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       if (closeAllTabs)
1483       {
1484         if (featureSettings != null && featureSettings.isOpen())
1485         {
1486           featureSettings.close();
1487           featureSettings = null;
1488         }
1489         /*
1490          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1491          * be called recursively, with the frame now in 'closed' state
1492          */
1493         this.setClosed(true);
1494       }
1495     } catch (Exception ex)
1496     {
1497       ex.printStackTrace();
1498     }
1499   }
1500
1501   /**
1502    * Close the specified panel and close up tabs appropriately.
1503    *
1504    * @param panelToClose
1505    */
1506   public void closeView(AlignmentPanel panelToClose)
1507   {
1508     int index = tabbedPane.getSelectedIndex();
1509     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1510     alignPanels.remove(panelToClose);
1511     panelToClose.closePanel();
1512     panelToClose = null;
1513
1514     tabbedPane.removeTabAt(closedindex);
1515     tabbedPane.validate();
1516
1517     if (index > closedindex || index == tabbedPane.getTabCount())
1518     {
1519       // modify currently selected tab index if necessary.
1520       index--;
1521     }
1522
1523     this.tabSelectionChanged(index);
1524   }
1525
1526   /**
1527    * DOCUMENT ME!
1528    */
1529   void updateEditMenuBar()
1530   {
1531
1532     if (viewport.getHistoryList().size() > 0)
1533     {
1534       undoMenuItem.setEnabled(true);
1535       CommandI command = viewport.getHistoryList().peek();
1536       undoMenuItem.setText(MessageManager
1537               .formatMessage("label.undo_command", new Object[]
1538               { command.getDescription() }));
1539     }
1540     else
1541     {
1542       undoMenuItem.setEnabled(false);
1543       undoMenuItem.setText(MessageManager.getString("action.undo"));
1544     }
1545
1546     if (viewport.getRedoList().size() > 0)
1547     {
1548       redoMenuItem.setEnabled(true);
1549
1550       CommandI command = viewport.getRedoList().peek();
1551       redoMenuItem.setText(MessageManager
1552               .formatMessage("label.redo_command", new Object[]
1553               { command.getDescription() }));
1554     }
1555     else
1556     {
1557       redoMenuItem.setEnabled(false);
1558       redoMenuItem.setText(MessageManager.getString("action.redo"));
1559     }
1560   }
1561
1562   @Override
1563   public void addHistoryItem(CommandI command)
1564   {
1565     if (command.getSize() > 0)
1566     {
1567       viewport.addToHistoryList(command);
1568       viewport.clearRedoList();
1569       updateEditMenuBar();
1570       viewport.updateHiddenColumns();
1571       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1572       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1573       // viewport.getColumnSelection()
1574       // .getHiddenColumns().size() > 0);
1575     }
1576   }
1577
1578   /**
1579    *
1580    * @return alignment objects for all views
1581    */
1582   AlignmentI[] getViewAlignments()
1583   {
1584     if (alignPanels != null)
1585     {
1586       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1587       int i = 0;
1588       for (AlignmentPanel ap : alignPanels)
1589       {
1590         als[i++] = ap.av.getAlignment();
1591       }
1592       return als;
1593     }
1594     if (viewport != null)
1595     {
1596       return new AlignmentI[] { viewport.getAlignment() };
1597     }
1598     return null;
1599   }
1600
1601   /**
1602    * DOCUMENT ME!
1603    *
1604    * @param e
1605    *          DOCUMENT ME!
1606    */
1607   @Override
1608   protected void undoMenuItem_actionPerformed(ActionEvent e)
1609   {
1610     if (viewport.getHistoryList().isEmpty())
1611     {
1612       return;
1613     }
1614     CommandI command = viewport.getHistoryList().pop();
1615     viewport.addToRedoList(command);
1616     command.undoCommand(getViewAlignments());
1617
1618     AlignmentViewport originalSource = getOriginatingSource(command);
1619     updateEditMenuBar();
1620
1621     if (originalSource != null)
1622     {
1623       if (originalSource != viewport)
1624       {
1625         Cache.log.warn(
1626                 "Implementation worry: mismatch of viewport origin for undo");
1627       }
1628       originalSource.updateHiddenColumns();
1629       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1630       // null
1631       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1632       // viewport.getColumnSelection()
1633       // .getHiddenColumns().size() > 0);
1634       originalSource.firePropertyChange("alignment", null,
1635               originalSource.getAlignment().getSequences());
1636     }
1637   }
1638
1639   /**
1640    * DOCUMENT ME!
1641    *
1642    * @param e
1643    *          DOCUMENT ME!
1644    */
1645   @Override
1646   protected void redoMenuItem_actionPerformed(ActionEvent e)
1647   {
1648     if (viewport.getRedoList().size() < 1)
1649     {
1650       return;
1651     }
1652
1653     CommandI command = viewport.getRedoList().pop();
1654     viewport.addToHistoryList(command);
1655     command.doCommand(getViewAlignments());
1656
1657     AlignmentViewport originalSource = getOriginatingSource(command);
1658     updateEditMenuBar();
1659
1660     if (originalSource != null)
1661     {
1662
1663       if (originalSource != viewport)
1664       {
1665         Cache.log.warn(
1666                 "Implementation worry: mismatch of viewport origin for redo");
1667       }
1668       originalSource.updateHiddenColumns();
1669       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1670       // null
1671       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1672       // viewport.getColumnSelection()
1673       // .getHiddenColumns().size() > 0);
1674       originalSource.firePropertyChange("alignment", null,
1675               originalSource.getAlignment().getSequences());
1676     }
1677   }
1678
1679   AlignmentViewport getOriginatingSource(CommandI command)
1680   {
1681     AlignmentViewport originalSource = null;
1682     // For sequence removal and addition, we need to fire
1683     // the property change event FROM the viewport where the
1684     // original alignment was altered
1685     AlignmentI al = null;
1686     if (command instanceof EditCommand)
1687     {
1688       EditCommand editCommand = (EditCommand) command;
1689       al = editCommand.getAlignment();
1690       List<Component> comps = PaintRefresher.components
1691               .get(viewport.getSequenceSetId());
1692
1693       for (Component comp : comps)
1694       {
1695         if (comp instanceof AlignmentPanel)
1696         {
1697           if (al == ((AlignmentPanel) comp).av.getAlignment())
1698           {
1699             originalSource = ((AlignmentPanel) comp).av;
1700             break;
1701           }
1702         }
1703       }
1704     }
1705
1706     if (originalSource == null)
1707     {
1708       // The original view is closed, we must validate
1709       // the current view against the closed view first
1710       if (al != null)
1711       {
1712         PaintRefresher.validateSequences(al, viewport.getAlignment());
1713       }
1714
1715       originalSource = viewport;
1716     }
1717
1718     return originalSource;
1719   }
1720
1721   /**
1722    * DOCUMENT ME!
1723    *
1724    * @param up
1725    *          DOCUMENT ME!
1726    */
1727   public void moveSelectedSequences(boolean up)
1728   {
1729     SequenceGroup sg = viewport.getSelectionGroup();
1730
1731     if (sg == null)
1732     {
1733       return;
1734     }
1735     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1736             viewport.getHiddenRepSequences(), up);
1737     alignPanel.paintAlignment(true, false);
1738   }
1739
1740   synchronized void slideSequences(boolean right, int size)
1741   {
1742     List<SequenceI> sg = new ArrayList<>();
1743     if (viewport.cursorMode)
1744     {
1745       sg.add(viewport.getAlignment()
1746               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1747     }
1748     else if (viewport.getSelectionGroup() != null
1749             && viewport.getSelectionGroup().getSize() != viewport
1750                     .getAlignment().getHeight())
1751     {
1752       sg = viewport.getSelectionGroup()
1753               .getSequences(viewport.getHiddenRepSequences());
1754     }
1755
1756     if (sg.size() < 1)
1757     {
1758       return;
1759     }
1760
1761     List<SequenceI> invertGroup = new ArrayList<>();
1762
1763     for (SequenceI seq : viewport.getAlignment().getSequences())
1764     {
1765       if (!sg.contains(seq))
1766       {
1767         invertGroup.add(seq);
1768       }
1769     }
1770
1771     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1772
1773     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1774     for (int i = 0; i < invertGroup.size(); i++)
1775     {
1776       seqs2[i] = invertGroup.get(i);
1777     }
1778
1779     SlideSequencesCommand ssc;
1780     if (right)
1781     {
1782       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1783               viewport.getGapCharacter());
1784     }
1785     else
1786     {
1787       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1788               viewport.getGapCharacter());
1789     }
1790
1791     int groupAdjustment = 0;
1792     if (ssc.getGapsInsertedBegin() && right)
1793     {
1794       if (viewport.cursorMode)
1795       {
1796         alignPanel.getSeqPanel().moveCursor(size, 0);
1797       }
1798       else
1799       {
1800         groupAdjustment = size;
1801       }
1802     }
1803     else if (!ssc.getGapsInsertedBegin() && !right)
1804     {
1805       if (viewport.cursorMode)
1806       {
1807         alignPanel.getSeqPanel().moveCursor(-size, 0);
1808       }
1809       else
1810       {
1811         groupAdjustment = -size;
1812       }
1813     }
1814
1815     if (groupAdjustment != 0)
1816     {
1817       viewport.getSelectionGroup().setStartRes(
1818               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1819       viewport.getSelectionGroup().setEndRes(
1820               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1821     }
1822
1823     /*
1824      * just extend the last slide command if compatible; but not if in
1825      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1826      */
1827     boolean appendHistoryItem = false;
1828     Deque<CommandI> historyList = viewport.getHistoryList();
1829     boolean inSplitFrame = getSplitViewContainer() != null;
1830     if (!inSplitFrame && historyList != null && historyList.size() > 0
1831             && historyList.peek() instanceof SlideSequencesCommand)
1832     {
1833       appendHistoryItem = ssc.appendSlideCommand(
1834               (SlideSequencesCommand) historyList.peek());
1835     }
1836
1837     if (!appendHistoryItem)
1838     {
1839       addHistoryItem(ssc);
1840     }
1841
1842     repaint();
1843   }
1844
1845   /**
1846    * DOCUMENT ME!
1847    *
1848    * @param e
1849    *          DOCUMENT ME!
1850    */
1851   @Override
1852   protected void copy_actionPerformed(ActionEvent e)
1853   {
1854     if (viewport.getSelectionGroup() == null)
1855     {
1856       return;
1857     }
1858     // TODO: preserve the ordering of displayed alignment annotation in any
1859     // internal paste (particularly sequence associated annotation)
1860     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1861     String[] omitHidden = null;
1862
1863     if (viewport.hasHiddenColumns())
1864     {
1865       omitHidden = viewport.getViewAsString(true);
1866     }
1867
1868     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1869             seqs, omitHidden, null);
1870
1871     StringSelection ss = new StringSelection(output);
1872
1873     try
1874     {
1875       jalview.gui.Desktop.internalCopy = true;
1876       // Its really worth setting the clipboard contents
1877       // to empty before setting the large StringSelection!!
1878       Toolkit.getDefaultToolkit().getSystemClipboard()
1879               .setContents(new StringSelection(""), null);
1880
1881       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1882               Desktop.instance);
1883     } catch (OutOfMemoryError er)
1884     {
1885       new OOMWarning("copying region", er);
1886       return;
1887     }
1888
1889     HiddenColumns hiddenColumns = null;
1890     if (viewport.hasHiddenColumns())
1891     {
1892       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1893       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1894
1895       // create new HiddenColumns object with copy of hidden regions
1896       // between startRes and endRes, offset by startRes
1897       hiddenColumns = new HiddenColumns(
1898               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1899               hiddenCutoff, hiddenOffset);
1900     }
1901
1902     Desktop.jalviewClipboard = new Object[] { seqs,
1903         viewport.getAlignment().getDataset(), hiddenColumns };
1904     statusBar.setText(MessageManager.formatMessage(
1905             "label.copied_sequences_to_clipboard", new Object[]
1906             { Integer.valueOf(seqs.length).toString() }));
1907   }
1908
1909   /**
1910    * DOCUMENT ME!
1911    *
1912    * @param e
1913    *          DOCUMENT ME!
1914    */
1915   @Override
1916   protected void pasteNew_actionPerformed(ActionEvent e)
1917   {
1918     paste(true);
1919   }
1920
1921   /**
1922    * DOCUMENT ME!
1923    *
1924    * @param e
1925    *          DOCUMENT ME!
1926    */
1927   @Override
1928   protected void pasteThis_actionPerformed(ActionEvent e)
1929   {
1930     paste(false);
1931   }
1932
1933   /**
1934    * Paste contents of Jalview clipboard
1935    *
1936    * @param newAlignment
1937    *          true to paste to a new alignment, otherwise add to this.
1938    */
1939   void paste(boolean newAlignment)
1940   {
1941     boolean externalPaste = true;
1942     try
1943     {
1944       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1945       Transferable contents = c.getContents(this);
1946
1947       if (contents == null)
1948       {
1949         return;
1950       }
1951
1952       String str;
1953       FileFormatI format;
1954       try
1955       {
1956         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957         if (str.length() < 1)
1958         {
1959           return;
1960         }
1961
1962         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1963
1964       } catch (OutOfMemoryError er)
1965       {
1966         new OOMWarning("Out of memory pasting sequences!!", er);
1967         return;
1968       }
1969
1970       SequenceI[] sequences;
1971       boolean annotationAdded = false;
1972       AlignmentI alignment = null;
1973
1974       if (Desktop.jalviewClipboard != null)
1975       {
1976         // The clipboard was filled from within Jalview, we must use the
1977         // sequences
1978         // And dataset from the copied alignment
1979         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980         // be doubly sure that we create *new* sequence objects.
1981         sequences = new SequenceI[newseq.length];
1982         for (int i = 0; i < newseq.length; i++)
1983         {
1984           sequences[i] = new Sequence(newseq[i]);
1985         }
1986         alignment = new Alignment(sequences);
1987         externalPaste = false;
1988       }
1989       else
1990       {
1991         // parse the clipboard as an alignment.
1992         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1993                 format);
1994         sequences = alignment.getSequencesArray();
1995       }
1996
1997       int alwidth = 0;
1998       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1999       int fgroup = -1;
2000
2001       if (newAlignment)
2002       {
2003
2004         if (Desktop.jalviewClipboard != null)
2005         {
2006           // dataset is inherited
2007           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2008         }
2009         else
2010         {
2011           // new dataset is constructed
2012           alignment.setDataset(null);
2013         }
2014         alwidth = alignment.getWidth() + 1;
2015       }
2016       else
2017       {
2018         AlignmentI pastedal = alignment; // preserve pasted alignment object
2019         // Add pasted sequences and dataset into existing alignment.
