2324   {
2325     copy_actionPerformed(null);
2326     delete_actionPerformed(null);
2327   }
2328
2329   /**
2330    * DOCUMENT ME!
2331    *
2332    * @param e
2333    *          DOCUMENT ME!
2334    */
2335   @Override
2336   protected void delete_actionPerformed(ActionEvent evt)
2337   {
2338
2339     SequenceGroup sg = viewport.getSelectionGroup();
2340     if (sg == null)
2341     {
2342       return;
2343     }
2344
2345     /*
2346      * If the cut affects all sequences, warn, remove highlighted columns
2347      */
2348     if (sg.getSize() == viewport.getAlignment().getHeight())
2349     {
2350       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2351               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2352       if (isEntireAlignWidth)
2353       {
2354         int confirm = JvOptionPane.showConfirmDialog(this,
2355                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2356                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2357                 JvOptionPane.OK_CANCEL_OPTION);
2358
2359         if (confirm == JvOptionPane.CANCEL_OPTION
2360                 || confirm == JvOptionPane.CLOSED_OPTION)
2361         {
2362           return;
2363         }
2364       }
2365       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2366               sg.getEndRes() + 1);
2367     }
2368     SequenceI[] cut = sg.getSequences()
2369             .toArray(new SequenceI[sg.getSize()]);
2370
2371     addHistoryItem(new EditCommand(
2372             MessageManager.getString("label.cut_sequences"), Action.CUT,
2373             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2374             viewport.getAlignment()));
2375
2376     viewport.setSelectionGroup(null);
2377     viewport.sendSelection();
2378     viewport.getAlignment().deleteGroup(sg);
2379
2380     viewport.firePropertyChange("alignment", null,
2381             viewport.getAlignment().getSequences());
2382     if (viewport.getAlignment().getHeight() < 1)
2383     {
2384       try
2385       {
2386         this.setClosed(true);
2387       } catch (Exception ex)
2388       {
2389       }
2390     }
2391   }
2392
2393   /**
2394    * DOCUMENT ME!
2395    *
2396    * @param e
2397    *          DOCUMENT ME!
2398    */
2399   @Override
2400   protected void deleteGroups_actionPerformed(ActionEvent e)
2401   {
2402     if (avc.deleteGroups())
2403     {
2404       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2405       alignPanel.updateAnnotation();
2406       alignPanel.paintAlignment(true, true);
2407     }
2408   }
2409
2410   /**
2411    * DOCUMENT ME!
2412    *
2413    * @param e
2414    *          DOCUMENT ME!
2415    */
2416   @Override
2417   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2418   {
2419     SequenceGroup sg = new SequenceGroup(
2420             viewport.getAlignment().getSequences());
2421
2422     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2423     viewport.setSelectionGroup(sg);
2424     viewport.isSelectionGroupChanged(true);
2425     viewport.sendSelection();
2426     // JAL-2034 - should delegate to
2427     // alignPanel to decide if overview needs
2428     // updating.
2429     alignPanel.paintAlignment(false, false);
2430     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2431   }
2432
2433   /**
2434    * DOCUMENT ME!
2435    *
2436    * @param e
2437    *          DOCUMENT ME!
2438    */
2439   @Override
2440   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441   {
2442     if (viewport.cursorMode)
2443     {
2444       alignPanel.getSeqPanel().keyboardNo1 = null;
2445       alignPanel.getSeqPanel().keyboardNo2 = null;
2446     }
2447     viewport.setSelectionGroup(null);
2448     viewport.getColumnSelection().clear();
2449     viewport.setSelectionGroup(null);
2450     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2451     // JAL-2034 - should delegate to
2452     // alignPanel to decide if overview needs
2453     // updating.
2454     alignPanel.paintAlignment(false, false);
2455     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2456     viewport.sendSelection();
2457   }
2458
2459   /**
2460    * DOCUMENT ME!
2461    *
2462    * @param e
2463    *          DOCUMENT ME!
2464    */
2465   @Override
2466   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2467   {
2468     SequenceGroup sg = viewport.getSelectionGroup();
2469
2470     if (sg == null)
2471     {
2472       selectAllSequenceMenuItem_actionPerformed(null);
2473
2474       return;
2475     }
2476
2477     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2478     {
2479       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2480     }
2481     // JAL-2034 - should delegate to
2482     // alignPanel to decide if overview needs
2483     // updating.
2484
2485     alignPanel.paintAlignment(true, false);
2486     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2487     viewport.sendSelection();
2488   }
2489
2490   @Override
2491   public void invertColSel_actionPerformed(ActionEvent e)
2492   {
2493     viewport.invertColumnSelection();
2494     alignPanel.paintAlignment(true, false);
2495     viewport.sendSelection();
2496   }
2497
2498   /**
2499    * DOCUMENT ME!
2500    *
2501    * @param e
2502    *          DOCUMENT ME!
2503    */
2504   @Override
2505   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506   {
2507     trimAlignment(true);
2508   }
2509
2510   /**
2511    * DOCUMENT ME!
2512    *
2513    * @param e
2514    *          DOCUMENT ME!
2515    */
2516   @Override
2517   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518   {
2519     trimAlignment(false);
2520   }
2521
2522   void trimAlignment(boolean trimLeft)
2523   {
2524     ColumnSelection colSel = viewport.getColumnSelection();
2525     int column;
2526
2527     if (!colSel.isEmpty())
2528     {
2529       if (trimLeft)
2530       {
2531         column = colSel.getMin();
2532       }
2533       else
2534       {
2535         column = colSel.getMax();
2536       }
2537
2538       SequenceI[] seqs;
2539       if (viewport.getSelectionGroup() != null)
2540       {
2541         seqs = viewport.getSelectionGroup()
2542                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2543       }
2544       else
2545       {
2546         seqs = viewport.getAlignment().getSequencesArray();
2547       }
2548
2549       TrimRegionCommand trimRegion;
2550       if (trimLeft)
2551       {
2552         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2553                 column, viewport.getAlignment());
2554         viewport.getRanges().setStartRes(0);
2555       }
2556       else
2557       {
2558         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2559                 column, viewport.getAlignment());
2560       }
2561
2562       statusBar.setText(MessageManager
2563               .formatMessage("label.removed_columns", new String[]
2564               { Integer.valueOf(trimRegion.getSize()).toString() }));
2565
2566       addHistoryItem(trimRegion);
2567
2568       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2569       {
2570         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2571                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2572         {
2573           viewport.getAlignment().deleteGroup(sg);
2574         }
2575       }
2576
2577       viewport.firePropertyChange("alignment", null,
2578               viewport.getAlignment().getSequences());
2579     }
2580   }
2581
2582   /**
2583    * DOCUMENT ME!
2584    *
2585    * @param e
2586    *          DOCUMENT ME!
2587    */
2588   @Override
2589   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2590   {
2591     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2592
2593     SequenceI[] seqs;
2594     if (viewport.getSelectionGroup() != null)
2595     {
2596       seqs = viewport.getSelectionGroup()
2597               .getSequencesAsArray(viewport.getHiddenRepSequences());
2598       start = viewport.getSelectionGroup().getStartRes();
2599       end = viewport.getSelectionGroup().getEndRes();
2600     }
2601     else
2602     {
2603       seqs = viewport.getAlignment().getSequencesArray();
2604     }
2605
2606     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2607             "Remove Gapped Columns", seqs, start, end,
2608             viewport.getAlignment());
2609
2610     addHistoryItem(removeGapCols);
2611
2612     statusBar.setText(MessageManager
2613             .formatMessage("label.removed_empty_columns", new Object[]
2614             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2615
2616     // This is to maintain viewport position on first residue
2617     // of first sequence
2618     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2619     ViewportRanges ranges = viewport.getRanges();
2620     int startRes = seq.findPosition(ranges.getStartRes());
2621     // ShiftList shifts;
2622     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2623     // edit.alColumnChanges=shifts.getInverse();
2624     // if (viewport.hasHiddenColumns)
2625     // viewport.getColumnSelection().compensateForEdits(shifts);
2626     ranges.setStartRes(seq.findIndex(startRes) - 1);
2627     viewport.firePropertyChange("alignment", null,
2628             viewport.getAlignment().getSequences());
2629
2630   }
2631
2632   /**
2633    * DOCUMENT ME!
2634    *
2635    * @param e
2636    *          DOCUMENT ME!
2637    */
2638   @Override
2639   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2640   {
2641     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2642
2643     SequenceI[] seqs;
2644     if (viewport.getSelectionGroup() != null)
2645     {
2646       seqs = viewport.getSelectionGroup()
2647               .getSequencesAsArray(viewport.getHiddenRepSequences());
2648       start = viewport.getSelectionGroup().getStartRes();
2649       end = viewport.getSelectionGroup().getEndRes();
2650     }
2651     else
2652     {
2653       seqs = viewport.getAlignment().getSequencesArray();
2654     }
2655
2656     // This is to maintain viewport position on first residue
2657     // of first sequence
2658     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2659     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2660
2661     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2662             viewport.getAlignment()));
2663
2664     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2665
2666     viewport.firePropertyChange("alignment", null,
2667             viewport.getAlignment().getSequences());
2668
2669   }
2670
2671   /**
2672    * DOCUMENT ME!
2673    *
2674    * @param e
2675    *          DOCUMENT ME!
2676    */
2677   @Override
2678   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2679   {
2680     viewport.setPadGaps(padGapsMenuitem.isSelected());
2681     viewport.firePropertyChange("alignment", null,
2682             viewport.getAlignment().getSequences());
2683   }
2684
2685   /**
2686    * Opens a Finder dialog
2687    *
2688    * @param e
2689    */
2690   @Override
2691   public void findMenuItem_actionPerformed(ActionEvent e)
2692   {
2693     new Finder(alignPanel);
2694   }
2695
2696   /**
2697    * Create a new view of the current alignment.
2698    */
2699   @Override
2700   public void newView_actionPerformed(ActionEvent e)
2701   {
2702     newView(null, true);
2703   }
2704
2705   /**
2706    * Creates and shows a new view of the current alignment.
2707    *
2708    * @param viewTitle
2709    *          title of newly created view; if null, one will be generated
2710    * @param copyAnnotation
2711    *          if true then duplicate all annnotation, groups and settings
2712    * @return new alignment panel, already displayed.
2713    */
2714   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2715   {
2716     /*
2717      * Create a new AlignmentPanel (with its own, new Viewport)
2718      */
2719     AlignmentPanel newap = new jalview.project.Jalview2XML()
2720             .copyAlignPanel(alignPanel);
2721     if (!copyAnnotation)
2722     {
2723       /*
2724        * remove all groups and annotation except for the automatic stuff
2725        */
2726       newap.av.getAlignment().deleteAllGroups();
2727       newap.av.getAlignment().deleteAllAnnotations(false);
2728     }
2729
2730     newap.av.setGatherViewsHere(false);
2731
2732     if (viewport.getViewName() == null)
2733     {
2734       viewport.setViewName(MessageManager
2735               .getString("label.view_name_original"));
2736     }
2737
2738     /*
2739      * Views share the same edits undo and redo stacks
2740      */
2741     newap.av.setHistoryList(viewport.getHistoryList());
2742     newap.av.setRedoList(viewport.getRedoList());
2743
2744     /*
2745      * copy any visualisation settings that are not saved in the project
2746      */
2747     newap.av.setColourAppliesToAllGroups(
2748             viewport.getColourAppliesToAllGroups());
2749
2750     /*
2751      * Views share the same mappings; need to deregister any new mappings
2752      * created by copyAlignPanel, and register the new reference to the shared
2753      * mappings
2754      */
2755     newap.av.replaceMappings(viewport.getAlignment());
2756
2757     /*
2758      * start up cDNA consensus (if applicable) now mappings are in place
2759      */
2760     if (newap.av.initComplementConsensus())
2761     {
2762       newap.refresh(true); // adjust layout of annotations
2763     }
2764
2765     newap.av.setViewName(getNewViewName(viewTitle));
2766
2767     addAlignmentPanel(newap, true);
2768     newap.alignmentChanged();
2769
2770     if (alignPanels.size() == 2)
2771     {
2772       viewport.setGatherViewsHere(true);
2773     }
2774     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2775     return newap;
2776   }
2777
2778   /**
2779    * Make a new name for the view, ensuring it is unique within the current
2780    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2781    * these now use viewId. Unique view names are still desirable for usability.)
