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.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.SimilarityParamsI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenColumns;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.io.AlignmentProperties;
  67 import jalview.io.AnnotationFile;
  68 import jalview.io.BackupFiles;
  69 import jalview.io.BioJsHTMLOutput;
  70 import jalview.io.DataSourceType;
  71 import jalview.io.FileFormat;
  72 import jalview.io.FileFormatI;
  73 import jalview.io.FileFormats;
  74 import jalview.io.FileLoader;
  75 import jalview.io.FileParse;
  76 import jalview.io.FormatAdapter;
  77 import jalview.io.HtmlSvgOutput;
  78 import jalview.io.IdentifyFile;
  79 import jalview.io.JPredFile;
  80 import jalview.io.JalviewFileChooser;
  81 import jalview.io.JalviewFileView;
  82 import jalview.io.JnetAnnotationMaker;
  83 import jalview.io.NewickFile;
  84 import jalview.io.ScoreMatrixFile;
  85 import jalview.io.TCoffeeScoreFile;
  86 import jalview.io.vcf.VCFLoader;
  87 import jalview.jbgui.GAlignFrame;
  88 import jalview.schemes.ColourSchemeI;
  89 import jalview.schemes.ColourSchemes;
  90 import jalview.schemes.ResidueColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.util.MessageManager;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.ws.DBRefFetcher;
  96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Rectangle;
 105 import java.awt.Toolkit;
 106 import java.awt.datatransfer.Clipboard;
 107 import java.awt.datatransfer.DataFlavor;
 108 import java.awt.datatransfer.StringSelection;
 109 import java.awt.datatransfer.Transferable;
 110 import java.awt.dnd.DnDConstants;
 111 import java.awt.dnd.DropTargetDragEvent;
 112 import java.awt.dnd.DropTargetDropEvent;
 113 import java.awt.dnd.DropTargetEvent;
 114 import java.awt.dnd.DropTargetListener;
 115 import java.awt.event.ActionEvent;
 116 import java.awt.event.ActionListener;
 117 import java.awt.event.FocusAdapter;
 118 import java.awt.event.FocusEvent;
 119 import java.awt.event.ItemEvent;
 120 import java.awt.event.ItemListener;
 121 import java.awt.event.KeyAdapter;
 122 import java.awt.event.KeyEvent;
 123 import java.awt.event.MouseEvent;
 124 import java.awt.print.PageFormat;
 125 import java.awt.print.PrinterJob;
 126 import java.beans.PropertyChangeEvent;
 127 import java.io.File;
 128 import java.io.FileWriter;
 129 import java.io.PrintWriter;
 130 import java.net.URL;
 131 import java.util.ArrayList;
 132 import java.util.Arrays;
 133 import java.util.Deque;
 134 import java.util.Enumeration;
 135 import java.util.Hashtable;
 136 import java.util.List;
 137 import java.util.Vector;
 138
 139 import javax.swing.ButtonGroup;
 140 import javax.swing.JCheckBoxMenuItem;
 141 import javax.swing.JEditorPane;
 142 import javax.swing.JInternalFrame;
 143 import javax.swing.JLayeredPane;
 144 import javax.swing.JMenu;
 145 import javax.swing.JMenuItem;
 146 import javax.swing.JScrollPane;
 147 import javax.swing.SwingUtilities;
 148
 149 /**
 150  * DOCUMENT ME!
 151  *
 152  * @author $author$
 153  * @version $Revision$
 154  */
 155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 156         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 157 {
 158
 159   public static final int DEFAULT_WIDTH = 700;
 160
 161   public static final int DEFAULT_HEIGHT = 500;
 162
 163   /*
 164    * The currently displayed panel (selected tabbed view if more than one)
 165    */
 166   public AlignmentPanel alignPanel;
 167
 168   AlignViewport viewport;
 169
 170   public AlignViewControllerI avc;
 171
 172   List<AlignmentPanel> alignPanels = new ArrayList<>();
 173
 174   /**
 175    * Last format used to load or save alignments in this window
 176    */
 177   FileFormatI currentFileFormat = null;
 178
 179   /**
 180    * Current filename for this alignment
 181    */
 182   String fileName = null;
 183
 184   /**
 185    * Creates a new AlignFrame object with specific width and height.
 186    *
 187    * @param al
 188    * @param width
 189    * @param height
 190    */
 191   public AlignFrame(AlignmentI al, int width, int height)
 192   {
 193     this(al, null, width, height);
 194   }
 195
 196   /**
 197    * Creates a new AlignFrame object with specific width, height and
 198    * sequenceSetId
 199    *
 200    * @param al
 201    * @param width
 202    * @param height
 203    * @param sequenceSetId
 204    */
 205   public AlignFrame(AlignmentI al, int width, int height,
 206           String sequenceSetId)
 207   {
 208     this(al, null, width, height, sequenceSetId);
 209   }
 210
 211   /**
 212    * Creates a new AlignFrame object with specific width, height and
 213    * sequenceSetId
 214    *
 215    * @param al
 216    * @param width
 217    * @param height
 218    * @param sequenceSetId
 219    * @param viewId
 220    */
 221   public AlignFrame(AlignmentI al, int width, int height,
 222           String sequenceSetId, String viewId)
 223   {
 224     this(al, null, width, height, sequenceSetId, viewId);
 225   }
 226
 227   /**
 228    * new alignment window with hidden columns
 229    *
 230    * @param al
 231    *          AlignmentI
 232    * @param hiddenColumns
 233    *          ColumnSelection or null
 234    * @param width
 235    *          Width of alignment frame
 236    * @param height
 237    *          height of frame.
 238    */
 239   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 240           int height)
 241   {
 242     this(al, hiddenColumns, width, height, null);
 243   }
 244
 245   /**
 246    * Create alignment frame for al with hiddenColumns, a specific width and
 247    * height, and specific sequenceId
 248    *
 249    * @param al
 250    * @param hiddenColumns
 251    * @param width
 252    * @param height
 253    * @param sequenceSetId
 254    *          (may be null)
 255    */
 256   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 257           int height, String sequenceSetId)
 258   {
 259     this(al, hiddenColumns, width, height, sequenceSetId, null);
 260   }
 261
 262   /**
 263    * Create alignment frame for al with hiddenColumns, a specific width and
 264    * height, and specific sequenceId
 265    *
 266    * @param al
 267    * @param hiddenColumns
 268    * @param width
 269    * @param height
 270    * @param sequenceSetId
 271    *          (may be null)
 272    * @param viewId
 273    *          (may be null)
 274    */
 275   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 276           int height, String sequenceSetId, String viewId)
 277   {
 278     setSize(width, height);
 279
 280     if (al.getDataset() == null)
 281     {
 282       al.setDataset(null);
 283     }
 284
 285     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 286
 287     alignPanel = new AlignmentPanel(this, viewport);
 288
 289     addAlignmentPanel(alignPanel, true);
 290     init();
 291   }
 292
 293   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 294           HiddenColumns hiddenColumns, int width, int height)
 295   {
 296     setSize(width, height);
 297
 298     if (al.getDataset() == null)
 299     {
 300       al.setDataset(null);
 301     }
 302
 303     viewport = new AlignViewport(al, hiddenColumns);
 304
 305     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 306     {
 307       viewport.hideSequence(hiddenSeqs);
 308     }
 309     alignPanel = new AlignmentPanel(this, viewport);
 310     addAlignmentPanel(alignPanel, true);
 311     init();
 312   }
 313
 314   /**
 315    * Make a new AlignFrame from existing alignmentPanels
 316    *
 317    * @param ap
 318    *          AlignmentPanel
 319    * @param av
 320    *          AlignViewport
 321    */
 322   public AlignFrame(AlignmentPanel ap)
 323   {
 324     viewport = ap.av;
 325     alignPanel = ap;
 326     addAlignmentPanel(ap, false);
 327     init();
 328   }
 329
 330   /**
 331    * initalise the alignframe from the underlying viewport data and the
 332    * configurations
 333    */
 334   void init()
 335   {
 336     if (!Jalview.isHeadlessMode())
 337     {
 338       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 339     }
 340
 341     avc = new jalview.controller.AlignViewController(this, viewport,
 342             alignPanel);
 343     if (viewport.getAlignmentConservationAnnotation() == null)
 344     {
 345       // BLOSUM62Colour.setEnabled(false);
 346       conservationMenuItem.setEnabled(false);
 347       modifyConservation.setEnabled(false);
 348       // PIDColour.setEnabled(false);
 349       // abovePIDThreshold.setEnabled(false);
 350       // modifyPID.setEnabled(false);
 351     }
 352
 353     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 354             "No sort");
 355
 356     if (sortby.equals("Id"))
 357     {
 358       sortIDMenuItem_actionPerformed(null);
 359     }
 360     else if (sortby.equals("Pairwise Identity"))
 361     {
 362       sortPairwiseMenuItem_actionPerformed(null);
 363     }
 364
 365     this.alignPanel.av
 366             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 367
 368     setMenusFromViewport(viewport);
 369     buildSortByAnnotationScoresMenu();
 370     calculateTree.addActionListener(new ActionListener()
 371     {
 372
 373       @Override
 374       public void actionPerformed(ActionEvent e)
 375       {
 376         openTreePcaDialog();
 377       }
 378     });
 379     buildColourMenu();
 380
 381     if (Desktop.desktop != null)
 382     {
 383       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 384       addServiceListeners();
 385       setGUINucleotide();
 386     }
 387
 388     if (viewport.getWrapAlignment())
 389     {
 390       wrapMenuItem_actionPerformed(null);
 391     }
 392
 393     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 394     {
 395       this.overviewMenuItem_actionPerformed(null);
 396     }
 397
 398     addKeyListener();
 399
 400     final List<AlignmentPanel> selviews = new ArrayList<>();
 401     final List<AlignmentPanel> origview = new ArrayList<>();
 402     final String menuLabel = MessageManager
 403             .getString("label.copy_format_from");
 404     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 405             new ViewSetProvider()
 406             {
 407
 408               @Override
 409               public AlignmentPanel[] getAllAlignmentPanels()
 410               {
 411                 origview.clear();
 412                 origview.add(alignPanel);
 413                 // make an array of all alignment panels except for this one
 414                 List<AlignmentPanel> aps = new ArrayList<>(
 415                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 416                 aps.remove(AlignFrame.this.alignPanel);
 417                 return aps.toArray(new AlignmentPanel[aps.size()]);
 418               }
 419             }, selviews, new ItemListener()
 420             {
 421
 422               @Override
 423               public void itemStateChanged(ItemEvent e)
 424               {
 425                 if (origview.size() > 0)
 426                 {
 427                   final AlignmentPanel ap = origview.get(0);
 428
 429                   /*
 430                    * Copy the ViewStyle of the selected panel to 'this one'.
 431                    * Don't change value of 'scaleProteinAsCdna' unless copying
 432                    * from a SplitFrame.
 433                    */
 434                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 435                           .getViewStyle();
 436                   boolean fromSplitFrame = selviews.get(0)
 437                           .getAlignViewport().getCodingComplement() != null;
 438                   if (!fromSplitFrame)
 439                   {
 440                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 441                             .getViewStyle().isScaleProteinAsCdna());
 442                   }
 443                   ap.getAlignViewport().setViewStyle(vs);
 444
 445                   /*
 446                    * Also rescale ViewStyle of SplitFrame complement if there is
 447                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 448                    * the whole ViewStyle (allow cDNA protein to have different
 449                    * fonts)
 450                    */
 451                   AlignViewportI complement = ap.getAlignViewport()
 452                           .getCodingComplement();
 453                   if (complement != null && vs.isScaleProteinAsCdna())
 454                   {
 455                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 456                     ((SplitFrame) af.getSplitViewContainer())
 457                             .adjustLayout();
 458                     af.setMenusForViewport();
 459                   }
 460
 461                   ap.updateLayout();
 462                   ap.setSelected(true);
 463                   ap.alignFrame.setMenusForViewport();
 464
 465                 }
 466               }
 467             });
 468     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 469             .indexOf("devel") > -1
 470             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 471                     .indexOf("test") > -1)
 472     {
 473       formatMenu.add(vsel);
 474     }
 475     addFocusListener(new FocusAdapter()
 476     {
 477       @Override
 478       public void focusGained(FocusEvent e)
 479       {
 480         Jalview.setCurrentAlignFrame(AlignFrame.this);
 481       }
 482     });
 483
 484   }
 485
 486   /**
 487    * Change the filename and format for the alignment, and enable the 'reload'
 488    * button functionality.
 489    *
 490    * @param file
 491    *          valid filename
 492    * @param format
 493    *          format of file
 494    */
 495   public void setFileName(String file, FileFormatI format)
 496   {
 497     fileName = file;
 498     setFileFormat(format);
 499     reload.setEnabled(true);
 500   }
 501
 502   /**
 503    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 504    * events
 505    */
 506   void addKeyListener()
 507   {
 508     addKeyListener(new KeyAdapter()
 509     {
 510       @Override
 511       public void keyPressed(KeyEvent evt)
 512       {
 513         if (viewport.cursorMode
 514                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 515                         && evt.getKeyCode() <= KeyEvent.VK_9)
 516                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 517                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 518                 && Character.isDigit(evt.getKeyChar()))
 519         {
 520           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 521         }
 522
 523         switch (evt.getKeyCode())
 524         {
 525
 526         case 27: // escape key
 527           deselectAllSequenceMenuItem_actionPerformed(null);
 528
 529           break;
 530
 531         case KeyEvent.VK_DOWN:
 532           if (evt.isAltDown() || !viewport.cursorMode)
 533           {
 534             moveSelectedSequences(false);
 535           }
 536           if (viewport.cursorMode)
 537           {
 538             alignPanel.getSeqPanel().moveCursor(0, 1);
 539           }
 540           break;
 541
 542         case KeyEvent.VK_UP:
 543           if (evt.isAltDown() || !viewport.cursorMode)
 544           {
 545             moveSelectedSequences(true);
 546           }
 547           if (viewport.cursorMode)
 548           {
 549             alignPanel.getSeqPanel().moveCursor(0, -1);
 550           }
 551
 552           break;
 553
 554         case KeyEvent.VK_LEFT:
 555           if (evt.isAltDown() || !viewport.cursorMode)
 556           {
 557             slideSequences(false,
 558                     alignPanel.getSeqPanel().getKeyboardNo1());
 559           }
 560           else
 561           {
 562             alignPanel.getSeqPanel().moveCursor(-1, 0);
 563           }
 564
 565           break;
 566
 567         case KeyEvent.VK_RIGHT:
 568           if (evt.isAltDown() || !viewport.cursorMode)
 569           {
 570             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 571           }
 572           else
 573           {
 574             alignPanel.getSeqPanel().moveCursor(1, 0);
 575           }
 576           break;
 577
 578         case KeyEvent.VK_SPACE:
 579           if (viewport.cursorMode)
 580           {
 581             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 582                     || evt.isShiftDown() || evt.isAltDown());
 583           }
 584           break;
 585
 586         // case KeyEvent.VK_A:
 587         // if (viewport.cursorMode)
 588         // {
 589         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 590         // //System.out.println("A");
 591         // }
 592         // break;
 593         /*
 594          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 595          * System.out.println("closing bracket"); } break;
 596          */
 597         case KeyEvent.VK_DELETE:
 598         case KeyEvent.VK_BACK_SPACE:
 599           if (!viewport.cursorMode)
 600           {
 601             cut_actionPerformed(null);
 602           }
 603           else
 604           {
 605             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 606                     || evt.isShiftDown() || evt.isAltDown());
 607           }
 608
 609           break;
 610
 611         case KeyEvent.VK_S:
 612           if (viewport.cursorMode)
 613           {
 614             alignPanel.getSeqPanel().setCursorRow();
 615           }
 616           break;
 617         case KeyEvent.VK_C:
 618           if (viewport.cursorMode && !evt.isControlDown())
 619           {
 620             alignPanel.getSeqPanel().setCursorColumn();
 621           }
 622           break;
 623         case KeyEvent.VK_P:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setCursorPosition();
 627           }
 628           break;
 629
 630         case KeyEvent.VK_ENTER:
 631         case KeyEvent.VK_COMMA:
 632           if (viewport.cursorMode)
 633           {
 634             alignPanel.getSeqPanel().setCursorRowAndColumn();
 635           }
 636           break;
 637
 638         case KeyEvent.VK_Q:
 639           if (viewport.cursorMode)
 640           {
 641             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 642           }
 643           break;
 644         case KeyEvent.VK_M:
 645           if (viewport.cursorMode)
 646           {
 647             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 648           }
 649           break;
 650
 651         case KeyEvent.VK_F2:
 652           viewport.cursorMode = !viewport.cursorMode;
 653           statusBar.setText(MessageManager
 654                   .formatMessage("label.keyboard_editing_mode", new String[]
 655                   { (viewport.cursorMode ? "on" : "off") }));
 656           if (viewport.cursorMode)
 657           {
 658             ViewportRanges ranges = viewport.getRanges();
 659             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 660                     .getStartRes();
 661             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 662                     .getStartSeq();
 663           }
 664           alignPanel.getSeqPanel().seqCanvas.repaint();
 665           break;
 666
 667         case KeyEvent.VK_F1:
 668           try
 669           {
 670             Help.showHelpWindow();
 671           } catch (Exception ex)
 672           {
 673             ex.printStackTrace();
 674           }
 675           break;
 676         case KeyEvent.VK_H:
 677         {
 678           boolean toggleSeqs = !evt.isControlDown();
 679           boolean toggleCols = !evt.isShiftDown();
 680           toggleHiddenRegions(toggleSeqs, toggleCols);
 681           break;
 682         }
 683         case KeyEvent.VK_B:
 684         {
 685           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 686           boolean modifyExisting = true; // always modify, don't clear
 687                                          // evt.isShiftDown();
 688           boolean invertHighlighted = evt.isAltDown();
 689           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 690                   toggleSel);
 691           break;
 692         }
 693         case KeyEvent.VK_PAGE_UP:
 694           viewport.getRanges().pageUp();
 695           break;
 696         case KeyEvent.VK_PAGE_DOWN:
 697           viewport.getRanges().pageDown();
 698           break;
 699         }
 700       }
 701
 702       @Override
 703       public void keyReleased(KeyEvent evt)
 704       {
 705         switch (evt.getKeyCode())
 706         {
 707         case KeyEvent.VK_LEFT:
 708           if (evt.isAltDown() || !viewport.cursorMode)
 709           {
 710             viewport.firePropertyChange("alignment", null,
 711                     viewport.getAlignment().getSequences());
 712           }
 713           break;
 714
 715         case KeyEvent.VK_RIGHT:
 716           if (evt.isAltDown() || !viewport.cursorMode)
 717           {
 718             viewport.firePropertyChange("alignment", null,
 719                     viewport.getAlignment().getSequences());
 720           }
 721           break;
 722         }
 723       }
 724     });
 725   }
 726
 727   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 728   {
 729     ap.alignFrame = this;
 730     avc = new jalview.controller.AlignViewController(this, viewport,
 731             alignPanel);
 732
 733     alignPanels.add(ap);
 734
 735     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 736
 737     int aSize = alignPanels.size();
 738
 739     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 740
 741     if (aSize == 1 && ap.av.getViewName() == null)
 742     {
 743       this.getContentPane().add(ap, BorderLayout.CENTER);
 744     }
 745     else
 746     {
 747       if (aSize == 2)
 748       {
 749         setInitialTabVisible();
 750       }
 751
 752       expandViews.setEnabled(true);
 753       gatherViews.setEnabled(true);
 754       tabbedPane.addTab(ap.av.getViewName(), ap);
 755
 756       ap.setVisible(false);
 757     }
 758
 759     if (newPanel)
 760     {
 761       if (ap.av.isPadGaps())
 762       {
 763         ap.av.getAlignment().padGaps();
 764       }
 765       ap.av.updateConservation(ap);
 766       ap.av.updateConsensus(ap);
 767       ap.av.updateStrucConsensus(ap);
 768     }
 769   }
 770
 771   public void setInitialTabVisible()
 772   {
 773     expandViews.setEnabled(true);
 774     gatherViews.setEnabled(true);
 775     tabbedPane.setVisible(true);
 776     AlignmentPanel first = alignPanels.get(0);
 777     tabbedPane.addTab(first.av.getViewName(), first);
 778     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 779   }
 780
 781   public AlignViewport getViewport()
 782   {
 783     return viewport;
 784   }
 785
 786   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 787   private void addServiceListeners()
 788   {
 789     final java.beans.PropertyChangeListener thisListener;
 790     Desktop.instance.addJalviewPropertyChangeListener("services",
 791             thisListener = new java.beans.PropertyChangeListener()
 792             {
 793               @Override
 794               public void propertyChange(PropertyChangeEvent evt)
 795               {
 796                 // // System.out.println("Discoverer property change.");
 797                 // if (evt.getPropertyName().equals("services"))
 798                 {
 799                   SwingUtilities.invokeLater(new Runnable()
 800                   {
 801
 802                     @Override
 803                     public void run()
 804                     {
 805                       System.err.println(
 806                               "Rebuild WS Menu for service change");
 807                       BuildWebServiceMenu();
 808                     }
 809
 810                   });
 811                 }
 812               }
 813             });
 814     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 815     {
 816       @Override
 817       public void internalFrameClosed(
 818               javax.swing.event.InternalFrameEvent evt)
 819       {
 820         // System.out.println("deregistering discoverer listener");
 821         Desktop.instance.removeJalviewPropertyChangeListener("services",
 822                 thisListener);
 823         closeMenuItem_actionPerformed(true);
 824       };
 825     });
 826     // Finally, build the menu once to get current service state
 827     new Thread(new Runnable()
 828     {
 829       @Override
 830       public void run()
 831       {
 832         BuildWebServiceMenu();
 833       }
 834     }).start();
 835   }
 836
 837   /**
 838    * Configure menu items that vary according to whether the alignment is
 839    * nucleotide or protein
 840    */
 841   public void setGUINucleotide()
 842   {
 843     AlignmentI al = getViewport().getAlignment();
 844     boolean nucleotide = al.isNucleotide();
 845
 846     loadVcf.setVisible(nucleotide);
 847     showTranslation.setVisible(nucleotide);
 848     showReverse.setVisible(nucleotide);
 849     showReverseComplement.setVisible(nucleotide);
 850     conservationMenuItem.setEnabled(!nucleotide);
 851     modifyConservation
 852             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 853     showGroupConservation.setEnabled(!nucleotide);
 854
 855     showComplementMenuItem
 856             .setText(nucleotide ? MessageManager.getString("label.protein")
 857                     : MessageManager.getString("label.nucleotide"));
 858   }
 859
 860   /**
 861    * set up menus for the current viewport. This may be called after any
 862    * operation that affects the data in the current view (selection changed,
 863    * etc) to update the menus to reflect the new state.