2020         alignment = viewport.getAlignment();
2021         alwidth = alignment.getWidth() + 1;
2022         // decide if we need to import sequences from an existing dataset
2023         boolean importDs = Desktop.jalviewClipboard != null
2024                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2025         // importDs==true instructs us to copy over new dataset sequences from
2026         // an existing alignment
2027         Vector newDs = (importDs) ? new Vector() : null; // used to create
2028         // minimum dataset set
2029
2030         for (int i = 0; i < sequences.length; i++)
2031         {
2032           if (importDs)
2033           {
2034             newDs.addElement(null);
2035           }
2036           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2037           // paste
2038           if (importDs && ds != null)
2039           {
2040             if (!newDs.contains(ds))
2041             {
2042               newDs.setElementAt(ds, i);
2043               ds = new Sequence(ds);
2044               // update with new dataset sequence
2045               sequences[i].setDatasetSequence(ds);
2046             }
2047             else
2048             {
2049               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2050             }
2051           }
2052           else
2053           {
2054             // copy and derive new dataset sequence
2055             sequences[i] = sequences[i].deriveSequence();
2056             alignment.getDataset()
2057                     .addSequence(sequences[i].getDatasetSequence());
2058             // TODO: avoid creation of duplicate dataset sequences with a
2059             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2060           }
2061           alignment.addSequence(sequences[i]); // merges dataset
2062         }
2063         if (newDs != null)
2064         {
2065           newDs.clear(); // tidy up
2066         }
2067         if (alignment.getAlignmentAnnotation() != null)
2068         {
2069           for (AlignmentAnnotation alan : alignment
2070                   .getAlignmentAnnotation())
2071           {
2072             if (alan.graphGroup > fgroup)
2073             {
2074               fgroup = alan.graphGroup;
2075             }
2076           }
2077         }
2078         if (pastedal.getAlignmentAnnotation() != null)
2079         {
2080           // Add any annotation attached to alignment.
2081           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2082           for (int i = 0; i < alann.length; i++)
2083           {
2084             annotationAdded = true;
2085             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2086             {
2087               AlignmentAnnotation newann = new AlignmentAnnotation(
2088                       alann[i]);
2089               if (newann.graphGroup > -1)
2090               {
2091                 if (newGraphGroups.size() <= newann.graphGroup
2092                         || newGraphGroups.get(newann.graphGroup) == null)
2093                 {
2094                   for (int q = newGraphGroups
2095                           .size(); q <= newann.graphGroup; q++)
2096                   {
2097                     newGraphGroups.add(q, null);
2098                   }
2099                   newGraphGroups.set(newann.graphGroup,
2100                           Integer.valueOf(++fgroup));
2101                 }
2102                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2103                         .intValue();
2104               }
2105
2106               newann.padAnnotation(alwidth);
2107               alignment.addAnnotation(newann);
2108             }
2109           }
2110         }
2111       }
2112       if (!newAlignment)
2113       {
2114         // /////
2115         // ADD HISTORY ITEM
2116         //
2117         addHistoryItem(new EditCommand(
2118                 MessageManager.getString("label.add_sequences"),
2119                 Action.PASTE, sequences, 0, alignment.getWidth(),
2120                 alignment));
2121       }
2122       // Add any annotations attached to sequences
2123       for (int i = 0; i < sequences.length; i++)
2124       {
2125         if (sequences[i].getAnnotation() != null)
2126         {
2127           AlignmentAnnotation newann;
2128           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2129           {
2130             annotationAdded = true;
2131             newann = sequences[i].getAnnotation()[a];
2132             newann.adjustForAlignment();
2133             newann.padAnnotation(alwidth);
2134             if (newann.graphGroup > -1)
2135             {
2136               if (newann.graphGroup > -1)
2137               {
2138                 if (newGraphGroups.size() <= newann.graphGroup
2139                         || newGraphGroups.get(newann.graphGroup) == null)
2140                 {
2141                   for (int q = newGraphGroups
2142                           .size(); q <= newann.graphGroup; q++)
2143                   {
2144                     newGraphGroups.add(q, null);
2145                   }
2146                   newGraphGroups.set(newann.graphGroup,
2147                           Integer.valueOf(++fgroup));
2148                 }
2149                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2150                         .intValue();
2151               }
2152             }
2153             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2154             // was
2155             // duplicated
2156             // earlier
2157             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2158                     a);
2159           }
2160         }
2161       }
2162       if (!newAlignment)
2163       {
2164
2165         // propagate alignment changed.
2166         viewport.getRanges().setEndSeq(alignment.getHeight());
2167         if (annotationAdded)
2168         {
2169           // Duplicate sequence annotation in all views.
2170           AlignmentI[] alview = this.getViewAlignments();
2171           for (int i = 0; i < sequences.length; i++)
2172           {
2173             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2174             if (sann == null)
2175             {
2176               continue;
2177             }
2178             for (int avnum = 0; avnum < alview.length; avnum++)
2179             {
2180               if (alview[avnum] != alignment)
2181               {
2182                 // duplicate in a view other than the one with input focus
2183                 int avwidth = alview[avnum].getWidth() + 1;
2184                 // this relies on sann being preserved after we
2185                 // modify the sequence's annotation array for each duplication
2186                 for (int a = 0; a < sann.length; a++)
2187                 {
2188                   AlignmentAnnotation newann = new AlignmentAnnotation(
2189                           sann[a]);
2190                   sequences[i].addAlignmentAnnotation(newann);
2191                   newann.padAnnotation(avwidth);
2192                   alview[avnum].addAnnotation(newann); // annotation was
2193                   // duplicated earlier
2194                   // TODO JAL-1145 graphGroups are not updated for sequence
2195                   // annotation added to several views. This may cause
2196                   // strangeness
2197                   alview[avnum].setAnnotationIndex(newann, a);
2198                 }
2199               }
2200             }
2201           }
2202           buildSortByAnnotationScoresMenu();
2203         }
2204         viewport.firePropertyChange("alignment", null,
2205                 alignment.getSequences());
2206         if (alignPanels != null)
2207         {
2208           for (AlignmentPanel ap : alignPanels)
2209           {
2210             ap.validateAnnotationDimensions(false);
2211           }
2212         }
2213         else
2214         {
2215           alignPanel.validateAnnotationDimensions(false);
2216         }
2217
2218       }
2219       else
2220       {
2221         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2222                 DEFAULT_HEIGHT);
2223         String newtitle = new String("Copied sequences");
2224
2225         if (Desktop.jalviewClipboard != null
2226                 && Desktop.jalviewClipboard[2] != null)
2227         {
2228           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2229           af.viewport.setHiddenColumns(hc);
2230         }
2231
2232         // >>>This is a fix for the moment, until a better solution is
2233         // found!!<<<
2234         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2235                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2236                         .getFeatureRenderer());
2237
2238         // TODO: maintain provenance of an alignment, rather than just make the
2239         // title a concatenation of operations.
2240         if (!externalPaste)
2241         {
2242           if (title.startsWith("Copied sequences"))
2243           {
2244             newtitle = title;
2245           }
2246           else
2247           {
2248             newtitle = newtitle.concat("- from " + title);
2249           }
2250         }
2251         else
2252         {
2253           newtitle = new String("Pasted sequences");
2254         }
2255
2256         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2257                 DEFAULT_HEIGHT);
2258
2259       }
2260
2261     } catch (Exception ex)
2262     {
2263       ex.printStackTrace();
2264       System.out.println("Exception whilst pasting: " + ex);
2265       // could be anything being pasted in here
2266     }
2267
2268   }
2269
2270   @Override
2271   protected void expand_newalign(ActionEvent e)
2272   {
2273     try
2274     {
2275       AlignmentI alignment = AlignmentUtils
2276               .expandContext(getViewport().getAlignment(), -1);
2277       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2278               DEFAULT_HEIGHT);
2279       String newtitle = new String("Flanking alignment");
2280
2281       if (Desktop.jalviewClipboard != null
2282               && Desktop.jalviewClipboard[2] != null)
2283       {
2284         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2285         af.viewport.setHiddenColumns(hc);
2286       }
2287
2288       // >>>This is a fix for the moment, until a better solution is
2289       // found!!<<<
2290       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2292                       .getFeatureRenderer());
2293
2294       // TODO: maintain provenance of an alignment, rather than just make the
2295       // title a concatenation of operations.
2296       {
2297         if (title.startsWith("Copied sequences"))
2298         {
2299           newtitle = title;
2300         }
2301         else
2302         {
2303           newtitle = newtitle.concat("- from " + title);
2304         }
2305       }
2306
2307       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2308
2309     } catch (Exception ex)
2310     {
2311       ex.printStackTrace();
2312       System.out.println("Exception whilst pasting: " + ex);
2313       // could be anything being pasted in here
2314     } catch (OutOfMemoryError oom)
2315     {
2316       new OOMWarning("Viewing flanking region of alignment", oom);
2317     }
2318   }
2319
2320   /**
2321    * DOCUMENT ME!
2322    *
2323    * @param e
2324    *          DOCUMENT ME!
2325    */
2326   @Override
2327   protected void cut_actionPerformed(ActionEvent e)
2328   {
2329     copy_actionPerformed(null);
2330     delete_actionPerformed(null);
2331   }
2332
2333   /**
2334    * DOCUMENT ME!
2335    *
2336    * @param e
2337    *          DOCUMENT ME!
2338    */
2339   @Override
2340   protected void delete_actionPerformed(ActionEvent evt)
2341   {
2342
2343     SequenceGroup sg = viewport.getSelectionGroup();
2344     if (sg == null)
2345     {
2346       return;
2347     }
2348
2349     /*
2350      * If the cut affects all sequences, warn, remove highlighted columns
2351      */
2352     if (sg.getSize() == viewport.getAlignment().getHeight())
2353     {
2354       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2355               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2356       if (isEntireAlignWidth)
2357       {
2358         int confirm = JvOptionPane.showConfirmDialog(this,
2359                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2360                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2361                 JvOptionPane.OK_CANCEL_OPTION);
2362
2363         if (confirm == JvOptionPane.CANCEL_OPTION
2364                 || confirm == JvOptionPane.CLOSED_OPTION)
2365         {
2366           return;
2367         }
2368       }
2369       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2370               sg.getEndRes() + 1);
2371     }
2372     SequenceI[] cut = sg.getSequences()
2373             .toArray(new SequenceI[sg.getSize()]);
2374
2375     addHistoryItem(new EditCommand(
2376             MessageManager.getString("label.cut_sequences"), Action.CUT,
2377             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2378             viewport.getAlignment()));
2379
2380     viewport.setSelectionGroup(null);
2381     viewport.sendSelection();
2382     viewport.getAlignment().deleteGroup(sg);
2383
2384     viewport.firePropertyChange("alignment", null,
2385             viewport.getAlignment().getSequences());
2386     if (viewport.getAlignment().getHeight() < 1)
2387     {
2388       try
2389       {
2390         this.setClosed(true);
2391       } catch (Exception ex)
2392       {
2393       }
2394     }
2395   }
2396
2397   /**
2398    * DOCUMENT ME!
2399    *
2400    * @param e
2401    *          DOCUMENT ME!
2402    */
2403   @Override
2404   protected void deleteGroups_actionPerformed(ActionEvent e)
2405   {
2406     if (avc.deleteGroups())
2407     {
2408       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2409       alignPanel.updateAnnotation();
2410       alignPanel.paintAlignment(true, true);
2411     }
2412   }
2413
2414   /**
2415    * DOCUMENT ME!
2416    *
2417    * @param e
2418    *          DOCUMENT ME!
2419    */
2420   @Override
2421   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2422   {
2423     SequenceGroup sg = new SequenceGroup(
2424             viewport.getAlignment().getSequences());
2425
2426     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2427     viewport.setSelectionGroup(sg);
2428     viewport.isSelectionGroupChanged(true);
2429     viewport.sendSelection();
2430     // JAL-2034 - should delegate to
2431     // alignPanel to decide if overview needs
2432     // updating.
2433     alignPanel.paintAlignment(false, false);
2434     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2435   }
2436
2437   /**
2438    * DOCUMENT ME!
2439    *
2440    * @param e
2441    *          DOCUMENT ME!
2442    */
2443   @Override
2444   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2445   {
2446     if (viewport.cursorMode)
2447     {
2448       alignPanel.getSeqPanel().keyboardNo1 = null;
2449       alignPanel.getSeqPanel().keyboardNo2 = null;
2450     }
2451     viewport.setSelectionGroup(null);
2452     viewport.getColumnSelection().clear();
2453     viewport.setSelectionGroup(null);
2454     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2455     // JAL-2034 - should delegate to
2456     // alignPanel to decide if overview needs
2457     // updating.
2458     alignPanel.paintAlignment(false, false);
2459     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2460     viewport.sendSelection();
2461   }
2462
2463   /**
2464    * DOCUMENT ME!
2465    *
2466    * @param e
2467    *          DOCUMENT ME!
2468    */
2469   @Override
2470   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2471   {
2472     SequenceGroup sg = viewport.getSelectionGroup();
2473
2474     if (sg == null)
2475     {
2476       selectAllSequenceMenuItem_actionPerformed(null);
2477
2478       return;
2479     }
2480
2481     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2482     {
2483       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2484     }
2485     // JAL-2034 - should delegate to
2486     // alignPanel to decide if overview needs
2487     // updating.
2488
2489     alignPanel.paintAlignment(true, false);
2490     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2491     viewport.sendSelection();
2492   }
2493
2494   @Override
2495   public void invertColSel_actionPerformed(ActionEvent e)
2496   {
2497     viewport.invertColumnSelection();
2498     alignPanel.paintAlignment(true, false);
2499     viewport.sendSelection();
2500   }
2501
2502   /**
2503    * DOCUMENT ME!
2504    *
2505    * @param e
2506    *          DOCUMENT ME!
2507    */
2508   @Override
2509   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2510   {
2511     trimAlignment(true);
2512   }
2513
2514   /**
2515    * DOCUMENT ME!
2516    *
2517    * @param e
2518    *          DOCUMENT ME!
2519    */
2520   @Override
2521   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2522   {
2523     trimAlignment(false);
2524   }
2525
2526   void trimAlignment(boolean trimLeft)
2527   {
2528     ColumnSelection colSel = viewport.getColumnSelection();
2529     int column;
2530
2531     if (!colSel.isEmpty())
2532     {
2533       if (trimLeft)
2534       {
2535         column = colSel.getMin();
2536       }
2537       else
2538       {
2539         column = colSel.getMax();
2540       }
2541
2542       SequenceI[] seqs;
2543       if (viewport.getSelectionGroup() != null)
2544       {
2545         seqs = viewport.getSelectionGroup()
2546                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2547       }
2548       else
2549       {
2550         seqs = viewport.getAlignment().getSequencesArray();
2551       }
2552
2553       TrimRegionCommand trimRegion;
2554       if (trimLeft)
2555       {
2556         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2557                 column, viewport.getAlignment());
2558         viewport.getRanges().setStartRes(0);
2559       }
2560       else
2561       {
2562         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2563                 column, viewport.getAlignment());
2564       }
2565
2566       statusBar.setText(MessageManager
2567               .formatMessage("label.removed_columns", new String[]
2568               { Integer.valueOf(trimRegion.getSize()).toString() }));
2569
2570       addHistoryItem(trimRegion);
2571
2572       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2573       {
2574         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2575                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2576         {
2577           viewport.getAlignment().deleteGroup(sg);
2578         }
2579       }
2580
2581       viewport.firePropertyChange("alignment", null,
2582               viewport.getAlignment().getSequences());
2583     }
2584   }
2585
2586   /**
2587    * DOCUMENT ME!
