src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.GeneticCodeI;
  28 import jalview.analysis.ParseProperties;
  29 import jalview.analysis.SequenceIdMatcher;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.FeatureSettingsModelI;
  37 import jalview.api.SplitContainerI;
  38 import jalview.api.ViewStyleI;
  39 import jalview.api.analysis.SimilarityParamsI;
  40 import jalview.bin.Cache;
  41 import jalview.bin.Jalview;
  42 import jalview.commands.CommandI;
  43 import jalview.commands.EditCommand;
  44 import jalview.commands.EditCommand.Action;
  45 import jalview.commands.OrderCommand;
  46 import jalview.commands.RemoveGapColCommand;
  47 import jalview.commands.RemoveGapsCommand;
  48 import jalview.commands.SlideSequencesCommand;
  49 import jalview.commands.TrimRegionCommand;
  50 import jalview.datamodel.AlignedCodonFrame;
  51 import jalview.datamodel.Alignment;
  52 import jalview.datamodel.AlignmentAnnotation;
  53 import jalview.datamodel.AlignmentExportData;
  54 import jalview.datamodel.AlignmentI;
  55 import jalview.datamodel.AlignmentOrder;
  56 import jalview.datamodel.AlignmentView;
  57 import jalview.datamodel.ColumnSelection;
  58 import jalview.datamodel.HiddenColumns;
  59 import jalview.datamodel.HiddenSequences;
  60 import jalview.datamodel.PDBEntry;
  61 import jalview.datamodel.SeqCigar;
  62 import jalview.datamodel.Sequence;
  63 import jalview.datamodel.SequenceGroup;
  64 import jalview.datamodel.SequenceI;
  65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  67 import jalview.io.AlignmentProperties;
  68 import jalview.io.AnnotationFile;
  69 import jalview.io.BackupFiles;
  70 import jalview.io.BioJsHTMLOutput;
  71 import jalview.io.DataSourceType;
  72 import jalview.io.FileFormat;
  73 import jalview.io.FileFormatI;
  74 import jalview.io.FileFormats;
  75 import jalview.io.FileLoader;
  76 import jalview.io.FileParse;
  77 import jalview.io.FormatAdapter;
  78 import jalview.io.HtmlSvgOutput;
  79 import jalview.io.IdentifyFile;
  80 import jalview.io.JPredFile;
  81 import jalview.io.JalviewFileChooser;
  82 import jalview.io.JalviewFileView;
  83 import jalview.io.JnetAnnotationMaker;
  84 import jalview.io.NewickFile;
  85 import jalview.io.ScoreMatrixFile;
  86 import jalview.io.TCoffeeScoreFile;
  87 import jalview.io.vcf.VCFLoader;
  88 import jalview.jbgui.GAlignFrame;
  89 import jalview.schemes.ColourSchemeI;
  90 import jalview.schemes.ColourSchemes;
  91 import jalview.schemes.ResidueColourScheme;
  92 import jalview.schemes.TCoffeeColourScheme;
  93 import jalview.util.MessageManager;
  94 import jalview.viewmodel.AlignmentViewport;
  95 import jalview.viewmodel.ViewportRanges;
  96 import jalview.ws.DBRefFetcher;
  97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  98 import jalview.ws.jws1.Discoverer;
  99 import jalview.ws.jws2.Jws2Discoverer;
 100 import jalview.ws.jws2.jabaws2.Jws2Instance;
 101 import jalview.ws.seqfetcher.DbSourceProxy;
 102
 103 import java.awt.BorderLayout;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseEvent;
 125 import java.awt.print.PageFormat;
 126 import java.awt.print.PrinterJob;
 127 import java.beans.PropertyChangeEvent;
 128 import java.io.File;
 129 import java.io.FileWriter;
 130 import java.io.PrintWriter;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.ButtonGroup;
 141 import javax.swing.JCheckBoxMenuItem;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLayeredPane;
 145 import javax.swing.JMenu;
 146 import javax.swing.JMenuItem;
 147 import javax.swing.JScrollPane;
 148 import javax.swing.SwingUtilities;
 149
 150 /**
 151  * DOCUMENT ME!
 152  *
 153  * @author $author$
 154  * @version $Revision$
 155  */
 156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 157         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 158 {
 159
 160   public static final int DEFAULT_WIDTH = 700;
 161
 162   public static final int DEFAULT_HEIGHT = 500;
 163
 164   /*
 165    * The currently displayed panel (selected tabbed view if more than one)
 166    */
 167   public AlignmentPanel alignPanel;
 168
 169   AlignViewport viewport;
 170
 171   public AlignViewControllerI avc;
 172
 173   List<AlignmentPanel> alignPanels = new ArrayList<>();
 174
 175   /**
 176    * Last format used to load or save alignments in this window
 177    */
 178   FileFormatI currentFileFormat = null;
 179
 180   /**
 181    * Current filename for this alignment
 182    */
 183   String fileName = null;
 184
 185   /**
 186    * Creates a new AlignFrame object with specific width and height.