2782    *
2783    * @param viewTitle
2784    * @return
2785    */
2786   protected String getNewViewName(String viewTitle)
2787   {
2788     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2789     boolean addFirstIndex = false;
2790     if (viewTitle == null || viewTitle.trim().length() == 0)
2791     {
2792       viewTitle = MessageManager.getString("action.view");
2793       addFirstIndex = true;
2794     }
2795     else
2796     {
2797       index = 1;// we count from 1 if given a specific name
2798     }
2799     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2800
2801     List<Component> comps = PaintRefresher.components
2802             .get(viewport.getSequenceSetId());
2803
2804     List<String> existingNames = getExistingViewNames(comps);
2805
2806     while (existingNames.contains(newViewName))
2807     {
2808       newViewName = viewTitle + " " + (++index);
2809     }
2810     return newViewName;
2811   }
2812
2813   /**
2814    * Returns a list of distinct view names found in the given list of
2815    * components. View names are held on the viewport of an AlignmentPanel.
2816    *
2817    * @param comps
2818    * @return
2819    */
2820   protected List<String> getExistingViewNames(List<Component> comps)
2821   {
2822     List<String> existingNames = new ArrayList<>();
2823     for (Component comp : comps)
2824     {
2825       if (comp instanceof AlignmentPanel)
2826       {
2827         AlignmentPanel ap = (AlignmentPanel) comp;
2828         if (!existingNames.contains(ap.av.getViewName()))
2829         {
2830           existingNames.add(ap.av.getViewName());
2831         }
2832       }
2833     }
2834     return existingNames;
2835   }
2836
2837   /**
2838    * Explode tabbed views into separate windows.
2839    */
2840   @Override
2841   public void expandViews_actionPerformed(ActionEvent e)
2842   {
2843     Desktop.explodeViews(this);
2844   }
2845
2846   /**
2847    * Gather views in separate windows back into a tabbed presentation.
2848    */
2849   @Override
2850   public void gatherViews_actionPerformed(ActionEvent e)
2851   {
2852     Desktop.instance.gatherViews(this);
2853   }
2854
2855   /**
2856    * DOCUMENT ME!
2857    *
2858    * @param e
2859    *          DOCUMENT ME!
2860    */
2861   @Override
2862   public void font_actionPerformed(ActionEvent e)
2863   {
2864     new FontChooser(alignPanel);
2865   }
2866
2867   /**
2868    * DOCUMENT ME!
2869    *
2870    * @param e
2871    *          DOCUMENT ME!
2872    */
2873   @Override
2874   protected void seqLimit_actionPerformed(ActionEvent e)
2875   {
2876     viewport.setShowJVSuffix(seqLimits.isSelected());
2877
2878     alignPanel.getIdPanel().getIdCanvas()
2879             .setPreferredSize(alignPanel.calculateIdWidth());
2880     alignPanel.paintAlignment(true, false);
2881   }
2882
2883   @Override
2884   public void idRightAlign_actionPerformed(ActionEvent e)
2885   {
2886     viewport.setRightAlignIds(idRightAlign.isSelected());
2887     alignPanel.paintAlignment(false, false);
2888   }
2889
2890   @Override
2891   public void centreColumnLabels_actionPerformed(ActionEvent e)
2892   {
2893     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2894     alignPanel.paintAlignment(false, false);
2895   }
2896
2897   /*
2898    * (non-Javadoc)
2899    *
2900    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2901    */
2902   @Override
2903   protected void followHighlight_actionPerformed()
2904   {
2905     /*
2906      * Set the 'follow' flag on the Viewport (and scroll to position if now
2907      * true).
2908      */
2909     final boolean state = this.followHighlightMenuItem.getState();
2910     viewport.setFollowHighlight(state);
2911     if (state)
2912     {
2913       alignPanel.scrollToPosition(viewport.getSearchResults());
2914     }
2915   }
2916
2917   /**
2918    * DOCUMENT ME!
2919    *
2920    * @param e
2921    *          DOCUMENT ME!
2922    */
2923   @Override
2924   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2925   {
2926     viewport.setColourText(colourTextMenuItem.isSelected());
2927     alignPanel.paintAlignment(false, false);
2928   }
2929
2930   /**
2931    * DOCUMENT ME!
2932    *
2933    * @param e
2934    *          DOCUMENT ME!
2935    */
2936   @Override
2937   public void wrapMenuItem_actionPerformed(ActionEvent e)
2938   {
2939     scaleAbove.setVisible(wrapMenuItem.isSelected());
2940     scaleLeft.setVisible(wrapMenuItem.isSelected());
2941     scaleRight.setVisible(wrapMenuItem.isSelected());
2942     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2943     alignPanel.updateLayout();
2944   }
2945
2946   @Override
2947   public void showAllSeqs_actionPerformed(ActionEvent e)
2948   {
2949     viewport.showAllHiddenSeqs();
2950   }
2951
2952   @Override
2953   public void showAllColumns_actionPerformed(ActionEvent e)
2954   {
2955     viewport.showAllHiddenColumns();
2956     alignPanel.paintAlignment(true, true);
2957     viewport.sendSelection();
2958   }
2959
2960   @Override
2961   public void hideSelSequences_actionPerformed(ActionEvent e)
2962   {
2963     viewport.hideAllSelectedSeqs();
2964   }
2965
2966   /**
2967    * called by key handler and the hide all/show all menu items
2968    *
2969    * @param toggleSeqs
2970    * @param toggleCols
2971    */
2972   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2973   {
2974
2975     boolean hide = false;
2976     SequenceGroup sg = viewport.getSelectionGroup();
2977     if (!toggleSeqs && !toggleCols)
2978     {
2979       // Hide everything by the current selection - this is a hack - we do the
2980       // invert and then hide
2981       // first check that there will be visible columns after the invert.
2982       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2983               && sg.getStartRes() <= sg.getEndRes()))
2984       {
2985         // now invert the sequence set, if required - empty selection implies
2986         // that no hiding is required.
2987         if (sg != null)
2988         {
2989           invertSequenceMenuItem_actionPerformed(null);
2990           sg = viewport.getSelectionGroup();
2991           toggleSeqs = true;
2992
2993         }
2994         viewport.expandColSelection(sg, true);
2995         // finally invert the column selection and get the new sequence
2996         // selection.
2997         invertColSel_actionPerformed(null);
2998         toggleCols = true;
2999       }
3000     }
3001
3002     if (toggleSeqs)
3003     {
3004       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3005       {
3006         hideSelSequences_actionPerformed(null);
3007         hide = true;
3008       }
3009       else if (!(toggleCols && viewport.hasSelectedColumns()))
3010       {
3011         showAllSeqs_actionPerformed(null);
3012       }
3013     }
3014
3015     if (toggleCols)
3016     {
3017       if (viewport.hasSelectedColumns())
3018       {
3019         hideSelColumns_actionPerformed(null);
3020         if (!toggleSeqs)
3021         {
3022           viewport.setSelectionGroup(sg);
3023         }
3024       }
3025       else if (!hide)
3026       {
3027         showAllColumns_actionPerformed(null);
3028       }
3029     }
3030   }
3031
3032   /*
3033    * (non-Javadoc)
3034    *
3035    * @see
3036    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3037    * event.ActionEvent)
3038    */
3039   @Override
3040   public void hideAllButSelection_actionPerformed(ActionEvent e)
3041   {
3042     toggleHiddenRegions(false, false);
3043     viewport.sendSelection();
3044   }
3045
3046   /*
3047    * (non-Javadoc)
3048    *
3049    * @see
3050    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3051    * .ActionEvent)
3052    */
3053   @Override
3054   public void hideAllSelection_actionPerformed(ActionEvent e)
3055   {
3056     SequenceGroup sg = viewport.getSelectionGroup();
3057     viewport.expandColSelection(sg, false);
3058     viewport.hideAllSelectedSeqs();
3059     viewport.hideSelectedColumns();
3060     alignPanel.updateLayout();
3061     alignPanel.paintAlignment(true, true);
3062     viewport.sendSelection();
3063   }
3064
3065   /*
3066    * (non-Javadoc)
3067    *
3068    * @see
3069    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3070    * ActionEvent)
3071    */
3072   @Override
3073   public void showAllhidden_actionPerformed(ActionEvent e)
3074   {
3075     viewport.showAllHiddenColumns();
3076     viewport.showAllHiddenSeqs();
3077     alignPanel.paintAlignment(true, true);
3078     viewport.sendSelection();
3079   }
3080
3081   @Override
3082   public void hideSelColumns_actionPerformed(ActionEvent e)
3083   {
3084     viewport.hideSelectedColumns();
3085     alignPanel.updateLayout();
3086     alignPanel.paintAlignment(true, true);
3087     viewport.sendSelection();
3088   }
3089
3090   @Override
3091   public void hiddenMarkers_actionPerformed(ActionEvent e)
3092   {
3093     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3094     repaint();
3095   }
3096
3097   /**
3098    * DOCUMENT ME!
3099    *
3100    * @param e
3101    *          DOCUMENT ME!
3102    */
3103   @Override
3104   protected void scaleAbove_actionPerformed(ActionEvent e)
3105   {
3106     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3107     alignPanel.updateLayout();
3108     alignPanel.paintAlignment(true, false);
3109   }
3110
3111   /**
3112    * DOCUMENT ME!
3113    *
3114    * @param e
3115    *          DOCUMENT ME!
3116    */
3117   @Override
3118   protected void scaleLeft_actionPerformed(ActionEvent e)
3119   {
3120     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3121     alignPanel.updateLayout();
3122     alignPanel.paintAlignment(true, false);
3123   }
3124
3125   /**
3126    * DOCUMENT ME!
3127    *
3128    * @param e
3129    *          DOCUMENT ME!
3130    */
3131   @Override
3132   protected void scaleRight_actionPerformed(ActionEvent e)
3133   {
3134     viewport.setScaleRightWrapped(scaleRight.isSelected());
3135     alignPanel.updateLayout();
3136     alignPanel.paintAlignment(true, false);
3137   }
3138
3139   /**
3140    * DOCUMENT ME!
3141    *
3142    * @param e
3143    *          DOCUMENT ME!
3144    */
3145   @Override
3146   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3147   {
3148     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3149     alignPanel.paintAlignment(false, false);
3150   }
3151
3152   /**
3153    * DOCUMENT ME!
3154    *
3155    * @param e
3156    *          DOCUMENT ME!
3157    */
3158   @Override
3159   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3160   {
3161     viewport.setShowText(viewTextMenuItem.isSelected());
3162     alignPanel.paintAlignment(false, false);
3163   }
3164
3165   /**
3166    * DOCUMENT ME!
3167    *
3168    * @param e
3169    *          DOCUMENT ME!
3170    */
3171   @Override
3172   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3173   {
3174     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3175     alignPanel.paintAlignment(false, false);
3176   }
3177
3178   public FeatureSettings featureSettings;
3179
3180   @Override
3181   public FeatureSettingsControllerI getFeatureSettingsUI()
3182   {
3183     return featureSettings;
3184   }
3185
3186   @Override
3187   public void featureSettings_actionPerformed(ActionEvent e)
3188   {
3189     if (featureSettings != null)
3190     {
3191       featureSettings.close();
3192       featureSettings = null;
3193     }
3194     if (!showSeqFeatures.isSelected())
3195     {
3196       // make sure features are actually displayed
3197       showSeqFeatures.setSelected(true);
3198       showSeqFeatures_actionPerformed(null);
3199     }
3200     featureSettings = new FeatureSettings(this);
3201   }
3202
3203   /**
3204    * Set or clear 'Show Sequence Features'
3205    *
3206    * @param evt
3207    *          DOCUMENT ME!