2588    *
2589    * @param e
2590    *          DOCUMENT ME!
2591    */
2592   @Override
2593   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2594   {
2595     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2596
2597     SequenceI[] seqs;
2598     if (viewport.getSelectionGroup() != null)
2599     {
2600       seqs = viewport.getSelectionGroup()
2601               .getSequencesAsArray(viewport.getHiddenRepSequences());
2602       start = viewport.getSelectionGroup().getStartRes();
2603       end = viewport.getSelectionGroup().getEndRes();
2604     }
2605     else
2606     {
2607       seqs = viewport.getAlignment().getSequencesArray();
2608     }
2609
2610     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2611             "Remove Gapped Columns", seqs, start, end,
2612             viewport.getAlignment());
2613
2614     addHistoryItem(removeGapCols);
2615
2616     statusBar.setText(MessageManager
2617             .formatMessage("label.removed_empty_columns", new Object[]
2618             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2619
2620     // This is to maintain viewport position on first residue
2621     // of first sequence
2622     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2623     ViewportRanges ranges = viewport.getRanges();
2624     int startRes = seq.findPosition(ranges.getStartRes());
2625     // ShiftList shifts;
2626     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2627     // edit.alColumnChanges=shifts.getInverse();
2628     // if (viewport.hasHiddenColumns)
2629     // viewport.getColumnSelection().compensateForEdits(shifts);
2630     ranges.setStartRes(seq.findIndex(startRes) - 1);
2631     viewport.firePropertyChange("alignment", null,
2632             viewport.getAlignment().getSequences());
2633
2634   }
2635
2636   /**
2637    * DOCUMENT ME!
2638    *
2639    * @param e
2640    *          DOCUMENT ME!
2641    */
2642   @Override
2643   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2644   {
2645     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2646
2647     SequenceI[] seqs;
2648     if (viewport.getSelectionGroup() != null)
2649     {
2650       seqs = viewport.getSelectionGroup()
2651               .getSequencesAsArray(viewport.getHiddenRepSequences());
2652       start = viewport.getSelectionGroup().getStartRes();
2653       end = viewport.getSelectionGroup().getEndRes();
2654     }
2655     else
2656     {
2657       seqs = viewport.getAlignment().getSequencesArray();
2658     }
2659
2660     // This is to maintain viewport position on first residue
2661     // of first sequence
2662     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2663     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2664
2665     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2666             viewport.getAlignment()));
2667
2668     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2669
2670     viewport.firePropertyChange("alignment", null,
2671             viewport.getAlignment().getSequences());
2672
2673   }
2674
2675   /**
2676    * DOCUMENT ME!
2677    *
2678    * @param e
2679    *          DOCUMENT ME!
2680    */
2681   @Override
2682   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2683   {
2684     viewport.setPadGaps(padGapsMenuitem.isSelected());
2685     viewport.firePropertyChange("alignment", null,
2686             viewport.getAlignment().getSequences());
2687   }
2688
2689   /**
2690    * Opens a Finder dialog
2691    *
2692    * @param e
2693    */
2694   @Override
2695   public void findMenuItem_actionPerformed(ActionEvent e)
2696   {
2697     new Finder(alignPanel);
2698   }
2699
2700   /**
2701    * Create a new view of the current alignment.
2702    */
2703   @Override
2704   public void newView_actionPerformed(ActionEvent e)
2705   {
2706     newView(null, true);
2707   }
2708
2709   /**
2710    * Creates and shows a new view of the current alignment.
2711    *
2712    * @param viewTitle
2713    *          title of newly created view; if null, one will be generated
2714    * @param copyAnnotation
2715    *          if true then duplicate all annnotation, groups and settings
2716    * @return new alignment panel, already displayed.
2717    */
2718   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2719   {
2720     /*
2721      * Create a new AlignmentPanel (with its own, new Viewport)
2722      */
2723     AlignmentPanel newap = new jalview.project.Jalview2XML()
2724             .copyAlignPanel(alignPanel);
2725     if (!copyAnnotation)
2726     {
2727       /*
2728        * remove all groups and annotation except for the automatic stuff
2729        */
2730       newap.av.getAlignment().deleteAllGroups();
2731       newap.av.getAlignment().deleteAllAnnotations(false);
2732     }
2733
2734     newap.av.setGatherViewsHere(false);
2735
2736     if (viewport.getViewName() == null)
2737     {
2738       viewport.setViewName(MessageManager
2739               .getString("label.view_name_original"));
2740     }
2741
2742     /*
2743      * Views share the same edits undo and redo stacks
2744      */
2745     newap.av.setHistoryList(viewport.getHistoryList());
2746     newap.av.setRedoList(viewport.getRedoList());
2747
2748     /*
2749      * copy any visualisation settings that are not saved in the project
2750      */
2751     newap.av.setColourAppliesToAllGroups(
2752             viewport.getColourAppliesToAllGroups());
2753
2754     /*
2755      * Views share the same mappings; need to deregister any new mappings
2756      * created by copyAlignPanel, and register the new reference to the shared
2757      * mappings
2758      */
2759     newap.av.replaceMappings(viewport.getAlignment());
2760
2761     /*
2762      * start up cDNA consensus (if applicable) now mappings are in place
2763      */
2764     if (newap.av.initComplementConsensus())
2765     {
2766       newap.refresh(true); // adjust layout of annotations
2767     }
2768
2769     newap.av.setViewName(getNewViewName(viewTitle));
2770
2771     addAlignmentPanel(newap, true);
2772     newap.alignmentChanged();
2773
2774     if (alignPanels.size() == 2)
2775     {
2776       viewport.setGatherViewsHere(true);
2777     }
2778     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2779     return newap;
2780   }
2781
2782   /**
2783    * Make a new name for the view, ensuring it is unique within the current
2784    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2785    * these now use viewId. Unique view names are still desirable for usability.)
2786    *
2787    * @param viewTitle
2788    * @return
2789    */
2790   protected String getNewViewName(String viewTitle)
2791   {
2792     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2793     boolean addFirstIndex = false;
2794     if (viewTitle == null || viewTitle.trim().length() == 0)
2795     {
2796       viewTitle = MessageManager.getString("action.view");
2797       addFirstIndex = true;
2798     }
2799     else
2800     {
2801       index = 1;// we count from 1 if given a specific name
2802     }
2803     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2804
2805     List<Component> comps = PaintRefresher.components
2806             .get(viewport.getSequenceSetId());
2807
2808     List<String> existingNames = getExistingViewNames(comps);
2809
2810     while (existingNames.contains(newViewName))
2811     {
2812       newViewName = viewTitle + " " + (++index);
2813     }
2814     return newViewName;
2815   }
2816
2817   /**
2818    * Returns a list of distinct view names found in the given list of
2819    * components. View names are held on the viewport of an AlignmentPanel.
2820    *
2821    * @param comps
2822    * @return
2823    */
2824   protected List<String> getExistingViewNames(List<Component> comps)
2825   {
2826     List<String> existingNames = new ArrayList<>();
2827     for (Component comp : comps)
2828     {
2829       if (comp instanceof AlignmentPanel)
2830       {
2831         AlignmentPanel ap = (AlignmentPanel) comp;
2832         if (!existingNames.contains(ap.av.getViewName()))
2833         {
2834           existingNames.add(ap.av.getViewName());
2835         }
2836       }
2837     }
2838     return existingNames;
2839   }
2840
2841   /**
2842    * Explode tabbed views into separate windows.
2843    */
2844   @Override
2845   public void expandViews_actionPerformed(ActionEvent e)
2846   {
2847     Desktop.explodeViews(this);
2848   }
2849
2850   /**
2851    * Gather views in separate windows back into a tabbed presentation.
2852    */
2853   @Override
2854   public void gatherViews_actionPerformed(ActionEvent e)
2855   {
2856     Desktop.instance.gatherViews(this);
2857   }
2858
2859   /**
2860    * DOCUMENT ME!
2861    *
2862    * @param e
2863    *          DOCUMENT ME!
2864    */
2865   @Override
2866   public void font_actionPerformed(ActionEvent e)
2867   {
2868     new FontChooser(alignPanel);
2869   }
2870
2871   /**
2872    * DOCUMENT ME!
2873    *
2874    * @param e
2875    *          DOCUMENT ME!
2876    */
2877   @Override
2878   protected void seqLimit_actionPerformed(ActionEvent e)
2879   {
2880     viewport.setShowJVSuffix(seqLimits.isSelected());
2881
2882     alignPanel.getIdPanel().getIdCanvas()
2883             .setPreferredSize(alignPanel.calculateIdWidth());
2884     alignPanel.paintAlignment(true, false);
2885   }
2886
2887   @Override
2888   public void idRightAlign_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setRightAlignIds(idRightAlign.isSelected());
2891     alignPanel.paintAlignment(false, false);
2892   }
2893
2894   @Override
2895   public void centreColumnLabels_actionPerformed(ActionEvent e)
2896   {
2897     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2898     alignPanel.paintAlignment(false, false);
2899   }
2900
2901   /*
2902    * (non-Javadoc)
2903    *
2904    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2905    */
2906   @Override
2907   protected void followHighlight_actionPerformed()
2908   {
2909     /*
2910      * Set the 'follow' flag on the Viewport (and scroll to position if now
2911      * true).
2912      */
2913     final boolean state = this.followHighlightMenuItem.getState();
2914     viewport.setFollowHighlight(state);
2915     if (state)
2916     {
2917       alignPanel.scrollToPosition(viewport.getSearchResults());
2918     }
2919   }
2920
2921   /**
2922    * DOCUMENT ME!
2923    *
2924    * @param e
2925    *          DOCUMENT ME!
2926    */
2927   @Override
2928   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2929   {
2930     viewport.setColourText(colourTextMenuItem.isSelected());
2931     alignPanel.paintAlignment(false, false);
2932   }
2933
2934   /**
2935    * DOCUMENT ME!
2936    *
2937    * @param e
2938    *          DOCUMENT ME!
2939    */
2940   @Override
2941   public void wrapMenuItem_actionPerformed(ActionEvent e)
2942   {
2943     scaleAbove.setVisible(wrapMenuItem.isSelected());
2944     scaleLeft.setVisible(wrapMenuItem.isSelected());
2945     scaleRight.setVisible(wrapMenuItem.isSelected());
2946     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2947     alignPanel.updateLayout();
2948   }
2949
2950   @Override
2951   public void showAllSeqs_actionPerformed(ActionEvent e)
2952   {
2953     viewport.showAllHiddenSeqs();
2954   }
2955
2956   @Override
2957   public void showAllColumns_actionPerformed(ActionEvent e)
2958   {
2959     viewport.showAllHiddenColumns();
2960     alignPanel.paintAlignment(true, true);
2961     viewport.sendSelection();
2962   }
2963
2964   @Override
2965   public void hideSelSequences_actionPerformed(ActionEvent e)
2966   {
2967     viewport.hideAllSelectedSeqs();
2968   }
2969
2970   /**
2971    * called by key handler and the hide all/show all menu items
2972    *
2973    * @param toggleSeqs
2974    * @param toggleCols
2975    */
2976   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2977   {
2978
2979     boolean hide = false;
2980     SequenceGroup sg = viewport.getSelectionGroup();
2981     if (!toggleSeqs && !toggleCols)
2982     {
2983       // Hide everything by the current selection - this is a hack - we do the
2984       // invert and then hide
2985       // first check that there will be visible columns after the invert.
2986       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2987               && sg.getStartRes() <= sg.getEndRes()))
2988       {
2989         // now invert the sequence set, if required - empty selection implies
2990         // that no hiding is required.
2991         if (sg != null)
2992         {
2993           invertSequenceMenuItem_actionPerformed(null);
2994           sg = viewport.getSelectionGroup();
2995           toggleSeqs = true;
2996
2997         }
2998         viewport.expandColSelection(sg, true);
2999         // finally invert the column selection and get the new sequence
3000         // selection.
3001         invertColSel_actionPerformed(null);
3002         toggleCols = true;
3003       }
3004     }
3005
3006     if (toggleSeqs)
3007     {
3008       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3009       {
3010         hideSelSequences_actionPerformed(null);
3011         hide = true;
3012       }
3013       else if (!(toggleCols && viewport.hasSelectedColumns()))
3014       {
3015         showAllSeqs_actionPerformed(null);
3016       }
3017     }
3018
3019     if (toggleCols)
3020     {
3021       if (viewport.hasSelectedColumns())
3022       {
3023         hideSelColumns_actionPerformed(null);
3024         if (!toggleSeqs)
3025         {
3026           viewport.setSelectionGroup(sg);
3027         }
3028       }
3029       else if (!hide)
3030       {
3031         showAllColumns_actionPerformed(null);
3032       }
3033     }
3034   }
3035
3036   /*
3037    * (non-Javadoc)
3038    *
3039    * @see
3040    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3041    * event.ActionEvent)
3042    */
3043   @Override
3044   public void hideAllButSelection_actionPerformed(ActionEvent e)
3045   {
3046     toggleHiddenRegions(false, false);
3047     viewport.sendSelection();
3048   }
3049
3050   /*
3051    * (non-Javadoc)
3052    *
3053    * @see
3054    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3055    * .ActionEvent)
3056    */
3057   @Override
3058   public void hideAllSelection_actionPerformed(ActionEvent e)
3059   {
3060     SequenceGroup sg = viewport.getSelectionGroup();
3061     viewport.expandColSelection(sg, false);
3062     viewport.hideAllSelectedSeqs();
3063     viewport.hideSelectedColumns();
3064     alignPanel.updateLayout();
3065     alignPanel.paintAlignment(true, true);
3066     viewport.sendSelection();
3067   }
3068
3069   /*
3070    * (non-Javadoc)
3071    *
3072    * @see
3073    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3074    * ActionEvent)
3075    */
3076   @Override
3077   public void showAllhidden_actionPerformed(ActionEvent e)
3078   {
3079     viewport.showAllHiddenColumns();
3080     viewport.showAllHiddenSeqs();
3081     alignPanel.paintAlignment(true, true);
3082     viewport.sendSelection();
3083   }
3084
3085   @Override
3086   public void hideSelColumns_actionPerformed(ActionEvent e)
3087   {
3088     viewport.hideSelectedColumns();
3089     alignPanel.updateLayout();
3090     alignPanel.paintAlignment(true, true);
3091     viewport.sendSelection();
3092   }
3093
3094   @Override
3095   public void hiddenMarkers_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3098     repaint();
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   protected void scaleAbove_actionPerformed(ActionEvent e)
3109   {
3110     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3111     alignPanel.updateLayout();
3112     alignPanel.paintAlignment(true, false);
3113   }
3114
3115   /**
3116    * DOCUMENT ME!