 187    *
 188    * @param al
 189    * @param width
 190    * @param height
 191    */
 192   public AlignFrame(AlignmentI al, int width, int height)
 193   {
 194     this(al, null, width, height);
 195   }
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width, height and
 199    * sequenceSetId
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    * @param sequenceSetId
 205    */
 206   public AlignFrame(AlignmentI al, int width, int height,
 207           String sequenceSetId)
 208   {
 209     this(al, null, width, height, sequenceSetId);
 210   }
 211
 212   /**
 213    * Creates a new AlignFrame object with specific width, height and
 214    * sequenceSetId
 215    *
 216    * @param al
 217    * @param width
 218    * @param height
 219    * @param sequenceSetId
 220    * @param viewId
 221    */
 222   public AlignFrame(AlignmentI al, int width, int height,
 223           String sequenceSetId, String viewId)
 224   {
 225     this(al, null, width, height, sequenceSetId, viewId);
 226   }
 227
 228   /**
 229    * new alignment window with hidden columns
 230    *
 231    * @param al
 232    *          AlignmentI
 233    * @param hiddenColumns
 234    *          ColumnSelection or null
 235    * @param width
 236    *          Width of alignment frame
 237    * @param height
 238    *          height of frame.
 239    */
 240   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 241           int height)
 242   {
 243     this(al, hiddenColumns, width, height, null);
 244   }
 245
 246   /**
 247    * Create alignment frame for al with hiddenColumns, a specific width and
 248    * height, and specific sequenceId
 249    *
 250    * @param al
 251    * @param hiddenColumns
 252    * @param width
 253    * @param height
 254    * @param sequenceSetId
 255    *          (may be null)
 256    */
 257   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 258           int height, String sequenceSetId)
 259   {
 260     this(al, hiddenColumns, width, height, sequenceSetId, null);
 261   }
 262
 263   /**
 264    * Create alignment frame for al with hiddenColumns, a specific width and
 265    * height, and specific sequenceId
 266    *
 267    * @param al
 268    * @param hiddenColumns
 269    * @param width
 270    * @param height
 271    * @param sequenceSetId
 272    *          (may be null)
 273    * @param viewId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 277           int height, String sequenceSetId, String viewId)
 278   {
 279     setSize(width, height);
 280
 281     if (al.getDataset() == null)
 282     {
 283       al.setDataset(null);
 284     }
 285
 286     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 287
 288     alignPanel = new AlignmentPanel(this, viewport);
 289
 290     addAlignmentPanel(alignPanel, true);
 291     init();
 292   }
 293
 294   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 295           HiddenColumns hiddenColumns, int width, int height)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns);
 305
 306     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 307     {
 308       viewport.hideSequence(hiddenSeqs);
 309     }
 310     alignPanel = new AlignmentPanel(this, viewport);
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   /**
 316    * Make a new AlignFrame from existing alignmentPanels
 317    *
 318    * @param ap
 319    *          AlignmentPanel
 320    * @param av
 321    *          AlignViewport
 322    */
 323   public AlignFrame(AlignmentPanel ap)
 324   {
 325     viewport = ap.av;
 326     alignPanel = ap;
 327     addAlignmentPanel(ap, false);
 328     init();
 329   }
 330
 331   /**
 332    * initalise the alignframe from the underlying viewport data and the
 333    * configurations
 334    */
 335   void init()
 336   {
 337     if (!Jalview.isHeadlessMode())
 338     {
 339       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 340     }
 341
 342     avc = new jalview.controller.AlignViewController(this, viewport,
 343             alignPanel);
 344     if (viewport.getAlignmentConservationAnnotation() == null)
 345     {
 346       // BLOSUM62Colour.setEnabled(false);
 347       conservationMenuItem.setEnabled(false);
 348       modifyConservation.setEnabled(false);
 349       // PIDColour.setEnabled(false);
 350       // abovePIDThreshold.setEnabled(false);
 351       // modifyPID.setEnabled(false);
 352     }
 353
 354     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 355             "No sort");
 356
 357     if (sortby.equals("Id"))
 358     {
 359       sortIDMenuItem_actionPerformed(null);
 360     }
 361     else if (sortby.equals("Pairwise Identity"))
 362     {
 363       sortPairwiseMenuItem_actionPerformed(null);
 364     }
 365
 366     this.alignPanel.av
 367             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 368
 369     setMenusFromViewport(viewport);
 370     buildSortByAnnotationScoresMenu();
 371     calculateTree.addActionListener(new ActionListener()
 372     {
 373
 374       @Override
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         openTreePcaDialog();
 378       }
 379     });
 380     buildColourMenu();
 381
 382     if (Desktop.desktop != null)
 383     {
 384       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 385       addServiceListeners();
 386       setGUINucleotide();
 387     }
 388
 389     if (viewport.getWrapAlignment())
 390     {
 391       wrapMenuItem_actionPerformed(null);
 392     }
 393
 394     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 395     {
 396       this.overviewMenuItem_actionPerformed(null);
 397     }
 398
 399     addKeyListener();
 400
 401     final List<AlignmentPanel> selviews = new ArrayList<>();
 402     final List<AlignmentPanel> origview = new ArrayList<>();
 403     final String menuLabel = MessageManager
 404             .getString("label.copy_format_from");
 405     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 406             new ViewSetProvider()
 407             {
 408
 409               @Override
 410               public AlignmentPanel[] getAllAlignmentPanels()
 411               {
 412                 origview.clear();
 413                 origview.add(alignPanel);
 414                 // make an array of all alignment panels except for this one
 415                 List<AlignmentPanel> aps = new ArrayList<>(
 416                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 417                 aps.remove(AlignFrame.this.alignPanel);
 418                 return aps.toArray(new AlignmentPanel[aps.size()]);
 419               }
 420             }, selviews, new ItemListener()
 421             {
 422
 423               @Override
 424               public void itemStateChanged(ItemEvent e)
 425               {
 426                 if (origview.size() > 0)
 427                 {
 428                   final AlignmentPanel ap = origview.get(0);
 429
 430                   /*
 431                    * Copy the ViewStyle of the selected panel to 'this one'.