3208    */
3209   @Override
3210   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3211   {
3212     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3213     alignPanel.paintAlignment(true, true);
3214   }
3215
3216   /**
3217    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3218    * the annotations panel as a whole.
3219    *
3220    * The options to show/hide all annotations should be enabled when the panel
3221    * is shown, and disabled when the panel is hidden.
3222    *
3223    * @param e
3224    */
3225   @Override
3226   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3227   {
3228     final boolean setVisible = annotationPanelMenuItem.isSelected();
3229     viewport.setShowAnnotation(setVisible);
3230     this.showAllSeqAnnotations.setEnabled(setVisible);
3231     this.hideAllSeqAnnotations.setEnabled(setVisible);
3232     this.showAllAlAnnotations.setEnabled(setVisible);
3233     this.hideAllAlAnnotations.setEnabled(setVisible);
3234     alignPanel.updateLayout();
3235   }
3236
3237   @Override
3238   public void alignmentProperties()
3239   {
3240     JEditorPane editPane = new JEditorPane("text/html", "");
3241     editPane.setEditable(false);
3242     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3243             .formatAsHtml();
3244     editPane.setText(
3245             MessageManager.formatMessage("label.html_content", new Object[]
3246             { contents.toString() }));
3247     JInternalFrame frame = new JInternalFrame();
3248     frame.getContentPane().add(new JScrollPane(editPane));
3249
3250     Desktop.addInternalFrame(frame, MessageManager
3251             .formatMessage("label.alignment_properties", new Object[]
3252             { getTitle() }), 500, 400);
3253   }
3254
3255   /**
3256    * DOCUMENT ME!
3257    *
3258    * @param e
3259    *          DOCUMENT ME!
3260    */
3261   @Override
3262   public void overviewMenuItem_actionPerformed(ActionEvent e)
3263   {
3264     if (alignPanel.overviewPanel != null)
3265     {
3266       return;
3267     }
3268
3269     JInternalFrame frame = new JInternalFrame();
3270     final OverviewPanel overview = new OverviewPanel(alignPanel);
3271     frame.setContentPane(overview);
3272     Desktop.addInternalFrame(frame, MessageManager
3273             .formatMessage("label.overview_params", new Object[]
3274             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3275             true, true);
3276     frame.pack();
3277     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3278     frame.addInternalFrameListener(
3279             new javax.swing.event.InternalFrameAdapter()
3280             {
3281               @Override
3282               public void internalFrameClosed(
3283                       javax.swing.event.InternalFrameEvent evt)
3284               {
3285                 overview.dispose();
3286                 alignPanel.setOverviewPanel(null);
3287               };
3288             });
3289     if (getKeyListeners().length > 0)
3290     {
3291       frame.addKeyListener(getKeyListeners()[0]);
3292     }
3293
3294     alignPanel.setOverviewPanel(overview);
3295   }
3296
3297   @Override
3298   public void textColour_actionPerformed()
3299   {
3300     new TextColourChooser().chooseColour(alignPanel, null);
3301   }
3302
3303   /*
3304    * public void covariationColour_actionPerformed() {
3305    * changeColour(new
3306    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3307    * ()[0])); }
3308    */
3309   @Override
3310   public void annotationColour_actionPerformed()
3311   {
3312     new AnnotationColourChooser(viewport, alignPanel);
3313   }
3314
3315   @Override
3316   public void annotationColumn_actionPerformed(ActionEvent e)
3317   {
3318     new AnnotationColumnChooser(viewport, alignPanel);
3319   }
3320
3321   /**
3322    * Action on the user checking or unchecking the option to apply the selected
3323    * colour scheme to all groups. If unchecked, groups may have their own
3324    * independent colour schemes.
3325    *
3326    * @param selected
3327    */
3328   @Override
3329   public void applyToAllGroups_actionPerformed(boolean selected)
3330   {
3331     viewport.setColourAppliesToAllGroups(selected);
3332   }
3333
3334   /**
3335    * Action on user selecting a colour from the colour menu
3336    *
3337    * @param name
3338    *          the name (not the menu item label!) of the colour scheme
3339    */
3340   @Override
3341   public void changeColour_actionPerformed(String name)
3342   {
3343     /*
3344      * 'User Defined' opens a panel to configure or load a
3345      * user-defined colour scheme
3346      */
3347     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3348     {
3349       new UserDefinedColours(alignPanel);
3350       return;
3351     }
3352
3353     /*
3354      * otherwise set the chosen colour scheme (or null for 'None')
3355      */
3356     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3357             viewport,
3358             viewport.getAlignment(), viewport.getHiddenRepSequences());
3359     changeColour(cs);
3360   }
3361
3362   /**
3363    * Actions on setting or changing the alignment colour scheme
3364    *
3365    * @param cs
3366    */
3367   @Override
3368   public void changeColour(ColourSchemeI cs)
3369   {
3370     // TODO: pull up to controller method
3371     ColourMenuHelper.setColourSelected(colourMenu, cs);
3372
3373     viewport.setGlobalColourScheme(cs);
3374
3375     alignPanel.paintAlignment(true, true);
3376   }
3377
3378   /**
3379    * Show the PID threshold slider panel
3380    */
3381   @Override
3382   protected void modifyPID_actionPerformed()
3383   {
3384     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3385             alignPanel.getViewName());
3386     SliderPanel.showPIDSlider();
3387   }
3388
3389   /**
3390    * Show the Conservation slider panel
3391    */
3392   @Override
3393   protected void modifyConservation_actionPerformed()
3394   {
3395     SliderPanel.setConservationSlider(alignPanel,
3396             viewport.getResidueShading(), alignPanel.getViewName());
3397     SliderPanel.showConservationSlider();
3398   }
3399
3400   /**
3401    * Action on selecting or deselecting (Colour) By Conservation
3402    */
3403   @Override
3404   public void conservationMenuItem_actionPerformed(boolean selected)
3405   {
3406     modifyConservation.setEnabled(selected);
3407     viewport.setConservationSelected(selected);
3408     viewport.getResidueShading().setConservationApplied(selected);
3409
3410     changeColour(viewport.getGlobalColourScheme());
3411     if (selected)
3412     {
3413       modifyConservation_actionPerformed();
3414     }
3415     else
3416     {
3417       SliderPanel.hideConservationSlider();
3418     }
3419   }
3420
3421   /**
3422    * Action on selecting or deselecting (Colour) Above PID Threshold
3423    */
3424   @Override
3425   public void abovePIDThreshold_actionPerformed(boolean selected)
3426   {
3427     modifyPID.setEnabled(selected);
3428     viewport.setAbovePIDThreshold(selected);
3429     if (!selected)
3430     {
3431       viewport.getResidueShading().setThreshold(0,
3432               viewport.isIgnoreGapsConsensus());
3433     }
3434
3435     changeColour(viewport.getGlobalColourScheme());
3436     if (selected)
3437     {
3438       modifyPID_actionPerformed();
3439     }
3440     else
3441     {
3442       SliderPanel.hidePIDSlider();
3443     }
3444   }
3445
3446   /**
3447    * DOCUMENT ME!
3448    *
3449    * @param e
3450    *          DOCUMENT ME!
3451    */
3452   @Override
3453   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3454   {
3455     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456     AlignmentSorter.sortByPID(viewport.getAlignment(),
3457             viewport.getAlignment().getSequenceAt(0));
3458     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3459             viewport.getAlignment()));
3460     alignPanel.paintAlignment(true, false);
3461   }
3462
3463   /**
3464    * DOCUMENT ME!
3465    *
3466    * @param e
3467    *          DOCUMENT ME!
3468    */
3469   @Override
3470   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3471   {
3472     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473     AlignmentSorter.sortByID(viewport.getAlignment());
3474     addHistoryItem(
3475             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3476     alignPanel.paintAlignment(true, false);
3477   }
3478
3479   /**
3480    * DOCUMENT ME!
3481    *
3482    * @param e
3483    *          DOCUMENT ME!
3484    */
3485   @Override
3486   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3487   {
3488     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489     AlignmentSorter.sortByLength(viewport.getAlignment());
3490     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3491             viewport.getAlignment()));
3492     alignPanel.paintAlignment(true, false);
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param e
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3503   {
3504     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505     AlignmentSorter.sortByGroup(viewport.getAlignment());
3506     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3507             viewport.getAlignment()));
3508
3509     alignPanel.paintAlignment(true, false);
3510   }
3511
3512   /**
3513    * DOCUMENT ME!
3514    *
3515    * @param e
3516    *          DOCUMENT ME!
3517    */
3518   @Override
3519   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3520   {
3521     new RedundancyPanel(alignPanel, this);
3522   }
3523
3524   /**
3525    * DOCUMENT ME!
3526    *
3527    * @param e
3528    *          DOCUMENT ME!
3529    */
3530   @Override
3531   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3532   {
3533     if ((viewport.getSelectionGroup() == null)
3534             || (viewport.getSelectionGroup().getSize() < 2))
3535     {
3536       JvOptionPane.showInternalMessageDialog(this,
3537               MessageManager.getString(
3538                       "label.you_must_select_least_two_sequences"),
3539               MessageManager.getString("label.invalid_selection"),
3540               JvOptionPane.WARNING_MESSAGE);
3541     }
3542     else
3543     {
3544       JInternalFrame frame = new JInternalFrame();
3545       frame.setContentPane(new PairwiseAlignPanel(viewport));
3546       Desktop.addInternalFrame(frame,
3547               MessageManager.getString("action.pairwise_alignment"), 600,
3548               500);
3549     }
3550   }
3551
3552   @Override
3553   public void autoCalculate_actionPerformed(ActionEvent e)
3554   {
3555     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3556     if (viewport.autoCalculateConsensus)
3557     {
3558       viewport.firePropertyChange("alignment", null,
3559               viewport.getAlignment().getSequences());
3560     }
3561   }
3562
3563   @Override
3564   public void sortByTreeOption_actionPerformed(ActionEvent e)
3565   {
3566     viewport.sortByTree = sortByTree.isSelected();
3567   }
3568
3569   @Override
3570   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3571   {
3572     viewport.followSelection = listenToViewSelections.isSelected();
3573   }
3574
3575   /**
3576    * Constructs a tree panel and adds it to the desktop
3577    *
3578    * @param type
3579    *          tree type (NJ or AV)
3580    * @param modelName
3581    *          name of score model used to compute the tree
3582    * @param options
3583    *          parameters for the distance or similarity calculation
3584    */
3585   void newTreePanel(String type, String modelName,
3586           SimilarityParamsI options)
3587   {
3588     String frameTitle = "";
3589     TreePanel tp;
3590
3591     boolean onSelection = false;
3592     if (viewport.getSelectionGroup() != null
3593             && viewport.getSelectionGroup().getSize() > 0)
3594     {
3595       SequenceGroup sg = viewport.getSelectionGroup();
3596
3597       /* Decide if the selection is a column region */
3598       for (SequenceI _s : sg.getSequences())
3599       {
3600         if (_s.getLength() < sg.getEndRes())
3601         {
3602           JvOptionPane.showMessageDialog(Desktop.desktop,
3603                   MessageManager.getString(
3604                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3605                   MessageManager.getString(
3606                           "label.sequences_selection_not_aligned"),
3607                   JvOptionPane.WARNING_MESSAGE);
3608
3609           return;
3610         }
3611       }
3612       onSelection = true;
3613     }
3614     else
3615     {
3616       if (viewport.getAlignment().getHeight() < 2)
3617       {
3618         return;
3619       }
3620     }
3621
3622     tp = new TreePanel(alignPanel, type, modelName, options);
3623     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3624
3625     frameTitle += " from ";
3626
3627     if (viewport.getViewName() != null)
3628     {
3629       frameTitle += viewport.getViewName() + " of ";
3630     }
3631
3632     frameTitle += this.title;
3633
3634     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3635   }
3636
3637   /**
3638    * DOCUMENT ME!