3117    *
3118    * @param e
3119    *          DOCUMENT ME!
3120    */
3121   @Override
3122   protected void scaleLeft_actionPerformed(ActionEvent e)
3123   {
3124     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3125     alignPanel.updateLayout();
3126     alignPanel.paintAlignment(true, false);
3127   }
3128
3129   /**
3130    * DOCUMENT ME!
3131    *
3132    * @param e
3133    *          DOCUMENT ME!
3134    */
3135   @Override
3136   protected void scaleRight_actionPerformed(ActionEvent e)
3137   {
3138     viewport.setScaleRightWrapped(scaleRight.isSelected());
3139     alignPanel.updateLayout();
3140     alignPanel.paintAlignment(true, false);
3141   }
3142
3143   /**
3144    * DOCUMENT ME!
3145    *
3146    * @param e
3147    *          DOCUMENT ME!
3148    */
3149   @Override
3150   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3151   {
3152     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3153     alignPanel.paintAlignment(false, false);
3154   }
3155
3156   /**
3157    * DOCUMENT ME!
3158    *
3159    * @param e
3160    *          DOCUMENT ME!
3161    */
3162   @Override
3163   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3164   {
3165     viewport.setShowText(viewTextMenuItem.isSelected());
3166     alignPanel.paintAlignment(false, false);
3167   }
3168
3169   /**
3170    * DOCUMENT ME!
3171    *
3172    * @param e
3173    *          DOCUMENT ME!
3174    */
3175   @Override
3176   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3177   {
3178     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3179     alignPanel.paintAlignment(false, false);
3180   }
3181
3182   public FeatureSettings featureSettings;
3183
3184   @Override
3185   public FeatureSettingsControllerI getFeatureSettingsUI()
3186   {
3187     return featureSettings;
3188   }
3189
3190   @Override
3191   public void featureSettings_actionPerformed(ActionEvent e)
3192   {
3193     showFeatureSettingsUI();
3194   }
3195
3196   @Override
3197   public FeatureSettingsControllerI showFeatureSettingsUI()
3198   {
3199     if (featureSettings != null)
3200     {
3201       featureSettings.closeOldSettings();
3202       featureSettings = null;
3203     }
3204     if (!showSeqFeatures.isSelected())
3205     {
3206       // make sure features are actually displayed
3207       showSeqFeatures.setSelected(true);
3208       showSeqFeatures_actionPerformed(null);
3209     }
3210     featureSettings = new FeatureSettings(this);
3211     return featureSettings;
3212   }
3213
3214   /**
3215    * Set or clear 'Show Sequence Features'
3216    *
3217    * @param evt
3218    *          DOCUMENT ME!
3219    */
3220   @Override
3221   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3222   {
3223     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3224     alignPanel.paintAlignment(true, true);
3225   }
3226
3227   /**
3228    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3229    * the annotations panel as a whole.
3230    *
3231    * The options to show/hide all annotations should be enabled when the panel
3232    * is shown, and disabled when the panel is hidden.
3233    *
3234    * @param e
3235    */
3236   @Override
3237   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3238   {
3239     final boolean setVisible = annotationPanelMenuItem.isSelected();
3240     viewport.setShowAnnotation(setVisible);
3241     this.showAllSeqAnnotations.setEnabled(setVisible);
3242     this.hideAllSeqAnnotations.setEnabled(setVisible);
3243     this.showAllAlAnnotations.setEnabled(setVisible);
3244     this.hideAllAlAnnotations.setEnabled(setVisible);
3245     alignPanel.updateLayout();
3246   }
3247
3248   @Override
3249   public void alignmentProperties()
3250   {
3251     JEditorPane editPane = new JEditorPane("text/html", "");
3252     editPane.setEditable(false);
3253     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3254             .formatAsHtml();
3255     editPane.setText(
3256             MessageManager.formatMessage("label.html_content", new Object[]
3257             { contents.toString() }));
3258     JInternalFrame frame = new JInternalFrame();
3259     frame.getContentPane().add(new JScrollPane(editPane));
3260
3261     Desktop.addInternalFrame(frame, MessageManager
3262             .formatMessage("label.alignment_properties", new Object[]
3263             { getTitle() }), 500, 400);
3264   }
3265
3266   /**
3267    * DOCUMENT ME!
3268    *
3269    * @param e
3270    *          DOCUMENT ME!
3271    */
3272   @Override
3273   public void overviewMenuItem_actionPerformed(ActionEvent e)
3274   {
3275     if (alignPanel.overviewPanel != null)
3276     {
3277       return;
3278     }
3279
3280     JInternalFrame frame = new JInternalFrame();
3281     final OverviewPanel overview = new OverviewPanel(alignPanel);
3282     frame.setContentPane(overview);
3283     Desktop.addInternalFrame(frame, MessageManager
3284             .formatMessage("label.overview_params", new Object[]
3285             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3286             true, true);
3287     frame.pack();
3288     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3289     frame.addInternalFrameListener(
3290             new javax.swing.event.InternalFrameAdapter()
3291             {
3292               @Override
3293               public void internalFrameClosed(
3294                       javax.swing.event.InternalFrameEvent evt)
3295               {
3296                 overview.dispose();
3297                 alignPanel.setOverviewPanel(null);
3298               };
3299             });
3300     if (getKeyListeners().length > 0)
3301     {
3302       frame.addKeyListener(getKeyListeners()[0]);
3303     }
3304
3305     alignPanel.setOverviewPanel(overview);
3306   }
3307
3308   @Override
3309   public void textColour_actionPerformed()
3310   {
3311     new TextColourChooser().chooseColour(alignPanel, null);
3312   }
3313
3314   /*
3315    * public void covariationColour_actionPerformed() {
3316    * changeColour(new
3317    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3318    * ()[0])); }
3319    */
3320   @Override
3321   public void annotationColour_actionPerformed()
3322   {
3323     new AnnotationColourChooser(viewport, alignPanel);
3324   }
3325
3326   @Override
3327   public void annotationColumn_actionPerformed(ActionEvent e)
3328   {
3329     new AnnotationColumnChooser(viewport, alignPanel);
3330   }
3331
3332   /**
3333    * Action on the user checking or unchecking the option to apply the selected
3334    * colour scheme to all groups. If unchecked, groups may have their own
3335    * independent colour schemes.
3336    *
3337    * @param selected
3338    */
3339   @Override
3340   public void applyToAllGroups_actionPerformed(boolean selected)
3341   {
3342     viewport.setColourAppliesToAllGroups(selected);
3343   }
3344
3345   /**
3346    * Action on user selecting a colour from the colour menu
3347    *
3348    * @param name
3349    *          the name (not the menu item label!) of the colour scheme
3350    */
3351   @Override
3352   public void changeColour_actionPerformed(String name)
3353   {
3354     /*
3355      * 'User Defined' opens a panel to configure or load a
3356      * user-defined colour scheme
3357      */
3358     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3359     {
3360       new UserDefinedColours(alignPanel);
3361       return;
3362     }
3363
3364     /*
3365      * otherwise set the chosen colour scheme (or null for 'None')
3366      */
3367     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3368             viewport,
3369             viewport.getAlignment(), viewport.getHiddenRepSequences());
3370     changeColour(cs);
3371   }
3372
3373   /**
3374    * Actions on setting or changing the alignment colour scheme
3375    *
3376    * @param cs
3377    */
3378   @Override
3379   public void changeColour(ColourSchemeI cs)
3380   {
3381     // TODO: pull up to controller method
3382     ColourMenuHelper.setColourSelected(colourMenu, cs);
3383
3384     viewport.setGlobalColourScheme(cs);
3385
3386     alignPanel.paintAlignment(true, true);
3387   }
3388
3389   /**
3390    * Show the PID threshold slider panel
3391    */
3392   @Override
3393   protected void modifyPID_actionPerformed()
3394   {
3395     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3396             alignPanel.getViewName());
3397     SliderPanel.showPIDSlider();
3398   }
3399
3400   /**
3401    * Show the Conservation slider panel
3402    */
3403   @Override
3404   protected void modifyConservation_actionPerformed()
3405   {
3406     SliderPanel.setConservationSlider(alignPanel,
3407             viewport.getResidueShading(), alignPanel.getViewName());
3408     SliderPanel.showConservationSlider();
3409   }
3410
3411   /**
3412    * Action on selecting or deselecting (Colour) By Conservation
3413    */
3414   @Override
3415   public void conservationMenuItem_actionPerformed(boolean selected)
3416   {
3417     modifyConservation.setEnabled(selected);
3418     viewport.setConservationSelected(selected);
3419     viewport.getResidueShading().setConservationApplied(selected);
3420
3421     changeColour(viewport.getGlobalColourScheme());
3422     if (selected)
3423     {
3424       modifyConservation_actionPerformed();
3425     }
3426     else
3427     {
3428       SliderPanel.hideConservationSlider();
3429     }
3430   }
3431
3432   /**
3433    * Action on selecting or deselecting (Colour) Above PID Threshold
3434    */
3435   @Override
3436   public void abovePIDThreshold_actionPerformed(boolean selected)
3437   {
3438     modifyPID.setEnabled(selected);
3439     viewport.setAbovePIDThreshold(selected);
3440     if (!selected)
3441     {
3442       viewport.getResidueShading().setThreshold(0,
3443               viewport.isIgnoreGapsConsensus());
3444     }
3445
3446     changeColour(viewport.getGlobalColourScheme());
3447     if (selected)
3448     {
3449       modifyPID_actionPerformed();
3450     }
3451     else
3452     {
3453       SliderPanel.hidePIDSlider();
3454     }
3455   }
3456
3457   /**
3458    * DOCUMENT ME!
3459    *
3460    * @param e
3461    *          DOCUMENT ME!
3462    */
3463   @Override
3464   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3465   {
3466     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3467     AlignmentSorter.sortByPID(viewport.getAlignment(),
3468             viewport.getAlignment().getSequenceAt(0));
3469     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3470             viewport.getAlignment()));
3471     alignPanel.paintAlignment(true, false);
3472   }
3473
3474   /**
3475    * DOCUMENT ME!
3476    *
3477    * @param e
3478    *          DOCUMENT ME!
3479    */
3480   @Override
3481   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3482   {
3483     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3484     AlignmentSorter.sortByID(viewport.getAlignment());
3485     addHistoryItem(
3486             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3487     alignPanel.paintAlignment(true, false);
3488   }
3489
3490   /**
3491    * DOCUMENT ME!
3492    *
3493    * @param e
3494    *          DOCUMENT ME!
3495    */
3496   @Override
3497   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3498   {
3499     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3500     AlignmentSorter.sortByLength(viewport.getAlignment());
3501     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3502             viewport.getAlignment()));
3503     alignPanel.paintAlignment(true, false);
3504   }
3505
3506   /**
3507    * DOCUMENT ME!
3508    *
3509    * @param e
3510    *          DOCUMENT ME!
3511    */
3512   @Override
3513   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3514   {
3515     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3516     AlignmentSorter.sortByGroup(viewport.getAlignment());
3517     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3518             viewport.getAlignment()));
3519
3520     alignPanel.paintAlignment(true, false);
3521   }
3522
3523   /**
3524    * DOCUMENT ME!
3525    *
3526    * @param e
3527    *          DOCUMENT ME!
3528    */
3529   @Override
3530   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3531   {
3532     new RedundancyPanel(alignPanel, this);
3533   }
3534
3535   /**
3536    * DOCUMENT ME!
3537    *
3538    * @param e
3539    *          DOCUMENT ME!
3540    */
3541   @Override
3542   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3543   {
3544     if ((viewport.getSelectionGroup() == null)
3545             || (viewport.getSelectionGroup().getSize() < 2))
3546     {
3547       JvOptionPane.showInternalMessageDialog(this,
3548               MessageManager.getString(
3549                       "label.you_must_select_least_two_sequences"),
3550               MessageManager.getString("label.invalid_selection"),
3551               JvOptionPane.WARNING_MESSAGE);
3552     }
3553     else
3554     {
3555       JInternalFrame frame = new JInternalFrame();
3556       frame.setContentPane(new PairwiseAlignPanel(viewport));
3557       Desktop.addInternalFrame(frame,
3558               MessageManager.getString("action.pairwise_alignment"), 600,
3559               500);
3560     }
3561   }
3562
3563   @Override
3564   public void autoCalculate_actionPerformed(ActionEvent e)
3565   {
3566     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3567     if (viewport.autoCalculateConsensus)
3568     {
3569       viewport.firePropertyChange("alignment", null,
3570               viewport.getAlignment().getSequences());
3571     }
3572   }
3573
3574   @Override
3575   public void sortByTreeOption_actionPerformed(ActionEvent e)
3576   {
3577     viewport.sortByTree = sortByTree.isSelected();
3578   }
3579
3580   @Override
3581   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3582   {
3583     viewport.followSelection = listenToViewSelections.isSelected();
3584   }
3585
3586   /**
3587    * Constructs a tree panel and adds it to the desktop
3588    *
3589    * @param type
3590    *          tree type (NJ or AV)
3591    * @param modelName
3592    *          name of score model used to compute the tree
3593    * @param options
3594    *          parameters for the distance or similarity calculation
3595    */
3596   void newTreePanel(String type, String modelName,
3597           SimilarityParamsI options)
3598   {
3599     String frameTitle = "";
3600     TreePanel tp;
3601
3602     boolean onSelection = false;
3603     if (viewport.getSelectionGroup() != null
3604             && viewport.getSelectionGroup().getSize() > 0)
3605     {
3606       SequenceGroup sg = viewport.getSelectionGroup();
3607
3608       /* Decide if the selection is a column region */
3609       for (SequenceI _s : sg.getSequences())
3610       {
3611         if (_s.getLength() < sg.getEndRes())
3612         {
3613           JvOptionPane.showMessageDialog(Desktop.desktop,
3614                   MessageManager.getString(
3615                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3616                   MessageManager.getString(
3617                           "label.sequences_selection_not_aligned"),
3618                   JvOptionPane.WARNING_MESSAGE);
3619
3620           return;
3621         }
3622       }
3623       onSelection = true;
3624     }
3625     else
3626     {
3627       if (viewport.getAlignment().getHeight() < 2)
3628       {
3629         return;
3630       }
3631     }
3632
3633     tp = new TreePanel(alignPanel, type, modelName, options);
3634     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3635
3636     frameTitle += " from ";
3637
3638     if (viewport.getViewName() != null)
3639     {
3640       frameTitle += viewport.getViewName() + " of ";
3641     }
3642
3643     frameTitle += this.title;
3644
3645     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3646   }
3647
3648   /**
3649    * DOCUMENT ME!
3650    *
3651    * @param title
3652    *          DOCUMENT ME!
3653    * @param order
3654    *          DOCUMENT ME!