 432                    * Don't change value of 'scaleProteinAsCdna' unless copying
 433                    * from a SplitFrame.
 434                    */
 435                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 436                           .getViewStyle();
 437                   boolean fromSplitFrame = selviews.get(0)
 438                           .getAlignViewport().getCodingComplement() != null;
 439                   if (!fromSplitFrame)
 440                   {
 441                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 442                             .getViewStyle().isScaleProteinAsCdna());
 443                   }
 444                   ap.getAlignViewport().setViewStyle(vs);
 445
 446                   /*
 447                    * Also rescale ViewStyle of SplitFrame complement if there is
 448                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 449                    * the whole ViewStyle (allow cDNA protein to have different
 450                    * fonts)
 451                    */
 452                   AlignViewportI complement = ap.getAlignViewport()
 453                           .getCodingComplement();
 454                   if (complement != null && vs.isScaleProteinAsCdna())
 455                   {
 456                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 457                     ((SplitFrame) af.getSplitViewContainer())
 458                             .adjustLayout();
 459                     af.setMenusForViewport();
 460                   }
 461
 462                   ap.updateLayout();
 463                   ap.setSelected(true);
 464                   ap.alignFrame.setMenusForViewport();
 465
 466                 }
 467               }
 468             });
 469     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 470             .indexOf("devel") > -1
 471             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 472                     .indexOf("test") > -1)
 473     {
 474       formatMenu.add(vsel);
 475     }
 476     addFocusListener(new FocusAdapter()
 477     {
 478       @Override
 479       public void focusGained(FocusEvent e)
 480       {
 481         Jalview.setCurrentAlignFrame(AlignFrame.this);
 482       }
 483     });
 484
 485   }
 486
 487   /**
 488    * Change the filename and format for the alignment, and enable the 'reload'
 489    * button functionality.
 490    *
 491    * @param file
 492    *          valid filename
 493    * @param format
 494    *          format of file
 495    */
 496   public void setFileName(String file, FileFormatI format)
 497   {
 498     fileName = file;
 499     setFileFormat(format);
 500     reload.setEnabled(true);
 501   }
 502
 503   /**
 504    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 505    * events
 506    */
 507   void addKeyListener()
 508   {
 509     addKeyListener(new KeyAdapter()
 510     {
 511       @Override
 512       public void keyPressed(KeyEvent evt)
 513       {
 514         if (viewport.cursorMode
 515                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 516                         && evt.getKeyCode() <= KeyEvent.VK_9)
 517                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 518                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 519                 && Character.isDigit(evt.getKeyChar()))
 520         {
 521           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 522         }
 523
 524         switch (evt.getKeyCode())
 525         {
 526
 527         case 27: // escape key
 528           deselectAllSequenceMenuItem_actionPerformed(null);
 529
 530           break;
 531
 532         case KeyEvent.VK_DOWN:
 533           if (evt.isAltDown() || !viewport.cursorMode)
 534           {
 535             moveSelectedSequences(false);
 536           }
 537           if (viewport.cursorMode)
 538           {
 539             alignPanel.getSeqPanel().moveCursor(0, 1);
 540           }
 541           break;
 542
 543         case KeyEvent.VK_UP:
 544           if (evt.isAltDown() || !viewport.cursorMode)
 545           {
 546             moveSelectedSequences(true);
 547           }
 548           if (viewport.cursorMode)
 549           {
 550             alignPanel.getSeqPanel().moveCursor(0, -1);
 551           }
 552
 553           break;
 554
 555         case KeyEvent.VK_LEFT:
 556           if (evt.isAltDown() || !viewport.cursorMode)
 557           {
 558             slideSequences(false,
 559                     alignPanel.getSeqPanel().getKeyboardNo1());
 560           }
 561           else
 562           {
 563             alignPanel.getSeqPanel().moveCursor(-1, 0);
 564           }
 565
 566           break;
 567
 568         case KeyEvent.VK_RIGHT:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 572           }
 573           else
 574           {
 575             alignPanel.getSeqPanel().moveCursor(1, 0);
 576           }
 577           break;
 578
 579         case KeyEvent.VK_SPACE:
 580           if (viewport.cursorMode)
 581           {
 582             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 583                     || evt.isShiftDown() || evt.isAltDown());
 584           }
 585           break;
 586
 587         // case KeyEvent.VK_A:
 588         // if (viewport.cursorMode)
 589         // {
 590         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 591         // //System.out.println("A");
 592         // }
 593         // break;
 594         /*
 595          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 596          * System.out.println("closing bracket"); } break;
 597          */
 598         case KeyEvent.VK_DELETE:
 599         case KeyEvent.VK_BACK_SPACE:
 600           if (!viewport.cursorMode)
 601           {
 602             cut_actionPerformed(null);
 603           }
 604           else
 605           {
 606             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 607                     || evt.isShiftDown() || evt.isAltDown());
 608           }
 609
 610           break;
 611
 612         case KeyEvent.VK_S:
 613           if (viewport.cursorMode)
 614           {
 615             alignPanel.getSeqPanel().setCursorRow();
 616           }
 617           break;
 618         case KeyEvent.VK_C:
 619           if (viewport.cursorMode && !evt.isControlDown())
 620           {
 621             alignPanel.getSeqPanel().setCursorColumn();
 622           }
 623           break;
 624         case KeyEvent.VK_P:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setCursorPosition();
 628           }
 629           break;
 630
 631         case KeyEvent.VK_ENTER:
 632         case KeyEvent.VK_COMMA:
 633           if (viewport.cursorMode)
 634           {
 635             alignPanel.getSeqPanel().setCursorRowAndColumn();
 636           }
 637           break;
 638
 639         case KeyEvent.VK_Q:
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 643           }
 644           break;
 645         case KeyEvent.VK_M:
 646           if (viewport.cursorMode)
 647           {
 648             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 649           }
 650           break;
 651
 652         case KeyEvent.VK_F2:
 653           viewport.cursorMode = !viewport.cursorMode;
 654           statusBar.setText(MessageManager
 655                   .formatMessage("label.keyboard_editing_mode", new String[]
 656                   { (viewport.cursorMode ? "on" : "off") }));
 657           if (viewport.cursorMode)
 658           {
 659             ViewportRanges ranges = viewport.getRanges();
 660             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 661                     .getStartRes();
 662             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 663                     .getStartSeq();
 664           }
 665           alignPanel.getSeqPanel().seqCanvas.repaint();
 666           break;
 667
 668         case KeyEvent.VK_F1:
 669           try
 670           {
 671             Help.showHelpWindow();
 672           } catch (Exception ex)
 673           {
 674             ex.printStackTrace();
 675           }
 676           break;
 677         case KeyEvent.VK_H:
 678         {
 679           boolean toggleSeqs = !evt.isControlDown();
 680           boolean toggleCols = !evt.isShiftDown();
 681           toggleHiddenRegions(toggleSeqs, toggleCols);
 682           break;
 683         }
 684         case KeyEvent.VK_B:
 685         {
 686           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 687           boolean modifyExisting = true; // always modify, don't clear
 688                                          // evt.isShiftDown();
 689           boolean invertHighlighted = evt.isAltDown();
 690           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 691                   toggleSel);
 692           break;
 693         }
 694         case KeyEvent.VK_PAGE_UP:
 695           viewport.getRanges().pageUp();
 696           break;
 697         case KeyEvent.VK_PAGE_DOWN:
 698           viewport.getRanges().pageDown();
 699           break;
 700         }
 701       }
 702
 703       @Override
 704       public void keyReleased(KeyEvent evt)
 705       {
 706         switch (evt.getKeyCode())
 707         {
 708         case KeyEvent.VK_LEFT:
 709           if (evt.isAltDown() || !viewport.cursorMode)
 710           {
 711             viewport.firePropertyChange("alignment", null,
 712                     viewport.getAlignment().getSequences());
 713           }
 714           break;
 715
 716         case KeyEvent.VK_RIGHT:
 717           if (evt.isAltDown() || !viewport.cursorMode)
 718           {
 719             viewport.firePropertyChange("alignment", null,
 720                     viewport.getAlignment().getSequences());
 721           }
 722           break;
 723         }
 724       }
 725     });
 726   }
 727
 728   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 729   {
 730     ap.alignFrame = this;
 731     avc = new jalview.controller.AlignViewController(this, viewport,
 732             alignPanel);
 733
 734     alignPanels.add(ap);
 735
 736     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 737
 738     int aSize = alignPanels.size();
 739
 740     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 741
 742     if (aSize == 1 && ap.av.getViewName() == null)
 743     {
 744       this.getContentPane().add(ap, BorderLayout.CENTER);
 745     }
 746     else
 747     {
 748       if (aSize == 2)
 749       {
 750         setInitialTabVisible();
 751       }
 752
 753       expandViews.setEnabled(true);
 754       gatherViews.setEnabled(true);
 755       tabbedPane.addTab(ap.av.getViewName(), ap);
 756
 757       ap.setVisible(false);
 758     }
 759
 760     if (newPanel)
 761     {
 762       if (ap.av.isPadGaps())
 763       {
 764         ap.av.getAlignment().padGaps();
 765       }
 766       ap.av.updateConservation(ap);
 767       ap.av.updateConsensus(ap);
 768       ap.av.updateStrucConsensus(ap);
 769     }
 770   }
 771
 772   public void setInitialTabVisible()
 773   {
 774     expandViews.setEnabled(true);
 775     gatherViews.setEnabled(true);
 776     tabbedPane.setVisible(true);
 777     AlignmentPanel first = alignPanels.get(0);
 778     tabbedPane.addTab(first.av.getViewName(), first);
 779     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 780   }
 781
 782   public AlignViewport getViewport()
 783   {
 784     return viewport;
 785   }
 786
 787   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 788   private void addServiceListeners()
 789   {
 790     final java.beans.PropertyChangeListener thisListener;
 791     Desktop.instance.addJalviewPropertyChangeListener("services",
 792             thisListener = new java.beans.PropertyChangeListener()
 793             {
 794               @Override
 795               public void propertyChange(PropertyChangeEvent evt)
 796               {
 797                 // // System.out.println("Discoverer property change.");
 798                 // if (evt.getPropertyName().equals("services"))
 799                 {
 800                   SwingUtilities.invokeLater(new Runnable()
 801                   {
 802
 803                     @Override