3639    *
3640    * @param title
3641    *          DOCUMENT ME!
3642    * @param order
3643    *          DOCUMENT ME!
3644    */
3645   public void addSortByOrderMenuItem(String title,
3646           final AlignmentOrder order)
3647   {
3648     final JMenuItem item = new JMenuItem(MessageManager
3649             .formatMessage("action.by_title_param", new Object[]
3650             { title }));
3651     sort.add(item);
3652     item.addActionListener(new java.awt.event.ActionListener()
3653     {
3654       @Override
3655       public void actionPerformed(ActionEvent e)
3656       {
3657         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3658
3659         // TODO: JBPNote - have to map order entries to curent SequenceI
3660         // pointers
3661         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3662
3663         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3664                 viewport.getAlignment()));
3665
3666         alignPanel.paintAlignment(true, false);
3667       }
3668     });
3669   }
3670
3671   /**
3672    * Add a new sort by annotation score menu item
3673    *
3674    * @param sort
3675    *          the menu to add the option to
3676    * @param scoreLabel
3677    *          the label used to retrieve scores for each sequence on the
3678    *          alignment
3679    */
3680   public void addSortByAnnotScoreMenuItem(JMenu sort,
3681           final String scoreLabel)
3682   {
3683     final JMenuItem item = new JMenuItem(scoreLabel);
3684     sort.add(item);
3685     item.addActionListener(new java.awt.event.ActionListener()
3686     {
3687       @Override
3688       public void actionPerformed(ActionEvent e)
3689       {
3690         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3691         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3692                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3693         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3694                 viewport.getAlignment()));
3695         alignPanel.paintAlignment(true, false);
3696       }
3697     });
3698   }
3699
3700   /**
3701    * last hash for alignment's annotation array - used to minimise cost of
3702    * rebuild.
3703    */
3704   protected int _annotationScoreVectorHash;
3705
3706   /**
3707    * search the alignment and rebuild the sort by annotation score submenu the
3708    * last alignment annotation vector hash is stored to minimize cost of
3709    * rebuilding in subsequence calls.
3710    *
3711    */
3712   @Override
3713   public void buildSortByAnnotationScoresMenu()
3714   {
3715     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3716     {
3717       return;
3718     }
3719
3720     if (viewport.getAlignment().getAlignmentAnnotation()
3721             .hashCode() != _annotationScoreVectorHash)
3722     {
3723       sortByAnnotScore.removeAll();
3724       // almost certainly a quicker way to do this - but we keep it simple
3725       Hashtable scoreSorts = new Hashtable();
3726       AlignmentAnnotation aann[];
3727       for (SequenceI sqa : viewport.getAlignment().getSequences())
3728       {
3729         aann = sqa.getAnnotation();
3730         for (int i = 0; aann != null && i < aann.length; i++)
3731         {
3732           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3733           {
3734             scoreSorts.put(aann[i].label, aann[i].label);
3735           }
3736         }
3737       }
3738       Enumeration labels = scoreSorts.keys();
3739       while (labels.hasMoreElements())
3740       {
3741         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3742                 (String) labels.nextElement());
3743       }
3744       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3745       scoreSorts.clear();
3746
3747       _annotationScoreVectorHash = viewport.getAlignment()
3748               .getAlignmentAnnotation().hashCode();
3749     }
3750   }
3751
3752   /**
3753    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3754    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3755    * call. Listeners are added to remove the menu item when the treePanel is
3756    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3757    * modified.
3758    */
3759   @Override
3760   public void buildTreeSortMenu()
3761   {
3762     sortByTreeMenu.removeAll();
3763
3764     List<Component> comps = PaintRefresher.components
3765             .get(viewport.getSequenceSetId());
3766     List<TreePanel> treePanels = new ArrayList<>();
3767     for (Component comp : comps)
3768     {
3769       if (comp instanceof TreePanel)
3770       {
3771         treePanels.add((TreePanel) comp);
3772       }
3773     }
3774
3775     if (treePanels.size() < 1)
3776     {
3777       sortByTreeMenu.setVisible(false);
3778       return;
3779     }
3780
3781     sortByTreeMenu.setVisible(true);
3782
3783     for (final TreePanel tp : treePanels)
3784     {
3785       final JMenuItem item = new JMenuItem(tp.getTitle());
3786       item.addActionListener(new java.awt.event.ActionListener()
3787       {
3788         @Override
3789         public void actionPerformed(ActionEvent e)
3790         {
3791           tp.sortByTree_actionPerformed();
3792           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3793
3794         }
3795       });
3796
3797       sortByTreeMenu.add(item);
3798     }
3799   }
3800
3801   public boolean sortBy(AlignmentOrder alorder, String undoname)
3802   {
3803     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3804     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3805     if (undoname != null)
3806     {
3807       addHistoryItem(new OrderCommand(undoname, oldOrder,
3808               viewport.getAlignment()));
3809     }
3810     alignPanel.paintAlignment(true, false);
3811     return true;
3812   }
3813
3814   /**
3815    * Work out whether the whole set of sequences or just the selected set will
3816    * be submitted for multiple alignment.
3817    *
3818    */
3819   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3820   {
3821     // Now, check we have enough sequences
3822     AlignmentView msa = null;
3823
3824     if ((viewport.getSelectionGroup() != null)
3825             && (viewport.getSelectionGroup().getSize() > 1))
3826     {
3827       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3828       // some common interface!
3829       /*
3830        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3831        * SequenceI[sz = seqs.getSize(false)];
3832        *
3833        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3834        * seqs.getSequenceAt(i); }
3835        */
3836       msa = viewport.getAlignmentView(true);
3837     }
3838     else if (viewport.getSelectionGroup() != null
3839             && viewport.getSelectionGroup().getSize() == 1)
3840     {
3841       int option = JvOptionPane.showConfirmDialog(this,
3842               MessageManager.getString("warn.oneseq_msainput_selection"),
3843               MessageManager.getString("label.invalid_selection"),
3844               JvOptionPane.OK_CANCEL_OPTION);
3845       if (option == JvOptionPane.OK_OPTION)
3846       {
3847         msa = viewport.getAlignmentView(false);
3848       }
3849     }
3850     else
3851     {
3852       msa = viewport.getAlignmentView(false);
3853     }
3854     return msa;
3855   }
3856
3857   /**
3858    * Decides what is submitted to a secondary structure prediction service: the
3859    * first sequence in the alignment, or in the current selection, or, if the
3860    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3861    * region or the whole alignment. (where the first sequence in the set is the
3862    * one that the prediction will be for).
3863    */
3864   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3865   {
3866     AlignmentView seqs = null;
3867
3868     if ((viewport.getSelectionGroup() != null)
3869             && (viewport.getSelectionGroup().getSize() > 0))
3870     {
3871       seqs = viewport.getAlignmentView(true);
3872     }
3873     else
3874     {
3875       seqs = viewport.getAlignmentView(false);
3876     }
3877     // limit sequences - JBPNote in future - could spawn multiple prediction
3878     // jobs
3879     // TODO: viewport.getAlignment().isAligned is a global state - the local
3880     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3881     if (!viewport.getAlignment().isAligned(false))
3882     {
3883       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3884       // TODO: if seqs.getSequences().length>1 then should really have warned
3885       // user!
3886
3887     }
3888     return seqs;
3889   }
3890
3891   /**
3892    * DOCUMENT ME!
3893    *
3894    * @param e
3895    *          DOCUMENT ME!
3896    */
3897   @Override
3898   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3899   {
3900     // Pick the tree file
3901     JalviewFileChooser chooser = new JalviewFileChooser(
3902             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3903     chooser.setFileView(new JalviewFileView());
3904     chooser.setDialogTitle(
3905             MessageManager.getString("label.select_newick_like_tree_file"));
3906     chooser.setToolTipText(
3907             MessageManager.getString("label.load_tree_file"));
3908
3909     int value = chooser.showOpenDialog(null);
3910
3911     if (value == JalviewFileChooser.APPROVE_OPTION)
3912     {
3913       String filePath = chooser.getSelectedFile().getPath();
3914       Cache.setProperty("LAST_DIRECTORY", filePath);
3915       NewickFile fin = null;
3916       try
3917       {
3918         fin = new NewickFile(filePath, DataSourceType.FILE);
3919         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3920       } catch (Exception ex)
3921       {
3922         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3923                 MessageManager.getString("label.problem_reading_tree_file"),
3924                 JvOptionPane.WARNING_MESSAGE);
3925         ex.printStackTrace();
3926       }
3927       if (fin != null && fin.hasWarningMessage())
3928       {
3929         JvOptionPane.showMessageDialog(Desktop.desktop,
3930                 fin.getWarningMessage(),
3931                 MessageManager
3932                         .getString("label.possible_problem_with_tree_file"),
3933                 JvOptionPane.WARNING_MESSAGE);
3934       }
3935     }
3936   }
3937
3938   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3939   {
3940     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3941   }
3942
3943   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3944           int h, int x, int y)
3945   {
3946     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3947   }
3948
3949   /**
3950    * Add a treeviewer for the tree extracted from a Newick file object to the
3951    * current alignment view
3952    *
3953    * @param nf
3954    *          the tree
3955    * @param title
3956    *          tree viewer title
3957    * @param input
3958    *          Associated alignment input data (or null)
3959    * @param w
3960    *          width
3961    * @param h
3962    *          height
3963    * @param x
3964    *          position
3965    * @param y
3966    *          position
3967    * @return TreePanel handle
3968    */
3969   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3970           AlignmentView input, int w, int h, int x, int y)
3971   {
3972     TreePanel tp = null;
3973
3974     try
3975     {
3976       nf.parse();
3977
3978       if (nf.getTree() != null)
3979       {
3980         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3981
3982         tp.setSize(w, h);
3983
3984         if (x > 0 && y > 0)
3985         {
3986           tp.setLocation(x, y);
3987         }
3988
3989         Desktop.addInternalFrame(tp, treeTitle, w, h);
3990       }
3991     } catch (Exception ex)
3992     {
3993       ex.printStackTrace();
3994     }
3995
3996     return tp;
3997   }
3998
3999   private boolean buildingMenu = false;
4000
4001   /**
4002    * Generates menu items and listener event actions for web service clients
4003    *
4004    */
4005   public void BuildWebServiceMenu()
4006   {
4007     while (buildingMenu)
4008     {
4009       try
4010       {
4011         System.err.println("Waiting for building menu to finish.");
4012         Thread.sleep(10);
4013       } catch (Exception e)
4014       {
4015       }
4016     }
4017     final AlignFrame me = this;
4018     buildingMenu = true;
4019     new Thread(new Runnable()
4020     {
4021       @Override
4022       public void run()
4023       {
4024         final List<JMenuItem> legacyItems = new ArrayList<>();
4025         try
4026         {
4027           // System.err.println("Building ws menu again "
4028           // + Thread.currentThread());
4029           // TODO: add support for context dependent disabling of services based
4030           // on
4031           // alignment and current selection
4032           // TODO: add additional serviceHandle parameter to specify abstract
4033           // handler
4034           // class independently of AbstractName
4035           // TODO: add in rediscovery GUI function to restart discoverer
4036           // TODO: group services by location as well as function and/or
4037           // introduce
4038           // object broker mechanism.