 864    */
 865   @Override
 866   public void setMenusForViewport()
 867   {
 868     setMenusFromViewport(viewport);
 869   }
 870
 871   /**
 872    * Need to call this method when tabs are selected for multiple views, or when
 873    * loading from Jalview2XML.java
 874    *
 875    * @param av
 876    *          AlignViewport
 877    */
 878   public void setMenusFromViewport(AlignViewport av)
 879   {
 880     padGapsMenuitem.setSelected(av.isPadGaps());
 881     colourTextMenuItem.setSelected(av.isShowColourText());
 882     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 883     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 884     conservationMenuItem.setSelected(av.getConservationSelected());
 885     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 886     seqLimits.setSelected(av.getShowJVSuffix());
 887     idRightAlign.setSelected(av.isRightAlignIds());
 888     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 889     renderGapsMenuItem.setSelected(av.isRenderGaps());
 890     wrapMenuItem.setSelected(av.getWrapAlignment());
 891     scaleAbove.setVisible(av.getWrapAlignment());
 892     scaleLeft.setVisible(av.getWrapAlignment());
 893     scaleRight.setVisible(av.getWrapAlignment());
 894     annotationPanelMenuItem.setState(av.isShowAnnotation());
 895     /*
 896      * Show/hide annotations only enabled if annotation panel is shown
 897      */
 898     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 902     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 903     viewTextMenuItem.setSelected(av.getShowText());
 904     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 905     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 906     showGroupConservation.setSelected(av.isShowGroupConservation());
 907     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 908     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 909     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 910
 911     ColourMenuHelper.setColourSelected(colourMenu,
 912             av.getGlobalColourScheme());
 913
 914     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 915     hiddenMarkers.setState(av.getShowHiddenMarkers());
 916     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 917     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 918     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 919     autoCalculate.setSelected(av.autoCalculateConsensus);
 920     sortByTree.setSelected(av.sortByTree);
 921     listenToViewSelections.setSelected(av.followSelection);
 922
 923     showProducts.setEnabled(canShowProducts());
 924     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 925
 926     updateEditMenuBar();
 927   }
 928
 929   /**
 930    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 931    *
 932    * @param b
 933    */
 934   public void setGroovyEnabled(boolean b)
 935   {
 936     runGroovy.setEnabled(b);
 937   }
 938
 939   private IProgressIndicator progressBar;
 940
 941   /*
 942    * (non-Javadoc)
 943    *
 944    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 945    */
 946   @Override
 947   public void setProgressBar(String message, long id)
 948   {
 949     progressBar.setProgressBar(message, id);
 950   }
 951
 952   @Override
 953   public void registerHandler(final long id,
 954           final IProgressIndicatorHandler handler)
 955   {
 956     progressBar.registerHandler(id, handler);
 957   }
 958
 959   /**
 960    *
 961    * @return true if any progress bars are still active
 962    */
 963   @Override
 964   public boolean operationInProgress()
 965   {
 966     return progressBar.operationInProgress();
 967   }
 968
 969   /**
 970    * Sets the text of the status bar. Note that setting a null or empty value
 971    * will cause the status bar to be hidden, with possibly undesirable flicker
 972    * of the screen layout.
 973    */
 974   @Override
 975   public void setStatus(String text)
 976   {
 977     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 978   }
 979
 980   /*
 981    * Added so Castor Mapping file can obtain Jalview Version
 982    */
 983   public String getVersion()
 984   {
 985     return jalview.bin.Cache.getProperty("VERSION");
 986   }
 987
 988   public FeatureRenderer getFeatureRenderer()
 989   {
 990     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 991   }
 992
 993   @Override
 994   public void fetchSequence_actionPerformed(ActionEvent e)
 995   {
 996     new jalview.gui.SequenceFetcher(this);
 997   }
 998
 999   @Override
1000   public void addFromFile_actionPerformed(ActionEvent e)
1001   {
1002     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1003   }
1004
1005   @Override
1006   public void reload_actionPerformed(ActionEvent e)
1007   {
1008     if (fileName != null)
1009     {
1010       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1011       // originating file's format
1012       // TODO: work out how to recover feature settings for correct view(s) when
1013       // file is reloaded.
1014       if (FileFormat.Jalview.equals(currentFileFormat))
1015       {
1016         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1017         for (int i = 0; i < frames.length; i++)
1018         {
1019           if (frames[i] instanceof AlignFrame && frames[i] != this
1020                   && ((AlignFrame) frames[i]).fileName != null
1021                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1022           {
1023             try
1024             {
1025               frames[i].setSelected(true);
1026               Desktop.instance.closeAssociatedWindows();
1027             } catch (java.beans.PropertyVetoException ex)
1028             {
1029             }
1030           }
1031
1032         }
1033         Desktop.instance.closeAssociatedWindows();
1034
1035         FileLoader loader = new FileLoader();
1036         DataSourceType protocol = fileName.startsWith("http:")
1037                 ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1040       }
1041       else
1042       {
1043         Rectangle bounds = this.getBounds();
1044
1045         FileLoader loader = new FileLoader();
1046         DataSourceType protocol = fileName.startsWith("http:")
1047                 ? DataSourceType.URL
1048                 : DataSourceType.FILE;
1049         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1050                 protocol, currentFileFormat);
1051
1052         newframe.setBounds(bounds);
1053         if (featureSettings != null && featureSettings.isShowing())
1054         {
1055           final Rectangle fspos = featureSettings.frame.getBounds();
1056           // TODO: need a 'show feature settings' function that takes bounds -
1057           // need to refactor Desktop.addFrame
1058           newframe.featureSettings_actionPerformed(null);
1059           final FeatureSettings nfs = newframe.featureSettings;
1060           SwingUtilities.invokeLater(new Runnable()
1061           {
1062             @Override
1063             public void run()
1064             {
1065               nfs.frame.setBounds(fspos);
1066             }
1067           });
1068           this.featureSettings.close();
1069           this.featureSettings = null;
1070         }
1071         this.closeMenuItem_actionPerformed(true);
1072       }
1073     }
1074   }
1075
1076   @Override
1077   public void addFromText_actionPerformed(ActionEvent e)
1078   {
1079     Desktop.instance
1080             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1081   }
1082
1083   @Override
1084   public void addFromURL_actionPerformed(ActionEvent e)
1085   {
1086     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1087   }
1088
1089   @Override
1090   public void save_actionPerformed(ActionEvent e)
1091   {
1092     if (fileName == null || (currentFileFormat == null)
1093             || fileName.startsWith("http"))
1094     {
1095       saveAs_actionPerformed(null);
1096     }
1097     else
1098     {
1099       saveAlignment(fileName, currentFileFormat);
1100     }
1101   }
1102
1103   /**
1104    * DOCUMENT ME!
1105    *
1106    * @param e
1107    *          DOCUMENT ME!
1108    */
1109   @Override
1110   public void saveAs_actionPerformed(ActionEvent e)
1111   {
1112     String format = currentFileFormat == null ? null
1113             : currentFileFormat.getName();
1114     JalviewFileChooser chooser = JalviewFileChooser
1115             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1116
1117     chooser.setFileView(new JalviewFileView());
1118     chooser.setDialogTitle(
1119             MessageManager.getString("label.save_alignment_to_file"));
1120     chooser.setToolTipText(MessageManager.getString("action.save"));
1121
1122     int value = chooser.showSaveDialog(this);
1123
1124     if (value == JalviewFileChooser.APPROVE_OPTION)
1125     {
1126       currentFileFormat = chooser.getSelectedFormat();
1127       while (currentFileFormat == null)
1128       {
1129         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1130                 MessageManager.getString(
1131                         "label.select_file_format_before_saving"),
1132                 MessageManager.getString("label.file_format_not_specified"),
1133                 JvOptionPane.WARNING_MESSAGE);
1134         currentFileFormat = chooser.getSelectedFormat();
1135         value = chooser.showSaveDialog(this);
1136         if (value != JalviewFileChooser.APPROVE_OPTION)
1137         {
1138           return;
1139         }
1140       }
1141
1142       fileName = chooser.getSelectedFile().getPath();
1143
1144       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1145
1146       Cache.setProperty("LAST_DIRECTORY", fileName);
1147       saveAlignment(fileName, currentFileFormat);
1148     }
1149   }
1150
1151   public boolean saveAlignment(String file, FileFormatI format)
1152   {
1153     boolean success = true;
1154
1155     if (FileFormat.Jalview.equals(format))
1156     {
1157       String shortName = title;
1158
1159       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160       {
1161         shortName = shortName.substring(
1162                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1163       }
1164
1165       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1166               shortName);
1167
1168       statusBar.setText(MessageManager.formatMessage(
1169               "label.successfully_saved_to_file_in_format", new Object[]
1170               { fileName, format }));
1171
1172     }
1173     else
1174     {
1175       AlignmentExportData exportData = getAlignmentForExport(format,
1176               viewport, null);
1177       if (exportData.getSettings().isCancelled())
1178       {
1179         return false;
1180       }
1181       FormatAdapter f = new FormatAdapter(alignPanel,
1182               exportData.getSettings());
1183       String output = f.formatSequences(format, exportData.getAlignment(), // class
1184                                                                            // cast
1185                                                                            // exceptions
1186                                                                            // will
1187               // occur in the distant future
1188               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1189               f.getCacheSuffixDefault(format),
1190               viewport.getAlignment().getHiddenColumns());
1191
1192       if (output == null)
1193       {
1194         success = false;
1195       }
1196       else
1197       {
1198         // create backupfiles object and get new temp filename destination
1199         BackupFiles backupfiles = new BackupFiles(file);
1200
1201         try
1202         {
1203           PrintWriter out = new PrintWriter(
1204                   new FileWriter(backupfiles.getTempFilePath()));
1205
1206           // TESTING code here
1207           boolean TESTING = true;
1208           if (TESTING)
1209           {
1210             out.print("; TESTSTART\n");
1211             int count = 20;
1212             for (int i = 0; i < count; i++)
1213             {
1214               // Thread.sleep(1000);
1215               out.println("; TEST: " + (count - 1 - i));
1216             }
1217           }
1218           out.print(output);
1219           if (TESTING)
1220           {
1221             out.print("; TESTEND\n");
1222           }
1223           out.close();
1224           this.setTitle(file);
1225           statusBar.setText(MessageManager.formatMessage(
1226                   "label.successfully_saved_to_file_in_format", new Object[]
1227                   { fileName, format.getName() }));
1228         } catch (Exception ex)
1229         {
1230           success = false;
1231           ex.printStackTrace();
1232         }
1233
1234         backupfiles.setWriteSuccess(success);
1235         // do the backup file roll and rename the temp file to actual file
1236         success = backupfiles.rollBackupsAndRenameTempFile();
1237
1238       }
1239     }
1240
1241     if (!success)
1242     {
1243       JvOptionPane.showInternalMessageDialog(this, MessageManager
1244               .formatMessage("label.couldnt_save_file", new Object[]
1245               { fileName }),
1246               MessageManager.getString("label.error_saving_file"),
1247               JvOptionPane.WARNING_MESSAGE);
1248     }
1249
1250     return success;
1251   }
1252
1253   private void warningMessage(String warning, String title)
1254   {
1255     if (new jalview.util.Platform().isHeadless())
1256     {
1257       System.err.println("Warning: " + title + "\nWarning: " + warning);
1258
1259     }
1260     else
1261     {
1262       JvOptionPane.showInternalMessageDialog(this, warning, title,
1263               JvOptionPane.WARNING_MESSAGE);
1264     }
1265     return;
1266   }
1267
1268   /**
1269    * DOCUMENT ME!
1270    *
1271    * @param e
1272    *          DOCUMENT ME!
1273    */
1274   @Override
1275   protected void outputText_actionPerformed(ActionEvent e)
1276   {
1277     FileFormatI fileFormat = FileFormats.getInstance()
1278             .forName(e.getActionCommand());
1279     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1280             viewport, null);
1281     if (exportData.getSettings().isCancelled())
1282     {
1283       return;
1284     }
1285     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1286     cap.setForInput(null);
1287     try
1288     {
1289       FileFormatI format = fileFormat;
1290       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1291               .formatSequences(format, exportData.getAlignment(),
1292                       exportData.getOmitHidden(),
1293                       exportData.getStartEndPostions(),
1294                       viewport.getAlignment().getHiddenColumns()));
1295       Desktop.addInternalFrame(cap, MessageManager
1296               .formatMessage("label.alignment_output_command", new Object[]
1297               { e.getActionCommand() }), 600, 500);
1298     } catch (OutOfMemoryError oom)
1299     {
1300       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1301               oom);
1302       cap.dispose();
1303     }
1304
1305   }
1306
1307   public static AlignmentExportData getAlignmentForExport(
1308           FileFormatI format, AlignViewportI viewport,
1309           AlignExportSettingI exportSettings)
1310   {
1311     AlignmentI alignmentToExport = null;
1312     AlignExportSettingI settings = exportSettings;
1313     String[] omitHidden = null;
1314
1315     HiddenSequences hiddenSeqs = viewport.getAlignment()
1316             .getHiddenSequences();
1317
1318     alignmentToExport = viewport.getAlignment();
1319
1320     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1321     if (settings == null)
1322     {
1323       settings = new AlignExportSettings(hasHiddenSeqs,
1324               viewport.hasHiddenColumns(), format);
1325     }
1326     // settings.isExportAnnotations();
1327
1328     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1329     {
1330       omitHidden = viewport.getViewAsString(false,
1331               settings.isExportHiddenSequences());
1332     }
1333
1334     int[] alignmentStartEnd = new int[2];
1335     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1336     {
1337       alignmentToExport = hiddenSeqs.getFullAlignment();
1338     }
1339     else
1340     {
1341       alignmentToExport = viewport.getAlignment();
1342     }
1343     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1344             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1345     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1346             omitHidden, alignmentStartEnd, settings);
1347     return ed;
1348   }
1349
1350   /**
1351    * DOCUMENT ME!
1352    *
1353    * @param e
1354    *          DOCUMENT ME!
1355    */
1356   @Override
1357   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1358   {
1359     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1360     htmlSVG.exportHTML(null);
1361   }
1362
1363   @Override
1364   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1365   {
1366     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1367     bjs.exportHTML(null);
1368   }
1369
1370   public void createImageMap(File file, String image)
1371   {
1372     alignPanel.makePNGImageMap(file, image);
1373   }
1374
1375   /**
1376    * DOCUMENT ME!
1377    *
1378    * @param e
1379    *          DOCUMENT ME!
1380    */
1381   @Override
1382   public void createPNG(File f)
1383   {
1384     alignPanel.makePNG(f);
1385   }
1386
1387   /**
1388    * DOCUMENT ME!
1389    *
1390    * @param e
1391    *          DOCUMENT ME!
1392    */
1393   @Override
1394   public void createEPS(File f)
1395   {
1396     alignPanel.makeEPS(f);
1397   }
1398
1399   @Override
1400   public void createSVG(File f)
1401   {
1402     alignPanel.makeSVG(f);
1403   }
1404
1405   @Override
1406   public void pageSetup_actionPerformed(ActionEvent e)
1407   {
1408     PrinterJob printJob = PrinterJob.getPrinterJob();
1409     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1410   }
1411
1412   /**
1413    * DOCUMENT ME!
1414    *
1415    * @param e
1416    *          DOCUMENT ME!
1417    */
1418   @Override
1419   public void printMenuItem_actionPerformed(ActionEvent e)
1420   {
1421     // Putting in a thread avoids Swing painting problems
1422     PrintThread thread = new PrintThread(alignPanel);
1423     thread.start();
1424   }
1425
1426   @Override
1427   public void exportFeatures_actionPerformed(ActionEvent e)
1428   {
1429     new AnnotationExporter(alignPanel).exportFeatures();
1430   }
1431
1432   @Override
1433   public void exportAnnotations_actionPerformed(ActionEvent e)
1434   {
1435     new AnnotationExporter(alignPanel).exportAnnotations();
1436   }
1437
1438   @Override
1439   public void associatedData_actionPerformed(ActionEvent e)
1440   {
1441     // Pick the tree file
1442     JalviewFileChooser chooser = new JalviewFileChooser(
1443             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1444     chooser.setFileView(new JalviewFileView());
1445     chooser.setDialogTitle(
1446             MessageManager.getString("label.load_jalview_annotations"));
1447     chooser.setToolTipText(
1448             MessageManager.getString("label.load_jalview_annotations"));
1449
1450     int value = chooser.showOpenDialog(null);
1451
1452     if (value == JalviewFileChooser.APPROVE_OPTION)
1453     {
1454       String choice = chooser.getSelectedFile().getPath();
1455       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1456       loadJalviewDataFile(choice, null, null, null);
1457     }
1458
1459   }
1460
1461   /**
1462    * Close the current view or all views in the alignment frame. If the frame
1463    * only contains one view then the alignment will be removed from memory.