3655    */
3656   public void addSortByOrderMenuItem(String title,
3657           final AlignmentOrder order)
3658   {
3659     final JMenuItem item = new JMenuItem(MessageManager
3660             .formatMessage("action.by_title_param", new Object[]
3661             { title }));
3662     sort.add(item);
3663     item.addActionListener(new java.awt.event.ActionListener()
3664     {
3665       @Override
3666       public void actionPerformed(ActionEvent e)
3667       {
3668         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3669
3670         // TODO: JBPNote - have to map order entries to curent SequenceI
3671         // pointers
3672         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3673
3674         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3675                 viewport.getAlignment()));
3676
3677         alignPanel.paintAlignment(true, false);
3678       }
3679     });
3680   }
3681
3682   /**
3683    * Add a new sort by annotation score menu item
3684    *
3685    * @param sort
3686    *          the menu to add the option to
3687    * @param scoreLabel
3688    *          the label used to retrieve scores for each sequence on the
3689    *          alignment
3690    */
3691   public void addSortByAnnotScoreMenuItem(JMenu sort,
3692           final String scoreLabel)
3693   {
3694     final JMenuItem item = new JMenuItem(scoreLabel);
3695     sort.add(item);
3696     item.addActionListener(new java.awt.event.ActionListener()
3697     {
3698       @Override
3699       public void actionPerformed(ActionEvent e)
3700       {
3701         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3702         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3703                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3704         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3705                 viewport.getAlignment()));
3706         alignPanel.paintAlignment(true, false);
3707       }
3708     });
3709   }
3710
3711   /**
3712    * last hash for alignment's annotation array - used to minimise cost of
3713    * rebuild.
3714    */
3715   protected int _annotationScoreVectorHash;
3716
3717   /**
3718    * search the alignment and rebuild the sort by annotation score submenu the
3719    * last alignment annotation vector hash is stored to minimize cost of
3720    * rebuilding in subsequence calls.
3721    *
3722    */
3723   @Override
3724   public void buildSortByAnnotationScoresMenu()
3725   {
3726     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3727     {
3728       return;
3729     }
3730
3731     if (viewport.getAlignment().getAlignmentAnnotation()
3732             .hashCode() != _annotationScoreVectorHash)
3733     {
3734       sortByAnnotScore.removeAll();
3735       // almost certainly a quicker way to do this - but we keep it simple
3736       Hashtable scoreSorts = new Hashtable();
3737       AlignmentAnnotation aann[];
3738       for (SequenceI sqa : viewport.getAlignment().getSequences())
3739       {
3740         aann = sqa.getAnnotation();
3741         for (int i = 0; aann != null && i < aann.length; i++)
3742         {
3743           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3744           {
3745             scoreSorts.put(aann[i].label, aann[i].label);
3746           }
3747         }
3748       }
3749       Enumeration labels = scoreSorts.keys();
3750       while (labels.hasMoreElements())
3751       {
3752         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3753                 (String) labels.nextElement());
3754       }
3755       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3756       scoreSorts.clear();
3757
3758       _annotationScoreVectorHash = viewport.getAlignment()
3759               .getAlignmentAnnotation().hashCode();
3760     }
3761   }
3762
3763   /**
3764    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3765    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3766    * call. Listeners are added to remove the menu item when the treePanel is
3767    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3768    * modified.
3769    */
3770   @Override
3771   public void buildTreeSortMenu()
3772   {
3773     sortByTreeMenu.removeAll();
3774
3775     List<Component> comps = PaintRefresher.components
3776             .get(viewport.getSequenceSetId());
3777     List<TreePanel> treePanels = new ArrayList<>();
3778     for (Component comp : comps)
3779     {
3780       if (comp instanceof TreePanel)
3781       {
3782         treePanels.add((TreePanel) comp);
3783       }
3784     }
3785
3786     if (treePanels.size() < 1)
3787     {
3788       sortByTreeMenu.setVisible(false);
3789       return;
3790     }
3791
3792     sortByTreeMenu.setVisible(true);
3793
3794     for (final TreePanel tp : treePanels)
3795     {
3796       final JMenuItem item = new JMenuItem(tp.getTitle());
3797       item.addActionListener(new java.awt.event.ActionListener()
3798       {
3799         @Override
3800         public void actionPerformed(ActionEvent e)
3801         {
3802           tp.sortByTree_actionPerformed();
3803           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3804
3805         }
3806       });
3807
3808       sortByTreeMenu.add(item);
3809     }
3810   }
3811
3812   public boolean sortBy(AlignmentOrder alorder, String undoname)
3813   {
3814     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3815     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3816     if (undoname != null)
3817     {
3818       addHistoryItem(new OrderCommand(undoname, oldOrder,
3819               viewport.getAlignment()));
3820     }
3821     alignPanel.paintAlignment(true, false);
3822     return true;
3823   }
3824
3825   /**
3826    * Work out whether the whole set of sequences or just the selected set will
3827    * be submitted for multiple alignment.
3828    *
3829    */
3830   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3831   {
3832     // Now, check we have enough sequences
3833     AlignmentView msa = null;
3834
3835     if ((viewport.getSelectionGroup() != null)
3836             && (viewport.getSelectionGroup().getSize() > 1))
3837     {
3838       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3839       // some common interface!
3840       /*
3841        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3842        * SequenceI[sz = seqs.getSize(false)];
3843        *
3844        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3845        * seqs.getSequenceAt(i); }
3846        */
3847       msa = viewport.getAlignmentView(true);
3848     }
3849     else if (viewport.getSelectionGroup() != null
3850             && viewport.getSelectionGroup().getSize() == 1)
3851     {
3852       int option = JvOptionPane.showConfirmDialog(this,
3853               MessageManager.getString("warn.oneseq_msainput_selection"),
3854               MessageManager.getString("label.invalid_selection"),
3855               JvOptionPane.OK_CANCEL_OPTION);
3856       if (option == JvOptionPane.OK_OPTION)
3857       {
3858         msa = viewport.getAlignmentView(false);
3859       }
3860     }
3861     else
3862     {
3863       msa = viewport.getAlignmentView(false);
3864     }
3865     return msa;
3866   }
3867
3868   /**
3869    * Decides what is submitted to a secondary structure prediction service: the
3870    * first sequence in the alignment, or in the current selection, or, if the
3871    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3872    * region or the whole alignment. (where the first sequence in the set is the
3873    * one that the prediction will be for).
3874    */
3875   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3876   {
3877     AlignmentView seqs = null;
3878
3879     if ((viewport.getSelectionGroup() != null)
3880             && (viewport.getSelectionGroup().getSize() > 0))
3881     {
3882       seqs = viewport.getAlignmentView(true);
3883     }
3884     else
3885     {
3886       seqs = viewport.getAlignmentView(false);
3887     }
3888     // limit sequences - JBPNote in future - could spawn multiple prediction
3889     // jobs
3890     // TODO: viewport.getAlignment().isAligned is a global state - the local
3891     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3892     if (!viewport.getAlignment().isAligned(false))
3893     {
3894       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3895       // TODO: if seqs.getSequences().length>1 then should really have warned
3896       // user!
3897
3898     }
3899     return seqs;
3900   }
3901
3902   /**
3903    * DOCUMENT ME!
3904    *
3905    * @param e
3906    *          DOCUMENT ME!
3907    */
3908   @Override
3909   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3910   {
3911     // Pick the tree file
3912     JalviewFileChooser chooser = new JalviewFileChooser(
3913             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3914     chooser.setFileView(new JalviewFileView());
3915     chooser.setDialogTitle(
3916             MessageManager.getString("label.select_newick_like_tree_file"));
3917     chooser.setToolTipText(
3918             MessageManager.getString("label.load_tree_file"));
3919
3920     int value = chooser.showOpenDialog(null);
3921
3922     if (value == JalviewFileChooser.APPROVE_OPTION)
3923     {
3924       String filePath = chooser.getSelectedFile().getPath();
3925       Cache.setProperty("LAST_DIRECTORY", filePath);
3926       NewickFile fin = null;
3927       try
3928       {
3929         fin = new NewickFile(filePath, DataSourceType.FILE);
3930         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3931       } catch (Exception ex)
3932       {
3933         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3934                 MessageManager.getString("label.problem_reading_tree_file"),
3935                 JvOptionPane.WARNING_MESSAGE);
3936         ex.printStackTrace();
3937       }
3938       if (fin != null && fin.hasWarningMessage())
3939       {
3940         JvOptionPane.showMessageDialog(Desktop.desktop,
3941                 fin.getWarningMessage(),
3942                 MessageManager
3943                         .getString("label.possible_problem_with_tree_file"),
3944                 JvOptionPane.WARNING_MESSAGE);
3945       }
3946     }
3947   }
3948
3949   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3950   {
3951     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3952   }
3953
3954   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3955           int h, int x, int y)
3956   {
3957     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3958   }
3959
3960   /**
3961    * Add a treeviewer for the tree extracted from a Newick file object to the
3962    * current alignment view
3963    *
3964    * @param nf
3965    *          the tree
3966    * @param title
3967    *          tree viewer title
3968    * @param input
3969    *          Associated alignment input data (or null)
3970    * @param w
3971    *          width
3972    * @param h
3973    *          height
3974    * @param x
3975    *          position
3976    * @param y
3977    *          position
3978    * @return TreePanel handle
3979    */
3980   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3981           AlignmentView input, int w, int h, int x, int y)
3982   {
3983     TreePanel tp = null;
3984
3985     try
3986     {
3987       nf.parse();
3988
3989       if (nf.getTree() != null)
3990       {
3991         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3992
3993         tp.setSize(w, h);
3994
3995         if (x > 0 && y > 0)
3996         {
3997           tp.setLocation(x, y);
3998         }
3999
4000         Desktop.addInternalFrame(tp, treeTitle, w, h);
4001       }
4002     } catch (Exception ex)
4003     {
4004       ex.printStackTrace();
4005     }
4006
4007     return tp;
4008   }
4009
4010   private boolean buildingMenu = false;
4011
4012   /**
4013    * Generates menu items and listener event actions for web service clients
4014    *
4015    */
4016   public void BuildWebServiceMenu()
4017   {
4018     while (buildingMenu)
4019     {
4020       try
4021       {
4022         System.err.println("Waiting for building menu to finish.");
4023         Thread.sleep(10);
4024       } catch (Exception e)
4025       {
4026       }
4027     }
4028     final AlignFrame me = this;
4029     buildingMenu = true;
4030     new Thread(new Runnable()
4031     {
4032       @Override
4033       public void run()
4034       {
4035         final List<JMenuItem> legacyItems = new ArrayList<>();
4036         try
4037         {
4038           // System.err.println("Building ws menu again "
4039           // + Thread.currentThread());
4040           // TODO: add support for context dependent disabling of services based
4041           // on
4042           // alignment and current selection
4043           // TODO: add additional serviceHandle parameter to specify abstract
4044           // handler
4045           // class independently of AbstractName
4046           // TODO: add in rediscovery GUI function to restart discoverer
4047           // TODO: group services by location as well as function and/or
4048           // introduce
4049           // object broker mechanism.
4050           final Vector<JMenu> wsmenu = new Vector<>();
4051           final IProgressIndicator af = me;
4052
4053           /*
4054            * do not i18n these strings - they are hard-coded in class
4055            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4056            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4057            */
4058           final JMenu msawsmenu = new JMenu("Alignment");
4059           final JMenu secstrmenu = new JMenu(
4060                   "Secondary Structure Prediction");
4061           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4062           final JMenu analymenu = new JMenu("Analysis");
4063           final JMenu dismenu = new JMenu("Protein Disorder");
4064           // JAL-940 - only show secondary structure prediction services from
4065           // the legacy server
4066           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4067               // &&
4068           Discoverer.services != null && (Discoverer.services.size() > 0))
4069           {
4070             // TODO: refactor to allow list of AbstractName/Handler bindings to
4071             // be
4072             // stored or retrieved from elsewhere
4073             // No MSAWS used any more:
4074             // Vector msaws = null; // (Vector)
4075             // Discoverer.services.get("MsaWS");
4076             Vector secstrpr = (Vector) Discoverer.services
4077                     .get("SecStrPred");
4078             if (secstrpr != null)
4079             {
4080               // Add any secondary structure prediction services
4081               for (int i = 0, j = secstrpr.size(); i < j; i++)
4082               {
4083                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4084                         .get(i);
4085                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4086                         .getServiceClient(sh);
4087                 int p = secstrmenu.getItemCount();
4088                 impl.attachWSMenuEntry(secstrmenu, me);
4089                 int q = secstrmenu.getItemCount();
4090                 for (int litm = p; litm < q; litm++)
4091                 {
4092                   legacyItems.add(secstrmenu.getItem(litm));
4093                 }
4094               }
4095             }
4096           }
4097
4098           // Add all submenus in the order they should appear on the web
4099           // services menu
4100           wsmenu.add(msawsmenu);
4101           wsmenu.add(secstrmenu);
4102           wsmenu.add(dismenu);
4103           wsmenu.add(analymenu);
4104           // No search services yet
4105           // wsmenu.add(seqsrchmenu);
4106
4107           javax.swing.SwingUtilities.invokeLater(new Runnable()
4108           {
4109             @Override
4110             public void run()
4111             {
4112               try
4113               {
4114                 webService.removeAll();
4115                 // first, add discovered services onto the webservices menu
4116                 if (wsmenu.size() > 0)
4117                 {
4118                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4119                   {
4120                     webService.add(wsmenu.get(i));
4121                   }
4122                 }
4123                 else
4124                 {
4125                   webService.add(me.webServiceNoServices);
4126                 }
4127                 // TODO: move into separate menu builder class.
4128                 boolean new_sspred = false;
4129                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4130                 {
4131                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4132                   if (jws2servs != null)
4133                   {
4134                     if (jws2servs.hasServices())
4135                     {
4136                       jws2servs.attachWSMenuEntry(webService, me);
4137                       for (Jws2Instance sv : jws2servs.getServices())
4138                       {
4139                         if (sv.description.toLowerCase().contains("jpred"))
4140                         {
4141                           for (JMenuItem jmi : legacyItems)
4142                           {
4143                             jmi.setVisible(false);
4144                           }
4145                         }
4146                       }
4147
4148                     }
4149                     if (jws2servs.isRunning())
4150                     {
4151                       JMenuItem tm = new JMenuItem(
4152                               "Still discovering JABA Services");
4153                       tm.setEnabled(false);
4154                       webService.add(tm);
4155                     }
4156                   }
4157                 }
4158                 build_urlServiceMenu(me.webService);
4159                 build_fetchdbmenu(webService);
4160                 for (JMenu item : wsmenu)
4161                 {
4162                   if (item.getItemCount() == 0)
4163                   {
4164                     item.setEnabled(false);
4165                   }
4166                   else
4167                   {
4168                     item.setEnabled(true);
4169                   }
4170                 }
4171               } catch (Exception e)
4172               {
4173                 Cache.log.debug(
4174                         "Exception during web service menu building process.",
4175                         e);
4176               }
4177             }
4178           });
4179         } catch (Exception e)
4180         {
4181         }
4182         buildingMenu = false;
4183       }
4184     }).start();
4185
4186   }
4187
4188   /**
4189    * construct any groupURL type service menu entries.