4039           final Vector<JMenu> wsmenu = new Vector<>();
4040           final IProgressIndicator af = me;
4041
4042           /*
4043            * do not i18n these strings - they are hard-coded in class
4044            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4045            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4046            */
4047           final JMenu msawsmenu = new JMenu("Alignment");
4048           final JMenu secstrmenu = new JMenu(
4049                   "Secondary Structure Prediction");
4050           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4051           final JMenu analymenu = new JMenu("Analysis");
4052           final JMenu dismenu = new JMenu("Protein Disorder");
4053           // JAL-940 - only show secondary structure prediction services from
4054           // the legacy server
4055           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4056               // &&
4057           Discoverer.services != null && (Discoverer.services.size() > 0))
4058           {
4059             // TODO: refactor to allow list of AbstractName/Handler bindings to
4060             // be
4061             // stored or retrieved from elsewhere
4062             // No MSAWS used any more:
4063             // Vector msaws = null; // (Vector)
4064             // Discoverer.services.get("MsaWS");
4065             Vector secstrpr = (Vector) Discoverer.services
4066                     .get("SecStrPred");
4067             if (secstrpr != null)
4068             {
4069               // Add any secondary structure prediction services
4070               for (int i = 0, j = secstrpr.size(); i < j; i++)
4071               {
4072                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4073                         .get(i);
4074                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4075                         .getServiceClient(sh);
4076                 int p = secstrmenu.getItemCount();
4077                 impl.attachWSMenuEntry(secstrmenu, me);
4078                 int q = secstrmenu.getItemCount();
4079                 for (int litm = p; litm < q; litm++)
4080                 {
4081                   legacyItems.add(secstrmenu.getItem(litm));
4082                 }
4083               }
4084             }
4085           }
4086
4087           // Add all submenus in the order they should appear on the web
4088           // services menu
4089           wsmenu.add(msawsmenu);
4090           wsmenu.add(secstrmenu);
4091           wsmenu.add(dismenu);
4092           wsmenu.add(analymenu);
4093           // No search services yet
4094           // wsmenu.add(seqsrchmenu);
4095
4096           javax.swing.SwingUtilities.invokeLater(new Runnable()
4097           {
4098             @Override
4099             public void run()
4100             {
4101               try
4102               {
4103                 webService.removeAll();
4104                 // first, add discovered services onto the webservices menu
4105                 if (wsmenu.size() > 0)
4106                 {
4107                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4108                   {
4109                     webService.add(wsmenu.get(i));
4110                   }
4111                 }
4112                 else
4113                 {
4114                   webService.add(me.webServiceNoServices);
4115                 }
4116                 // TODO: move into separate menu builder class.
4117                 boolean new_sspred = false;
4118                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4119                 {
4120                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4121                   if (jws2servs != null)
4122                   {
4123                     if (jws2servs.hasServices())
4124                     {
4125                       jws2servs.attachWSMenuEntry(webService, me);
4126                       for (Jws2Instance sv : jws2servs.getServices())
4127                       {
4128                         if (sv.description.toLowerCase().contains("jpred"))
4129                         {
4130                           for (JMenuItem jmi : legacyItems)
4131                           {
4132                             jmi.setVisible(false);
4133                           }
4134                         }
4135                       }
4136
4137                     }
4138                     if (jws2servs.isRunning())
4139                     {
4140                       JMenuItem tm = new JMenuItem(
4141                               "Still discovering JABA Services");
4142                       tm.setEnabled(false);
4143                       webService.add(tm);
4144                     }
4145                   }
4146                 }
4147                 build_urlServiceMenu(me.webService);
4148                 build_fetchdbmenu(webService);
4149                 for (JMenu item : wsmenu)
4150                 {
4151                   if (item.getItemCount() == 0)
4152                   {
4153                     item.setEnabled(false);
4154                   }
4155                   else
4156                   {
4157                     item.setEnabled(true);
4158                   }
4159                 }
4160               } catch (Exception e)
4161               {
4162                 Cache.log.debug(
4163                         "Exception during web service menu building process.",
4164                         e);
4165               }
4166             }
4167           });
4168         } catch (Exception e)
4169         {
4170         }
4171         buildingMenu = false;
4172       }
4173     }).start();
4174
4175   }
4176
4177   /**
4178    * construct any groupURL type service menu entries.
4179    *
4180    * @param webService
4181    */
4182   private void build_urlServiceMenu(JMenu webService)
4183   {
4184     // TODO: remove this code when 2.7 is released
4185     // DEBUG - alignmentView
4186     /*
4187      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4188      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4189      *
4190      * @Override public void actionPerformed(ActionEvent e) {
4191      * jalview.datamodel.AlignmentView
4192      * .testSelectionViews(af.viewport.getAlignment(),
4193      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4194      *
4195      * }); webService.add(testAlView);
4196      */
4197     // TODO: refactor to RestClient discoverer and merge menu entries for
4198     // rest-style services with other types of analysis/calculation service
4199     // SHmmr test client - still being implemented.
4200     // DEBUG - alignmentView
4201
4202     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4203             .getRestClients())
4204     {
4205       client.attachWSMenuEntry(
4206               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4207               this);
4208     }
4209   }
4210
4211   /**
4212    * Searches the alignment sequences for xRefs and builds the Show
4213    * Cross-References menu (formerly called Show Products), with database
4214    * sources for which cross-references are found (protein sources for a
4215    * nucleotide alignment and vice versa)
4216    *
4217    * @return true if Show Cross-references menu should be enabled
4218    */
4219   public boolean canShowProducts()
4220   {
4221     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4222     AlignmentI dataset = viewport.getAlignment().getDataset();
4223
4224     showProducts.removeAll();
4225     final boolean dna = viewport.getAlignment().isNucleotide();
4226
4227     if (seqs == null || seqs.length == 0)
4228     {
4229       // nothing to see here.
4230       return false;
4231     }
4232
4233     boolean showp = false;
4234     try
4235     {
4236       List<String> ptypes = new CrossRef(seqs, dataset)
4237               .findXrefSourcesForSequences(dna);
4238
4239       for (final String source : ptypes)
4240       {
4241         showp = true;
4242         final AlignFrame af = this;
4243         JMenuItem xtype = new JMenuItem(source);
4244         xtype.addActionListener(new ActionListener()
4245         {
4246           @Override
4247           public void actionPerformed(ActionEvent e)
4248           {
4249             showProductsFor(af.viewport.getSequenceSelection(), dna,
4250                     source);
4251           }
4252         });
4253         showProducts.add(xtype);
4254       }
4255       showProducts.setVisible(showp);
4256       showProducts.setEnabled(showp);
4257     } catch (Exception e)
4258     {
4259       Cache.log.warn(
4260               "canShowProducts threw an exception - please report to help@jalview.org",
4261               e);
4262       return false;
4263     }
4264     return showp;
4265   }
4266
4267   /**
4268    * Finds and displays cross-references for the selected sequences (protein
4269    * products for nucleotide sequences, dna coding sequences for peptides).
4270    *
4271    * @param sel
4272    *          the sequences to show cross-references for
4273    * @param dna
4274    *          true if from a nucleotide alignment (so showing proteins)
4275    * @param source
4276    *          the database to show cross-references for
4277    */
4278   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4279           final String source)
4280   {
4281     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4282             .start();
4283   }
4284
4285   /**
4286    * Construct and display a new frame containing the translation of this
4287    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4288    */
4289   @Override
4290   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4291   {
4292     AlignmentI al = null;
4293     try
4294     {
4295       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4296
4297       al = dna.translateCdna(codeTable);
4298     } catch (Exception ex)
4299     {
4300       jalview.bin.Cache.log.error(
4301               "Exception during translation. Please report this !", ex);
4302       final String msg = MessageManager.getString(
4303               "label.error_when_translating_sequences_submit_bug_report");
4304       final String errorTitle = MessageManager
4305               .getString("label.implementation_error")
4306               + MessageManager.getString("label.translation_failed");
4307       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4308               JvOptionPane.ERROR_MESSAGE);
4309       return;
4310     }
4311     if (al == null || al.getHeight() == 0)
4312     {
4313       final String msg = MessageManager.getString(
4314               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4315       final String errorTitle = MessageManager
4316               .getString("label.translation_failed");
4317       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4318               JvOptionPane.WARNING_MESSAGE);
4319     }
4320     else
4321     {
4322       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4323       af.setFileFormat(this.currentFileFormat);
4324       final String newTitle = MessageManager
4325               .formatMessage("label.translation_of_params", new Object[]
4326               { this.getTitle(), codeTable.getId() });
4327       af.setTitle(newTitle);
4328       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4329       {
4330         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4331         viewport.openSplitFrame(af, new Alignment(seqs));
4332       }
4333       else
4334       {
4335         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4336                 DEFAULT_HEIGHT);
4337       }
4338     }
4339   }
4340
4341   /**
4342    * Set the file format
4343    *
4344    * @param format
4345    */
4346   public void setFileFormat(FileFormatI format)
4347   {
4348     this.currentFileFormat = format;
4349   }
4350
4351   /**
4352    * Try to load a features file onto the alignment.
4353    *
4354    * @param file
4355    *          contents or path to retrieve file
4356    * @param sourceType
4357    *          access mode of file (see jalview.io.AlignFile)
4358    * @return true if features file was parsed correctly.
4359    */
4360   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4361   {
4362     return avc.parseFeaturesFile(file, sourceType,
4363             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4364
4365   }
4366
4367   @Override
4368   public void refreshFeatureUI(boolean enableIfNecessary)
4369   {
4370     // note - currently this is only still here rather than in the controller
4371     // because of the featureSettings hard reference that is yet to be
4372     // abstracted
4373     if (enableIfNecessary)
4374     {
4375       viewport.setShowSequenceFeatures(true);
4376       showSeqFeatures.setSelected(true);
4377     }
4378
4379   }
4380
4381   @Override
4382   public void dragEnter(DropTargetDragEvent evt)
4383   {
4384   }
4385
4386   @Override
4387   public void dragExit(DropTargetEvent evt)
4388   {
4389   }
4390
4391   @Override
4392   public void dragOver(DropTargetDragEvent evt)
4393   {
4394   }
4395
4396   @Override
4397   public void dropActionChanged(DropTargetDragEvent evt)
4398   {
4399   }
4400
4401   @Override
4402   public void drop(DropTargetDropEvent evt)
4403   {
4404     // JAL-1552 - acceptDrop required before getTransferable call for
4405     // Java's Transferable for native dnd
4406     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4407     Transferable t = evt.getTransferable();
4408     final AlignFrame thisaf = this;
4409     final List<String> files = new ArrayList<>();
4410     List<DataSourceType> protocols = new ArrayList<>();
4411
4412     try
4413     {
4414       Desktop.transferFromDropTarget(files, protocols, evt, t);
4415     } catch (Exception e)
4416     {
4417       e.printStackTrace();
4418     }
4419     if (files != null)
4420     {
4421       new Thread(new Runnable()
4422       {
4423         @Override
4424         public void run()
4425         {
4426           try
4427           {
4428             // check to see if any of these files have names matching sequences
4429             // in
4430             // the alignment
4431             SequenceIdMatcher idm = new SequenceIdMatcher(
4432                     viewport.getAlignment().getSequencesArray());
4433             /**
4434              * Object[] { String,SequenceI}
4435              */
4436             ArrayList<Object[]> filesmatched = new ArrayList<>();
4437             ArrayList<String> filesnotmatched = new ArrayList<>();
4438             for (int i = 0; i < files.size(); i++)
4439             {
4440               String file = files.get(i).toString();
4441               String pdbfn = "";
4442               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4443               if (protocol == DataSourceType.FILE)
4444               {
4445                 File fl = new File(file);
4446                 pdbfn = fl.getName();
4447               }
4448               else if (protocol == DataSourceType.URL)
4449               {
4450                 URL url = new URL(file);
4451                 pdbfn = url.getFile();
4452               }
4453               if (pdbfn.length() > 0)
4454               {
4455                 // attempt to find a match in the alignment
4456                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4457                 int l = 0, c = pdbfn.indexOf(".");
4458                 while (mtch == null && c != -1)
4459                 {
4460                   do
4461                   {
4462                     l = c;
4463                   } while ((c = pdbfn.indexOf(".", l)) > l);
4464                   if (l > -1)
4465                   {
4466                     pdbfn = pdbfn.substring(0, l);
4467                   }
4468                   mtch = idm.findAllIdMatches(pdbfn);
4469                 }
4470                 if (mtch != null)
4471                 {
4472                   FileFormatI type = null;
4473                   try
4474                   {
4475                     type = new IdentifyFile().identify(file, protocol);
4476                   } catch (Exception ex)
4477                   {
4478                     type = null;
4479                   }
4480                   if (type != null && type.isStructureFile())
4481                   {
4482                     filesmatched.add(new Object[] { file, protocol, mtch });
4483                     continue;
4484                   }
4485                 }
4486                 // File wasn't named like one of the sequences or wasn't a PDB
4487                 // file.