1464    *
1465    * @param closeAllTabs
1466    */
1467   @Override
1468   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1469   {
1470     if (alignPanels != null && alignPanels.size() < 2)
1471     {
1472       closeAllTabs = true;
1473     }
1474
1475     try
1476     {
1477       if (alignPanels != null)
1478       {
1479         if (closeAllTabs)
1480         {
1481           if (this.isClosed())
1482           {
1483             // really close all the windows - otherwise wait till
1484             // setClosed(true) is called
1485             for (int i = 0; i < alignPanels.size(); i++)
1486             {
1487               AlignmentPanel ap = alignPanels.get(i);
1488               ap.closePanel();
1489             }
1490           }
1491         }
1492         else
1493         {
1494           closeView(alignPanel);
1495         }
1496       }
1497
1498       if (closeAllTabs)
1499       {
1500         /*
1501          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1502          * be called recursively, with the frame now in 'closed' state
1503          */
1504         this.setClosed(true);
1505       }
1506     } catch (Exception ex)
1507     {
1508       ex.printStackTrace();
1509     }
1510   }
1511
1512   /**
1513    * Close the specified panel and close up tabs appropriately.
1514    *
1515    * @param panelToClose
1516    */
1517   public void closeView(AlignmentPanel panelToClose)
1518   {
1519     int index = tabbedPane.getSelectedIndex();
1520     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1521     alignPanels.remove(panelToClose);
1522     panelToClose.closePanel();
1523     panelToClose = null;
1524
1525     tabbedPane.removeTabAt(closedindex);
1526     tabbedPane.validate();
1527
1528     if (index > closedindex || index == tabbedPane.getTabCount())
1529     {
1530       // modify currently selected tab index if necessary.
1531       index--;
1532     }
1533
1534     this.tabSelectionChanged(index);
1535   }
1536
1537   /**
1538    * DOCUMENT ME!
1539    */
1540   void updateEditMenuBar()
1541   {
1542
1543     if (viewport.getHistoryList().size() > 0)
1544     {
1545       undoMenuItem.setEnabled(true);
1546       CommandI command = viewport.getHistoryList().peek();
1547       undoMenuItem.setText(MessageManager
1548               .formatMessage("label.undo_command", new Object[]
1549               { command.getDescription() }));
1550     }
1551     else
1552     {
1553       undoMenuItem.setEnabled(false);
1554       undoMenuItem.setText(MessageManager.getString("action.undo"));
1555     }
1556
1557     if (viewport.getRedoList().size() > 0)
1558     {
1559       redoMenuItem.setEnabled(true);
1560
1561       CommandI command = viewport.getRedoList().peek();
1562       redoMenuItem.setText(MessageManager
1563               .formatMessage("label.redo_command", new Object[]
1564               { command.getDescription() }));
1565     }
1566     else
1567     {
1568       redoMenuItem.setEnabled(false);
1569       redoMenuItem.setText(MessageManager.getString("action.redo"));
1570     }
1571   }
1572
1573   @Override
1574   public void addHistoryItem(CommandI command)
1575   {
1576     if (command.getSize() > 0)
1577     {
1578       viewport.addToHistoryList(command);
1579       viewport.clearRedoList();
1580       updateEditMenuBar();
1581       viewport.updateHiddenColumns();
1582       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1583       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1584       // viewport.getColumnSelection()
1585       // .getHiddenColumns().size() > 0);
1586     }
1587   }
1588
1589   /**
1590    *
1591    * @return alignment objects for all views
1592    */
1593   AlignmentI[] getViewAlignments()
1594   {
1595     if (alignPanels != null)
1596     {
1597       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1598       int i = 0;
1599       for (AlignmentPanel ap : alignPanels)
1600       {
1601         als[i++] = ap.av.getAlignment();
1602       }
1603       return als;
1604     }
1605     if (viewport != null)
1606     {
1607       return new AlignmentI[] { viewport.getAlignment() };
1608     }
1609     return null;
1610   }
1611
1612   /**
1613    * DOCUMENT ME!
1614    *
1615    * @param e
1616    *          DOCUMENT ME!
1617    */
1618   @Override
1619   protected void undoMenuItem_actionPerformed(ActionEvent e)
1620   {
1621     if (viewport.getHistoryList().isEmpty())
1622     {
1623       return;
1624     }
1625     CommandI command = viewport.getHistoryList().pop();
1626     viewport.addToRedoList(command);
1627     command.undoCommand(getViewAlignments());
1628
1629     AlignmentViewport originalSource = getOriginatingSource(command);
1630     updateEditMenuBar();
1631
1632     if (originalSource != null)
1633     {
1634       if (originalSource != viewport)
1635       {
1636         Cache.log.warn(
1637                 "Implementation worry: mismatch of viewport origin for undo");
1638       }
1639       originalSource.updateHiddenColumns();
1640       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1641       // null
1642       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1643       // viewport.getColumnSelection()
1644       // .getHiddenColumns().size() > 0);
1645       originalSource.firePropertyChange("alignment", null,
1646               originalSource.getAlignment().getSequences());
1647     }
1648   }
1649
1650   /**
1651    * DOCUMENT ME!
1652    *
1653    * @param e
1654    *          DOCUMENT ME!
1655    */
1656   @Override
1657   protected void redoMenuItem_actionPerformed(ActionEvent e)
1658   {
1659     if (viewport.getRedoList().size() < 1)
1660     {
1661       return;
1662     }
1663
1664     CommandI command = viewport.getRedoList().pop();
1665     viewport.addToHistoryList(command);
1666     command.doCommand(getViewAlignments());
1667
1668     AlignmentViewport originalSource = getOriginatingSource(command);
1669     updateEditMenuBar();
1670
1671     if (originalSource != null)
1672     {
1673
1674       if (originalSource != viewport)
1675       {
1676         Cache.log.warn(
1677                 "Implementation worry: mismatch of viewport origin for redo");
1678       }
1679       originalSource.updateHiddenColumns();
1680       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1681       // null
1682       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1683       // viewport.getColumnSelection()
1684       // .getHiddenColumns().size() > 0);
1685       originalSource.firePropertyChange("alignment", null,
1686               originalSource.getAlignment().getSequences());
1687     }
1688   }
1689
1690   AlignmentViewport getOriginatingSource(CommandI command)
1691   {
1692     AlignmentViewport originalSource = null;
1693     // For sequence removal and addition, we need to fire
1694     // the property change event FROM the viewport where the
1695     // original alignment was altered
1696     AlignmentI al = null;
1697     if (command instanceof EditCommand)
1698     {
1699       EditCommand editCommand = (EditCommand) command;
1700       al = editCommand.getAlignment();
1701       List<Component> comps = PaintRefresher.components
1702               .get(viewport.getSequenceSetId());
1703
1704       for (Component comp : comps)
1705       {
1706         if (comp instanceof AlignmentPanel)
1707         {
1708           if (al == ((AlignmentPanel) comp).av.getAlignment())
1709           {
1710             originalSource = ((AlignmentPanel) comp).av;
1711             break;
1712           }
1713         }
1714       }
1715     }
1716
1717     if (originalSource == null)
1718     {
1719       // The original view is closed, we must validate
1720       // the current view against the closed view first
1721       if (al != null)
1722       {
1723         PaintRefresher.validateSequences(al, viewport.getAlignment());
1724       }
1725
1726       originalSource = viewport;
1727     }
1728
1729     return originalSource;
1730   }
1731
1732   /**
1733    * DOCUMENT ME!
1734    *
1735    * @param up
1736    *          DOCUMENT ME!
1737    */
1738   public void moveSelectedSequences(boolean up)
1739   {
1740     SequenceGroup sg = viewport.getSelectionGroup();
1741
1742     if (sg == null)
1743     {
1744       return;
1745     }
1746     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1747             viewport.getHiddenRepSequences(), up);
1748     alignPanel.paintAlignment(true, false);
1749   }
1750
1751   synchronized void slideSequences(boolean right, int size)
1752   {
1753     List<SequenceI> sg = new ArrayList<>();
1754     if (viewport.cursorMode)
1755     {
1756       sg.add(viewport.getAlignment()
1757               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1758     }
1759     else if (viewport.getSelectionGroup() != null
1760             && viewport.getSelectionGroup().getSize() != viewport
1761                     .getAlignment().getHeight())
1762     {
1763       sg = viewport.getSelectionGroup()
1764               .getSequences(viewport.getHiddenRepSequences());
1765     }
1766
1767     if (sg.size() < 1)
1768     {
1769       return;
1770     }
1771
1772     List<SequenceI> invertGroup = new ArrayList<>();
1773
1774     for (SequenceI seq : viewport.getAlignment().getSequences())
1775     {
1776       if (!sg.contains(seq))
1777       {
1778         invertGroup.add(seq);
1779       }
1780     }
1781
1782     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1783
1784     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1785     for (int i = 0; i < invertGroup.size(); i++)
1786     {
1787       seqs2[i] = invertGroup.get(i);
1788     }
1789
1790     SlideSequencesCommand ssc;
1791     if (right)
1792     {
1793       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1794               viewport.getGapCharacter());
1795     }
1796     else
1797     {
1798       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1799               viewport.getGapCharacter());
1800     }
1801
1802     int groupAdjustment = 0;
1803     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     else if (!ssc.getGapsInsertedBegin() && !right)
1815     {
1816       if (viewport.cursorMode)
1817       {
1818         alignPanel.getSeqPanel().moveCursor(-size, 0);
1819       }
1820       else
1821       {
1822         groupAdjustment = -size;
1823       }
1824     }
1825
1826     if (groupAdjustment != 0)
1827     {
1828       viewport.getSelectionGroup().setStartRes(
1829               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1830       viewport.getSelectionGroup().setEndRes(
1831               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1832     }
1833
1834     /*
1835      * just extend the last slide command if compatible; but not if in
1836      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1837      */
1838     boolean appendHistoryItem = false;
1839     Deque<CommandI> historyList = viewport.getHistoryList();
1840     boolean inSplitFrame = getSplitViewContainer() != null;
1841     if (!inSplitFrame && historyList != null && historyList.size() > 0
1842             && historyList.peek() instanceof SlideSequencesCommand)
1843     {
1844       appendHistoryItem = ssc.appendSlideCommand(
1845               (SlideSequencesCommand) historyList.peek());
1846     }
1847
1848     if (!appendHistoryItem)
1849     {
1850       addHistoryItem(ssc);
1851     }
1852
1853     repaint();
1854   }
1855
1856   /**
1857    * DOCUMENT ME!
1858    *
1859    * @param e
1860    *          DOCUMENT ME!
1861    */
1862   @Override
1863   protected void copy_actionPerformed(ActionEvent e)
1864   {
1865     if (viewport.getSelectionGroup() == null)
1866     {
1867       return;
1868     }
1869     // TODO: preserve the ordering of displayed alignment annotation in any
1870     // internal paste (particularly sequence associated annotation)
1871     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1872     String[] omitHidden = null;
1873
1874     if (viewport.hasHiddenColumns())
1875     {
1876       omitHidden = viewport.getViewAsString(true);
1877     }
1878
1879     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1880             seqs, omitHidden, null);
1881
1882     StringSelection ss = new StringSelection(output);
1883
1884     try
1885     {
1886       jalview.gui.Desktop.internalCopy = true;
1887       // Its really worth setting the clipboard contents
1888       // to empty before setting the large StringSelection!!
1889       Toolkit.getDefaultToolkit().getSystemClipboard()
1890               .setContents(new StringSelection(""), null);
1891
1892       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1893               Desktop.instance);
1894     } catch (OutOfMemoryError er)
1895     {
1896       new OOMWarning("copying region", er);
1897       return;
1898     }
1899
1900     HiddenColumns hiddenColumns = null;
1901     if (viewport.hasHiddenColumns())
1902     {
1903       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1904       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1905
1906       // create new HiddenColumns object with copy of hidden regions
1907       // between startRes and endRes, offset by startRes
1908       hiddenColumns = new HiddenColumns(
1909               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1910               hiddenCutoff, hiddenOffset);
1911     }
1912
1913     Desktop.jalviewClipboard = new Object[] { seqs,
1914         viewport.getAlignment().getDataset(), hiddenColumns };
1915     statusBar.setText(MessageManager.formatMessage(
1916             "label.copied_sequences_to_clipboard", new Object[]
1917             { Integer.valueOf(seqs.length).toString() }));
1918   }
1919
1920   /**
1921    * DOCUMENT ME!
1922    *
1923    * @param e
1924    *          DOCUMENT ME!
1925    */
1926   @Override
1927   protected void pasteNew_actionPerformed(ActionEvent e)
1928   {
1929     paste(true);
1930   }
1931
1932   /**
1933    * DOCUMENT ME!
1934    *
1935    * @param e
1936    *          DOCUMENT ME!
1937    */
1938   @Override
1939   protected void pasteThis_actionPerformed(ActionEvent e)
1940   {
1941     paste(false);
1942   }
1943
1944   /**
1945    * Paste contents of Jalview clipboard
1946    *
1947    * @param newAlignment
1948    *          true to paste to a new alignment, otherwise add to this.
1949    */
1950   void paste(boolean newAlignment)
1951   {
1952     boolean externalPaste = true;
1953     try
1954     {
1955       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1956       Transferable contents = c.getContents(this);
1957
1958       if (contents == null)
1959       {
1960         return;
1961       }
1962
1963       String str;
1964       FileFormatI format;
1965       try
1966       {
1967         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1968         if (str.length() < 1)
1969         {
1970           return;
1971         }
1972
1973         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1974
1975       } catch (OutOfMemoryError er)
1976       {
1977         new OOMWarning("Out of memory pasting sequences!!", er);
1978         return;
1979       }
1980
1981       SequenceI[] sequences;
1982       boolean annotationAdded = false;
1983       AlignmentI alignment = null;
1984
1985       if (Desktop.jalviewClipboard != null)
1986       {
1987         // The clipboard was filled from within Jalview, we must use the
1988         // sequences
1989         // And dataset from the copied alignment
1990         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1991         // be doubly sure that we create *new* sequence objects.
1992         sequences = new SequenceI[newseq.length];
1993         for (int i = 0; i < newseq.length; i++)
1994         {
1995           sequences[i] = new Sequence(newseq[i]);
1996         }
1997         alignment = new Alignment(sequences);
1998         externalPaste = false;
1999       }
2000       else
2001       {
2002         // parse the clipboard as an alignment.
2003         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2004                 format);
2005         sequences = alignment.getSequencesArray();
2006       }
2007
2008       int alwidth = 0;
2009       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2010       int fgroup = -1;
2011
2012       if (newAlignment)
2013       {
2014
2015         if (Desktop.jalviewClipboard != null)
2016         {
2017           // dataset is inherited
2018           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2019         }
2020         else
2021         {
2022           // new dataset is constructed
2023           alignment.setDataset(null);
2024         }
2025         alwidth = alignment.getWidth() + 1;
2026       }
2027       else
2028       {
2029         AlignmentI pastedal = alignment; // preserve pasted alignment object
2030         // Add pasted sequences and dataset into existing alignment.
2031         alignment = viewport.getAlignment();
2032         alwidth = alignment.getWidth() + 1;
2033         // decide if we need to import sequences from an existing dataset
2034         boolean importDs = Desktop.jalviewClipboard != null
2035                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2036         // importDs==true instructs us to copy over new dataset sequences from
2037         // an existing alignment
2038         Vector newDs = (importDs) ? new Vector() : null; // used to create
2039         // minimum dataset set
2040
2041         for (int i = 0; i < sequences.length; i++)
2042         {
2043           if (importDs)
2044           {
2045             newDs.addElement(null);
2046           }
2047           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2048           // paste
2049           if (importDs && ds != null)
2050           {
2051             if (!newDs.contains(ds))
2052             {
2053               newDs.setElementAt(ds, i);
2054               ds = new Sequence(ds);
2055               // update with new dataset sequence
2056               sequences[i].setDatasetSequence(ds);
2057             }
2058             else
2059             {
2060               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2061             }
2062           }
2063           else
2064           {
2065             // copy and derive new dataset sequence
2066             sequences[i] = sequences[i].deriveSequence();
2067             alignment.getDataset()
2068                     .addSequence(sequences[i].getDatasetSequence());
2069             // TODO: avoid creation of duplicate dataset sequences with a
2070             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2071           }
2072           alignment.addSequence(sequences[i]); // merges dataset
2073         }
2074         if (newDs != null)
2075         {
2076           newDs.clear(); // tidy up
2077         }
2078         if (alignment.getAlignmentAnnotation() != null)
2079         {
2080           for (AlignmentAnnotation alan : alignment
2081                   .getAlignmentAnnotation())
2082           {
2083             if (alan.graphGroup > fgroup)
2084             {
2085               fgroup = alan.graphGroup;
2086             }
2087           }
2088         }
2089         if (pastedal.getAlignmentAnnotation() != null)
2090         {
2091           // Add any annotation attached to alignment.
2092           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2093           for (int i = 0; i < alann.length; i++)
2094           {
2095             annotationAdded = true;
2096             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2097             {
2098               AlignmentAnnotation newann = new AlignmentAnnotation(
2099                       alann[i]);
2100               if (newann.graphGroup > -1)
2101               {
2102                 if (newGraphGroups.size() <= newann.graphGroup
2103                         || newGraphGroups.get(newann.graphGroup) == null)
2104                 {
2105                   for (int q = newGraphGroups
2106                           .size(); q <= newann.graphGroup; q++)
2107                   {
2108                     newGraphGroups.add(q, null);
2109                   }
2110                   newGraphGroups.set(newann.graphGroup,
2111                           Integer.valueOf(++fgroup));
2112                 }
2113                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2114                         .intValue();
2115               }
2116
2117               newann.padAnnotation(alwidth);
2118               alignment.addAnnotation(newann);
2119             }
2120           }
2121         }
2122       }
2123       if (!newAlignment)
2124       {
2125         // /////
2126         // ADD HISTORY ITEM
2127         //
2128         addHistoryItem(new EditCommand(
2129                 MessageManager.getString("label.add_sequences"),
2130                 Action.PASTE, sequences, 0, alignment.getWidth(),
2131                 alignment));
2132       }
2133       // Add any annotations attached to sequences
2134       for (int i = 0; i < sequences.length; i++)
2135       {
2136         if (sequences[i].getAnnotation() != null)
2137         {
2138           AlignmentAnnotation newann;
2139           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2140           {
2141             annotationAdded = true;
2142             newann = sequences[i].getAnnotation()[a];
2143             newann.adjustForAlignment();
2144             newann.padAnnotation(alwidth);
2145             if (newann.graphGroup > -1)
2146             {
2147               if (newann.graphGroup > -1)
2148               {
2149                 if (newGraphGroups.size() <= newann.graphGroup
2150                         || newGraphGroups.get(newann.graphGroup) == null)
2151                 {
2152                   for (int q = newGraphGroups
2153                           .size(); q <= newann.graphGroup; q++)
2154                   {
2155                     newGraphGroups.add(q, null);
2156                   }
2157                   newGraphGroups.set(newann.graphGroup,
2158                           Integer.valueOf(++fgroup));
2159                 }
2160                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2161                         .intValue();
2162               }
2163             }
2164             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2165             // was
2166             // duplicated
2167             // earlier
2168             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2169                     a);
2170           }
2171         }
2172       }
2173       if (!newAlignment)
2174       {
2175
2176         // propagate alignment changed.
2177         viewport.getRanges().setEndSeq(alignment.getHeight());
2178         if (annotationAdded)
2179         {
2180           // Duplicate sequence annotation in all views.