4190    *
4191    * @param webService
4192    */
4193   private void build_urlServiceMenu(JMenu webService)
4194   {
4195     // TODO: remove this code when 2.7 is released
4196     // DEBUG - alignmentView
4197     /*
4198      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4199      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4200      *
4201      * @Override public void actionPerformed(ActionEvent e) {
4202      * jalview.datamodel.AlignmentView
4203      * .testSelectionViews(af.viewport.getAlignment(),
4204      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4205      *
4206      * }); webService.add(testAlView);
4207      */
4208     // TODO: refactor to RestClient discoverer and merge menu entries for
4209     // rest-style services with other types of analysis/calculation service
4210     // SHmmr test client - still being implemented.
4211     // DEBUG - alignmentView
4212
4213     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4214             .getRestClients())
4215     {
4216       client.attachWSMenuEntry(
4217               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4218               this);
4219     }
4220   }
4221
4222   /**
4223    * Searches the alignment sequences for xRefs and builds the Show
4224    * Cross-References menu (formerly called Show Products), with database
4225    * sources for which cross-references are found (protein sources for a
4226    * nucleotide alignment and vice versa)
4227    *
4228    * @return true if Show Cross-references menu should be enabled
4229    */
4230   public boolean canShowProducts()
4231   {
4232     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4233     AlignmentI dataset = viewport.getAlignment().getDataset();
4234
4235     showProducts.removeAll();
4236     final boolean dna = viewport.getAlignment().isNucleotide();
4237
4238     if (seqs == null || seqs.length == 0)
4239     {
4240       // nothing to see here.
4241       return false;
4242     }
4243
4244     boolean showp = false;
4245     try
4246     {
4247       List<String> ptypes = new CrossRef(seqs, dataset)
4248               .findXrefSourcesForSequences(dna);
4249
4250       for (final String source : ptypes)
4251       {
4252         showp = true;
4253         final AlignFrame af = this;
4254         JMenuItem xtype = new JMenuItem(source);
4255         xtype.addActionListener(new ActionListener()
4256         {
4257           @Override
4258           public void actionPerformed(ActionEvent e)
4259           {
4260             showProductsFor(af.viewport.getSequenceSelection(), dna,
4261                     source);
4262           }
4263         });
4264         showProducts.add(xtype);
4265       }
4266       showProducts.setVisible(showp);
4267       showProducts.setEnabled(showp);
4268     } catch (Exception e)
4269     {
4270       Cache.log.warn(
4271               "canShowProducts threw an exception - please report to help@jalview.org",
4272               e);
4273       return false;
4274     }
4275     return showp;
4276   }
4277
4278   /**
4279    * Finds and displays cross-references for the selected sequences (protein
4280    * products for nucleotide sequences, dna coding sequences for peptides).
4281    *
4282    * @param sel
4283    *          the sequences to show cross-references for
4284    * @param dna
4285    *          true if from a nucleotide alignment (so showing proteins)
4286    * @param source
4287    *          the database to show cross-references for
4288    */
4289   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4290           final String source)
4291   {
4292     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4293             .start();
4294   }
4295
4296   /**
4297    * Construct and display a new frame containing the translation of this
4298    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4299    */
4300   @Override
4301   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4302   {
4303     AlignmentI al = null;
4304     try
4305     {
4306       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4307
4308       al = dna.translateCdna(codeTable);
4309     } catch (Exception ex)
4310     {
4311       jalview.bin.Cache.log.error(
4312               "Exception during translation. Please report this !", ex);
4313       final String msg = MessageManager.getString(
4314               "label.error_when_translating_sequences_submit_bug_report");
4315       final String errorTitle = MessageManager
4316               .getString("label.implementation_error")
4317               + MessageManager.getString("label.translation_failed");
4318       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4319               JvOptionPane.ERROR_MESSAGE);
4320       return;
4321     }
4322     if (al == null || al.getHeight() == 0)
4323     {
4324       final String msg = MessageManager.getString(
4325               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4326       final String errorTitle = MessageManager
4327               .getString("label.translation_failed");
4328       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4329               JvOptionPane.WARNING_MESSAGE);
4330     }
4331     else
4332     {
4333       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4334       af.setFileFormat(this.currentFileFormat);
4335       final String newTitle = MessageManager
4336               .formatMessage("label.translation_of_params", new Object[]
4337               { this.getTitle(), codeTable.getId() });
4338       af.setTitle(newTitle);
4339       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4340       {
4341         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4342         viewport.openSplitFrame(af, new Alignment(seqs));
4343       }
4344       else
4345       {
4346         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4347                 DEFAULT_HEIGHT);
4348       }
4349     }
4350   }
4351
4352   /**
4353    * Set the file format
4354    *
4355    * @param format
4356    */
4357   public void setFileFormat(FileFormatI format)
4358   {
4359     this.currentFileFormat = format;
4360   }
4361
4362   /**
4363    * Try to load a features file onto the alignment.
4364    *
4365    * @param file
4366    *          contents or path to retrieve file
4367    * @param sourceType
4368    *          access mode of file (see jalview.io.AlignFile)
4369    * @return true if features file was parsed correctly.
4370    */
4371   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4372   {
4373     return avc.parseFeaturesFile(file, sourceType,
4374             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4375
4376   }
4377
4378   @Override
4379   public void refreshFeatureUI(boolean enableIfNecessary)
4380   {
4381     // note - currently this is only still here rather than in the controller
4382     // because of the featureSettings hard reference that is yet to be
4383     // abstracted
4384     if (enableIfNecessary)
4385     {
4386       viewport.setShowSequenceFeatures(true);
4387       showSeqFeatures.setSelected(true);
4388     }
4389
4390   }
4391
4392   @Override
4393   public void dragEnter(DropTargetDragEvent evt)
4394   {
4395   }
4396
4397   @Override
4398   public void dragExit(DropTargetEvent evt)
4399   {
4400   }
4401
4402   @Override
4403   public void dragOver(DropTargetDragEvent evt)
4404   {
4405   }
4406
4407   @Override
4408   public void dropActionChanged(DropTargetDragEvent evt)
4409   {
4410   }
4411
4412   @Override
4413   public void drop(DropTargetDropEvent evt)
4414   {
4415     // JAL-1552 - acceptDrop required before getTransferable call for
4416     // Java's Transferable for native dnd
4417     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4418     Transferable t = evt.getTransferable();
4419     final AlignFrame thisaf = this;
4420     final List<String> files = new ArrayList<>();
4421     List<DataSourceType> protocols = new ArrayList<>();
4422
4423     try
4424     {
4425       Desktop.transferFromDropTarget(files, protocols, evt, t);
4426     } catch (Exception e)
4427     {
4428       e.printStackTrace();
4429     }
4430     if (files != null)
4431     {
4432       new Thread(new Runnable()
4433       {
4434         @Override
4435         public void run()
4436         {
4437           try
4438           {
4439             // check to see if any of these files have names matching sequences
4440             // in
4441             // the alignment
4442             SequenceIdMatcher idm = new SequenceIdMatcher(
4443                     viewport.getAlignment().getSequencesArray());
4444             /**
4445              * Object[] { String,SequenceI}
4446              */
4447             ArrayList<Object[]> filesmatched = new ArrayList<>();
4448             ArrayList<String> filesnotmatched = new ArrayList<>();
4449             for (int i = 0; i < files.size(); i++)
4450             {
4451               String file = files.get(i).toString();
4452               String pdbfn = "";
4453               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4454               if (protocol == DataSourceType.FILE)
4455               {
4456                 File fl = new File(file);
4457                 pdbfn = fl.getName();
4458               }
4459               else if (protocol == DataSourceType.URL)
4460               {
4461                 URL url = new URL(file);
4462                 pdbfn = url.getFile();
4463               }
4464               if (pdbfn.length() > 0)
4465               {
4466                 // attempt to find a match in the alignment
4467                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4468                 int l = 0, c = pdbfn.indexOf(".");
4469                 while (mtch == null && c != -1)
4470                 {
4471                   do
4472                   {
4473                     l = c;
4474                   } while ((c = pdbfn.indexOf(".", l)) > l);
4475                   if (l > -1)
4476                   {
4477                     pdbfn = pdbfn.substring(0, l);
4478                   }
4479                   mtch = idm.findAllIdMatches(pdbfn);
4480                 }
4481                 if (mtch != null)
4482                 {
4483                   FileFormatI type = null;
4484                   try
4485                   {
4486                     type = new IdentifyFile().identify(file, protocol);
4487                   } catch (Exception ex)
4488                   {
4489                     type = null;
4490                   }
4491                   if (type != null && type.isStructureFile())
4492                   {
4493                     filesmatched.add(new Object[] { file, protocol, mtch });
4494                     continue;
4495                   }
4496                 }
4497                 // File wasn't named like one of the sequences or wasn't a PDB
4498                 // file.
4499                 filesnotmatched.add(file);
4500               }
4501             }
4502             int assocfiles = 0;
4503             if (filesmatched.size() > 0)
4504             {
4505               boolean autoAssociate = Cache
4506                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4507               if (!autoAssociate)
4508               {
4509                 String msg = MessageManager.formatMessage(
4510                         "label.automatically_associate_structure_files_with_sequences_same_name",
4511                         new Object[]
4512                         { Integer.valueOf(filesmatched.size())
4513                                 .toString() });
4514                 String ttl = MessageManager.getString(
4515                         "label.automatically_associate_structure_files_by_name");
4516                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4517                         ttl, JvOptionPane.YES_NO_OPTION);
4518                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4519               }
4520               if (autoAssociate)
4521               {
4522                 for (Object[] fm : filesmatched)
4523                 {
4524                   // try and associate
4525                   // TODO: may want to set a standard ID naming formalism for
4526                   // associating PDB files which have no IDs.
4527                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4528                   {
4529                     PDBEntry pe = new AssociatePdbFileWithSeq()
4530                             .associatePdbWithSeq((String) fm[0],
4531                                     (DataSourceType) fm[1], toassoc, false,
4532                                     Desktop.instance);
4533                     if (pe != null)
4534                     {
4535                       System.err.println("Associated file : "
4536                               + ((String) fm[0]) + " with "
4537                               + toassoc.getDisplayId(true));
4538                       assocfiles++;
4539                     }
4540                   }
4541                   // TODO: do we need to update overview ? only if features are
4542                   // shown I guess
4543                   alignPanel.paintAlignment(true, false);
4544                 }
4545               }
4546               else
4547               {
4548                 /*
4549                  * add declined structures as sequences
4550                  */
4551                 for (Object[] o : filesmatched)
4552                 {
4553                   filesnotmatched.add((String) o[0]);
4554                 }
4555               }
4556             }
4557             if (filesnotmatched.size() > 0)
4558             {
4559               if (assocfiles > 0 && (Cache.getDefault(
4560                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4561                       || JvOptionPane.showConfirmDialog(thisaf,
4562                               "<html>" + MessageManager.formatMessage(
4563                                       "label.ignore_unmatched_dropped_files_info",
4564                                       new Object[]
4565                                       { Integer.valueOf(
4566                                               filesnotmatched.size())
4567                                               .toString() })
4568                                       + "</html>",
4569                               MessageManager.getString(
4570                                       "label.ignore_unmatched_dropped_files"),
4571                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4572               {
4573                 return;
4574               }
4575               for (String fn : filesnotmatched)
4576               {
4577                 loadJalviewDataFile(fn, null, null, null);
4578               }
4579
4580             }
4581           } catch (Exception ex)
4582           {
4583             ex.printStackTrace();
4584           }
4585         }
4586       }).start();
4587     }
4588   }
4589
4590   /**
4591    * Attempt to load a "dropped" file or URL string, by testing in turn for
4592    * <ul>
4593    * <li>an Annotation file</li>
4594    * <li>a JNet file</li>
4595    * <li>a features file</li>
4596    * <li>else try to interpret as an alignment file</li>
4597    * </ul>
4598    *
4599    * @param file
4600    *          either a filename or a URL string.
4601    */
4602   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4603           FileFormatI format, SequenceI assocSeq)
4604   {
4605     try
4606     {
4607       if (sourceType == null)
4608       {
4609         sourceType = FormatAdapter.checkProtocol(file);
4610       }
4611       // if the file isn't identified, or not positively identified as some
4612       // other filetype (PFAM is default unidentified alignment file type) then
4613       // try to parse as annotation.
4614       boolean isAnnotation = (format == null
4615               || FileFormat.Pfam.equals(format))
4616                       ? new AnnotationFile().annotateAlignmentView(viewport,
4617                               file, sourceType)
4618                       : false;
4619
4620       if (!isAnnotation)
4621       {
4622         // first see if its a T-COFFEE score file
4623         TCoffeeScoreFile tcf = null;
4624         try
4625         {
4626           tcf = new TCoffeeScoreFile(file, sourceType);
4627           if (tcf.isValid())
4628           {
4629             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4630             {
4631               buildColourMenu();
4632               changeColour(
4633                       new TCoffeeColourScheme(viewport.getAlignment()));
4634               isAnnotation = true;
4635               statusBar.setText(MessageManager.getString(
4636                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4637             }
4638             else
4639             {
4640               // some problem - if no warning its probable that the ID matching
4641               // process didn't work
4642               JvOptionPane.showMessageDialog(Desktop.desktop,
4643                       tcf.getWarningMessage() == null
4644                               ? MessageManager.getString(
4645                                       "label.check_file_matches_sequence_ids_alignment")
4646                               : tcf.getWarningMessage(),
4647                       MessageManager.getString(
4648                               "label.problem_reading_tcoffee_score_file"),
4649                       JvOptionPane.WARNING_MESSAGE);
4650             }
4651           }
4652           else
4653           {
4654             tcf = null;
4655           }
4656         } catch (Exception x)
4657         {
4658           Cache.log.debug(
4659                   "Exception when processing data source as T-COFFEE score file",
4660                   x);
4661           tcf = null;
4662         }
4663         if (tcf == null)
4664         {
4665           // try to see if its a JNet 'concise' style annotation file *before*
4666           // we
4667           // try to parse it as a features file
4668           if (format == null)
4669           {
4670             format = new IdentifyFile().identify(file, sourceType);
4671           }
4672           if (FileFormat.ScoreMatrix == format)
4673           {
4674             ScoreMatrixFile sm = new ScoreMatrixFile(
4675                     new FileParse(file, sourceType));
4676             sm.parse();
4677             // todo: i18n this message
4678             statusBar.setText(MessageManager.formatMessage(
4679                     "label.successfully_loaded_matrix",
4680                     sm.getMatrixName()));
4681           }
4682           else if (FileFormat.Jnet.equals(format))
4683           {
4684             JPredFile predictions = new JPredFile(file, sourceType);
4685             new JnetAnnotationMaker();
4686             JnetAnnotationMaker.add_annotation(predictions,
4687                     viewport.getAlignment(), 0, false);
4688             viewport.getAlignment().setupJPredAlignment();
4689             isAnnotation = true;
4690           }
4691           // else if (IdentifyFile.FeaturesFile.equals(format))
4692           else if (FileFormat.Features.equals(format))
4693           {
4694             if (parseFeaturesFile(file, sourceType))
4695             {
4696               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4697               if (splitFrame != null)
4698               {
4699                 splitFrame.repaint();
4700               }
4701               else
4702               {
4703                 alignPanel.paintAlignment(true, true);
4704               }
4705             }
4706           }
4707           else
4708           {
4709             new FileLoader().LoadFile(viewport, file, sourceType, format);
4710           }
4711         }
4712       }
4713       if (isAnnotation)
4714       {
4715
4716         alignPanel.adjustAnnotationHeight();
4717         viewport.updateSequenceIdColours();
4718         buildSortByAnnotationScoresMenu();
4719         alignPanel.paintAlignment(true, true);
4720       }
4721     } catch (Exception ex)
4722     {
4723       ex.printStackTrace();
4724     } catch (OutOfMemoryError oom)
4725     {
4726       try
4727       {
4728         System.gc();
4729       } catch (Exception x)
4730       {
4731       }
4732       new OOMWarning(
4733               "loading data "
4734                       + (sourceType != null
4735                               ? (sourceType == DataSourceType.PASTE
4736                                       ? "from clipboard."