4488                 filesnotmatched.add(file);
4489               }
4490             }
4491             int assocfiles = 0;
4492             if (filesmatched.size() > 0)
4493             {
4494               boolean autoAssociate = Cache
4495                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4496               if (!autoAssociate)
4497               {
4498                 String msg = MessageManager.formatMessage(
4499                         "label.automatically_associate_structure_files_with_sequences_same_name",
4500                         new Object[]
4501                         { Integer.valueOf(filesmatched.size())
4502                                 .toString() });
4503                 String ttl = MessageManager.getString(
4504                         "label.automatically_associate_structure_files_by_name");
4505                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4506                         ttl, JvOptionPane.YES_NO_OPTION);
4507                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4508               }
4509               if (autoAssociate)
4510               {
4511                 for (Object[] fm : filesmatched)
4512                 {
4513                   // try and associate
4514                   // TODO: may want to set a standard ID naming formalism for
4515                   // associating PDB files which have no IDs.
4516                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4517                   {
4518                     PDBEntry pe = new AssociatePdbFileWithSeq()
4519                             .associatePdbWithSeq((String) fm[0],
4520                                     (DataSourceType) fm[1], toassoc, false,
4521                                     Desktop.instance);
4522                     if (pe != null)
4523                     {
4524                       System.err.println("Associated file : "
4525                               + ((String) fm[0]) + " with "
4526                               + toassoc.getDisplayId(true));
4527                       assocfiles++;
4528                     }
4529                   }
4530                   // TODO: do we need to update overview ? only if features are
4531                   // shown I guess
4532                   alignPanel.paintAlignment(true, false);
4533                 }
4534               }
4535               else
4536               {
4537                 /*
4538                  * add declined structures as sequences
4539                  */
4540                 for (Object[] o : filesmatched)
4541                 {
4542                   filesnotmatched.add((String) o[0]);
4543                 }
4544               }
4545             }
4546             if (filesnotmatched.size() > 0)
4547             {
4548               if (assocfiles > 0 && (Cache.getDefault(
4549                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4550                       || JvOptionPane.showConfirmDialog(thisaf,
4551                               "<html>" + MessageManager.formatMessage(
4552                                       "label.ignore_unmatched_dropped_files_info",
4553                                       new Object[]
4554                                       { Integer.valueOf(
4555                                               filesnotmatched.size())
4556                                               .toString() })
4557                                       + "</html>",
4558                               MessageManager.getString(
4559                                       "label.ignore_unmatched_dropped_files"),
4560                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4561               {
4562                 return;
4563               }
4564               for (String fn : filesnotmatched)
4565               {
4566                 loadJalviewDataFile(fn, null, null, null);
4567               }
4568
4569             }
4570           } catch (Exception ex)
4571           {
4572             ex.printStackTrace();
4573           }
4574         }
4575       }).start();
4576     }
4577   }
4578
4579   /**
4580    * Attempt to load a "dropped" file or URL string, by testing in turn for
4581    * <ul>
4582    * <li>an Annotation file</li>
4583    * <li>a JNet file</li>
4584    * <li>a features file</li>
4585    * <li>else try to interpret as an alignment file</li>
4586    * </ul>
4587    *
4588    * @param file
4589    *          either a filename or a URL string.
4590    */
4591   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4592           FileFormatI format, SequenceI assocSeq)
4593   {
4594     try
4595     {
4596       if (sourceType == null)
4597       {
4598         sourceType = FormatAdapter.checkProtocol(file);
4599       }
4600       // if the file isn't identified, or not positively identified as some
4601       // other filetype (PFAM is default unidentified alignment file type) then
4602       // try to parse as annotation.
4603       boolean isAnnotation = (format == null
4604               || FileFormat.Pfam.equals(format))
4605                       ? new AnnotationFile().annotateAlignmentView(viewport,
4606                               file, sourceType)
4607                       : false;
4608
4609       if (!isAnnotation)
4610       {
4611         // first see if its a T-COFFEE score file
4612         TCoffeeScoreFile tcf = null;
4613         try
4614         {
4615           tcf = new TCoffeeScoreFile(file, sourceType);
4616           if (tcf.isValid())
4617           {
4618             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4619             {
4620               buildColourMenu();
4621               changeColour(
4622                       new TCoffeeColourScheme(viewport.getAlignment()));
4623               isAnnotation = true;
4624               statusBar.setText(MessageManager.getString(
4625                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4626             }
4627             else
4628             {
4629               // some problem - if no warning its probable that the ID matching
4630               // process didn't work
4631               JvOptionPane.showMessageDialog(Desktop.desktop,
4632                       tcf.getWarningMessage() == null
4633                               ? MessageManager.getString(
4634                                       "label.check_file_matches_sequence_ids_alignment")
4635                               : tcf.getWarningMessage(),
4636                       MessageManager.getString(
4637                               "label.problem_reading_tcoffee_score_file"),
4638                       JvOptionPane.WARNING_MESSAGE);
4639             }
4640           }
4641           else
4642           {
4643             tcf = null;
4644           }
4645         } catch (Exception x)
4646         {
4647           Cache.log.debug(
4648                   "Exception when processing data source as T-COFFEE score file",
4649                   x);
4650           tcf = null;
4651         }
4652         if (tcf == null)
4653         {
4654           // try to see if its a JNet 'concise' style annotation file *before*
4655           // we
4656           // try to parse it as a features file
4657           if (format == null)
4658           {
4659             format = new IdentifyFile().identify(file, sourceType);
4660           }
4661           if (FileFormat.ScoreMatrix == format)
4662           {
4663             ScoreMatrixFile sm = new ScoreMatrixFile(
4664                     new FileParse(file, sourceType));
4665             sm.parse();
4666             // todo: i18n this message
4667             statusBar.setText(MessageManager.formatMessage(
4668                     "label.successfully_loaded_matrix",
4669                     sm.getMatrixName()));
4670           }
4671           else if (FileFormat.Jnet.equals(format))
4672           {
4673             JPredFile predictions = new JPredFile(file, sourceType);
4674             new JnetAnnotationMaker();
4675             JnetAnnotationMaker.add_annotation(predictions,
4676                     viewport.getAlignment(), 0, false);
4677             viewport.getAlignment().setupJPredAlignment();
4678             isAnnotation = true;
4679           }
4680           // else if (IdentifyFile.FeaturesFile.equals(format))
4681           else if (FileFormat.Features.equals(format))
4682           {
4683             if (parseFeaturesFile(file, sourceType))
4684             {
4685               alignPanel.paintAlignment(true, true);
4686             }
4687           }
4688           else
4689           {
4690             new FileLoader().LoadFile(viewport, file, sourceType, format);
4691           }
4692         }
4693       }
4694       if (isAnnotation)
4695       {
4696
4697         alignPanel.adjustAnnotationHeight();
4698         viewport.updateSequenceIdColours();
4699         buildSortByAnnotationScoresMenu();
4700         alignPanel.paintAlignment(true, true);
4701       }
4702     } catch (Exception ex)
4703     {
4704       ex.printStackTrace();
4705     } catch (OutOfMemoryError oom)
4706     {
4707       try
4708       {
4709         System.gc();
4710       } catch (Exception x)
4711       {
4712       }
4713       new OOMWarning(
4714               "loading data "
4715                       + (sourceType != null
4716                               ? (sourceType == DataSourceType.PASTE
4717                                       ? "from clipboard."
4718                                       : "using " + sourceType + " from "
4719                                               + file)
4720                               : ".")
4721                       + (format != null
4722                               ? "(parsing as '" + format + "' file)"
4723                               : ""),
4724               oom, Desktop.desktop);
4725     }
4726   }
4727
4728   /**
4729    * Method invoked by the ChangeListener on the tabbed pane, in other words
4730    * when a different tabbed pane is selected by the user or programmatically.
4731    */
4732   @Override
4733   public void tabSelectionChanged(int index)
4734   {
4735     if (index > -1)
4736     {
4737       alignPanel = alignPanels.get(index);
4738       viewport = alignPanel.av;
4739       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4740       setMenusFromViewport(viewport);
4741     }
4742
4743     /*
4744      * 'focus' any colour slider that is open to the selected viewport
4745      */
4746     if (viewport.getConservationSelected())
4747     {
4748       SliderPanel.setConservationSlider(alignPanel,
4749               viewport.getResidueShading(), alignPanel.getViewName());
4750     }
4751     else
4752     {
4753       SliderPanel.hideConservationSlider();
4754     }
4755     if (viewport.getAbovePIDThreshold())
4756     {
4757       SliderPanel.setPIDSliderSource(alignPanel,
4758               viewport.getResidueShading(), alignPanel.getViewName());
4759     }
4760     else
4761     {
4762       SliderPanel.hidePIDSlider();
4763     }
4764
4765     /*
4766      * If there is a frame linked to this one in a SplitPane, switch it to the
4767      * same view tab index. No infinite recursion of calls should happen, since
4768      * tabSelectionChanged() should not get invoked on setting the selected
4769      * index to an unchanged value. Guard against setting an invalid index
4770      * before the new view peer tab has been created.
4771      */
4772     final AlignViewportI peer = viewport.getCodingComplement();
4773     if (peer != null)
4774     {
4775       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4776               .getAlignPanel().alignFrame;
4777       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4778       {
4779         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4780       }
4781     }
4782   }
4783
4784   /**
4785    * On right mouse click on view tab, prompt for and set new view name.
4786    */
4787   @Override
4788   public void tabbedPane_mousePressed(MouseEvent e)
4789   {
4790     if (e.isPopupTrigger())
4791     {
4792       String msg = MessageManager.getString("label.enter_view_name");
4793       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4794               JvOptionPane.QUESTION_MESSAGE);
4795
4796       if (reply != null)
4797       {
4798         viewport.setViewName(reply);
4799         // TODO warn if reply is in getExistingViewNames()?
4800         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4801       }
4802     }
4803   }
4804
4805   public AlignViewport getCurrentView()
4806   {
4807     return viewport;
4808   }
4809
4810   /**
4811    * Open the dialog for regex description parsing.
4812    */
4813   @Override
4814   protected void extractScores_actionPerformed(ActionEvent e)
4815   {
4816     ParseProperties pp = new jalview.analysis.ParseProperties(
4817             viewport.getAlignment());
4818     // TODO: verify regex and introduce GUI dialog for version 2.5
4819     // if (pp.getScoresFromDescription("col", "score column ",
4820     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4821     // true)>0)
4822     if (pp.getScoresFromDescription("description column",
4823             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4824     {
4825       buildSortByAnnotationScoresMenu();
4826     }
4827   }
4828
4829   /*
4830    * (non-Javadoc)
4831    *
4832    * @see
4833    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4834    * )
4835    */
4836   @Override
4837   protected void showDbRefs_actionPerformed(ActionEvent e)
4838   {
4839     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4840   }
4841
4842   /*
4843    * (non-Javadoc)
4844    *
4845    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4846    * ActionEvent)
4847    */
4848   @Override
4849   protected void showNpFeats_actionPerformed(ActionEvent e)
4850   {
4851     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4852   }
4853
4854   /**
4855    * find the viewport amongst the tabs in this alignment frame and close that
4856    * tab
4857    *
4858    * @param av
4859    */
4860   public boolean closeView(AlignViewportI av)
4861   {
4862     if (viewport == av)
4863     {
4864       this.closeMenuItem_actionPerformed(false);
4865       return true;
4866     }
4867     Component[] comp = tabbedPane.getComponents();
4868     for (int i = 0; comp != null && i < comp.length; i++)
4869     {
4870       if (comp[i] instanceof AlignmentPanel)
4871       {
4872         if (((AlignmentPanel) comp[i]).av == av)
4873         {
4874           // close the view.