2181           AlignmentI[] alview = this.getViewAlignments();
2182           for (int i = 0; i < sequences.length; i++)
2183           {
2184             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2185             if (sann == null)
2186             {
2187               continue;
2188             }
2189             for (int avnum = 0; avnum < alview.length; avnum++)
2190             {
2191               if (alview[avnum] != alignment)
2192               {
2193                 // duplicate in a view other than the one with input focus
2194                 int avwidth = alview[avnum].getWidth() + 1;
2195                 // this relies on sann being preserved after we
2196                 // modify the sequence's annotation array for each duplication
2197                 for (int a = 0; a < sann.length; a++)
2198                 {
2199                   AlignmentAnnotation newann = new AlignmentAnnotation(
2200                           sann[a]);
2201                   sequences[i].addAlignmentAnnotation(newann);
2202                   newann.padAnnotation(avwidth);
2203                   alview[avnum].addAnnotation(newann); // annotation was
2204                   // duplicated earlier
2205                   // TODO JAL-1145 graphGroups are not updated for sequence
2206                   // annotation added to several views. This may cause
2207                   // strangeness
2208                   alview[avnum].setAnnotationIndex(newann, a);
2209                 }
2210               }
2211             }
2212           }
2213           buildSortByAnnotationScoresMenu();
2214         }
2215         viewport.firePropertyChange("alignment", null,
2216                 alignment.getSequences());
2217         if (alignPanels != null)
2218         {
2219           for (AlignmentPanel ap : alignPanels)
2220           {
2221             ap.validateAnnotationDimensions(false);
2222           }
2223         }
2224         else
2225         {
2226           alignPanel.validateAnnotationDimensions(false);
2227         }
2228
2229       }
2230       else
2231       {
2232         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2233                 DEFAULT_HEIGHT);
2234         String newtitle = new String("Copied sequences");
2235
2236         if (Desktop.jalviewClipboard != null
2237                 && Desktop.jalviewClipboard[2] != null)
2238         {
2239           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2240           af.viewport.setHiddenColumns(hc);
2241         }
2242
2243         // >>>This is a fix for the moment, until a better solution is
2244         // found!!<<<
2245         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2246                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2247                         .getFeatureRenderer());
2248
2249         // TODO: maintain provenance of an alignment, rather than just make the
2250         // title a concatenation of operations.
2251         if (!externalPaste)
2252         {
2253           if (title.startsWith("Copied sequences"))
2254           {
2255             newtitle = title;
2256           }
2257           else
2258           {
2259             newtitle = newtitle.concat("- from " + title);
2260           }
2261         }
2262         else
2263         {
2264           newtitle = new String("Pasted sequences");
2265         }
2266
2267         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2268                 DEFAULT_HEIGHT);
2269
2270       }
2271
2272     } catch (Exception ex)
2273     {
2274       ex.printStackTrace();
2275       System.out.println("Exception whilst pasting: " + ex);
2276       // could be anything being pasted in here
2277     }
2278
2279   }
2280
2281   @Override
2282   protected void expand_newalign(ActionEvent e)
2283   {
2284     try
2285     {
2286       AlignmentI alignment = AlignmentUtils
2287               .expandContext(getViewport().getAlignment(), -1);
2288       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2289               DEFAULT_HEIGHT);
2290       String newtitle = new String("Flanking alignment");
2291
2292       if (Desktop.jalviewClipboard != null
2293               && Desktop.jalviewClipboard[2] != null)
2294       {
2295         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2296         af.viewport.setHiddenColumns(hc);
2297       }
2298
2299       // >>>This is a fix for the moment, until a better solution is
2300       // found!!<<<
2301       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2302               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2303                       .getFeatureRenderer());
2304
2305       // TODO: maintain provenance of an alignment, rather than just make the
2306       // title a concatenation of operations.
2307       {
2308         if (title.startsWith("Copied sequences"))
2309         {
2310           newtitle = title;
2311         }
2312         else
2313         {
2314           newtitle = newtitle.concat("- from " + title);
2315         }
2316       }
2317
2318       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2319
2320     } catch (Exception ex)
2321     {
2322       ex.printStackTrace();
2323       System.out.println("Exception whilst pasting: " + ex);
2324       // could be anything being pasted in here
2325     } catch (OutOfMemoryError oom)
2326     {
2327       new OOMWarning("Viewing flanking region of alignment", oom);
2328     }
2329   }
2330
2331   /**
2332    * DOCUMENT ME!
2333    *
2334    * @param e
2335    *          DOCUMENT ME!
2336    */
2337   @Override
2338   protected void cut_actionPerformed(ActionEvent e)
2339   {
2340     copy_actionPerformed(null);
2341     delete_actionPerformed(null);
2342   }
2343
2344   /**
2345    * DOCUMENT ME!
2346    *
2347    * @param e
2348    *          DOCUMENT ME!
2349    */
2350   @Override
2351   protected void delete_actionPerformed(ActionEvent evt)
2352   {
2353
2354     SequenceGroup sg = viewport.getSelectionGroup();
2355     if (sg == null)
2356     {
2357       return;
2358     }
2359
2360     /*
2361      * If the cut affects all sequences, warn, remove highlighted columns
2362      */
2363     if (sg.getSize() == viewport.getAlignment().getHeight())
2364     {
2365       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2366               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2367       if (isEntireAlignWidth)
2368       {
2369         int confirm = JvOptionPane.showConfirmDialog(this,
2370                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2371                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2372                 JvOptionPane.OK_CANCEL_OPTION);
2373
2374         if (confirm == JvOptionPane.CANCEL_OPTION
2375                 || confirm == JvOptionPane.CLOSED_OPTION)
2376         {
2377           return;
2378         }
2379       }
2380       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2381               sg.getEndRes() + 1);
2382     }
2383     SequenceI[] cut = sg.getSequences()
2384             .toArray(new SequenceI[sg.getSize()]);
2385
2386     addHistoryItem(new EditCommand(
2387             MessageManager.getString("label.cut_sequences"), Action.CUT,
2388             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2389             viewport.getAlignment()));
2390
2391     viewport.setSelectionGroup(null);
2392     viewport.sendSelection();
2393     viewport.getAlignment().deleteGroup(sg);
2394
2395     viewport.firePropertyChange("alignment", null,
2396             viewport.getAlignment().getSequences());
2397     if (viewport.getAlignment().getHeight() < 1)
2398     {
2399       try
2400       {
2401         this.setClosed(true);
2402       } catch (Exception ex)
2403       {
2404       }
2405     }
2406   }
2407
2408   /**
2409    * DOCUMENT ME!
2410    *
2411    * @param e
2412    *          DOCUMENT ME!
2413    */
2414   @Override
2415   protected void deleteGroups_actionPerformed(ActionEvent e)
2416   {
2417     if (avc.deleteGroups())
2418     {
2419       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2420       alignPanel.updateAnnotation();
2421       alignPanel.paintAlignment(true, true);
2422     }
2423   }
2424
2425   /**
2426    * DOCUMENT ME!
2427    *
2428    * @param e
2429    *          DOCUMENT ME!
2430    */
2431   @Override
2432   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2433   {
2434     SequenceGroup sg = new SequenceGroup(
2435             viewport.getAlignment().getSequences());
2436
2437     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2438     viewport.setSelectionGroup(sg);
2439     viewport.isSelectionGroupChanged(true);
2440     viewport.sendSelection();
2441     // JAL-2034 - should delegate to
2442     // alignPanel to decide if overview needs
2443     // updating.
2444     alignPanel.paintAlignment(false, false);
2445     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2446   }
2447
2448   /**
2449    * DOCUMENT ME!
2450    *
2451    * @param e
2452    *          DOCUMENT ME!
2453    */
2454   @Override
2455   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2456   {
2457     if (viewport.cursorMode)
2458     {
2459       alignPanel.getSeqPanel().keyboardNo1 = null;
2460       alignPanel.getSeqPanel().keyboardNo2 = null;
2461     }
2462     viewport.setSelectionGroup(null);
2463     viewport.getColumnSelection().clear();
2464     viewport.setSelectionGroup(null);
2465     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2466     // JAL-2034 - should delegate to
2467     // alignPanel to decide if overview needs
2468     // updating.
2469     alignPanel.paintAlignment(false, false);
2470     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2471     viewport.sendSelection();
2472   }
2473
2474   /**
2475    * DOCUMENT ME!
2476    *
2477    * @param e
2478    *          DOCUMENT ME!
2479    */
2480   @Override
2481   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2482   {
2483     SequenceGroup sg = viewport.getSelectionGroup();
2484
2485     if (sg == null)
2486     {
2487       selectAllSequenceMenuItem_actionPerformed(null);
2488
2489       return;
2490     }
2491
2492     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2493     {
2494       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2495     }
2496     // JAL-2034 - should delegate to
2497     // alignPanel to decide if overview needs
2498     // updating.
2499
2500     alignPanel.paintAlignment(true, false);
2501     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2502     viewport.sendSelection();
2503   }
2504
2505   @Override
2506   public void invertColSel_actionPerformed(ActionEvent e)
2507   {
2508     viewport.invertColumnSelection();
2509     alignPanel.paintAlignment(true, false);
2510     viewport.sendSelection();
2511   }
2512
2513   /**
2514    * DOCUMENT ME!
2515    *
2516    * @param e
2517    *          DOCUMENT ME!
2518    */
2519   @Override
2520   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2521   {
2522     trimAlignment(true);
2523   }
2524
2525   /**
2526    * DOCUMENT ME!
2527    *
2528    * @param e
2529    *          DOCUMENT ME!
2530    */
2531   @Override
2532   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2533   {
2534     trimAlignment(false);
2535   }
2536
2537   void trimAlignment(boolean trimLeft)
2538   {
2539     ColumnSelection colSel = viewport.getColumnSelection();
2540     int column;
2541
2542     if (!colSel.isEmpty())
2543     {
2544       if (trimLeft)
2545       {
2546         column = colSel.getMin();
2547       }
2548       else
2549       {
2550         column = colSel.getMax();
2551       }
2552
2553       SequenceI[] seqs;
2554       if (viewport.getSelectionGroup() != null)
2555       {
2556         seqs = viewport.getSelectionGroup()
2557                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2558       }
2559       else
2560       {
2561         seqs = viewport.getAlignment().getSequencesArray();
2562       }
2563
2564       TrimRegionCommand trimRegion;
2565       if (trimLeft)
2566       {
2567         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2568                 column, viewport.getAlignment());
2569         viewport.getRanges().setStartRes(0);
2570       }
2571       else
2572       {
2573         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2574                 column, viewport.getAlignment());
2575       }
2576
2577       statusBar.setText(MessageManager
2578               .formatMessage("label.removed_columns", new String[]
2579               { Integer.valueOf(trimRegion.getSize()).toString() }));
2580
2581       addHistoryItem(trimRegion);
2582
2583       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2584       {
2585         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2586                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2587         {
2588           viewport.getAlignment().deleteGroup(sg);
2589         }
2590       }
2591
2592       viewport.firePropertyChange("alignment", null,
2593               viewport.getAlignment().getSequences());
2594     }
2595   }
2596
2597   /**
2598    * DOCUMENT ME!
2599    *
2600    * @param e
2601    *          DOCUMENT ME!
2602    */
2603   @Override
2604   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2605   {
2606     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2607
2608     SequenceI[] seqs;
2609     if (viewport.getSelectionGroup() != null)
2610     {
2611       seqs = viewport.getSelectionGroup()
2612               .getSequencesAsArray(viewport.getHiddenRepSequences());
2613       start = viewport.getSelectionGroup().getStartRes();
2614       end = viewport.getSelectionGroup().getEndRes();
2615     }
2616     else
2617     {
2618       seqs = viewport.getAlignment().getSequencesArray();
2619     }
2620
2621     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2622             "Remove Gapped Columns", seqs, start, end,
2623             viewport.getAlignment());
2624
2625     addHistoryItem(removeGapCols);
2626
2627     statusBar.setText(MessageManager
2628             .formatMessage("label.removed_empty_columns", new Object[]
2629             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2630
2631     // This is to maintain viewport position on first residue
2632     // of first sequence
2633     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2634     ViewportRanges ranges = viewport.getRanges();
2635     int startRes = seq.findPosition(ranges.getStartRes());
2636     // ShiftList shifts;
2637     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2638     // edit.alColumnChanges=shifts.getInverse();
2639     // if (viewport.hasHiddenColumns)
2640     // viewport.getColumnSelection().compensateForEdits(shifts);
2641     ranges.setStartRes(seq.findIndex(startRes) - 1);
2642     viewport.firePropertyChange("alignment", null,
2643             viewport.getAlignment().getSequences());
2644
2645   }
2646
2647   /**
2648    * DOCUMENT ME!
2649    *
2650    * @param e
2651    *          DOCUMENT ME!
2652    */
2653   @Override
2654   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2655   {
2656     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2657
2658     SequenceI[] seqs;
2659     if (viewport.getSelectionGroup() != null)
2660     {
2661       seqs = viewport.getSelectionGroup()
2662               .getSequencesAsArray(viewport.getHiddenRepSequences());
2663       start = viewport.getSelectionGroup().getStartRes();
2664       end = viewport.getSelectionGroup().getEndRes();
2665     }
2666     else
2667     {
2668       seqs = viewport.getAlignment().getSequencesArray();
2669     }
2670
2671     // This is to maintain viewport position on first residue
2672     // of first sequence
2673     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2674     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2675
2676     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2677             viewport.getAlignment()));
2678
2679     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2680
2681     viewport.firePropertyChange("alignment", null,
2682             viewport.getAlignment().getSequences());
2683
2684   }
2685
2686   /**
2687    * DOCUMENT ME!
2688    *
2689    * @param e
2690    *          DOCUMENT ME!
2691    */
2692   @Override
2693   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2694   {
2695     viewport.setPadGaps(padGapsMenuitem.isSelected());
2696     viewport.firePropertyChange("alignment", null,
2697             viewport.getAlignment().getSequences());
2698   }
2699
2700   /**
2701    * DOCUMENT ME!
2702    *
2703    * @param e
2704    *          DOCUMENT ME!
2705    */
2706   @Override
2707   public void findMenuItem_actionPerformed(ActionEvent e)
2708   {
2709     new Finder();
2710   }
2711
2712   /**
2713    * Create a new view of the current alignment.
2714    */
2715   @Override
2716   public void newView_actionPerformed(ActionEvent e)
2717   {
2718     newView(null, true);
2719   }
2720
2721   /**
2722    * Creates and shows a new view of the current alignment.
2723    *
2724    * @param viewTitle
2725    *          title of newly created view; if null, one will be generated
2726    * @param copyAnnotation
2727    *          if true then duplicate all annnotation, groups and settings
2728    * @return new alignment panel, already displayed.
2729    */
2730   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2731   {
2732     /*
2733      * Create a new AlignmentPanel (with its own, new Viewport)
2734      */
2735     AlignmentPanel newap = new jalview.project.Jalview2XML()
2736             .copyAlignPanel(alignPanel);
2737     if (!copyAnnotation)
2738     {
2739       /*
2740        * remove all groups and annotation except for the automatic stuff
2741        */
2742       newap.av.getAlignment().deleteAllGroups();
2743       newap.av.getAlignment().deleteAllAnnotations(false);
2744     }
2745
2746     newap.av.setGatherViewsHere(false);
2747
2748     if (viewport.getViewName() == null)
2749     {
2750       viewport.setViewName(MessageManager
2751               .getString("label.view_name_original"));
2752     }
2753
2754     /*
2755      * Views share the same edits undo and redo stacks
2756      */
2757     newap.av.setHistoryList(viewport.getHistoryList());
2758     newap.av.setRedoList(viewport.getRedoList());
2759
2760     /*
2761      * copy any visualisation settings that are not saved in the project
2762      */
2763     newap.av.setColourAppliesToAllGroups(
2764             viewport.getColourAppliesToAllGroups());
2765
2766     /*
2767      * Views share the same mappings; need to deregister any new mappings
2768      * created by copyAlignPanel, and register the new reference to the shared
2769      * mappings
2770      */
2771     newap.av.replaceMappings(viewport.getAlignment());
2772
2773     /*
2774      * start up cDNA consensus (if applicable) now mappings are in place
2775      */
2776     if (newap.av.initComplementConsensus())
2777     {
2778       newap.refresh(true); // adjust layout of annotations
2779     }
2780
2781     newap.av.setViewName(getNewViewName(viewTitle));
2782
2783     addAlignmentPanel(newap, true);
2784     newap.alignmentChanged();
2785
2786     if (alignPanels.size() == 2)
2787     {
2788       viewport.setGatherViewsHere(true);
2789     }
2790     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2791     return newap;
2792   }
2793
2794   /**
2795    * Make a new name for the view, ensuring it is unique within the current
2796    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2797    * these now use viewId. Unique view names are still desirable for usability.)
2798    *
2799    * @param viewTitle
2800    * @return
2801    */
2802   protected String getNewViewName(String viewTitle)
2803   {
2804     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2805     boolean addFirstIndex = false;
2806     if (viewTitle == null || viewTitle.trim().length() == 0)
2807     {
2808       viewTitle = MessageManager.getString("action.view");
2809       addFirstIndex = true;
2810     }
2811     else
2812     {
2813       index = 1;// we count from 1 if given a specific name
2814     }
2815     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2816
2817     List<Component> comps = PaintRefresher.components
2818             .get(viewport.getSequenceSetId());
2819
2820     List<String> existingNames = getExistingViewNames(comps);
2821
2822     while (existingNames.contains(newViewName))
2823     {
2824       newViewName = viewTitle + " " + (++index);
2825     }
2826     return newViewName;
2827   }
2828
2829   /**
2830    * Returns a list of distinct view names found in the given list of
2831    * components. View names are held on the viewport of an AlignmentPanel.
2832    *
2833    * @param comps
2834    * @return
2835    */
2836   protected List<String> getExistingViewNames(List<Component> comps)
2837   {
2838     List<String> existingNames = new ArrayList<>();
2839     for (Component comp : comps)
2840     {
2841       if (comp instanceof AlignmentPanel)
2842       {
2843         AlignmentPanel ap = (AlignmentPanel) comp;
2844         if (!existingNames.contains(ap.av.getViewName()))
2845         {
2846           existingNames.add(ap.av.getViewName());
2847         }
2848       }
2849     }
2850     return existingNames;
2851   }
2852
2853   /**
2854    * Explode tabbed views into separate windows.
2855    */
2856   @Override
2857   public void expandViews_actionPerformed(ActionEvent e)
2858   {
2859     Desktop.explodeViews(this);
2860   }
2861
2862   /**
2863    * Gather views in separate windows back into a tabbed presentation.
2864    */
2865   @Override
2866   public void gatherViews_actionPerformed(ActionEvent e)
2867   {
2868     Desktop.instance.gatherViews(this);
2869   }
2870
2871   /**
2872    * DOCUMENT ME!
2873    *
2874    * @param e
2875    *          DOCUMENT ME!
2876    */
2877   @Override
2878   public void font_actionPerformed(ActionEvent e)
2879   {
2880     new FontChooser(alignPanel);
2881   }
2882
2883   /**
2884    * DOCUMENT ME!
2885    *
2886    * @param e
2887    *          DOCUMENT ME!