 804                     public void run()
 805                     {
 806                       System.err.println(
 807                               "Rebuild WS Menu for service change");
 808                       BuildWebServiceMenu();
 809                     }
 810
 811                   });
 812                 }
 813               }
 814             });
 815     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 816     {
 817       @Override
 818       public void internalFrameClosed(
 819               javax.swing.event.InternalFrameEvent evt)
 820       {
 821         // System.out.println("deregistering discoverer listener");
 822         Desktop.instance.removeJalviewPropertyChangeListener("services",
 823                 thisListener);
 824         closeMenuItem_actionPerformed(true);
 825       };
 826     });
 827     // Finally, build the menu once to get current service state
 828     new Thread(new Runnable()
 829     {
 830       @Override
 831       public void run()
 832       {
 833         BuildWebServiceMenu();
 834       }
 835     }).start();
 836   }
 837
 838   /**
 839    * Configure menu items that vary according to whether the alignment is
 840    * nucleotide or protein
 841    */
 842   public void setGUINucleotide()
 843   {
 844     AlignmentI al = getViewport().getAlignment();
 845     boolean nucleotide = al.isNucleotide();
 846
 847     loadVcf.setVisible(nucleotide);
 848     showTranslation.setVisible(nucleotide);
 849     showReverse.setVisible(nucleotide);
 850     showReverseComplement.setVisible(nucleotide);
 851     conservationMenuItem.setEnabled(!nucleotide);
 852     modifyConservation
 853             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 854     showGroupConservation.setEnabled(!nucleotide);
 855
 856     showComplementMenuItem
 857             .setText(nucleotide ? MessageManager.getString("label.protein")
 858                     : MessageManager.getString("label.nucleotide"));
 859   }
 860
 861   /**
 862    * set up menus for the current viewport. This may be called after any
 863    * operation that affects the data in the current view (selection changed,
 864    * etc) to update the menus to reflect the new state.
 865    */
 866   @Override
 867   public void setMenusForViewport()
 868   {
 869     setMenusFromViewport(viewport);
 870   }
 871
 872   /**
 873    * Need to call this method when tabs are selected for multiple views, or when
 874    * loading from Jalview2XML.java
 875    *
 876    * @param av
 877    *          AlignViewport
 878    */
 879   public void setMenusFromViewport(AlignViewport av)
 880   {
 881     padGapsMenuitem.setSelected(av.isPadGaps());
 882     colourTextMenuItem.setSelected(av.isShowColourText());
 883     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 884     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 885     conservationMenuItem.setSelected(av.getConservationSelected());
 886     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 887     seqLimits.setSelected(av.getShowJVSuffix());
 888     idRightAlign.setSelected(av.isRightAlignIds());
 889     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 890     renderGapsMenuItem.setSelected(av.isRenderGaps());
 891     wrapMenuItem.setSelected(av.getWrapAlignment());
 892     scaleAbove.setVisible(av.getWrapAlignment());
 893     scaleLeft.setVisible(av.getWrapAlignment());
 894     scaleRight.setVisible(av.getWrapAlignment());
 895     annotationPanelMenuItem.setState(av.isShowAnnotation());
 896     /*
 897      * Show/hide annotations only enabled if annotation panel is shown
 898      */
 899     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 902     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 904     viewTextMenuItem.setSelected(av.getShowText());
 905     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 906     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 907     showGroupConservation.setSelected(av.isShowGroupConservation());
 908     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 909     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 910     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 911
 912     ColourMenuHelper.setColourSelected(colourMenu,
 913             av.getGlobalColourScheme());
 914
 915     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 916     hiddenMarkers.setState(av.getShowHiddenMarkers());
 917     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 918     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 919     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 920     autoCalculate.setSelected(av.autoCalculateConsensus);
 921     sortByTree.setSelected(av.sortByTree);
 922     listenToViewSelections.setSelected(av.followSelection);
 923
 924     showProducts.setEnabled(canShowProducts());
 925     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 926
 927     updateEditMenuBar();
 928   }
 929
 930   /**
 931    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 932    *
 933    * @param b
 934    */
 935   public void setGroovyEnabled(boolean b)
 936   {
 937     runGroovy.setEnabled(b);
 938   }
 939
 940   private IProgressIndicator progressBar;
 941
 942   /*
 943    * (non-Javadoc)
 944    *
 945    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 946    */
 947   @Override
 948   public void setProgressBar(String message, long id)
 949   {
 950     progressBar.setProgressBar(message, id);
 951   }
 952
 953   @Override
 954   public void registerHandler(final long id,
 955           final IProgressIndicatorHandler handler)
 956   {
 957     progressBar.registerHandler(id, handler);
 958   }
 959
 960   /**
 961    *
 962    * @return true if any progress bars are still active
 963    */
 964   @Override
 965   public boolean operationInProgress()
 966   {
 967     return progressBar.operationInProgress();
 968   }
 969
 970   /**
 971    * Sets the text of the status bar. Note that setting a null or empty value
 972    * will cause the status bar to be hidden, with possibly undesirable flicker
 973    * of the screen layout.