4875           closeView((AlignmentPanel) comp[i]);
4876           return true;
4877         }
4878       }
4879     }
4880     return false;
4881   }
4882
4883   protected void build_fetchdbmenu(JMenu webService)
4884   {
4885     // Temporary hack - DBRef Fetcher always top level ws entry.
4886     // TODO We probably want to store a sequence database checklist in
4887     // preferences and have checkboxes.. rather than individual sources selected
4888     // here
4889     final JMenu rfetch = new JMenu(
4890             MessageManager.getString("action.fetch_db_references"));
4891     rfetch.setToolTipText(MessageManager.getString(
4892             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4893     webService.add(rfetch);
4894
4895     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4896             MessageManager.getString("option.trim_retrieved_seqs"));
4897     trimrs.setToolTipText(
4898             MessageManager.getString("label.trim_retrieved_sequences"));
4899     trimrs.setSelected(
4900             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4901     trimrs.addActionListener(new ActionListener()
4902     {
4903       @Override
4904       public void actionPerformed(ActionEvent e)
4905       {
4906         trimrs.setSelected(trimrs.isSelected());
4907         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4908                 Boolean.valueOf(trimrs.isSelected()).toString());
4909       };
4910     });
4911     rfetch.add(trimrs);
4912     JMenuItem fetchr = new JMenuItem(
4913             MessageManager.getString("label.standard_databases"));
4914     fetchr.setToolTipText(
4915             MessageManager.getString("label.fetch_embl_uniprot"));
4916     fetchr.addActionListener(new ActionListener()
4917     {
4918
4919       @Override
4920       public void actionPerformed(ActionEvent e)
4921       {
4922         new Thread(new Runnable()
4923         {
4924           @Override
4925           public void run()
4926           {
4927             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4928                     .getAlignment().isNucleotide();
4929             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4930                     alignPanel.av.getSequenceSelection(),
4931                     alignPanel.alignFrame, null,
4932                     alignPanel.alignFrame.featureSettings, isNucleotide);
4933             dbRefFetcher.addListener(new FetchFinishedListenerI()
4934             {
4935               @Override
4936               public void finished()
4937               {
4938
4939                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
4940                         .getFeatureSettingsModels())
4941                 {
4942
4943                   alignPanel.av.mergeFeaturesStyle(srcSettings);
4944                 }
4945                 AlignFrame.this.setMenusForViewport();
4946               }
4947             });
4948             dbRefFetcher.fetchDBRefs(false);
4949           }
4950         }).start();
4951
4952       }
4953
4954     });
4955     rfetch.add(fetchr);
4956     final AlignFrame me = this;
4957     new Thread(new Runnable()
4958     {
4959       @Override
4960       public void run()
4961       {
4962         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4963                 .getSequenceFetcherSingleton(me);
4964         javax.swing.SwingUtilities.invokeLater(new Runnable()
4965         {
4966           @Override
4967           public void run()
4968           {
4969             String[] dbclasses = sf.getOrderedSupportedSources();
4970             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4971             // jalview.util.QuickSort.sort(otherdb, otherdb);
4972             List<DbSourceProxy> otherdb;
4973             JMenu dfetch = new JMenu();
4974             JMenu ifetch = new JMenu();
4975             JMenuItem fetchr = null;
4976             int comp = 0, icomp = 0, mcomp = 15;
4977             String mname = null;
4978             int dbi = 0;
4979             for (String dbclass : dbclasses)
4980             {
4981               otherdb = sf.getSourceProxy(dbclass);
4982               // add a single entry for this class, or submenu allowing 'fetch
4983               // all' or pick one
4984               if (otherdb == null || otherdb.size() < 1)
4985               {
4986                 continue;
4987               }
4988               // List<DbSourceProxy> dbs=otherdb;
4989               // otherdb=new ArrayList<DbSourceProxy>();
4990               // for (DbSourceProxy db:dbs)
4991               // {
4992               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4993               // }
4994               if (mname == null)
4995               {
4996                 mname = "From " + dbclass;
4997               }
4998               if (otherdb.size() == 1)
4999               {
5000                 final DbSourceProxy[] dassource = otherdb
5001                         .toArray(new DbSourceProxy[0]);
5002                 DbSourceProxy src = otherdb.get(0);
5003                 fetchr = new JMenuItem(src.getDbSource());
5004                 fetchr.addActionListener(new ActionListener()
5005                 {
5006
5007                   @Override
5008                   public void actionPerformed(ActionEvent e)
5009                   {
5010                     new Thread(new Runnable()
5011                     {
5012
5013                       @Override
5014                       public void run()
5015                       {
5016                         boolean isNucleotide = alignPanel.alignFrame
5017                                 .getViewport().getAlignment()
5018                                 .isNucleotide();
5019                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5020                                 alignPanel.av.getSequenceSelection(),
5021                                 alignPanel.alignFrame, dassource,
5022                                 alignPanel.alignFrame.featureSettings,
5023                                 isNucleotide);
5024                         dbRefFetcher
5025                                 .addListener(new FetchFinishedListenerI()
5026                                 {
5027                                   @Override
5028                                   public void finished()
5029                                   {
5030                                     FeatureSettingsModelI srcSettings = dassource[0]
5031                                             .getFeatureColourScheme();
5032                                     alignPanel.av.mergeFeaturesStyle(
5033                                             srcSettings);
5034                                     AlignFrame.this.setMenusForViewport();
5035                                   }
5036                                 });
5037                         dbRefFetcher.fetchDBRefs(false);
5038                       }
5039                     }).start();
5040                   }
5041
5042                 });
5043                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5044                         MessageManager.formatMessage(
5045                                 "label.fetch_retrieve_from", new Object[]
5046                                 { src.getDbName() })));
5047                 dfetch.add(fetchr);
5048                 comp++;
5049               }
5050               else
5051               {
5052                 final DbSourceProxy[] dassource = otherdb
5053                         .toArray(new DbSourceProxy[0]);
5054                 // fetch all entry
5055                 DbSourceProxy src = otherdb.get(0);
5056                 fetchr = new JMenuItem(MessageManager
5057                         .formatMessage("label.fetch_all_param", new Object[]
5058                         { src.getDbSource() }));
5059                 fetchr.addActionListener(new ActionListener()
5060                 {
5061                   @Override
5062                   public void actionPerformed(ActionEvent e)
5063                   {
5064                     new Thread(new Runnable()
5065                     {
5066
5067                       @Override
5068                       public void run()
5069                       {
5070                         boolean isNucleotide = alignPanel.alignFrame
5071                                 .getViewport().getAlignment()
5072                                 .isNucleotide();
5073                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5074                                 alignPanel.av.getSequenceSelection(),
5075                                 alignPanel.alignFrame, dassource,
5076                                 alignPanel.alignFrame.featureSettings,
5077                                 isNucleotide);
5078                         dbRefFetcher
5079                                 .addListener(new FetchFinishedListenerI()
5080                                 {
5081                                   @Override
5082                                   public void finished()
5083                                   {
5084                                     AlignFrame.this.setMenusForViewport();
5085                                   }
5086                                 });
5087                         dbRefFetcher.fetchDBRefs(false);
5088                       }
5089                     }).start();
5090                   }
5091                 });
5092
5093                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5094                         MessageManager.formatMessage(
5095                                 "label.fetch_retrieve_from_all_sources",
5096                                 new Object[]
5097                                 { Integer.valueOf(otherdb.size())
5098                                         .toString(),
5099                                     src.getDbSource(), src.getDbName() })));
5100                 dfetch.add(fetchr);
5101                 comp++;
5102                 // and then build the rest of the individual menus
5103                 ifetch = new JMenu(MessageManager.formatMessage(
5104                         "label.source_from_db_source", new Object[]
5105                         { src.getDbSource() }));
5106                 icomp = 0;
5107                 String imname = null;
5108                 int i = 0;
5109                 for (DbSourceProxy sproxy : otherdb)
5110                 {
5111                   String dbname = sproxy.getDbName();
5112                   String sname = dbname.length() > 5
5113                           ? dbname.substring(0, 5) + "..."
5114                           : dbname;
5115                   String msname = dbname.length() > 10
5116                           ? dbname.substring(0, 10) + "..."
5117                           : dbname;
5118                   if (imname == null)
5119                   {
5120                     imname = MessageManager
5121                             .formatMessage("label.from_msname", new Object[]
5122                             { sname });
5123                   }
5124                   fetchr = new JMenuItem(msname);
5125                   final DbSourceProxy[] dassrc = { sproxy };
5126                   fetchr.addActionListener(new ActionListener()
5127                   {
5128
5129                     @Override
5130                     public void actionPerformed(ActionEvent e)
5131                     {
5132                       new Thread(new Runnable()
5133                       {
5134
5135                         @Override
5136                         public void run()
5137                         {
5138                           boolean isNucleotide = alignPanel.alignFrame
5139                                   .getViewport().getAlignment()
5140                                   .isNucleotide();
5141                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5142                                   alignPanel.av.getSequenceSelection(),
5143                                   alignPanel.alignFrame, dassrc,
5144                                   alignPanel.alignFrame.featureSettings,
5145                                   isNucleotide);
5146                           dbRefFetcher
5147                                   .addListener(new FetchFinishedListenerI()
5148                                   {
5149                                     @Override
5150                                     public void finished()
5151                                     {
5152                                       AlignFrame.this.setMenusForViewport();
5153                                     }
5154                                   });
5155                           dbRefFetcher.fetchDBRefs(false);
5156                         }
5157                       }).start();
5158                     }
5159
5160                   });
5161                   fetchr.setToolTipText(
5162                           "<html>" + MessageManager.formatMessage(
5163                                   "label.fetch_retrieve_from", new Object[]
5164                                   { dbname }));
5165                   ifetch.add(fetchr);
5166                   ++i;
5167                   if (++icomp >= mcomp || i == (otherdb.size()))
5168                   {
5169                     ifetch.setText(MessageManager.formatMessage(
5170                             "label.source_to_target", imname, sname));
5171                     dfetch.add(ifetch);
5172                     ifetch = new JMenu();
5173                     imname = null;
5174                     icomp = 0;
5175                     comp++;
5176                   }
5177                 }
5178               }
5179               ++dbi;
5180               if (comp >= mcomp || dbi >= (dbclasses.length))
5181               {
5182                 dfetch.setText(MessageManager.formatMessage(
5183                         "label.source_to_target", mname, dbclass));
5184                 rfetch.add(dfetch);
5185                 dfetch = new JMenu();
5186                 mname = null;
5187                 comp = 0;
5188               }
5189             }
5190           }
5191         });
5192       }
5193     }).start();
5194
5195   }
5196
5197   /**
5198    * Left justify the whole alignment.
5199    */
5200   @Override
5201   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5202   {
5203     AlignmentI al = viewport.getAlignment();
5204     al.justify(false);
5205     viewport.firePropertyChange("alignment", null, al);
5206   }
5207
5208   /**
5209    * Right justify the whole alignment.