2888    */
2889   @Override
2890   protected void seqLimit_actionPerformed(ActionEvent e)
2891   {
2892     viewport.setShowJVSuffix(seqLimits.isSelected());
2893
2894     alignPanel.getIdPanel().getIdCanvas()
2895             .setPreferredSize(alignPanel.calculateIdWidth());
2896     alignPanel.paintAlignment(true, false);
2897   }
2898
2899   @Override
2900   public void idRightAlign_actionPerformed(ActionEvent e)
2901   {
2902     viewport.setRightAlignIds(idRightAlign.isSelected());
2903     alignPanel.paintAlignment(false, false);
2904   }
2905
2906   @Override
2907   public void centreColumnLabels_actionPerformed(ActionEvent e)
2908   {
2909     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2910     alignPanel.paintAlignment(false, false);
2911   }
2912
2913   /*
2914    * (non-Javadoc)
2915    *
2916    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2917    */
2918   @Override
2919   protected void followHighlight_actionPerformed()
2920   {
2921     /*
2922      * Set the 'follow' flag on the Viewport (and scroll to position if now
2923      * true).
2924      */
2925     final boolean state = this.followHighlightMenuItem.getState();
2926     viewport.setFollowHighlight(state);
2927     if (state)
2928     {
2929       alignPanel.scrollToPosition(viewport.getSearchResults());
2930     }
2931   }
2932
2933   /**
2934    * DOCUMENT ME!
2935    *
2936    * @param e
2937    *          DOCUMENT ME!
2938    */
2939   @Override
2940   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2941   {
2942     viewport.setColourText(colourTextMenuItem.isSelected());
2943     alignPanel.paintAlignment(false, false);
2944   }
2945
2946   /**
2947    * DOCUMENT ME!
2948    *
2949    * @param e
2950    *          DOCUMENT ME!
2951    */
2952   @Override
2953   public void wrapMenuItem_actionPerformed(ActionEvent e)
2954   {
2955     scaleAbove.setVisible(wrapMenuItem.isSelected());
2956     scaleLeft.setVisible(wrapMenuItem.isSelected());
2957     scaleRight.setVisible(wrapMenuItem.isSelected());
2958     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2959     alignPanel.updateLayout();
2960   }
2961
2962   @Override
2963   public void showAllSeqs_actionPerformed(ActionEvent e)
2964   {
2965     viewport.showAllHiddenSeqs();
2966   }
2967
2968   @Override
2969   public void showAllColumns_actionPerformed(ActionEvent e)
2970   {
2971     viewport.showAllHiddenColumns();
2972     alignPanel.paintAlignment(true, true);
2973     viewport.sendSelection();
2974   }
2975
2976   @Override
2977   public void hideSelSequences_actionPerformed(ActionEvent e)
2978   {
2979     viewport.hideAllSelectedSeqs();
2980   }
2981
2982   /**
2983    * called by key handler and the hide all/show all menu items
2984    *
2985    * @param toggleSeqs
2986    * @param toggleCols
2987    */
2988   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2989   {
2990
2991     boolean hide = false;
2992     SequenceGroup sg = viewport.getSelectionGroup();
2993     if (!toggleSeqs && !toggleCols)
2994     {
2995       // Hide everything by the current selection - this is a hack - we do the
2996       // invert and then hide
2997       // first check that there will be visible columns after the invert.
2998       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2999               && sg.getStartRes() <= sg.getEndRes()))
3000       {
3001         // now invert the sequence set, if required - empty selection implies
3002         // that no hiding is required.
3003         if (sg != null)
3004         {
3005           invertSequenceMenuItem_actionPerformed(null);
3006           sg = viewport.getSelectionGroup();
3007           toggleSeqs = true;
3008
3009         }
3010         viewport.expandColSelection(sg, true);
3011         // finally invert the column selection and get the new sequence
3012         // selection.
3013         invertColSel_actionPerformed(null);
3014         toggleCols = true;
3015       }
3016     }
3017
3018     if (toggleSeqs)
3019     {
3020       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3021       {
3022         hideSelSequences_actionPerformed(null);
3023         hide = true;
3024       }
3025       else if (!(toggleCols && viewport.hasSelectedColumns()))
3026       {
3027         showAllSeqs_actionPerformed(null);
3028       }
3029     }
3030
3031     if (toggleCols)
3032     {
3033       if (viewport.hasSelectedColumns())
3034       {
3035         hideSelColumns_actionPerformed(null);
3036         if (!toggleSeqs)
3037         {
3038           viewport.setSelectionGroup(sg);
3039         }
3040       }
3041       else if (!hide)
3042       {
3043         showAllColumns_actionPerformed(null);
3044       }
3045     }
3046   }
3047
3048   /*
3049    * (non-Javadoc)
3050    *
3051    * @see
3052    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3053    * event.ActionEvent)
3054    */
3055   @Override
3056   public void hideAllButSelection_actionPerformed(ActionEvent e)
3057   {
3058     toggleHiddenRegions(false, false);
3059     viewport.sendSelection();
3060   }
3061
3062   /*
3063    * (non-Javadoc)
3064    *
3065    * @see
3066    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3067    * .ActionEvent)
3068    */
3069   @Override
3070   public void hideAllSelection_actionPerformed(ActionEvent e)
3071   {
3072     SequenceGroup sg = viewport.getSelectionGroup();
3073     viewport.expandColSelection(sg, false);
3074     viewport.hideAllSelectedSeqs();
3075     viewport.hideSelectedColumns();
3076     alignPanel.updateLayout();
3077     alignPanel.paintAlignment(true, true);
3078     viewport.sendSelection();
3079   }
3080
3081   /*
3082    * (non-Javadoc)
3083    *
3084    * @see
3085    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3086    * ActionEvent)
3087    */
3088   @Override
3089   public void showAllhidden_actionPerformed(ActionEvent e)
3090   {
3091     viewport.showAllHiddenColumns();
3092     viewport.showAllHiddenSeqs();
3093     alignPanel.paintAlignment(true, true);
3094     viewport.sendSelection();
3095   }
3096
3097   @Override
3098   public void hideSelColumns_actionPerformed(ActionEvent e)
3099   {
3100     viewport.hideSelectedColumns();
3101     alignPanel.updateLayout();
3102     alignPanel.paintAlignment(true, true);
3103     viewport.sendSelection();
3104   }
3105
3106   @Override
3107   public void hiddenMarkers_actionPerformed(ActionEvent e)
3108   {
3109     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3110     repaint();
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   @Override
3120   protected void scaleAbove_actionPerformed(ActionEvent e)
3121   {
3122     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3123     alignPanel.updateLayout();
3124     alignPanel.paintAlignment(true, false);
3125   }
3126
3127   /**
3128    * DOCUMENT ME!
3129    *
3130    * @param e
3131    *          DOCUMENT ME!
3132    */
3133   @Override
3134   protected void scaleLeft_actionPerformed(ActionEvent e)
3135   {
3136     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3137     alignPanel.updateLayout();
3138     alignPanel.paintAlignment(true, false);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   protected void scaleRight_actionPerformed(ActionEvent e)
3149   {
3150     viewport.setScaleRightWrapped(scaleRight.isSelected());
3151     alignPanel.updateLayout();
3152     alignPanel.paintAlignment(true, false);
3153   }
3154
3155   /**
3156    * DOCUMENT ME!
3157    *
3158    * @param e
3159    *          DOCUMENT ME!
3160    */
3161   @Override
3162   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3163   {
3164     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3165     alignPanel.paintAlignment(false, false);
3166   }
3167
3168   /**
3169    * DOCUMENT ME!
3170    *
3171    * @param e
3172    *          DOCUMENT ME!
3173    */
3174   @Override
3175   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3176   {
3177     viewport.setShowText(viewTextMenuItem.isSelected());
3178     alignPanel.paintAlignment(false, false);
3179   }
3180
3181   /**
3182    * DOCUMENT ME!
3183    *
3184    * @param e
3185    *          DOCUMENT ME!
3186    */
3187   @Override
3188   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3189   {
3190     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3191     alignPanel.paintAlignment(false, false);
3192   }
3193
3194   public FeatureSettings featureSettings;
3195
3196   @Override
3197   public FeatureSettingsControllerI getFeatureSettingsUI()
3198   {
3199     return featureSettings;
3200   }
3201
3202   @Override
3203   public void featureSettings_actionPerformed(ActionEvent e)
3204   {
3205     if (featureSettings != null)
3206     {
3207       featureSettings.close();
3208       featureSettings = null;
3209     }
3210     if (!showSeqFeatures.isSelected())
3211     {
3212       // make sure features are actually displayed
3213       showSeqFeatures.setSelected(true);
3214       showSeqFeatures_actionPerformed(null);
3215     }
3216     featureSettings = new FeatureSettings(this);
3217   }
3218
3219   /**
3220    * Set or clear 'Show Sequence Features'
3221    *
3222    * @param evt
3223    *          DOCUMENT ME!
3224    */
3225   @Override
3226   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3227   {
3228     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3229     alignPanel.paintAlignment(true, true);
3230   }
3231
3232   /**
3233    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3234    * the annotations panel as a whole.
3235    *
3236    * The options to show/hide all annotations should be enabled when the panel
3237    * is shown, and disabled when the panel is hidden.
3238    *
3239    * @param e
3240    */
3241   @Override
3242   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3243   {
3244     final boolean setVisible = annotationPanelMenuItem.isSelected();
3245     viewport.setShowAnnotation(setVisible);
3246     this.showAllSeqAnnotations.setEnabled(setVisible);
3247     this.hideAllSeqAnnotations.setEnabled(setVisible);
3248     this.showAllAlAnnotations.setEnabled(setVisible);
3249     this.hideAllAlAnnotations.setEnabled(setVisible);
3250     alignPanel.updateLayout();
3251   }
3252
3253   @Override
3254   public void alignmentProperties()
3255   {
3256     JEditorPane editPane = new JEditorPane("text/html", "");
3257     editPane.setEditable(false);
3258     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3259             .formatAsHtml();
3260     editPane.setText(
3261             MessageManager.formatMessage("label.html_content", new Object[]
3262             { contents.toString() }));
3263     JInternalFrame frame = new JInternalFrame();
3264     frame.getContentPane().add(new JScrollPane(editPane));
3265
3266     Desktop.addInternalFrame(frame, MessageManager
3267             .formatMessage("label.alignment_properties", new Object[]
3268             { getTitle() }), 500, 400);
3269   }
3270
3271   /**
3272    * DOCUMENT ME!
3273    *
3274    * @param e
3275    *          DOCUMENT ME!
3276    */
3277   @Override
3278   public void overviewMenuItem_actionPerformed(ActionEvent e)
3279   {
3280     if (alignPanel.overviewPanel != null)
3281     {
3282       return;
3283     }
3284
3285     JInternalFrame frame = new JInternalFrame();
3286     final OverviewPanel overview = new OverviewPanel(alignPanel);
3287     frame.setContentPane(overview);
3288     Desktop.addInternalFrame(frame, MessageManager
3289             .formatMessage("label.overview_params", new Object[]
3290             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3291             true, true);
3292     frame.pack();
3293     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3294     frame.addInternalFrameListener(
3295             new javax.swing.event.InternalFrameAdapter()
3296             {
3297               @Override
3298               public void internalFrameClosed(
3299                       javax.swing.event.InternalFrameEvent evt)
3300               {
3301                 overview.dispose();
3302                 alignPanel.setOverviewPanel(null);
3303               };
3304             });
3305     if (getKeyListeners().length > 0)
3306     {
3307       frame.addKeyListener(getKeyListeners()[0]);
3308     }
3309
3310     alignPanel.setOverviewPanel(overview);
3311   }
3312
3313   @Override
3314   public void textColour_actionPerformed()
3315   {
3316     new TextColourChooser().chooseColour(alignPanel, null);
3317   }
3318
3319   /*
3320    * public void covariationColour_actionPerformed() {
3321    * changeColour(new
3322    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3323    * ()[0])); }
3324    */
3325   @Override
3326   public void annotationColour_actionPerformed()
3327   {
3328     new AnnotationColourChooser(viewport, alignPanel);
3329   }
3330
3331   @Override
3332   public void annotationColumn_actionPerformed(ActionEvent e)
3333   {
3334     new AnnotationColumnChooser(viewport, alignPanel);
3335   }
3336
3337   /**
3338    * Action on the user checking or unchecking the option to apply the selected
3339    * colour scheme to all groups. If unchecked, groups may have their own
3340    * independent colour schemes.
3341    *
3342    * @param selected
3343    */
3344   @Override
3345   public void applyToAllGroups_actionPerformed(boolean selected)
3346   {
3347     viewport.setColourAppliesToAllGroups(selected);
3348   }
3349
3350   /**
3351    * Action on user selecting a colour from the colour menu
3352    *
3353    * @param name
3354    *          the name (not the menu item label!) of the colour scheme
3355    */
3356   @Override
3357   public void changeColour_actionPerformed(String name)
3358   {
3359     /*
3360      * 'User Defined' opens a panel to configure or load a
3361      * user-defined colour scheme
3362      */
3363     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3364     {
3365       new UserDefinedColours(alignPanel);
3366       return;
3367     }
3368
3369     /*
3370      * otherwise set the chosen colour scheme (or null for 'None')
3371      */
3372     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3373             viewport,
3374             viewport.getAlignment(), viewport.getHiddenRepSequences());
3375     changeColour(cs);
3376   }
3377
3378   /**
3379    * Actions on setting or changing the alignment colour scheme
3380    *
3381    * @param cs
3382    */
3383   @Override
3384   public void changeColour(ColourSchemeI cs)
3385   {
3386     // TODO: pull up to controller method
3387     ColourMenuHelper.setColourSelected(colourMenu, cs);
3388
3389     viewport.setGlobalColourScheme(cs);
3390
3391     alignPanel.paintAlignment(true, true);
3392   }
3393
3394   /**
3395    * Show the PID threshold slider panel
3396    */
3397   @Override
3398   protected void modifyPID_actionPerformed()
3399   {
3400     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3401             alignPanel.getViewName());
3402     SliderPanel.showPIDSlider();
3403   }
3404
3405   /**
3406    * Show the Conservation slider panel
3407    */
3408   @Override
3409   protected void modifyConservation_actionPerformed()
3410   {
3411     SliderPanel.setConservationSlider(alignPanel,
3412             viewport.getResidueShading(), alignPanel.getViewName());
3413     SliderPanel.showConservationSlider();
3414   }
3415
3416   /**
3417    * Action on selecting or deselecting (Colour) By Conservation
3418    */
3419   @Override
3420   public void conservationMenuItem_actionPerformed(boolean selected)
3421   {
3422     modifyConservation.setEnabled(selected);
3423     viewport.setConservationSelected(selected);
3424     viewport.getResidueShading().setConservationApplied(selected);
3425
3426     changeColour(viewport.getGlobalColourScheme());
3427     if (selected)
3428     {
3429       modifyConservation_actionPerformed();
3430     }
3431     else
3432     {
3433       SliderPanel.hideConservationSlider();
3434     }
3435   }
3436
3437   /**
3438    * Action on selecting or deselecting (Colour) Above PID Threshold
3439    */
3440   @Override
3441   public void abovePIDThreshold_actionPerformed(boolean selected)
3442   {
3443     modifyPID.setEnabled(selected);
3444     viewport.setAbovePIDThreshold(selected);
3445     if (!selected)
3446     {
3447       viewport.getResidueShading().setThreshold(0,
3448               viewport.isIgnoreGapsConsensus());
3449     }
3450
3451     changeColour(viewport.getGlobalColourScheme());
3452     if (selected)
3453     {
3454       modifyPID_actionPerformed();
3455     }
3456     else
3457     {
3458       SliderPanel.hidePIDSlider();
3459     }
3460   }
3461
3462   /**
3463    * DOCUMENT ME!
3464    *
3465    * @param e
3466    *          DOCUMENT ME!
3467    */
3468   @Override
3469   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3470   {
3471     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472     AlignmentSorter.sortByPID(viewport.getAlignment(),
3473             viewport.getAlignment().getSequenceAt(0));
3474     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3475             viewport.getAlignment()));
3476     alignPanel.paintAlignment(true, false);
3477   }
3478
3479   /**
3480    * DOCUMENT ME!
3481    *
3482    * @param e
3483    *          DOCUMENT ME!
3484    */
3485   @Override
3486   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3487   {
3488     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489     AlignmentSorter.sortByID(viewport.getAlignment());
3490     addHistoryItem(
3491             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3492     alignPanel.paintAlignment(true, false);
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param e
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3503   {
3504     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505     AlignmentSorter.sortByLength(viewport.getAlignment());
3506     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3507             viewport.getAlignment()));
3508     alignPanel.paintAlignment(true, false);
3509   }
3510
3511   /**
3512    * DOCUMENT ME!
3513    *
3514    * @param e
3515    *          DOCUMENT ME!
3516    */
3517   @Override
3518   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3519   {
3520     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3521     AlignmentSorter.sortByGroup(viewport.getAlignment());
3522     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3523             viewport.getAlignment()));
3524
3525     alignPanel.paintAlignment(true, false);
3526   }
3527
3528   /**
3529    * DOCUMENT ME!
3530    *
3531    * @param e
3532    *          DOCUMENT ME!
3533    */
3534   @Override
3535   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3536   {
3537     new RedundancyPanel(alignPanel, this);
3538   }
3539
3540   /**
3541    * DOCUMENT ME!
3542    *
3543    * @param e
3544    *          DOCUMENT ME!
3545    */
3546   @Override
3547   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3548   {
3549     if ((viewport.getSelectionGroup() == null)
3550             || (viewport.getSelectionGroup().getSize() < 2))
3551     {
3552       JvOptionPane.showInternalMessageDialog(this,
3553               MessageManager.getString(
3554                       "label.you_must_select_least_two_sequences"),
3555               MessageManager.getString("label.invalid_selection"),
3556               JvOptionPane.WARNING_MESSAGE);
3557     }
3558     else
3559     {
3560       JInternalFrame frame = new JInternalFrame();
3561       frame.setContentPane(new PairwiseAlignPanel(viewport));
3562       Desktop.addInternalFrame(frame,
3563               MessageManager.getString("action.pairwise_alignment"), 600,
3564               500);
3565     }
3566   }
3567
3568   @Override
3569   public void autoCalculate_actionPerformed(ActionEvent e)
3570   {
3571     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3572     if (viewport.autoCalculateConsensus)
3573     {
3574       viewport.firePropertyChange("alignment", null,
3575               viewport.getAlignment().getSequences());
3576     }
3577   }
3578
3579   @Override
3580   public void sortByTreeOption_actionPerformed(ActionEvent e)
3581   {
3582     viewport.sortByTree = sortByTree.isSelected();
3583   }
3584
3585   @Override
3586   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3587   {
3588     viewport.followSelection = listenToViewSelections.isSelected();
3589   }
3590
3591   /**
3592    * Constructs a tree panel and adds it to the desktop
3593    *
3594    * @param type
3595    *          tree type (NJ or AV)
3596    * @param modelName
3597    *          name of score model used to compute the tree
3598    * @param options
3599    *          parameters for the distance or similarity calculation
3600    */
3601   void newTreePanel(String type, String modelName,
3602           SimilarityParamsI options)
3603   {
3604     String frameTitle = "";
3605     TreePanel tp;
3606
3607     boolean onSelection = false;
3608     if (viewport.getSelectionGroup() != null
3609             && viewport.getSelectionGroup().getSize() > 0)
3610     {
3611       SequenceGroup sg = viewport.getSelectionGroup();
3612
3613       /* Decide if the selection is a column region */
3614       for (SequenceI _s : sg.getSequences())
3615       {
3616         if (_s.getLength() < sg.getEndRes())
3617         {
3618           JvOptionPane.showMessageDialog(Desktop.desktop,
3619                   MessageManager.getString(
3620                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3621                   MessageManager.getString(
3622                           "label.sequences_selection_not_aligned"),
3623                   JvOptionPane.WARNING_MESSAGE);
3624
3625           return;
3626         }
3627       }
3628       onSelection = true;
3629     }
3630     else
3631     {
3632       if (viewport.getAlignment().getHeight() < 2)
3633       {
3634         return;
3635       }
3636     }
3637
3638     tp = new TreePanel(alignPanel, type, modelName, options);
3639     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3640
3641     frameTitle += " from ";
3642
3643     if (viewport.getViewName() != null)
3644     {
3645       frameTitle += viewport.getViewName() + " of ";
3646     }
3647
3648     frameTitle += this.title;
3649
3650     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3651   }
3652
3653   /**
3654    * DOCUMENT ME!