4737                                       : "using " + sourceType + " from "
4738                                               + file)
4739                               : ".")
4740                       + (format != null
4741                               ? "(parsing as '" + format + "' file)"
4742                               : ""),
4743               oom, Desktop.desktop);
4744     }
4745   }
4746
4747   /**
4748    * Method invoked by the ChangeListener on the tabbed pane, in other words
4749    * when a different tabbed pane is selected by the user or programmatically.
4750    */
4751   @Override
4752   public void tabSelectionChanged(int index)
4753   {
4754     if (index > -1)
4755     {
4756       alignPanel = alignPanels.get(index);
4757       viewport = alignPanel.av;
4758       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4759       setMenusFromViewport(viewport);
4760       if (featureSettings != null && featureSettings.isOpen()
4761               && featureSettings.fr.getViewport() != viewport)
4762       {
4763         if (viewport.isShowSequenceFeatures())
4764         {
4765           // refresh the featureSettings to reflect UI change
4766           showFeatureSettingsUI();
4767         }
4768         else
4769         {
4770           // close feature settings for this view.
4771           featureSettings.close();
4772         }
4773       }
4774
4775     }
4776
4777     /*
4778      * 'focus' any colour slider that is open to the selected viewport
4779      */
4780     if (viewport.getConservationSelected())
4781     {
4782       SliderPanel.setConservationSlider(alignPanel,
4783               viewport.getResidueShading(), alignPanel.getViewName());
4784     }
4785     else
4786     {
4787       SliderPanel.hideConservationSlider();
4788     }
4789     if (viewport.getAbovePIDThreshold())
4790     {
4791       SliderPanel.setPIDSliderSource(alignPanel,
4792               viewport.getResidueShading(), alignPanel.getViewName());
4793     }
4794     else
4795     {
4796       SliderPanel.hidePIDSlider();
4797     }
4798
4799     /*
4800      * If there is a frame linked to this one in a SplitPane, switch it to the
4801      * same view tab index. No infinite recursion of calls should happen, since
4802      * tabSelectionChanged() should not get invoked on setting the selected
4803      * index to an unchanged value. Guard against setting an invalid index
4804      * before the new view peer tab has been created.
4805      */
4806     final AlignViewportI peer = viewport.getCodingComplement();
4807     if (peer != null)
4808     {
4809       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4810               .getAlignPanel().alignFrame;
4811       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4812       {
4813         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4814       }
4815     }
4816   }
4817
4818   /**
4819    * On right mouse click on view tab, prompt for and set new view name.
4820    */
4821   @Override
4822   public void tabbedPane_mousePressed(MouseEvent e)
4823   {
4824     if (e.isPopupTrigger())
4825     {
4826       String msg = MessageManager.getString("label.enter_view_name");
4827       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4828               JvOptionPane.QUESTION_MESSAGE);
4829
4830       if (reply != null)
4831       {
4832         viewport.setViewName(reply);
4833         // TODO warn if reply is in getExistingViewNames()?
4834         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4835       }
4836     }
4837   }
4838
4839   public AlignViewport getCurrentView()
4840   {
4841     return viewport;
4842   }
4843
4844   /**
4845    * Open the dialog for regex description parsing.
4846    */
4847   @Override
4848   protected void extractScores_actionPerformed(ActionEvent e)
4849   {
4850     ParseProperties pp = new jalview.analysis.ParseProperties(
4851             viewport.getAlignment());
4852     // TODO: verify regex and introduce GUI dialog for version 2.5
4853     // if (pp.getScoresFromDescription("col", "score column ",
4854     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4855     // true)>0)
4856     if (pp.getScoresFromDescription("description column",
4857             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4858     {
4859       buildSortByAnnotationScoresMenu();
4860     }
4861   }
4862
4863   /*
4864    * (non-Javadoc)
4865    *
4866    * @see
4867    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4868    * )
4869    */
4870   @Override
4871   protected void showDbRefs_actionPerformed(ActionEvent e)
4872   {
4873     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4874   }
4875
4876   /*
4877    * (non-Javadoc)
4878    *
4879    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4880    * ActionEvent)
4881    */
4882   @Override
4883   protected void showNpFeats_actionPerformed(ActionEvent e)
4884   {
4885     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4886   }
4887
4888   /**
4889    * find the viewport amongst the tabs in this alignment frame and close that
4890    * tab
4891    *
4892    * @param av
4893    */
4894   public boolean closeView(AlignViewportI av)
4895   {
4896     if (viewport == av)
4897     {
4898       this.closeMenuItem_actionPerformed(false);
4899       return true;
4900     }
4901     Component[] comp = tabbedPane.getComponents();
4902     for (int i = 0; comp != null && i < comp.length; i++)
4903     {
4904       if (comp[i] instanceof AlignmentPanel)
4905       {
4906         if (((AlignmentPanel) comp[i]).av == av)
4907         {
4908           // close the view.
4909           closeView((AlignmentPanel) comp[i]);
4910           return true;
4911         }
4912       }
4913     }
4914     return false;
4915   }
4916
4917   protected void build_fetchdbmenu(JMenu webService)
4918   {
4919     // Temporary hack - DBRef Fetcher always top level ws entry.
4920     // TODO We probably want to store a sequence database checklist in
4921     // preferences and have checkboxes.. rather than individual sources selected
4922     // here
4923     final JMenu rfetch = new JMenu(
4924             MessageManager.getString("action.fetch_db_references"));
4925     rfetch.setToolTipText(MessageManager.getString(
4926             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4927     webService.add(rfetch);
4928
4929     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4930             MessageManager.getString("option.trim_retrieved_seqs"));
4931     trimrs.setToolTipText(
4932             MessageManager.getString("label.trim_retrieved_sequences"));
4933     trimrs.setSelected(
4934             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4935     trimrs.addActionListener(new ActionListener()
4936     {
4937       @Override
4938       public void actionPerformed(ActionEvent e)
4939       {
4940         trimrs.setSelected(trimrs.isSelected());
4941         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4942                 Boolean.valueOf(trimrs.isSelected()).toString());
4943       };
4944     });
4945     rfetch.add(trimrs);
4946     JMenuItem fetchr = new JMenuItem(
4947             MessageManager.getString("label.standard_databases"));
4948     fetchr.setToolTipText(
4949             MessageManager.getString("label.fetch_embl_uniprot"));
4950     fetchr.addActionListener(new ActionListener()
4951     {
4952
4953       @Override
4954       public void actionPerformed(ActionEvent e)
4955       {
4956         new Thread(new Runnable()
4957         {
4958           @Override
4959           public void run()
4960           {
4961             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4962                     .getAlignment().isNucleotide();
4963             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4964                     alignPanel.av.getSequenceSelection(),
4965                     alignPanel.alignFrame, null,
4966                     alignPanel.alignFrame.featureSettings, isNucleotide);
4967             dbRefFetcher.addListener(new FetchFinishedListenerI()
4968             {
4969               @Override
4970               public void finished()
4971               {
4972
4973                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
4974                         .getFeatureSettingsModels())
4975                 {
4976
4977                   alignPanel.av.mergeFeaturesStyle(srcSettings);
4978                 }
4979                 AlignFrame.this.setMenusForViewport();
4980               }
4981             });
4982             dbRefFetcher.fetchDBRefs(false);
4983           }
4984         }).start();
4985
4986       }
4987
4988     });
4989     rfetch.add(fetchr);
4990     final AlignFrame me = this;
4991     new Thread(new Runnable()
4992     {
4993       @Override
4994       public void run()
4995       {
4996         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4997                 .getSequenceFetcherSingleton(me);
4998         javax.swing.SwingUtilities.invokeLater(new Runnable()
4999         {
5000           @Override
5001           public void run()
5002           {
5003             String[] dbclasses = sf.getOrderedSupportedSources();
5004             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5005             // jalview.util.QuickSort.sort(otherdb, otherdb);
5006             List<DbSourceProxy> otherdb;
5007             JMenu dfetch = new JMenu();
5008             JMenu ifetch = new JMenu();
5009             JMenuItem fetchr = null;
5010             int comp = 0, icomp = 0, mcomp = 15;
5011             String mname = null;
5012             int dbi = 0;
5013             for (String dbclass : dbclasses)
5014             {
5015               otherdb = sf.getSourceProxy(dbclass);
5016               // add a single entry for this class, or submenu allowing 'fetch
5017               // all' or pick one
5018               if (otherdb == null || otherdb.size() < 1)
5019               {
5020                 continue;
5021               }
5022               // List<DbSourceProxy> dbs=otherdb;
5023               // otherdb=new ArrayList<DbSourceProxy>();
5024               // for (DbSourceProxy db:dbs)
5025               // {
5026               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5027               // }
5028               if (mname == null)
5029               {
5030                 mname = "From " + dbclass;
5031               }
5032               if (otherdb.size() == 1)
5033               {
5034                 final DbSourceProxy[] dassource = otherdb
5035                         .toArray(new DbSourceProxy[0]);
5036                 DbSourceProxy src = otherdb.get(0);
5037                 fetchr = new JMenuItem(src.getDbSource());
5038                 fetchr.addActionListener(new ActionListener()
5039                 {
5040
5041                   @Override
5042                   public void actionPerformed(ActionEvent e)
5043                   {
5044                     new Thread(new Runnable()
5045                     {
5046
5047                       @Override
5048                       public void run()
5049                       {
5050                         boolean isNucleotide = alignPanel.alignFrame
5051                                 .getViewport().getAlignment()
5052                                 .isNucleotide();
5053                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5054                                 alignPanel.av.getSequenceSelection(),
5055                                 alignPanel.alignFrame, dassource,
5056                                 alignPanel.alignFrame.featureSettings,
5057                                 isNucleotide);
5058                         dbRefFetcher
5059                                 .addListener(new FetchFinishedListenerI()
5060                                 {
5061                                   @Override
5062                                   public void finished()
5063                                   {
5064                                     FeatureSettingsModelI srcSettings = dassource[0]
5065                                             .getFeatureColourScheme();
5066                                     alignPanel.av.mergeFeaturesStyle(
5067                                             srcSettings);
5068                                     AlignFrame.this.setMenusForViewport();
5069                                   }
5070                                 });
5071                         dbRefFetcher.fetchDBRefs(false);
5072                       }
5073                     }).start();
5074                   }
5075
5076                 });
5077                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5078                         MessageManager.formatMessage(
5079                                 "label.fetch_retrieve_from", new Object[]
5080                                 { src.getDbName() })));
5081                 dfetch.add(fetchr);
5082                 comp++;
5083               }
5084               else
5085               {
5086                 final DbSourceProxy[] dassource = otherdb
5087                         .toArray(new DbSourceProxy[0]);
5088                 // fetch all entry
5089                 DbSourceProxy src = otherdb.get(0);
5090                 fetchr = new JMenuItem(MessageManager
5091                         .formatMessage("label.fetch_all_param", new Object[]
5092                         { src.getDbSource() }));
5093                 fetchr.addActionListener(new ActionListener()
5094                 {
5095                   @Override
5096                   public void actionPerformed(ActionEvent e)
5097                   {
5098                     new Thread(new Runnable()
5099                     {
5100
5101                       @Override
5102                       public void run()
5103                       {
5104                         boolean isNucleotide = alignPanel.alignFrame
5105                                 .getViewport().getAlignment()
5106                                 .isNucleotide();
5107                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5108                                 alignPanel.av.getSequenceSelection(),
5109                                 alignPanel.alignFrame, dassource,
5110                                 alignPanel.alignFrame.featureSettings,
5111                                 isNucleotide);
5112                         dbRefFetcher
5113                                 .addListener(new FetchFinishedListenerI()
5114                                 {
5115                                   @Override
5116                                   public void finished()
5117                                   {
5118                                     AlignFrame.this.setMenusForViewport();
5119                                   }
5120                                 });
5121                         dbRefFetcher.fetchDBRefs(false);
5122                       }
5123                     }).start();
5124                   }
5125                 });
5126
5127                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5128                         MessageManager.formatMessage(
5129                                 "label.fetch_retrieve_from_all_sources",
5130                                 new Object[]
5131                                 { Integer.valueOf(otherdb.size())
5132                                         .toString(),
5133                                     src.getDbSource(), src.getDbName() })));
5134                 dfetch.add(fetchr);
5135                 comp++;
5136                 // and then build the rest of the individual menus
5137                 ifetch = new JMenu(MessageManager.formatMessage(
5138                         "label.source_from_db_source", new Object[]
5139                         { src.getDbSource() }));
5140                 icomp = 0;
5141                 String imname = null;
5142                 int i = 0;
5143                 for (DbSourceProxy sproxy : otherdb)
5144                 {
5145                   String dbname = sproxy.getDbName();
5146                   String sname = dbname.length() > 5
5147                           ? dbname.substring(0, 5) + "..."
5148                           : dbname;
5149                   String msname = dbname.length() > 10
5150                           ? dbname.substring(0, 10) + "..."