 974    */
 975   @Override
 976   public void setStatus(String text)
 977   {
 978     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 979   }
 980
 981   /*
 982    * Added so Castor Mapping file can obtain Jalview Version
 983    */
 984   public String getVersion()
 985   {
 986     return jalview.bin.Cache.getProperty("VERSION");
 987   }
 988
 989   public FeatureRenderer getFeatureRenderer()
 990   {
 991     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 992   }
 993
 994   @Override
 995   public void fetchSequence_actionPerformed(ActionEvent e)
 996   {
 997     new jalview.gui.SequenceFetcher(this);
 998   }
 999
1000   @Override
1001   public void addFromFile_actionPerformed(ActionEvent e)
1002   {
1003     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1004   }
1005
1006   @Override
1007   public void reload_actionPerformed(ActionEvent e)
1008   {
1009     if (fileName != null)
1010     {
1011       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1012       // originating file's format
1013       // TODO: work out how to recover feature settings for correct view(s) when
1014       // file is reloaded.
1015       if (FileFormat.Jalview.equals(currentFileFormat))
1016       {
1017         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1018         for (int i = 0; i < frames.length; i++)
1019         {
1020           if (frames[i] instanceof AlignFrame && frames[i] != this
1021                   && ((AlignFrame) frames[i]).fileName != null
1022                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1023           {
1024             try
1025             {
1026               frames[i].setSelected(true);
1027               Desktop.instance.closeAssociatedWindows();
1028             } catch (java.beans.PropertyVetoException ex)
1029             {
1030             }
1031           }
1032
1033         }
1034         Desktop.instance.closeAssociatedWindows();
1035
1036         FileLoader loader = new FileLoader();
1037         DataSourceType protocol = fileName.startsWith("http:")
1038                 ? DataSourceType.URL
1039                 : DataSourceType.FILE;
1040         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1041       }
1042       else
1043       {
1044         Rectangle bounds = this.getBounds();
1045
1046         FileLoader loader = new FileLoader();
1047         DataSourceType protocol = fileName.startsWith("http:")
1048                 ? DataSourceType.URL
1049                 : DataSourceType.FILE;
1050         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1051                 protocol, currentFileFormat);
1052
1053         newframe.setBounds(bounds);
1054         if (featureSettings != null && featureSettings.isShowing())
1055         {
1056           final Rectangle fspos = featureSettings.frame.getBounds();
1057           // TODO: need a 'show feature settings' function that takes bounds -
1058           // need to refactor Desktop.addFrame
1059           newframe.featureSettings_actionPerformed(null);
1060           final FeatureSettings nfs = newframe.featureSettings;
1061           SwingUtilities.invokeLater(new Runnable()
1062           {
1063             @Override
1064             public void run()
1065             {
1066               nfs.frame.setBounds(fspos);
1067             }
1068           });
1069           this.featureSettings.close();
1070           this.featureSettings = null;
1071         }
1072         this.closeMenuItem_actionPerformed(true);
1073       }
1074     }
1075   }
1076
1077   @Override
1078   public void addFromText_actionPerformed(ActionEvent e)
1079   {
1080     Desktop.instance
1081             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1082   }
1083
1084   @Override
1085   public void addFromURL_actionPerformed(ActionEvent e)
1086   {
1087     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1088   }
1089
1090   @Override
1091   public void save_actionPerformed(ActionEvent e)
1092   {
1093     if (fileName == null || (currentFileFormat == null)
1094             || fileName.startsWith("http"))
1095     {
1096       saveAs_actionPerformed(null);
1097     }
1098     else
1099     {
1100       saveAlignment(fileName, currentFileFormat);
1101     }
1102   }
1103
1104   /**
1105    * DOCUMENT ME!
1106    *
1107    * @param e
1108    *          DOCUMENT ME!