3655    *
3656    * @param title
3657    *          DOCUMENT ME!
3658    * @param order
3659    *          DOCUMENT ME!
3660    */
3661   public void addSortByOrderMenuItem(String title,
3662           final AlignmentOrder order)
3663   {
3664     final JMenuItem item = new JMenuItem(MessageManager
3665             .formatMessage("action.by_title_param", new Object[]
3666             { title }));
3667     sort.add(item);
3668     item.addActionListener(new java.awt.event.ActionListener()
3669     {
3670       @Override
3671       public void actionPerformed(ActionEvent e)
3672       {
3673         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3674
3675         // TODO: JBPNote - have to map order entries to curent SequenceI
3676         // pointers
3677         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3678
3679         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3680                 viewport.getAlignment()));
3681
3682         alignPanel.paintAlignment(true, false);
3683       }
3684     });
3685   }
3686
3687   /**
3688    * Add a new sort by annotation score menu item
3689    *
3690    * @param sort
3691    *          the menu to add the option to
3692    * @param scoreLabel
3693    *          the label used to retrieve scores for each sequence on the
3694    *          alignment
3695    */
3696   public void addSortByAnnotScoreMenuItem(JMenu sort,
3697           final String scoreLabel)
3698   {
3699     final JMenuItem item = new JMenuItem(scoreLabel);
3700     sort.add(item);
3701     item.addActionListener(new java.awt.event.ActionListener()
3702     {
3703       @Override
3704       public void actionPerformed(ActionEvent e)
3705       {
3706         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3707         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3708                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3709         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3710                 viewport.getAlignment()));
3711         alignPanel.paintAlignment(true, false);
3712       }
3713     });
3714   }
3715
3716   /**
3717    * last hash for alignment's annotation array - used to minimise cost of
3718    * rebuild.
3719    */
3720   protected int _annotationScoreVectorHash;
3721
3722   /**
3723    * search the alignment and rebuild the sort by annotation score submenu the
3724    * last alignment annotation vector hash is stored to minimize cost of
3725    * rebuilding in subsequence calls.
3726    *
3727    */
3728   @Override
3729   public void buildSortByAnnotationScoresMenu()
3730   {
3731     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3732     {
3733       return;
3734     }
3735
3736     if (viewport.getAlignment().getAlignmentAnnotation()
3737             .hashCode() != _annotationScoreVectorHash)
3738     {
3739       sortByAnnotScore.removeAll();
3740       // almost certainly a quicker way to do this - but we keep it simple
3741       Hashtable scoreSorts = new Hashtable();
3742       AlignmentAnnotation aann[];
3743       for (SequenceI sqa : viewport.getAlignment().getSequences())
3744       {
3745         aann = sqa.getAnnotation();
3746         for (int i = 0; aann != null && i < aann.length; i++)
3747         {
3748           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3749           {
3750             scoreSorts.put(aann[i].label, aann[i].label);
3751           }
3752         }
3753       }
3754       Enumeration labels = scoreSorts.keys();
3755       while (labels.hasMoreElements())
3756       {
3757         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3758                 (String) labels.nextElement());
3759       }
3760       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3761       scoreSorts.clear();
3762
3763       _annotationScoreVectorHash = viewport.getAlignment()
3764               .getAlignmentAnnotation().hashCode();
3765     }
3766   }
3767
3768   /**
3769    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3770    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3771    * call. Listeners are added to remove the menu item when the treePanel is
3772    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3773    * modified.
3774    */
3775   @Override
3776   public void buildTreeSortMenu()
3777   {
3778     sortByTreeMenu.removeAll();
3779
3780     List<Component> comps = PaintRefresher.components
3781             .get(viewport.getSequenceSetId());
3782     List<TreePanel> treePanels = new ArrayList<>();
3783     for (Component comp : comps)
3784     {
3785       if (comp instanceof TreePanel)
3786       {
3787         treePanels.add((TreePanel) comp);
3788       }
3789     }
3790
3791     if (treePanels.size() < 1)
3792     {
3793       sortByTreeMenu.setVisible(false);
3794       return;
3795     }
3796
3797     sortByTreeMenu.setVisible(true);
3798
3799     for (final TreePanel tp : treePanels)
3800     {
3801       final JMenuItem item = new JMenuItem(tp.getTitle());
3802       item.addActionListener(new java.awt.event.ActionListener()
3803       {
3804         @Override
3805         public void actionPerformed(ActionEvent e)
3806         {
3807           tp.sortByTree_actionPerformed();
3808           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3809
3810         }
3811       });
3812
3813       sortByTreeMenu.add(item);
3814     }
3815   }
3816
3817   public boolean sortBy(AlignmentOrder alorder, String undoname)
3818   {
3819     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3820     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3821     if (undoname != null)
3822     {
3823       addHistoryItem(new OrderCommand(undoname, oldOrder,
3824               viewport.getAlignment()));
3825     }
3826     alignPanel.paintAlignment(true, false);
3827     return true;
3828   }
3829
3830   /**
3831    * Work out whether the whole set of sequences or just the selected set will
3832    * be submitted for multiple alignment.
3833    *
3834    */
3835   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3836   {
3837     // Now, check we have enough sequences
3838     AlignmentView msa = null;
3839
3840     if ((viewport.getSelectionGroup() != null)
3841             && (viewport.getSelectionGroup().getSize() > 1))
3842     {
3843       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3844       // some common interface!
3845       /*
3846        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3847        * SequenceI[sz = seqs.getSize(false)];
3848        *
3849        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3850        * seqs.getSequenceAt(i); }
3851        */
3852       msa = viewport.getAlignmentView(true);
3853     }
3854     else if (viewport.getSelectionGroup() != null
3855             && viewport.getSelectionGroup().getSize() == 1)
3856     {
3857       int option = JvOptionPane.showConfirmDialog(this,
3858               MessageManager.getString("warn.oneseq_msainput_selection"),
3859               MessageManager.getString("label.invalid_selection"),
3860               JvOptionPane.OK_CANCEL_OPTION);
3861       if (option == JvOptionPane.OK_OPTION)
3862       {
3863         msa = viewport.getAlignmentView(false);
3864       }
3865     }
3866     else
3867     {
3868       msa = viewport.getAlignmentView(false);
3869     }
3870     return msa;
3871   }
3872
3873   /**
3874    * Decides what is submitted to a secondary structure prediction service: the
3875    * first sequence in the alignment, or in the current selection, or, if the
3876    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3877    * region or the whole alignment. (where the first sequence in the set is the
3878    * one that the prediction will be for).
3879    */
3880   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3881   {
3882     AlignmentView seqs = null;
3883
3884     if ((viewport.getSelectionGroup() != null)
3885             && (viewport.getSelectionGroup().getSize() > 0))
3886     {
3887       seqs = viewport.getAlignmentView(true);
3888     }
3889     else
3890     {
3891       seqs = viewport.getAlignmentView(false);
3892     }
3893     // limit sequences - JBPNote in future - could spawn multiple prediction
3894     // jobs
3895     // TODO: viewport.getAlignment().isAligned is a global state - the local
3896     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3897     if (!viewport.getAlignment().isAligned(false))
3898     {
3899       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3900       // TODO: if seqs.getSequences().length>1 then should really have warned
3901       // user!
3902
3903     }
3904     return seqs;
3905   }
3906
3907   /**
3908    * DOCUMENT ME!
3909    *
3910    * @param e
3911    *          DOCUMENT ME!
3912    */
3913   @Override
3914   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3915   {
3916     // Pick the tree file
3917     JalviewFileChooser chooser = new JalviewFileChooser(
3918             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3919     chooser.setFileView(new JalviewFileView());
3920     chooser.setDialogTitle(
3921             MessageManager.getString("label.select_newick_like_tree_file"));
3922     chooser.setToolTipText(
3923             MessageManager.getString("label.load_tree_file"));
3924
3925     int value = chooser.showOpenDialog(null);
3926
3927     if (value == JalviewFileChooser.APPROVE_OPTION)
3928     {
3929       String filePath = chooser.getSelectedFile().getPath();
3930       Cache.setProperty("LAST_DIRECTORY", filePath);
3931       NewickFile fin = null;
3932       try
3933       {
3934         fin = new NewickFile(filePath, DataSourceType.FILE);
3935         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3936       } catch (Exception ex)
3937       {
3938         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3939                 MessageManager.getString("label.problem_reading_tree_file"),
3940                 JvOptionPane.WARNING_MESSAGE);
3941         ex.printStackTrace();
3942       }
3943       if (fin != null && fin.hasWarningMessage())
3944       {
3945         JvOptionPane.showMessageDialog(Desktop.desktop,
3946                 fin.getWarningMessage(),
3947                 MessageManager
3948                         .getString("label.possible_problem_with_tree_file"),
3949                 JvOptionPane.WARNING_MESSAGE);
3950       }
3951     }
3952   }
3953
3954   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3955   {
3956     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3957   }
3958
3959   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3960           int h, int x, int y)
3961   {
3962     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3963   }
3964
3965   /**
3966    * Add a treeviewer for the tree extracted from a Newick file object to the
3967    * current alignment view
3968    *
3969    * @param nf
3970    *          the tree
3971    * @param title
3972    *          tree viewer title
3973    * @param input
3974    *          Associated alignment input data (or null)
3975    * @param w
3976    *          width
3977    * @param h
3978    *          height
3979    * @param x
3980    *          position
3981    * @param y
3982    *          position
3983    * @return TreePanel handle
3984    */
3985   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3986           AlignmentView input, int w, int h, int x, int y)
3987   {
3988     TreePanel tp = null;
3989
3990     try
3991     {
3992       nf.parse();
3993
3994       if (nf.getTree() != null)
3995       {
3996         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3997
3998         tp.setSize(w, h);
3999
4000         if (x > 0 && y > 0)
4001         {
4002           tp.setLocation(x, y);
4003         }
4004
4005         Desktop.addInternalFrame(tp, treeTitle, w, h);
4006       }
4007     } catch (Exception ex)
4008     {
4009       ex.printStackTrace();
4010     }
4011
4012     return tp;
4013   }
4014
4015   private boolean buildingMenu = false;
4016
4017   /**
4018    * Generates menu items and listener event actions for web service clients
4019    *
4020    */
4021   public void BuildWebServiceMenu()
4022   {
4023     while (buildingMenu)
4024     {
4025       try
4026       {
4027         System.err.println("Waiting for building menu to finish.");
4028         Thread.sleep(10);
4029       } catch (Exception e)
4030       {
4031       }
4032     }
4033     final AlignFrame me = this;
4034     buildingMenu = true;
4035     new Thread(new Runnable()
4036     {
4037       @Override
4038       public void run()
4039       {
4040         final List<JMenuItem> legacyItems = new ArrayList<>();
4041         try
4042         {
4043           // System.err.println("Building ws menu again "
4044           // + Thread.currentThread());
4045           // TODO: add support for context dependent disabling of services based
4046           // on
4047           // alignment and current selection
4048           // TODO: add additional serviceHandle parameter to specify abstract
4049           // handler
4050           // class independently of AbstractName
4051           // TODO: add in rediscovery GUI function to restart discoverer
4052           // TODO: group services by location as well as function and/or
4053           // introduce
4054           // object broker mechanism.
4055           final Vector<JMenu> wsmenu = new Vector<>();
4056           final IProgressIndicator af = me;
4057
4058           /*
4059            * do not i18n these strings - they are hard-coded in class
4060            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4061            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4062            */
4063           final JMenu msawsmenu = new JMenu("Alignment");
4064           final JMenu secstrmenu = new JMenu(
4065                   "Secondary Structure Prediction");
4066           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4067           final JMenu analymenu = new JMenu("Analysis");
4068           final JMenu dismenu = new JMenu("Protein Disorder");
4069           // JAL-940 - only show secondary structure prediction services from
4070           // the legacy server
4071           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4072               // &&
4073           Discoverer.services != null && (Discoverer.services.size() > 0))
4074           {
4075             // TODO: refactor to allow list of AbstractName/Handler bindings to
4076             // be
4077             // stored or retrieved from elsewhere
4078             // No MSAWS used any more:
4079             // Vector msaws = null; // (Vector)
4080             // Discoverer.services.get("MsaWS");
4081             Vector secstrpr = (Vector) Discoverer.services
4082                     .get("SecStrPred");
4083             if (secstrpr != null)
4084             {
4085               // Add any secondary structure prediction services
4086               for (int i = 0, j = secstrpr.size(); i < j; i++)
4087               {
4088                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4089                         .get(i);
4090                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4091                         .getServiceClient(sh);
4092                 int p = secstrmenu.getItemCount();
4093                 impl.attachWSMenuEntry(secstrmenu, me);
4094                 int q = secstrmenu.getItemCount();
4095                 for (int litm = p; litm < q; litm++)
4096                 {
4097                   legacyItems.add(secstrmenu.getItem(litm));
4098                 }
4099               }
4100             }
4101           }
4102
4103           // Add all submenus in the order they should appear on the web
4104           // services menu
4105           wsmenu.add(msawsmenu);
4106           wsmenu.add(secstrmenu);
4107           wsmenu.add(dismenu);
4108           wsmenu.add(analymenu);
4109           // No search services yet
4110           // wsmenu.add(seqsrchmenu);
4111
4112           javax.swing.SwingUtilities.invokeLater(new Runnable()
4113           {
4114             @Override
4115             public void run()
4116             {
4117               try
4118               {
4119                 webService.removeAll();
4120                 // first, add discovered services onto the webservices menu
4121                 if (wsmenu.size() > 0)
4122                 {
4123                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4124                   {
4125                     webService.add(wsmenu.get(i));
4126                   }
4127                 }
4128                 else
4129                 {
4130                   webService.add(me.webServiceNoServices);
4131                 }
4132                 // TODO: move into separate menu builder class.
4133                 boolean new_sspred = false;
4134                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4135                 {
4136                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4137                   if (jws2servs != null)
4138                   {
4139                     if (jws2servs.hasServices())
4140                     {
4141                       jws2servs.attachWSMenuEntry(webService, me);
4142                       for (Jws2Instance sv : jws2servs.getServices())
4143                       {
4144                         if (sv.description.toLowerCase().contains("jpred"))
4145                         {
4146                           for (JMenuItem jmi : legacyItems)
4147                           {
4148                             jmi.setVisible(false);
4149                           }
4150                         }
4151                       }
4152
4153                     }
4154                     if (jws2servs.isRunning())
4155                     {
4156                       JMenuItem tm = new JMenuItem(
4157                               "Still discovering JABA Services");
4158                       tm.setEnabled(false);
4159                       webService.add(tm);
4160                     }
4161                   }
4162                 }
4163                 build_urlServiceMenu(me.webService);
4164                 build_fetchdbmenu(webService);
4165                 for (JMenu item : wsmenu)
4166                 {
4167                   if (item.getItemCount() == 0)
4168                   {
4169                     item.setEnabled(false);
4170                   }
4171                   else
4172                   {
4173                     item.setEnabled(true);
4174                   }
4175                 }
4176               } catch (Exception e)
4177               {
4178                 Cache.log.debug(
4179                         "Exception during web service menu building process.",
4180                         e);
4181               }
4182             }
4183           });
4184         } catch (Exception e)
4185         {
4186         }
4187         buildingMenu = false;
4188       }
4189     }).start();
4190
4191   }
4192
4193   /**
4194    * construct any groupURL type service menu entries.
4195    *
4196    * @param webService
4197    */
4198   private void build_urlServiceMenu(JMenu webService)
4199   {
4200     // TODO: remove this code when 2.7 is released
4201     // DEBUG - alignmentView
4202     /*
4203      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4204      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4205      *
4206      * @Override public void actionPerformed(ActionEvent e) {
4207      * jalview.datamodel.AlignmentView
4208      * .testSelectionViews(af.viewport.getAlignment(),
4209      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4210      *
4211      * }); webService.add(testAlView);
4212      */
4213     // TODO: refactor to RestClient discoverer and merge menu entries for
4214     // rest-style services with other types of analysis/calculation service
4215     // SHmmr test client - still being implemented.
4216     // DEBUG - alignmentView
4217
4218     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4219             .getRestClients())
4220     {
4221       client.attachWSMenuEntry(
4222               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4223               this);
4224     }
4225   }
4226
4227   /**
4228    * Searches the alignment sequences for xRefs and builds the Show
4229    * Cross-References menu (formerly called Show Products), with database
4230    * sources for which cross-references are found (protein sources for a
4231    * nucleotide alignment and vice versa)
4232    *
4233    * @return true if Show Cross-references menu should be enabled
4234    */
4235   public boolean canShowProducts()
4236   {
4237     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4238     AlignmentI dataset = viewport.getAlignment().getDataset();
4239
4240     showProducts.removeAll();
4241     final boolean dna = viewport.getAlignment().isNucleotide();
4242
4243     if (seqs == null || seqs.length == 0)
4244     {
4245       // nothing to see here.
4246       return false;
4247     }
4248
4249     boolean showp = false;
4250     try
4251     {
4252       List<String> ptypes = new CrossRef(seqs, dataset)
4253               .findXrefSourcesForSequences(dna);
4254
4255       for (final String source : ptypes)
4256       {
4257         showp = true;
4258         final AlignFrame af = this;
4259         JMenuItem xtype = new JMenuItem(source);
4260         xtype.addActionListener(new ActionListener()
4261         {
4262           @Override
4263           public void actionPerformed(ActionEvent e)
4264           {
4265             showProductsFor(af.viewport.getSequenceSelection(), dna,
4266                     source);
4267           }
4268         });
4269         showProducts.add(xtype);
4270       }
4271       showProducts.setVisible(showp);
4272       showProducts.setEnabled(showp);
4273     } catch (Exception e)
4274     {
4275       Cache.log.warn(
4276               "canShowProducts threw an exception - please report to help@jalview.org",
4277               e);
4278       return false;
4279     }
4280     return showp;
4281   }
4282
4283   /**
4284    * Finds and displays cross-references for the selected sequences (protein
4285    * products for nucleotide sequences, dna coding sequences for peptides).
4286    *
4287    * @param sel
4288    *          the sequences to show cross-references for
4289    * @param dna
4290    *          true if from a nucleotide alignment (so showing proteins)
4291    * @param source
4292    *          the database to show cross-references for
4293    */
4294   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4295           final String source)
4296   {
4297     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4298             .start();
4299   }
4300
4301   /**
4302    * Construct and display a new frame containing the translation of this
4303    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4304    */
4305   @Override
4306   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4307   {
4308     AlignmentI al = null;
4309     try
4310     {
4311       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4312
4313       al = dna.translateCdna(codeTable);
4314     } catch (Exception ex)
4315     {
4316       jalview.bin.Cache.log.error(
4317               "Exception during translation. Please report this !", ex);
4318       final String msg = MessageManager.getString(
4319               "label.error_when_translating_sequences_submit_bug_report");
4320       final String errorTitle = MessageManager
4321               .getString("label.implementation_error")
4322               + MessageManager.getString("label.translation_failed");
4323       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4324               JvOptionPane.ERROR_MESSAGE);
4325       return;
4326     }
4327     if (al == null || al.getHeight() == 0)
4328     {
4329       final String msg = MessageManager.getString(
4330               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4331       final String errorTitle = MessageManager
4332               .getString("label.translation_failed");
4333       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4334               JvOptionPane.WARNING_MESSAGE);
4335     }
4336     else
4337     {
4338       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4339       af.setFileFormat(this.currentFileFormat);
4340       final String newTitle = MessageManager
4341               .formatMessage("label.translation_of_params", new Object[]
4342               { this.getTitle(), codeTable.getId() });
4343       af.setTitle(newTitle);
4344       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4345       {
4346         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4347         viewport.openSplitFrame(af, new Alignment(seqs));
4348       }
4349       else
4350       {
4351         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4352                 DEFAULT_HEIGHT);
4353       }
4354     }
4355   }
4356
4357   /**
4358    * Set the file format
4359    *
4360    * @param format
4361    */
4362   public void setFileFormat(FileFormatI format)
4363   {
4364     this.currentFileFormat = format;
4365   }
4366
4367   /**
4368    * Try to load a features file onto the alignment.