5151                           : dbname;
5152                   if (imname == null)
5153                   {
5154                     imname = MessageManager
5155                             .formatMessage("label.from_msname", new Object[]
5156                             { sname });
5157                   }
5158                   fetchr = new JMenuItem(msname);
5159                   final DbSourceProxy[] dassrc = { sproxy };
5160                   fetchr.addActionListener(new ActionListener()
5161                   {
5162
5163                     @Override
5164                     public void actionPerformed(ActionEvent e)
5165                     {
5166                       new Thread(new Runnable()
5167                       {
5168
5169                         @Override
5170                         public void run()
5171                         {
5172                           boolean isNucleotide = alignPanel.alignFrame
5173                                   .getViewport().getAlignment()
5174                                   .isNucleotide();
5175                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5176                                   alignPanel.av.getSequenceSelection(),
5177                                   alignPanel.alignFrame, dassrc,
5178                                   alignPanel.alignFrame.featureSettings,
5179                                   isNucleotide);
5180                           dbRefFetcher
5181                                   .addListener(new FetchFinishedListenerI()
5182                                   {
5183                                     @Override
5184                                     public void finished()
5185                                     {
5186                                       AlignFrame.this.setMenusForViewport();
5187                                     }
5188                                   });
5189                           dbRefFetcher.fetchDBRefs(false);
5190                         }
5191                       }).start();
5192                     }
5193
5194                   });
5195                   fetchr.setToolTipText(
5196                           "<html>" + MessageManager.formatMessage(
5197                                   "label.fetch_retrieve_from", new Object[]
5198                                   { dbname }));
5199                   ifetch.add(fetchr);
5200                   ++i;
5201                   if (++icomp >= mcomp || i == (otherdb.size()))
5202                   {
5203                     ifetch.setText(MessageManager.formatMessage(
5204                             "label.source_to_target", imname, sname));
5205                     dfetch.add(ifetch);
5206                     ifetch = new JMenu();
5207                     imname = null;
5208                     icomp = 0;
5209                     comp++;
5210                   }
5211                 }
5212               }
5213               ++dbi;
5214               if (comp >= mcomp || dbi >= (dbclasses.length))
5215               {
5216                 dfetch.setText(MessageManager.formatMessage(
5217                         "label.source_to_target", mname, dbclass));
5218                 rfetch.add(dfetch);
5219                 dfetch = new JMenu();
5220                 mname = null;
5221                 comp = 0;
5222               }
5223             }
5224           }
5225         });
5226       }
5227     }).start();
5228
5229   }
5230
5231   /**
5232    * Left justify the whole alignment.
5233    */
5234   @Override
5235   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5236   {
5237     AlignmentI al = viewport.getAlignment();
5238     al.justify(false);
5239     viewport.firePropertyChange("alignment", null, al);
5240   }
5241
5242   /**
5243    * Right justify the whole alignment.
5244    */
5245   @Override
5246   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5247   {
5248     AlignmentI al = viewport.getAlignment();
5249     al.justify(true);
5250     viewport.firePropertyChange("alignment", null, al);
5251   }
5252
5253   @Override
5254   public void setShowSeqFeatures(boolean b)
5255   {
5256     showSeqFeatures.setSelected(b);
5257     viewport.setShowSequenceFeatures(b);
5258   }
5259
5260   /*
5261    * (non-Javadoc)
5262    *
5263    * @see
5264    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5265    * awt.event.ActionEvent)
5266    */
5267   @Override
5268   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5269   {
5270     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5271     alignPanel.paintAlignment(false, false);
5272   }
5273
5274   /*
5275    * (non-Javadoc)
5276    *
5277    * @see
5278    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5279    * .ActionEvent)
5280    */
5281   @Override
5282   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5283   {
5284     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5285     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5286
5287   }
5288
5289   /*
5290    * (non-Javadoc)
5291    *
5292    * @see
5293    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5294    * .event.ActionEvent)
5295    */
5296   @Override
5297   protected void showGroupConservation_actionPerformed(ActionEvent e)
5298   {
5299     viewport.setShowGroupConservation(showGroupConservation.getState());
5300     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5301   }
5302
5303   /*
5304    * (non-Javadoc)
5305    *
5306    * @see
5307    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5308    * .event.ActionEvent)
5309    */
5310   @Override
5311   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5312   {
5313     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5314     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5315   }
5316
5317   /*
5318    * (non-Javadoc)
5319    *
5320    * @see
5321    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5322    * .event.ActionEvent)
5323    */
5324   @Override
5325   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5326   {
5327     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5328     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5329   }
5330
5331   @Override
5332   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5333   {
5334     showSequenceLogo.setState(true);
5335     viewport.setShowSequenceLogo(true);
5336     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5337     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5338   }
5339
5340   @Override
5341   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5342   {
5343     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5344   }
5345
5346   /*
5347    * (non-Javadoc)
5348    *
5349    * @see
5350    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5351    * .event.ActionEvent)
5352    */
5353   @Override
5354   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5355   {
5356     if (avc.makeGroupsFromSelection())
5357     {
5358       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5359       alignPanel.updateAnnotation();
5360       alignPanel.paintAlignment(true,
5361               viewport.needToUpdateStructureViews());
5362     }
5363   }
5364
5365   public void clearAlignmentSeqRep()
5366   {
5367     // TODO refactor alignmentseqrep to controller
5368     if (viewport.getAlignment().hasSeqrep())
5369     {
5370       viewport.getAlignment().setSeqrep(null);
5371       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5372       alignPanel.updateAnnotation();
5373       alignPanel.paintAlignment(true, true);
5374     }
5375   }
5376
5377   @Override
5378   protected void createGroup_actionPerformed(ActionEvent e)
5379   {
5380     if (avc.createGroup())
5381     {
5382       if (applyAutoAnnotationSettings.isSelected())
5383       {
5384         alignPanel.updateAnnotation(true, false);
5385       }
5386       alignPanel.alignmentChanged();
5387     }
5388   }
5389
5390   @Override
5391   protected void unGroup_actionPerformed(ActionEvent e)
5392   {
5393     if (avc.unGroup())
5394     {
5395       alignPanel.alignmentChanged();
5396     }
5397   }
5398
5399   /**
5400    * make the given alignmentPanel the currently selected tab
5401    *
5402    * @param alignmentPanel
5403    */
5404   public void setDisplayedView(AlignmentPanel alignmentPanel)
5405   {
5406     if (!viewport.getSequenceSetId()
5407             .equals(alignmentPanel.av.getSequenceSetId()))
5408     {
5409       throw new Error(MessageManager.getString(
5410               "error.implementation_error_cannot_show_view_alignment_frame"));
5411     }
5412     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5413             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5414     {
5415       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5416     }
5417   }
5418
5419   /**
5420    * Action on selection of menu options to Show or Hide annotations.
5421    *
5422    * @param visible
5423    * @param forSequences
5424    *          update sequence-related annotations
5425    * @param forAlignment
5426    *          update non-sequence-related annotations
5427    */
5428   @Override
5429   protected void setAnnotationsVisibility(boolean visible,
5430           boolean forSequences, boolean forAlignment)
5431   {
5432     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5433             .getAlignmentAnnotation();
5434     if (anns == null)
5435     {
5436       return;
5437     }
5438     for (AlignmentAnnotation aa : anns)
5439     {
5440       /*
5441        * don't display non-positional annotations on an alignment
5442        */
5443       if (aa.annotations == null)
5444       {
5445         continue;
5446       }
5447       boolean apply = (aa.sequenceRef == null && forAlignment)
5448               || (aa.sequenceRef != null && forSequences);
5449       if (apply)
5450       {
5451         aa.visible = visible;
5452       }
5453     }
5454     alignPanel.validateAnnotationDimensions(true);
5455     alignPanel.alignmentChanged();
5456   }
5457
5458   /**
5459    * Store selected annotation sort order for the view and repaint.
5460    */
5461   @Override
5462   protected void sortAnnotations_actionPerformed()
5463   {
5464     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5465     this.alignPanel.av
5466             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5467     alignPanel.paintAlignment(false, false);
5468   }
5469
5470   /**
5471    *
5472    * @return alignment panels in this alignment frame
5473    */
5474   public List<? extends AlignmentViewPanel> getAlignPanels()
5475   {
5476     // alignPanels is never null
5477     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5478     return alignPanels;
5479   }
5480
5481   /**
5482    * Open a new alignment window, with the cDNA associated with this (protein)
5483    * alignment, aligned as is the protein.
5484    */
5485   protected void viewAsCdna_actionPerformed()
5486   {
5487     // TODO no longer a menu action - refactor as required
5488     final AlignmentI alignment = getViewport().getAlignment();
5489     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5490     if (mappings == null)
5491     {
5492       return;
5493     }
5494     List<SequenceI> cdnaSeqs = new ArrayList<>();
5495     for (SequenceI aaSeq : alignment.getSequences())
5496     {
5497       for (AlignedCodonFrame acf : mappings)
5498       {
5499         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5500         if (dnaSeq != null)
5501         {
5502           /*
5503            * There is a cDNA mapping for this protein sequence - add to new
5504            * alignment. It will share the same dataset sequence as other mapped
5505            * cDNA (no new mappings need to be created).
5506            */
5507           final Sequence newSeq = new Sequence(dnaSeq);
5508           newSeq.setDatasetSequence(dnaSeq);
5509           cdnaSeqs.add(newSeq);
5510         }
5511       }
5512     }
5513     if (cdnaSeqs.size() == 0)
5514     {
5515       // show a warning dialog no mapped cDNA
5516       return;
5517     }
5518     AlignmentI cdna = new Alignment(
5519             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5520     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5521             AlignFrame.DEFAULT_HEIGHT);
5522     cdna.alignAs(alignment);
5523     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5524             + this.title;
5525     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5526             AlignFrame.DEFAULT_HEIGHT);
5527   }
5528
5529   /**
5530    * Set visibility of dna/protein complement view (available when shown in a
5531    * split frame).
5532    *
5533    * @param show
5534    */
5535   @Override
5536   protected void showComplement_actionPerformed(boolean show)
5537   {
5538     SplitContainerI sf = getSplitViewContainer();
5539     if (sf != null)
5540     {
5541       sf.setComplementVisible(this, show);
5542     }
5543   }
5544
5545   /**
5546    * Generate the reverse (optionally complemented) of the selected sequences,
5547    * and add them to the alignment
5548    */
5549   @Override
5550   protected void showReverse_actionPerformed(boolean complement)
5551   {
5552     AlignmentI al = null;
5553     try
5554     {
5555       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5556       al = dna.reverseCdna(complement);
5557       viewport.addAlignment(al, "");
5558       addHistoryItem(new EditCommand(
5559               MessageManager.getString("label.add_sequences"), Action.PASTE,
5560               al.getSequencesArray(), 0, al.getWidth(),
5561               viewport.getAlignment()));
5562     } catch (Exception ex)
5563     {
5564       System.err.println(ex.getMessage());
5565       return;
5566     }
5567   }
5568
5569   /**
5570    * Try to run a script in the Groovy console, having first ensured that this
5571    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5572    * be targeted at this alignment.
5573    */
5574   @Override
5575   protected void runGroovy_actionPerformed()
5576   {
5577     Jalview.setCurrentAlignFrame(this);
5578     groovy.ui.Console console = Desktop.getGroovyConsole();
5579     if (console != null)
5580     {
5581       try
5582       {
5583         console.runScript();
5584       } catch (Exception ex)
5585       {
5586         System.err.println((ex.toString()));
5587         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5588                 MessageManager.getString("label.couldnt_run_groovy_script"),
5589                 MessageManager.getString("label.groovy_support_failed"),
5590                 JvOptionPane.ERROR_MESSAGE);
5591       }
5592     }
5593     else
5594     {
5595       System.err.println("Can't run Groovy script as console not found");
5596     }
5597   }
5598
5599   /**
5600    * Hides columns containing (or not containing) a specified feature, provided
5601    * that would not leave all columns hidden
5602    *
5603    * @param featureType
5604    * @param columnsContaining
5605    * @return
5606    */
5607   public boolean hideFeatureColumns(String featureType,
5608           boolean columnsContaining)
5609   {
5610     boolean notForHiding = avc.markColumnsContainingFeatures(
5611             columnsContaining, false, false, featureType);
5612     if (notForHiding)
5613     {
5614       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5615               false, featureType))
5616       {
5617         getViewport().hideSelectedColumns();
5618         return true;
5619       }
5620     }
5621     return false;
5622   }
5623
5624   @Override
5625   protected void selectHighlightedColumns_actionPerformed(
5626           ActionEvent actionEvent)
5627   {
5628     // include key modifier check in case user selects from menu
5629     avc.markHighlightedColumns(
5630             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5631             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5632                     | ActionEvent.CTRL_MASK)) != 0);
5633   }
5634
5635   /**
5636    * Rebuilds the Colour menu, including any user-defined colours which have
5637    * been loaded either on startup or during the session
5638    */
5639   public void buildColourMenu()
5640   {
5641     colourMenu.removeAll();
5642
5643     colourMenu.add(applyToAllGroups);
5644     colourMenu.add(textColour);
5645     colourMenu.addSeparator();
5646
5647     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5648             viewport.getAlignment(), false);
5649
5650     colourMenu.add(annotationColour);
5651     bg.add(annotationColour);
5652     colourMenu.addSeparator();
5653     colourMenu.add(conservationMenuItem);
5654     colourMenu.add(modifyConservation);
5655     colourMenu.add(abovePIDThreshold);
5656     colourMenu.add(modifyPID);
5657
5658     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5659     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5660   }
5661
5662   /**
5663    * Open a dialog (if not already open) that allows the user to select and
5664    * calculate PCA or Tree analysis
5665    */
5666   protected void openTreePcaDialog()
5667   {
5668     if (alignPanel.getCalculationDialog() == null)
5669     {
5670       new CalculationChooser(AlignFrame.this);
5671     }
5672   }
5673
5674   @Override
5675   protected void loadVcf_actionPerformed()
5676   {
5677     JalviewFileChooser chooser = new JalviewFileChooser(
5678             Cache.getProperty("LAST_DIRECTORY"));
5679     chooser.setFileView(new JalviewFileView());
5680     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5681     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5682
5683     int value = chooser.showOpenDialog(null);
5684
5685     if (value == JalviewFileChooser.APPROVE_OPTION)
5686     {
5687       String choice = chooser.getSelectedFile().getPath();
5688       Cache.setProperty("LAST_DIRECTORY", choice);
5689       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5690       new VCFLoader(choice).loadVCF(seqs, this);
5691     }
5692
5693   }
5694
5695   private Rectangle lastFeatureSettingsBounds = null;
5696   @Override
5697   public void setFeatureSettingsGeometry(Rectangle bounds)
5698   {
5699     lastFeatureSettingsBounds = bounds;
5700   }
5701
5702   @Override
5703   public Rectangle getFeatureSettingsGeometry()
5704   {
5705     return lastFeatureSettingsBounds;
5706   }
5707 }
5708
5709 class PrintThread extends Thread
5710 {
5711   AlignmentPanel ap;
5712
5713   public PrintThread(AlignmentPanel ap)
5714   {
5715     this.ap = ap;
5716   }
5717
5718   static PageFormat pf;
5719
5720   @Override
5721   public void run()
5722   {
5723     PrinterJob printJob = PrinterJob.getPrinterJob();
5724
5725     if (pf != null)
5726     {
5727       printJob.setPrintable(ap, pf);
5728     }
5729     else
5730     {
5731       printJob.setPrintable(ap);
5732     }
5733
5734     if (printJob.printDialog())
5735     {
5736       try
5737       {
5738         printJob.print();
5739       } catch (Exception PrintException)
5740       {
5741         PrintException.printStackTrace();
5742       }
5743     }
5744   }
5745 }