1109    */
1110   @Override
1111   public void saveAs_actionPerformed(ActionEvent e)
1112   {
1113     String format = currentFileFormat == null ? null
1114             : currentFileFormat.getName();
1115     JalviewFileChooser chooser = JalviewFileChooser
1116             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1117
1118     chooser.setFileView(new JalviewFileView());
1119     chooser.setDialogTitle(
1120             MessageManager.getString("label.save_alignment_to_file"));
1121     chooser.setToolTipText(MessageManager.getString("action.save"));
1122
1123     int value = chooser.showSaveDialog(this);
1124
1125     if (value == JalviewFileChooser.APPROVE_OPTION)
1126     {
1127       currentFileFormat = chooser.getSelectedFormat();
1128       while (currentFileFormat == null)
1129       {
1130         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1131                 MessageManager.getString(
1132                         "label.select_file_format_before_saving"),
1133                 MessageManager.getString("label.file_format_not_specified"),
1134                 JvOptionPane.WARNING_MESSAGE);
1135         currentFileFormat = chooser.getSelectedFormat();
1136         value = chooser.showSaveDialog(this);
1137         if (value != JalviewFileChooser.APPROVE_OPTION)
1138         {
1139           return;
1140         }
1141       }
1142
1143       fileName = chooser.getSelectedFile().getPath();
1144
1145       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1146
1147       Cache.setProperty("LAST_DIRECTORY", fileName);
1148       saveAlignment(fileName, currentFileFormat);
1149     }
1150   }
1151
1152   public boolean saveAlignment(String file, FileFormatI format)
1153   {
1154     boolean success = true;
1155
1156     if (FileFormat.Jalview.equals(format))
1157     {
1158       String shortName = title;
1159
1160       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161       {
1162         shortName = shortName.substring(
1163                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1164       }
1165
1166       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1167               shortName);
1168
1169       statusBar.setText(MessageManager.formatMessage(
1170               "label.successfully_saved_to_file_in_format", new Object[]
1171               { fileName, format }));
1172
1173     }
1174     else
1175     {
1176       AlignmentExportData exportData = getAlignmentForExport(format,
1177               viewport, null);
1178       if (exportData.getSettings().isCancelled())
1179       {
1180         return false;
1181       }
1182       FormatAdapter f = new FormatAdapter(alignPanel,
1183               exportData.getSettings());
1184       String output = f.formatSequences(format, exportData.getAlignment(), // class
1185                                                                            // cast
1186                                                                            // exceptions
1187                                                                            // will
1188               // occur in the distant future
1189               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1190               f.getCacheSuffixDefault(format),
1191               viewport.getAlignment().getHiddenColumns());
1192
1193       if (output == null)
1194       {
1195         success = false;
1196       }
1197       else
1198       {
1199         // create backupfiles object and get new temp filename destination
1200         BackupFiles backupfiles = new BackupFiles(file);
1201
1202         try
1203         {
1204           PrintWriter out = new PrintWriter(
1205                   new FileWriter(backupfiles.getTempFilePath()));
1206
1207           out.print(output);
1208           out.close();
1209           this.setTitle(file);
1210           statusBar.setText(MessageManager.formatMessage(
1211                   "label.successfully_saved_to_file_in_format", new Object[]
1212                   { fileName, format.getName() }));
1213         } catch (Exception ex)
1214         {
1215           success = false;
1216           ex.printStackTrace();
1217         }
1218
1219         backupfiles.setWriteSuccess(success);
1220         // do the backup file roll and rename the temp file to actual file
1221         success = backupfiles.rollBackupsAndRenameTempFile();
1222
1223       }
1224     }
1225
1226     if (!success)
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, MessageManager
1229               .formatMessage("label.couldnt_save_file", new Object[]
1230               { fileName }),
1231               MessageManager.getString("label.error_saving_file"),
1232               JvOptionPane.WARNING_MESSAGE);
1233     }
1234
1235     return success;
1236   }
1237
1238   private void warningMessage(String warning, String title)
1239   {
1240     if (new jalview.util.Platform().isHeadless())
1241     {
1242       System.err.println("Warning: " + title + "\nWarning: " + warning);
1243
1244     }
1245     else
1246     {
1247       JvOptionPane.showInternalMessageDialog(this, warning, title,
1248               JvOptionPane.WARNING_MESSAGE);
1249     }
1250     return;
1251   }
1252
1253   /**
1254    * DOCUMENT ME!
1255    *
1256    * @param e
1257    *          DOCUMENT ME!
1258    */
1259   @Override
1260   protected void outputText_actionPerformed(ActionEvent e)
1261   {
1262     FileFormatI fileFormat = FileFormats.getInstance()
1263             .forName(e.getActionCommand());
1264     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1265             viewport, null);
1266     if (exportData.getSettings().isCancelled())
1267     {
1268       return;
1269     }
1270     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1271     cap.setForInput(null);
1272     try
1273     {
1274       FileFormatI format = fileFormat;
1275       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1276               .formatSequences(format, exportData.getAlignment(),
1277                       exportData.getOmitHidden(),
1278                       exportData.getStartEndPostions(),
1279                       viewport.getAlignment().getHiddenColumns()));
1280       Desktop.addInternalFrame(cap, MessageManager
1281               .formatMessage("label.alignment_output_command", new Object[]
1282               { e.getActionCommand() }), 600, 500);
1283     } catch (OutOfMemoryError oom)
1284     {
1285       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1286               oom);
1287       cap.dispose();
1288     }
1289
1290   }
1291
1292   public static AlignmentExportData getAlignmentForExport(
1293           FileFormatI format, AlignViewportI viewport,
1294           AlignExportSettingI exportSettings)
1295   {
1296     AlignmentI alignmentToExport = null;
1297     AlignExportSettingI settings = exportSettings;
1298     String[] omitHidden = null;
1299
1300     HiddenSequences hiddenSeqs = viewport.getAlignment()
1301             .getHiddenSequences();
1302
1303     alignmentToExport = viewport.getAlignment();
1304
1305     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1306     if (settings == null)
1307     {
1308       settings = new AlignExportSettings(hasHiddenSeqs,
1309               viewport.hasHiddenColumns(), format);
1310     }
1311     // settings.isExportAnnotations();
1312
1313     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1314     {
1315       omitHidden = viewport.getViewAsString(false,
1316               settings.isExportHiddenSequences());
1317     }
1318
1319     int[] alignmentStartEnd = new int[2];
1320     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1321     {
1322       alignmentToExport = hiddenSeqs.getFullAlignment();
1323     }
1324     else
1325     {
1326       alignmentToExport = viewport.getAlignment();
1327     }
1328     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1329             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1330     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1331             omitHidden, alignmentStartEnd, settings);
1332     return ed;
1333   }
1334
1335   /**
1336    * DOCUMENT ME!