4369    *
4370    * @param file
4371    *          contents or path to retrieve file
4372    * @param sourceType
4373    *          access mode of file (see jalview.io.AlignFile)
4374    * @return true if features file was parsed correctly.
4375    */
4376   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4377   {
4378     return avc.parseFeaturesFile(file, sourceType,
4379             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4380
4381   }
4382
4383   @Override
4384   public void refreshFeatureUI(boolean enableIfNecessary)
4385   {
4386     // note - currently this is only still here rather than in the controller
4387     // because of the featureSettings hard reference that is yet to be
4388     // abstracted
4389     if (enableIfNecessary)
4390     {
4391       viewport.setShowSequenceFeatures(true);
4392       showSeqFeatures.setSelected(true);
4393     }
4394
4395   }
4396
4397   @Override
4398   public void dragEnter(DropTargetDragEvent evt)
4399   {
4400   }
4401
4402   @Override
4403   public void dragExit(DropTargetEvent evt)
4404   {
4405   }
4406
4407   @Override
4408   public void dragOver(DropTargetDragEvent evt)
4409   {
4410   }
4411
4412   @Override
4413   public void dropActionChanged(DropTargetDragEvent evt)
4414   {
4415   }
4416
4417   @Override
4418   public void drop(DropTargetDropEvent evt)
4419   {
4420     // JAL-1552 - acceptDrop required before getTransferable call for
4421     // Java's Transferable for native dnd
4422     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4423     Transferable t = evt.getTransferable();
4424     final AlignFrame thisaf = this;
4425     final List<String> files = new ArrayList<>();
4426     List<DataSourceType> protocols = new ArrayList<>();
4427
4428     try
4429     {
4430       Desktop.transferFromDropTarget(files, protocols, evt, t);
4431     } catch (Exception e)
4432     {
4433       e.printStackTrace();
4434     }
4435     if (files != null)
4436     {
4437       new Thread(new Runnable()
4438       {
4439         @Override
4440         public void run()
4441         {
4442           try
4443           {
4444             // check to see if any of these files have names matching sequences
4445             // in
4446             // the alignment
4447             SequenceIdMatcher idm = new SequenceIdMatcher(
4448                     viewport.getAlignment().getSequencesArray());
4449             /**
4450              * Object[] { String,SequenceI}
4451              */
4452             ArrayList<Object[]> filesmatched = new ArrayList<>();
4453             ArrayList<String> filesnotmatched = new ArrayList<>();
4454             for (int i = 0; i < files.size(); i++)
4455             {
4456               String file = files.get(i).toString();
4457               String pdbfn = "";
4458               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4459               if (protocol == DataSourceType.FILE)
4460               {
4461                 File fl = new File(file);
4462                 pdbfn = fl.getName();
4463               }
4464               else if (protocol == DataSourceType.URL)
4465               {
4466                 URL url = new URL(file);
4467                 pdbfn = url.getFile();
4468               }
4469               if (pdbfn.length() > 0)
4470               {
4471                 // attempt to find a match in the alignment
4472                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4473                 int l = 0, c = pdbfn.indexOf(".");
4474                 while (mtch == null && c != -1)
4475                 {
4476                   do
4477                   {
4478                     l = c;
4479                   } while ((c = pdbfn.indexOf(".", l)) > l);
4480                   if (l > -1)
4481                   {
4482                     pdbfn = pdbfn.substring(0, l);
4483                   }
4484                   mtch = idm.findAllIdMatches(pdbfn);
4485                 }
4486                 if (mtch != null)
4487                 {
4488                   FileFormatI type = null;
4489                   try
4490                   {
4491                     type = new IdentifyFile().identify(file, protocol);
4492                   } catch (Exception ex)
4493                   {
4494                     type = null;
4495                   }
4496                   if (type != null && type.isStructureFile())
4497                   {
4498                     filesmatched.add(new Object[] { file, protocol, mtch });
4499                     continue;
4500                   }
4501                 }
4502                 // File wasn't named like one of the sequences or wasn't a PDB
4503                 // file.
4504                 filesnotmatched.add(file);
4505               }
4506             }
4507             int assocfiles = 0;
4508             if (filesmatched.size() > 0)
4509             {
4510               boolean autoAssociate = Cache
4511                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4512               if (!autoAssociate)
4513               {
4514                 String msg = MessageManager.formatMessage(
4515                         "label.automatically_associate_structure_files_with_sequences_same_name",
4516                         new Object[]
4517                         { Integer.valueOf(filesmatched.size())
4518                                 .toString() });
4519                 String ttl = MessageManager.getString(
4520                         "label.automatically_associate_structure_files_by_name");
4521                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4522                         ttl, JvOptionPane.YES_NO_OPTION);
4523                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4524               }
4525               if (autoAssociate)
4526               {
4527                 for (Object[] fm : filesmatched)
4528                 {
4529                   // try and associate
4530                   // TODO: may want to set a standard ID naming formalism for
4531                   // associating PDB files which have no IDs.
4532                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4533                   {
4534                     PDBEntry pe = new AssociatePdbFileWithSeq()
4535                             .associatePdbWithSeq((String) fm[0],
4536                                     (DataSourceType) fm[1], toassoc, false,
4537                                     Desktop.instance);
4538                     if (pe != null)
4539                     {
4540                       System.err.println("Associated file : "
4541                               + ((String) fm[0]) + " with "
4542                               + toassoc.getDisplayId(true));
4543                       assocfiles++;
4544                     }
4545                   }
4546                   // TODO: do we need to update overview ? only if features are
4547                   // shown I guess
4548                   alignPanel.paintAlignment(true, false);
4549                 }
4550               }
4551               else
4552               {
4553                 /*
4554                  * add declined structures as sequences
4555                  */
4556                 for (Object[] o : filesmatched)
4557                 {
4558                   filesnotmatched.add((String) o[0]);
4559                 }
4560               }
4561             }
4562             if (filesnotmatched.size() > 0)
4563             {
4564               if (assocfiles > 0 && (Cache.getDefault(
4565                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4566                       || JvOptionPane.showConfirmDialog(thisaf,
4567                               "<html>" + MessageManager.formatMessage(
4568                                       "label.ignore_unmatched_dropped_files_info",
4569                                       new Object[]
4570                                       { Integer.valueOf(
4571                                               filesnotmatched.size())
4572                                               .toString() })
4573                                       + "</html>",
4574                               MessageManager.getString(
4575                                       "label.ignore_unmatched_dropped_files"),
4576                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4577               {
4578                 return;
4579               }
4580               for (String fn : filesnotmatched)
4581               {
4582                 loadJalviewDataFile(fn, null, null, null);
4583               }
4584
4585             }
4586           } catch (Exception ex)
4587           {
4588             ex.printStackTrace();
4589           }
4590         }
4591       }).start();
4592     }
4593   }
4594
4595   /**
4596    * Attempt to load a "dropped" file or URL string, by testing in turn for
4597    * <ul>
4598    * <li>an Annotation file</li>
4599    * <li>a JNet file</li>
4600    * <li>a features file</li>
4601    * <li>else try to interpret as an alignment file</li>
4602    * </ul>
4603    *
4604    * @param file
4605    *          either a filename or a URL string.
4606    */
4607   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4608           FileFormatI format, SequenceI assocSeq)
4609   {
4610     try
4611     {
4612       if (sourceType == null)
4613       {
4614         sourceType = FormatAdapter.checkProtocol(file);
4615       }
4616       // if the file isn't identified, or not positively identified as some
4617       // other filetype (PFAM is default unidentified alignment file type) then
4618       // try to parse as annotation.
4619       boolean isAnnotation = (format == null
4620               || FileFormat.Pfam.equals(format))
4621                       ? new AnnotationFile().annotateAlignmentView(viewport,
4622                               file, sourceType)
4623                       : false;
4624
4625       if (!isAnnotation)
4626       {
4627         // first see if its a T-COFFEE score file
4628         TCoffeeScoreFile tcf = null;
4629         try
4630         {
4631           tcf = new TCoffeeScoreFile(file, sourceType);
4632           if (tcf.isValid())
4633           {
4634             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4635             {
4636               buildColourMenu();
4637               changeColour(
4638                       new TCoffeeColourScheme(viewport.getAlignment()));
4639               isAnnotation = true;
4640               statusBar.setText(MessageManager.getString(
4641                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4642             }
4643             else
4644             {
4645               // some problem - if no warning its probable that the ID matching
4646               // process didn't work
4647               JvOptionPane.showMessageDialog(Desktop.desktop,
4648                       tcf.getWarningMessage() == null
4649                               ? MessageManager.getString(
4650                                       "label.check_file_matches_sequence_ids_alignment")
4651                               : tcf.getWarningMessage(),
4652                       MessageManager.getString(
4653                               "label.problem_reading_tcoffee_score_file"),
4654                       JvOptionPane.WARNING_MESSAGE);
4655             }
4656           }
4657           else
4658           {
4659             tcf = null;
4660           }
4661         } catch (Exception x)
4662         {
4663           Cache.log.debug(
4664                   "Exception when processing data source as T-COFFEE score file",
4665                   x);
4666           tcf = null;
4667         }
4668         if (tcf == null)
4669         {
4670           // try to see if its a JNet 'concise' style annotation file *before*
4671           // we
4672           // try to parse it as a features file
4673           if (format == null)
4674           {
4675             format = new IdentifyFile().identify(file, sourceType);
4676           }
4677           if (FileFormat.ScoreMatrix == format)
4678           {
4679             ScoreMatrixFile sm = new ScoreMatrixFile(
4680                     new FileParse(file, sourceType));
4681             sm.parse();
4682             // todo: i18n this message
4683             statusBar.setText(MessageManager.formatMessage(
4684                     "label.successfully_loaded_matrix",
4685                     sm.getMatrixName()));
4686           }
4687           else if (FileFormat.Jnet.equals(format))
4688           {
4689             JPredFile predictions = new JPredFile(file, sourceType);
4690             new JnetAnnotationMaker();
4691             JnetAnnotationMaker.add_annotation(predictions,
4692                     viewport.getAlignment(), 0, false);
4693             viewport.getAlignment().setupJPredAlignment();
4694             isAnnotation = true;
4695           }
4696           // else if (IdentifyFile.FeaturesFile.equals(format))
4697           else if (FileFormat.Features.equals(format))
4698           {
4699             if (parseFeaturesFile(file, sourceType))
4700             {
4701               alignPanel.paintAlignment(true, true);
4702             }
4703           }
4704           else
4705           {
4706             new FileLoader().LoadFile(viewport, file, sourceType, format);
4707           }
4708         }
4709       }
4710       if (isAnnotation)
4711       {
4712
4713         alignPanel.adjustAnnotationHeight();
4714         viewport.updateSequenceIdColours();
4715         buildSortByAnnotationScoresMenu();
4716         alignPanel.paintAlignment(true, true);
4717       }
4718     } catch (Exception ex)
4719     {
4720       ex.printStackTrace();
4721     } catch (OutOfMemoryError oom)
4722     {
4723       try
4724       {
4725         System.gc();
4726       } catch (Exception x)
4727       {
4728       }
4729       new OOMWarning(
4730               "loading data "
4731                       + (sourceType != null
4732                               ? (sourceType == DataSourceType.PASTE
4733                                       ? "from clipboard."
4734                                       : "using " + sourceType + " from "
4735                                               + file)
4736                               : ".")
4737                       + (format != null
4738                               ? "(parsing as '" + format + "' file)"
4739                               : ""),
4740               oom, Desktop.desktop);
4741     }
4742   }
4743
4744   /**
4745    * Method invoked by the ChangeListener on the tabbed pane, in other words
4746    * when a different tabbed pane is selected by the user or programmatically.
4747    */
4748   @Override
4749   public void tabSelectionChanged(int index)
4750   {
4751     if (index > -1)
4752     {
4753       alignPanel = alignPanels.get(index);
4754       viewport = alignPanel.av;
4755       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4756       setMenusFromViewport(viewport);
4757     }
4758
4759     /*
4760      * 'focus' any colour slider that is open to the selected viewport
4761      */
4762     if (viewport.getConservationSelected())
4763     {
4764       SliderPanel.setConservationSlider(alignPanel,
4765               viewport.getResidueShading(), alignPanel.getViewName());
4766     }
4767     else
4768     {
4769       SliderPanel.hideConservationSlider();
4770     }
4771     if (viewport.getAbovePIDThreshold())
4772     {
4773       SliderPanel.setPIDSliderSource(alignPanel,
4774               viewport.getResidueShading(), alignPanel.getViewName());
4775     }
4776     else
4777     {
4778       SliderPanel.hidePIDSlider();
4779     }
4780
4781     /*
4782      * If there is a frame linked to this one in a SplitPane, switch it to the
4783      * same view tab index. No infinite recursion of calls should happen, since
4784      * tabSelectionChanged() should not get invoked on setting the selected
4785      * index to an unchanged value. Guard against setting an invalid index
4786      * before the new view peer tab has been created.
4787      */
4788     final AlignViewportI peer = viewport.getCodingComplement();
4789     if (peer != null)
4790     {
4791       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4792               .getAlignPanel().alignFrame;
4793       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4794       {
4795         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4796       }
4797     }
4798   }
4799
4800   /**
4801    * On right mouse click on view tab, prompt for and set new view name.
4802    */
4803   @Override
4804   public void tabbedPane_mousePressed(MouseEvent e)
4805   {
4806     if (e.isPopupTrigger())
4807     {
4808       String msg = MessageManager.getString("label.enter_view_name");
4809       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4810               JvOptionPane.QUESTION_MESSAGE);
4811
4812       if (reply != null)
4813       {
4814         viewport.setViewName(reply);
4815         // TODO warn if reply is in getExistingViewNames()?
4816         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4817       }
4818     }
4819   }
4820
4821   public AlignViewport getCurrentView()
4822   {
4823     return viewport;
4824   }
4825
4826   /**
4827    * Open the dialog for regex description parsing.
4828    */
4829   @Override
4830   protected void extractScores_actionPerformed(ActionEvent e)
4831   {
4832     ParseProperties pp = new jalview.analysis.ParseProperties(
4833             viewport.getAlignment());
4834     // TODO: verify regex and introduce GUI dialog for version 2.5
4835     // if (pp.getScoresFromDescription("col", "score column ",
4836     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4837     // true)>0)
4838     if (pp.getScoresFromDescription("description column",
4839             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4840     {
4841       buildSortByAnnotationScoresMenu();
4842     }
4843   }
4844
4845   /*
4846    * (non-Javadoc)
4847    *
4848    * @see
4849    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4850    * )
4851    */
4852   @Override
4853   protected void showDbRefs_actionPerformed(ActionEvent e)
4854   {
4855     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4856   }
4857
4858   /*
4859    * (non-Javadoc)
4860    *
4861    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4862    * ActionEvent)
4863    */
4864   @Override
4865   protected void showNpFeats_actionPerformed(ActionEvent e)
4866   {
4867     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4868   }
4869
4870   /**
4871    * find the viewport amongst the tabs in this alignment frame and close that
4872    * tab
4873    *
4874    * @param av
4875    */
4876   public boolean closeView(AlignViewportI av)
4877   {
4878     if (viewport == av)
4879     {
4880       this.closeMenuItem_actionPerformed(false);
4881       return true;
4882     }
4883     Component[] comp = tabbedPane.getComponents();
4884     for (int i = 0; comp != null && i < comp.length; i++)
4885     {
4886       if (comp[i] instanceof AlignmentPanel)
4887       {
4888         if (((AlignmentPanel) comp[i]).av == av)
4889         {
4890           // close the view.
4891           closeView((AlignmentPanel) comp[i]);
4892           return true;
4893         }
4894       }
4895     }
4896     return false;
4897   }
4898
4899   protected void build_fetchdbmenu(JMenu webService)
4900   {
4901     // Temporary hack - DBRef Fetcher always top level ws entry.