5210    */
5211   @Override
5212   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5213   {
5214     AlignmentI al = viewport.getAlignment();
5215     al.justify(true);
5216     viewport.firePropertyChange("alignment", null, al);
5217   }
5218
5219   @Override
5220   public void setShowSeqFeatures(boolean b)
5221   {
5222     showSeqFeatures.setSelected(b);
5223     viewport.setShowSequenceFeatures(b);
5224   }
5225
5226   /*
5227    * (non-Javadoc)
5228    *
5229    * @see
5230    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5231    * awt.event.ActionEvent)
5232    */
5233   @Override
5234   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5235   {
5236     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5237     alignPanel.paintAlignment(false, false);
5238   }
5239
5240   /*
5241    * (non-Javadoc)
5242    *
5243    * @see
5244    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5245    * .ActionEvent)
5246    */
5247   @Override
5248   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5249   {
5250     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5251     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5252
5253   }
5254
5255   /*
5256    * (non-Javadoc)
5257    *
5258    * @see
5259    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5260    * .event.ActionEvent)
5261    */
5262   @Override
5263   protected void showGroupConservation_actionPerformed(ActionEvent e)
5264   {
5265     viewport.setShowGroupConservation(showGroupConservation.getState());
5266     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5267   }
5268
5269   /*
5270    * (non-Javadoc)
5271    *
5272    * @see
5273    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5274    * .event.ActionEvent)
5275    */
5276   @Override
5277   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5278   {
5279     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5280     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5281   }
5282
5283   /*
5284    * (non-Javadoc)
5285    *
5286    * @see
5287    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5288    * .event.ActionEvent)
5289    */
5290   @Override
5291   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5292   {
5293     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5294     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5295   }
5296
5297   @Override
5298   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5299   {
5300     showSequenceLogo.setState(true);
5301     viewport.setShowSequenceLogo(true);
5302     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5303     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5304   }
5305
5306   @Override
5307   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5308   {
5309     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310   }
5311
5312   /*
5313    * (non-Javadoc)
5314    *
5315    * @see
5316    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5317    * .event.ActionEvent)
5318    */
5319   @Override
5320   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5321   {
5322     if (avc.makeGroupsFromSelection())
5323     {
5324       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5325       alignPanel.updateAnnotation();
5326       alignPanel.paintAlignment(true,
5327               viewport.needToUpdateStructureViews());
5328     }
5329   }
5330
5331   public void clearAlignmentSeqRep()
5332   {
5333     // TODO refactor alignmentseqrep to controller
5334     if (viewport.getAlignment().hasSeqrep())
5335     {
5336       viewport.getAlignment().setSeqrep(null);
5337       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5338       alignPanel.updateAnnotation();
5339       alignPanel.paintAlignment(true, true);
5340     }
5341   }
5342
5343   @Override
5344   protected void createGroup_actionPerformed(ActionEvent e)
5345   {
5346     if (avc.createGroup())
5347     {
5348       if (applyAutoAnnotationSettings.isSelected())
5349       {
5350         alignPanel.updateAnnotation(true, false);
5351       }
5352       alignPanel.alignmentChanged();
5353     }
5354   }
5355
5356   @Override
5357   protected void unGroup_actionPerformed(ActionEvent e)
5358   {
5359     if (avc.unGroup())
5360     {
5361       alignPanel.alignmentChanged();
5362     }
5363   }
5364
5365   /**
5366    * make the given alignmentPanel the currently selected tab
5367    *
5368    * @param alignmentPanel
5369    */
5370   public void setDisplayedView(AlignmentPanel alignmentPanel)
5371   {
5372     if (!viewport.getSequenceSetId()
5373             .equals(alignmentPanel.av.getSequenceSetId()))
5374     {
5375       throw new Error(MessageManager.getString(
5376               "error.implementation_error_cannot_show_view_alignment_frame"));
5377     }
5378     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5379             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5380     {
5381       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5382     }
5383   }
5384
5385   /**
5386    * Action on selection of menu options to Show or Hide annotations.
5387    *
5388    * @param visible
5389    * @param forSequences
5390    *          update sequence-related annotations
5391    * @param forAlignment
5392    *          update non-sequence-related annotations
5393    */
5394   @Override
5395   protected void setAnnotationsVisibility(boolean visible,
5396           boolean forSequences, boolean forAlignment)
5397   {
5398     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5399             .getAlignmentAnnotation();
5400     if (anns == null)
5401     {
5402       return;
5403     }
5404     for (AlignmentAnnotation aa : anns)
5405     {
5406       /*
5407        * don't display non-positional annotations on an alignment
5408        */
5409       if (aa.annotations == null)
5410       {
5411         continue;
5412       }
5413       boolean apply = (aa.sequenceRef == null && forAlignment)
5414               || (aa.sequenceRef != null && forSequences);
5415       if (apply)
5416       {
5417         aa.visible = visible;
5418       }
5419     }
5420     alignPanel.validateAnnotationDimensions(true);
5421     alignPanel.alignmentChanged();
5422   }
5423
5424   /**
5425    * Store selected annotation sort order for the view and repaint.
5426    */
5427   @Override
5428   protected void sortAnnotations_actionPerformed()
5429   {
5430     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5431     this.alignPanel.av
5432             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5433     alignPanel.paintAlignment(false, false);
5434   }
5435
5436   /**
5437    *
5438    * @return alignment panels in this alignment frame
5439    */
5440   public List<? extends AlignmentViewPanel> getAlignPanels()
5441   {
5442     // alignPanels is never null
5443     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5444     return alignPanels;
5445   }
5446
5447   /**
5448    * Open a new alignment window, with the cDNA associated with this (protein)
5449    * alignment, aligned as is the protein.
5450    */
5451   protected void viewAsCdna_actionPerformed()
5452   {
5453     // TODO no longer a menu action - refactor as required
5454     final AlignmentI alignment = getViewport().getAlignment();
5455     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5456     if (mappings == null)
5457     {
5458       return;
5459     }
5460     List<SequenceI> cdnaSeqs = new ArrayList<>();
5461     for (SequenceI aaSeq : alignment.getSequences())
5462     {
5463       for (AlignedCodonFrame acf : mappings)
5464       {
5465         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5466         if (dnaSeq != null)
5467         {
5468           /*
5469            * There is a cDNA mapping for this protein sequence - add to new
5470            * alignment. It will share the same dataset sequence as other mapped
5471            * cDNA (no new mappings need to be created).
5472            */
5473           final Sequence newSeq = new Sequence(dnaSeq);
5474           newSeq.setDatasetSequence(dnaSeq);
5475           cdnaSeqs.add(newSeq);
5476         }
5477       }
5478     }
5479     if (cdnaSeqs.size() == 0)
5480     {
5481       // show a warning dialog no mapped cDNA
5482       return;
5483     }
5484     AlignmentI cdna = new Alignment(
5485             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5486     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5487             AlignFrame.DEFAULT_HEIGHT);
5488     cdna.alignAs(alignment);
5489     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5490             + this.title;
5491     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5492             AlignFrame.DEFAULT_HEIGHT);
5493   }
5494
5495   /**
5496    * Set visibility of dna/protein complement view (available when shown in a
5497    * split frame).
5498    *
5499    * @param show
5500    */
5501   @Override
5502   protected void showComplement_actionPerformed(boolean show)
5503   {
5504     SplitContainerI sf = getSplitViewContainer();
5505     if (sf != null)
5506     {
5507       sf.setComplementVisible(this, show);
5508     }
5509   }
5510
5511   /**
5512    * Generate the reverse (optionally complemented) of the selected sequences,
5513    * and add them to the alignment
5514    */
5515   @Override
5516   protected void showReverse_actionPerformed(boolean complement)
5517   {
5518     AlignmentI al = null;
5519     try
5520     {
5521       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5522       al = dna.reverseCdna(complement);
5523       viewport.addAlignment(al, "");
5524       addHistoryItem(new EditCommand(
5525               MessageManager.getString("label.add_sequences"), Action.PASTE,
5526               al.getSequencesArray(), 0, al.getWidth(),
5527               viewport.getAlignment()));
5528     } catch (Exception ex)
5529     {
5530       System.err.println(ex.getMessage());
5531       return;
5532     }
5533   }
5534
5535   /**
5536    * Try to run a script in the Groovy console, having first ensured that this
5537    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5538    * be targeted at this alignment.
5539    */
5540   @Override
5541   protected void runGroovy_actionPerformed()
5542   {
5543     Jalview.setCurrentAlignFrame(this);
5544     groovy.ui.Console console = Desktop.getGroovyConsole();
5545     if (console != null)
5546     {
5547       try
5548       {
5549         console.runScript();
5550       } catch (Exception ex)
5551       {
5552         System.err.println((ex.toString()));
5553         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5554                 MessageManager.getString("label.couldnt_run_groovy_script"),
5555                 MessageManager.getString("label.groovy_support_failed"),
5556                 JvOptionPane.ERROR_MESSAGE);
5557       }
5558     }
5559     else
5560     {
5561       System.err.println("Can't run Groovy script as console not found");
5562     }
5563   }
5564
5565   /**
5566    * Hides columns containing (or not containing) a specified feature, provided
5567    * that would not leave all columns hidden
5568    *
5569    * @param featureType
5570    * @param columnsContaining
5571    * @return
5572    */
5573   public boolean hideFeatureColumns(String featureType,
5574           boolean columnsContaining)
5575   {
5576     boolean notForHiding = avc.markColumnsContainingFeatures(
5577             columnsContaining, false, false, featureType);
5578     if (notForHiding)
5579     {
5580       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5581               false, featureType))
5582       {
5583         getViewport().hideSelectedColumns();
5584         return true;
5585       }
5586     }
5587     return false;
5588   }
5589
5590   @Override
5591   protected void selectHighlightedColumns_actionPerformed(
5592           ActionEvent actionEvent)
5593   {
5594     // include key modifier check in case user selects from menu
5595     avc.markHighlightedColumns(
5596             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5597             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5598                     | ActionEvent.CTRL_MASK)) != 0);
5599   }
5600
5601   /**
5602    * Rebuilds the Colour menu, including any user-defined colours which have
5603    * been loaded either on startup or during the session
5604    */
5605   public void buildColourMenu()
5606   {
5607     colourMenu.removeAll();
5608
5609     colourMenu.add(applyToAllGroups);
5610     colourMenu.add(textColour);
5611     colourMenu.addSeparator();
5612
5613     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5614             viewport.getAlignment(), false);
5615
5616     colourMenu.add(annotationColour);
5617     bg.add(annotationColour);
5618     colourMenu.addSeparator();
5619     colourMenu.add(conservationMenuItem);
5620     colourMenu.add(modifyConservation);
5621     colourMenu.add(abovePIDThreshold);
5622     colourMenu.add(modifyPID);
5623
5624     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5625     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5626   }
5627
5628   /**
5629    * Open a dialog (if not already open) that allows the user to select and
5630    * calculate PCA or Tree analysis
5631    */
5632   protected void openTreePcaDialog()
5633   {
5634     if (alignPanel.getCalculationDialog() == null)
5635     {
5636       new CalculationChooser(AlignFrame.this);
5637     }
5638   }
5639
5640   @Override
5641   protected void loadVcf_actionPerformed()
5642   {
5643     JalviewFileChooser chooser = new JalviewFileChooser(
5644             Cache.getProperty("LAST_DIRECTORY"));
5645     chooser.setFileView(new JalviewFileView());
5646     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5647     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5648
5649     int value = chooser.showOpenDialog(null);
5650
5651     if (value == JalviewFileChooser.APPROVE_OPTION)
5652     {
5653       String choice = chooser.getSelectedFile().getPath();
5654       Cache.setProperty("LAST_DIRECTORY", choice);
5655       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5656       new VCFLoader(choice).loadVCF(seqs, this);
5657     }
5658
5659   }
5660 }
5661
5662 class PrintThread extends Thread
5663 {
5664   AlignmentPanel ap;
5665
5666   public PrintThread(AlignmentPanel ap)
5667   {
5668     this.ap = ap;
5669   }
5670
5671   static PageFormat pf;
5672
5673   @Override
5674   public void run()
5675   {
5676     PrinterJob printJob = PrinterJob.getPrinterJob();
5677
5678     if (pf != null)
5679     {
5680       printJob.setPrintable(ap, pf);
5681     }
5682     else
5683     {
5684       printJob.setPrintable(ap);
5685     }
5686
5687     if (printJob.printDialog())
5688     {
5689       try
5690       {
5691         printJob.print();
5692       } catch (Exception PrintException)
5693       {
5694         PrintException.printStackTrace();
5695       }
5696     }
5697   }
5698 }