4902     // TODO We probably want to store a sequence database checklist in
4903     // preferences and have checkboxes.. rather than individual sources selected
4904     // here
4905     final JMenu rfetch = new JMenu(
4906             MessageManager.getString("action.fetch_db_references"));
4907     rfetch.setToolTipText(MessageManager.getString(
4908             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4909     webService.add(rfetch);
4910
4911     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4912             MessageManager.getString("option.trim_retrieved_seqs"));
4913     trimrs.setToolTipText(
4914             MessageManager.getString("label.trim_retrieved_sequences"));
4915     trimrs.setSelected(
4916             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4917     trimrs.addActionListener(new ActionListener()
4918     {
4919       @Override
4920       public void actionPerformed(ActionEvent e)
4921       {
4922         trimrs.setSelected(trimrs.isSelected());
4923         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4924                 Boolean.valueOf(trimrs.isSelected()).toString());
4925       };
4926     });
4927     rfetch.add(trimrs);
4928     JMenuItem fetchr = new JMenuItem(
4929             MessageManager.getString("label.standard_databases"));
4930     fetchr.setToolTipText(
4931             MessageManager.getString("label.fetch_embl_uniprot"));
4932     fetchr.addActionListener(new ActionListener()
4933     {
4934
4935       @Override
4936       public void actionPerformed(ActionEvent e)
4937       {
4938         new Thread(new Runnable()
4939         {
4940           @Override
4941           public void run()
4942           {
4943             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4944                     .getAlignment().isNucleotide();
4945             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4946                     alignPanel.av.getSequenceSelection(),
4947                     alignPanel.alignFrame, null,
4948                     alignPanel.alignFrame.featureSettings, isNucleotide);
4949             dbRefFetcher.addListener(new FetchFinishedListenerI()
4950             {
4951               @Override
4952               public void finished()
4953               {
4954                 AlignFrame.this.setMenusForViewport();
4955               }
4956             });
4957             dbRefFetcher.fetchDBRefs(false);
4958           }
4959         }).start();
4960
4961       }
4962
4963     });
4964     rfetch.add(fetchr);
4965     final AlignFrame me = this;
4966     new Thread(new Runnable()
4967     {
4968       @Override
4969       public void run()
4970       {
4971         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4972                 .getSequenceFetcherSingleton(me);
4973         javax.swing.SwingUtilities.invokeLater(new Runnable()
4974         {
4975           @Override
4976           public void run()
4977           {
4978             String[] dbclasses = sf.getOrderedSupportedSources();
4979             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4980             // jalview.util.QuickSort.sort(otherdb, otherdb);
4981             List<DbSourceProxy> otherdb;
4982             JMenu dfetch = new JMenu();
4983             JMenu ifetch = new JMenu();
4984             JMenuItem fetchr = null;
4985             int comp = 0, icomp = 0, mcomp = 15;
4986             String mname = null;
4987             int dbi = 0;
4988             for (String dbclass : dbclasses)
4989             {
4990               otherdb = sf.getSourceProxy(dbclass);
4991               // add a single entry for this class, or submenu allowing 'fetch
4992               // all' or pick one
4993               if (otherdb == null || otherdb.size() < 1)
4994               {
4995                 continue;
4996               }
4997               // List<DbSourceProxy> dbs=otherdb;
4998               // otherdb=new ArrayList<DbSourceProxy>();
4999               // for (DbSourceProxy db:dbs)
5000               // {
5001               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5002               // }
5003               if (mname == null)
5004               {
5005                 mname = "From " + dbclass;
5006               }
5007               if (otherdb.size() == 1)
5008               {
5009                 final DbSourceProxy[] dassource = otherdb
5010                         .toArray(new DbSourceProxy[0]);
5011                 DbSourceProxy src = otherdb.get(0);
5012                 fetchr = new JMenuItem(src.getDbSource());
5013                 fetchr.addActionListener(new ActionListener()
5014                 {
5015
5016                   @Override
5017                   public void actionPerformed(ActionEvent e)
5018                   {
5019                     new Thread(new Runnable()
5020                     {
5021
5022                       @Override
5023                       public void run()
5024                       {
5025                         boolean isNucleotide = alignPanel.alignFrame
5026                                 .getViewport().getAlignment()
5027                                 .isNucleotide();
5028                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5029                                 alignPanel.av.getSequenceSelection(),
5030                                 alignPanel.alignFrame, dassource,
5031                                 alignPanel.alignFrame.featureSettings,
5032                                 isNucleotide);
5033                         dbRefFetcher
5034                                 .addListener(new FetchFinishedListenerI()
5035                                 {
5036                                   @Override
5037                                   public void finished()
5038                                   {
5039                                     AlignFrame.this.setMenusForViewport();
5040                                   }
5041                                 });
5042                         dbRefFetcher.fetchDBRefs(false);
5043                       }
5044                     }).start();
5045                   }
5046
5047                 });
5048                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5049                         MessageManager.formatMessage(
5050                                 "label.fetch_retrieve_from", new Object[]
5051                                 { src.getDbName() })));
5052                 dfetch.add(fetchr);
5053                 comp++;
5054               }
5055               else
5056               {
5057                 final DbSourceProxy[] dassource = otherdb
5058                         .toArray(new DbSourceProxy[0]);
5059                 // fetch all entry
5060                 DbSourceProxy src = otherdb.get(0);
5061                 fetchr = new JMenuItem(MessageManager
5062                         .formatMessage("label.fetch_all_param", new Object[]
5063                         { src.getDbSource() }));
5064                 fetchr.addActionListener(new ActionListener()
5065                 {
5066                   @Override
5067                   public void actionPerformed(ActionEvent e)
5068                   {
5069                     new Thread(new Runnable()
5070                     {
5071
5072                       @Override
5073                       public void run()
5074                       {
5075                         boolean isNucleotide = alignPanel.alignFrame
5076                                 .getViewport().getAlignment()
5077                                 .isNucleotide();
5078                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5079                                 alignPanel.av.getSequenceSelection(),
5080                                 alignPanel.alignFrame, dassource,
5081                                 alignPanel.alignFrame.featureSettings,
5082                                 isNucleotide);
5083                         dbRefFetcher
5084                                 .addListener(new FetchFinishedListenerI()
5085                                 {
5086                                   @Override
5087                                   public void finished()
5088                                   {
5089                                     AlignFrame.this.setMenusForViewport();
5090                                   }
5091                                 });
5092                         dbRefFetcher.fetchDBRefs(false);
5093                       }
5094                     }).start();
5095                   }
5096                 });
5097
5098                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5099                         MessageManager.formatMessage(
5100                                 "label.fetch_retrieve_from_all_sources",
5101                                 new Object[]
5102                                 { Integer.valueOf(otherdb.size())
5103                                         .toString(),
5104                                     src.getDbSource(), src.getDbName() })));
5105                 dfetch.add(fetchr);
5106                 comp++;
5107                 // and then build the rest of the individual menus
5108                 ifetch = new JMenu(MessageManager.formatMessage(
5109                         "label.source_from_db_source", new Object[]
5110                         { src.getDbSource() }));
5111                 icomp = 0;
5112                 String imname = null;
5113                 int i = 0;
5114                 for (DbSourceProxy sproxy : otherdb)
5115                 {
5116                   String dbname = sproxy.getDbName();
5117                   String sname = dbname.length() > 5
5118                           ? dbname.substring(0, 5) + "..."
5119                           : dbname;
5120                   String msname = dbname.length() > 10
5121                           ? dbname.substring(0, 10) + "..."
5122                           : dbname;
5123                   if (imname == null)
5124                   {
5125                     imname = MessageManager
5126                             .formatMessage("label.from_msname", new Object[]
5127                             { sname });
5128                   }
5129                   fetchr = new JMenuItem(msname);
5130                   final DbSourceProxy[] dassrc = { sproxy };
5131                   fetchr.addActionListener(new ActionListener()
5132                   {
5133
5134                     @Override
5135                     public void actionPerformed(ActionEvent e)
5136                     {
5137                       new Thread(new Runnable()
5138                       {
5139
5140                         @Override
5141                         public void run()
5142                         {
5143                           boolean isNucleotide = alignPanel.alignFrame
5144                                   .getViewport().getAlignment()
5145                                   .isNucleotide();
5146                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5147                                   alignPanel.av.getSequenceSelection(),
5148                                   alignPanel.alignFrame, dassrc,
5149                                   alignPanel.alignFrame.featureSettings,
5150                                   isNucleotide);
5151                           dbRefFetcher
5152                                   .addListener(new FetchFinishedListenerI()
5153                                   {
5154                                     @Override
5155                                     public void finished()
5156                                     {
5157                                       AlignFrame.this.setMenusForViewport();
5158                                     }
5159                                   });
5160                           dbRefFetcher.fetchDBRefs(false);
5161                         }
5162                       }).start();
5163                     }
5164
5165                   });
5166                   fetchr.setToolTipText(
5167                           "<html>" + MessageManager.formatMessage(
5168                                   "label.fetch_retrieve_from", new Object[]
5169                                   { dbname }));
5170                   ifetch.add(fetchr);
5171                   ++i;
5172                   if (++icomp >= mcomp || i == (otherdb.size()))
5173                   {
5174                     ifetch.setText(MessageManager.formatMessage(
5175                             "label.source_to_target", imname, sname));
5176                     dfetch.add(ifetch);
5177                     ifetch = new JMenu();
5178                     imname = null;
5179                     icomp = 0;
5180                     comp++;
5181                   }
5182                 }
5183               }
5184               ++dbi;
5185               if (comp >= mcomp || dbi >= (dbclasses.length))
5186               {
5187                 dfetch.setText(MessageManager.formatMessage(
5188                         "label.source_to_target", mname, dbclass));
5189                 rfetch.add(dfetch);
5190                 dfetch = new JMenu();
5191                 mname = null;
5192                 comp = 0;
5193               }
5194             }
5195           }
5196         });
5197       }
5198     }).start();
5199
5200   }
5201
5202   /**
5203    * Left justify the whole alignment.
5204    */
5205   @Override
5206   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5207   {
5208     AlignmentI al = viewport.getAlignment();
5209     al.justify(false);
5210     viewport.firePropertyChange("alignment", null, al);
5211   }
5212
5213   /**
5214    * Right justify the whole alignment.
5215    */
5216   @Override
5217   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5218   {
5219     AlignmentI al = viewport.getAlignment();
5220     al.justify(true);
5221     viewport.firePropertyChange("alignment", null, al);
5222   }
5223
5224   @Override
5225   public void setShowSeqFeatures(boolean b)
5226   {
5227     showSeqFeatures.setSelected(b);
5228     viewport.setShowSequenceFeatures(b);
5229   }
5230
5231   /*
5232    * (non-Javadoc)
5233    *
5234    * @see
5235    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5236    * awt.event.ActionEvent)
5237    */
5238   @Override
5239   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5240   {
5241     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5242     alignPanel.paintAlignment(false, false);
5243   }
5244
5245   /*
5246    * (non-Javadoc)
5247    *
5248    * @see
5249    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5250    * .ActionEvent)
5251    */
5252   @Override
5253   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5254   {
5255     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5256     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5257
5258   }
5259
5260   /*
5261    * (non-Javadoc)
5262    *
5263    * @see
5264    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5265    * .event.ActionEvent)
5266    */
5267   @Override
5268   protected void showGroupConservation_actionPerformed(ActionEvent e)
5269   {
5270     viewport.setShowGroupConservation(showGroupConservation.getState());
5271     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5272   }
5273
5274   /*
5275    * (non-Javadoc)
5276    *
5277    * @see
5278    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5279    * .event.ActionEvent)
5280    */
5281   @Override
5282   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5283   {
5284     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5285     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5286   }
5287
5288   /*
5289    * (non-Javadoc)
5290    *
5291    * @see
5292    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5293    * .event.ActionEvent)
5294    */
5295   @Override
5296   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5297   {
5298     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5299     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5300   }
5301
5302   @Override
5303   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5304   {
5305     showSequenceLogo.setState(true);
5306     viewport.setShowSequenceLogo(true);
5307     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5308     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5309   }
5310
5311   @Override
5312   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5313   {
5314     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5315   }
5316
5317   /*
5318    * (non-Javadoc)
5319    *
5320    * @see
5321    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5322    * .event.ActionEvent)
5323    */
5324   @Override
5325   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5326   {
5327     if (avc.makeGroupsFromSelection())
5328     {
5329       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5330       alignPanel.updateAnnotation();
5331       alignPanel.paintAlignment(true,
5332               viewport.needToUpdateStructureViews());
5333     }
5334   }
5335
5336   public void clearAlignmentSeqRep()
5337   {
5338     // TODO refactor alignmentseqrep to controller
5339     if (viewport.getAlignment().hasSeqrep())
5340     {
5341       viewport.getAlignment().setSeqrep(null);
5342       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5343       alignPanel.updateAnnotation();
5344       alignPanel.paintAlignment(true, true);
5345     }
5346   }
5347
5348   @Override
5349   protected void createGroup_actionPerformed(ActionEvent e)
5350   {
5351     if (avc.createGroup())
5352     {
5353       if (applyAutoAnnotationSettings.isSelected())
5354       {
5355         alignPanel.updateAnnotation(true, false);
5356       }
5357       alignPanel.alignmentChanged();
5358     }
5359   }
5360
5361   @Override
5362   protected void unGroup_actionPerformed(ActionEvent e)
5363   {
5364     if (avc.unGroup())
5365     {
5366       alignPanel.alignmentChanged();
5367     }
5368   }
5369
5370   /**
5371    * make the given alignmentPanel the currently selected tab
5372    *
5373    * @param alignmentPanel
5374    */
5375   public void setDisplayedView(AlignmentPanel alignmentPanel)
5376   {
5377     if (!viewport.getSequenceSetId()
5378             .equals(alignmentPanel.av.getSequenceSetId()))
5379     {
5380       throw new Error(MessageManager.getString(
5381               "error.implementation_error_cannot_show_view_alignment_frame"));
5382     }
5383     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5384             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5385     {
5386       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5387     }
5388   }
5389
5390   /**
5391    * Action on selection of menu options to Show or Hide annotations.
5392    *
5393    * @param visible
5394    * @param forSequences
5395    *          update sequence-related annotations
5396    * @param forAlignment
5397    *          update non-sequence-related annotations
5398    */
5399   @Override
5400   protected void setAnnotationsVisibility(boolean visible,
5401           boolean forSequences, boolean forAlignment)
5402   {
5403     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5404             .getAlignmentAnnotation();
5405     if (anns == null)
5406     {
5407       return;
5408     }
5409     for (AlignmentAnnotation aa : anns)
5410     {
5411       /*
5412        * don't display non-positional annotations on an alignment
5413        */
5414       if (aa.annotations == null)
5415       {
5416         continue;
5417       }
5418       boolean apply = (aa.sequenceRef == null && forAlignment)
5419               || (aa.sequenceRef != null && forSequences);
5420       if (apply)
5421       {
5422         aa.visible = visible;
5423       }
5424     }
5425     alignPanel.validateAnnotationDimensions(true);
5426     alignPanel.alignmentChanged();
5427   }
5428
5429   /**
5430    * Store selected annotation sort order for the view and repaint.
5431    */
5432   @Override
5433   protected void sortAnnotations_actionPerformed()
5434   {
5435     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5436     this.alignPanel.av
5437             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5438     alignPanel.paintAlignment(false, false);
5439   }
5440
5441   /**
5442    *
5443    * @return alignment panels in this alignment frame
5444    */
5445   public List<? extends AlignmentViewPanel> getAlignPanels()
5446   {
5447     // alignPanels is never null
5448     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5449     return alignPanels;
5450   }
5451
5452   /**
5453    * Open a new alignment window, with the cDNA associated with this (protein)
5454    * alignment, aligned as is the protein.
5455    */
5456   protected void viewAsCdna_actionPerformed()
5457   {
5458     // TODO no longer a menu action - refactor as required
5459     final AlignmentI alignment = getViewport().getAlignment();
5460     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5461     if (mappings == null)
5462     {
5463       return;
5464     }
5465     List<SequenceI> cdnaSeqs = new ArrayList<>();
5466     for (SequenceI aaSeq : alignment.getSequences())
5467     {
5468       for (AlignedCodonFrame acf : mappings)
5469       {
5470         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5471         if (dnaSeq != null)
5472         {
5473           /*
5474            * There is a cDNA mapping for this protein sequence - add to new
5475            * alignment. It will share the same dataset sequence as other mapped
5476            * cDNA (no new mappings need to be created).
5477            */
5478           final Sequence newSeq = new Sequence(dnaSeq);
5479           newSeq.setDatasetSequence(dnaSeq);
5480           cdnaSeqs.add(newSeq);
5481         }
5482       }
5483     }
5484     if (cdnaSeqs.size() == 0)
5485     {
5486       // show a warning dialog no mapped cDNA
5487       return;
5488     }
5489     AlignmentI cdna = new Alignment(
5490             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5491     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5492             AlignFrame.DEFAULT_HEIGHT);
5493     cdna.alignAs(alignment);
5494     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5495             + this.title;
5496     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5497             AlignFrame.DEFAULT_HEIGHT);
5498   }
5499
5500   /**
5501    * Set visibility of dna/protein complement view (available when shown in a
5502    * split frame).
5503    *
5504    * @param show
5505    */
5506   @Override
5507   protected void showComplement_actionPerformed(boolean show)
5508   {
5509     SplitContainerI sf = getSplitViewContainer();
5510     if (sf != null)
5511     {
5512       sf.setComplementVisible(this, show);
5513     }
5514   }
5515
5516   /**
5517    * Generate the reverse (optionally complemented) of the selected sequences,
5518    * and add them to the alignment
5519    */
5520   @Override
5521   protected void showReverse_actionPerformed(boolean complement)
5522   {
5523     AlignmentI al = null;
5524     try
5525     {
5526       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5527       al = dna.reverseCdna(complement);
5528       viewport.addAlignment(al, "");
5529       addHistoryItem(new EditCommand(
5530               MessageManager.getString("label.add_sequences"), Action.PASTE,
5531               al.getSequencesArray(), 0, al.getWidth(),
5532               viewport.getAlignment()));
5533     } catch (Exception ex)
5534     {
5535       System.err.println(ex.getMessage());
5536       return;
5537     }
5538   }
5539
5540   /**
5541    * Try to run a script in the Groovy console, having first ensured that this
5542    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5543    * be targeted at this alignment.
5544    */
5545   @Override
5546   protected void runGroovy_actionPerformed()
5547   {
5548     Jalview.setCurrentAlignFrame(this);
5549     groovy.ui.Console console = Desktop.getGroovyConsole();
5550     if (console != null)
5551     {
5552       try
5553       {
5554         console.runScript();
5555       } catch (Exception ex)
5556       {
5557         System.err.println((ex.toString()));
5558         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5559                 MessageManager.getString("label.couldnt_run_groovy_script"),
5560                 MessageManager.getString("label.groovy_support_failed"),
5561                 JvOptionPane.ERROR_MESSAGE);
5562       }
5563     }
5564     else
5565     {
5566       System.err.println("Can't run Groovy script as console not found");
5567     }
5568   }
5569
5570   /**
5571    * Hides columns containing (or not containing) a specified feature, provided
5572    * that would not leave all columns hidden
5573    *
5574    * @param featureType
5575    * @param columnsContaining
5576    * @return
5577    */
5578   public boolean hideFeatureColumns(String featureType,
5579           boolean columnsContaining)
5580   {
5581     boolean notForHiding = avc.markColumnsContainingFeatures(
5582             columnsContaining, false, false, featureType);
5583     if (notForHiding)
5584     {
5585       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5586               false, featureType))
5587       {
5588         getViewport().hideSelectedColumns();
5589         return true;
5590       }
5591     }
5592     return false;
5593   }
5594
5595   @Override
5596   protected void selectHighlightedColumns_actionPerformed(
5597           ActionEvent actionEvent)
5598   {
5599     // include key modifier check in case user selects from menu
5600     avc.markHighlightedColumns(
5601             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5602             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5603                     | ActionEvent.CTRL_MASK)) != 0);
5604   }
5605
5606   /**
5607    * Rebuilds the Colour menu, including any user-defined colours which have
5608    * been loaded either on startup or during the session
5609    */
5610   public void buildColourMenu()
5611   {
5612     colourMenu.removeAll();
5613
5614     colourMenu.add(applyToAllGroups);
5615     colourMenu.add(textColour);
5616     colourMenu.addSeparator();
5617
5618     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5619             viewport.getAlignment(), false);
5620
5621     colourMenu.add(annotationColour);
5622     bg.add(annotationColour);
5623     colourMenu.addSeparator();
5624     colourMenu.add(conservationMenuItem);
5625     colourMenu.add(modifyConservation);
5626     colourMenu.add(abovePIDThreshold);
5627     colourMenu.add(modifyPID);
5628
5629     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5630     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5631   }
5632
5633   /**
5634    * Open a dialog (if not already open) that allows the user to select and
5635    * calculate PCA or Tree analysis
5636    */
5637   protected void openTreePcaDialog()
5638   {
5639     if (alignPanel.getCalculationDialog() == null)
5640     {
5641       new CalculationChooser(AlignFrame.this);
5642     }
5643   }
5644
5645   @Override
5646   protected void loadVcf_actionPerformed()
5647   {
5648     JalviewFileChooser chooser = new JalviewFileChooser(
5649             Cache.getProperty("LAST_DIRECTORY"));
5650     chooser.setFileView(new JalviewFileView());
5651     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5652     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5653
5654     int value = chooser.showOpenDialog(null);
5655
5656     if (value == JalviewFileChooser.APPROVE_OPTION)
5657     {
5658       String choice = chooser.getSelectedFile().getPath();
5659       Cache.setProperty("LAST_DIRECTORY", choice);
5660       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5661       new VCFLoader(choice).loadVCF(seqs, this);
5662     }
5663
5664   }
5665 }
5666
5667 class PrintThread extends Thread
5668 {
5669   AlignmentPanel ap;
5670
5671   public PrintThread(AlignmentPanel ap)
5672   {
5673     this.ap = ap;
5674   }
5675
5676   static PageFormat pf;
5677
5678   @Override
5679   public void run()
5680   {
5681     PrinterJob printJob = PrinterJob.getPrinterJob();
5682
5683     if (pf != null)
5684     {
5685       printJob.setPrintable(ap, pf);
5686     }
5687     else
5688     {
5689       printJob.setPrintable(ap);
5690     }
5691
5692     if (printJob.printDialog())
5693     {
5694       try
5695       {
5696         printJob.print();
5697       } catch (Exception PrintException)
5698       {
5699         PrintException.printStackTrace();
5700       }
5701     }
5702   }
5703 }