1337    *
1338    * @param e
1339    *          DOCUMENT ME!
1340    */
1341   @Override
1342   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343   {
1344     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1345     htmlSVG.exportHTML(null);
1346   }
1347
1348   @Override
1349   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350   {
1351     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1352     bjs.exportHTML(null);
1353   }
1354
1355   public void createImageMap(File file, String image)
1356   {
1357     alignPanel.makePNGImageMap(file, image);
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   @Override
1367   public void createPNG(File f)
1368   {
1369     alignPanel.makePNG(f);
1370   }
1371
1372   /**
1373    * DOCUMENT ME!
1374    *
1375    * @param e
1376    *          DOCUMENT ME!
1377    */
1378   @Override
1379   public void createEPS(File f)
1380   {
1381     alignPanel.makeEPS(f);
1382   }
1383
1384   @Override
1385   public void createSVG(File f)
1386   {
1387     alignPanel.makeSVG(f);
1388   }
1389
1390   @Override
1391   public void pageSetup_actionPerformed(ActionEvent e)
1392   {
1393     PrinterJob printJob = PrinterJob.getPrinterJob();
1394     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1395   }
1396
1397   /**
1398    * DOCUMENT ME!
1399    *
1400    * @param e
1401    *          DOCUMENT ME!
1402    */
1403   @Override
1404   public void printMenuItem_actionPerformed(ActionEvent e)
1405   {
1406     // Putting in a thread avoids Swing painting problems
1407     PrintThread thread = new PrintThread(alignPanel);
1408     thread.start();
1409   }
1410
1411   @Override
1412   public void exportFeatures_actionPerformed(ActionEvent e)
1413   {
1414     new AnnotationExporter(alignPanel).exportFeatures();
1415   }
1416
1417   @Override
1418   public void exportAnnotations_actionPerformed(ActionEvent e)
1419   {
1420     new AnnotationExporter(alignPanel).exportAnnotations();
1421   }
1422
1423   @Override
1424   public void associatedData_actionPerformed(ActionEvent e)
1425   {
1426     // Pick the tree file
1427     JalviewFileChooser chooser = new JalviewFileChooser(
1428             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429     chooser.setFileView(new JalviewFileView());
1430     chooser.setDialogTitle(
1431             MessageManager.getString("label.load_jalview_annotations"));
1432     chooser.setToolTipText(
1433             MessageManager.getString("label.load_jalview_annotations"));
1434
1435     int value = chooser.showOpenDialog(null);
1436
1437     if (value == JalviewFileChooser.APPROVE_OPTION)
1438     {
1439       String choice = chooser.getSelectedFile().getPath();
1440       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441       loadJalviewDataFile(choice, null, null, null);
1442     }
1443
1444   }
1445
1446   /**
1447    * Close the current view or all views in the alignment frame. If the frame
1448    * only contains one view then the alignment will be removed from memory.
1449    *
1450    * @param closeAllTabs
1451    */
1452   @Override
1453   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454   {
1455     if (alignPanels != null && alignPanels.size() < 2)
1456     {
1457       closeAllTabs = true;
1458     }
1459
1460     try
1461     {
1462       if (alignPanels != null)
1463       {
1464         if (closeAllTabs)
1465         {
1466           if (this.isClosed())
1467           {
1468             // really close all the windows - otherwise wait till
1469             // setClosed(true) is called
1470             for (int i = 0; i < alignPanels.size(); i++)
1471             {
1472               AlignmentPanel ap = alignPanels.get(i);
1473               ap.closePanel();
1474             }
1475           }
1476         }
1477         else
1478         {
1479           closeView(alignPanel);
1480         }
1481       }
1482
1483       if (closeAllTabs)
1484       {
1485         /*
1486          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1487          * be called recursively, with the frame now in 'closed' state
1488          */
1489         this.setClosed(true);
1490       }
1491     } catch (Exception ex)
1492     {
1493       ex.printStackTrace();
1494     }
1495   }
1496
1497   /**
1498    * Close the specified panel and close up tabs appropriately.
1499    *
1500    * @param panelToClose
1501    */
1502   public void closeView(AlignmentPanel panelToClose)
1503   {
1504     int index = tabbedPane.getSelectedIndex();
1505     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1506     alignPanels.remove(panelToClose);
1507     panelToClose.closePanel();
1508     panelToClose = null;
1509
1510     tabbedPane.removeTabAt(closedindex);
1511     tabbedPane.validate();
1512
1513     if (index > closedindex || index == tabbedPane.getTabCount())
1514     {
1515       // modify currently selected tab index if necessary.
1516       index--;
1517     }
1518
1519     this.tabSelectionChanged(index);
1520   }
1521
1522   /**
1523    * DOCUMENT ME!
1524    */
1525   void updateEditMenuBar()
1526   {
1527
1528     if (viewport.getHistoryList().size() > 0)
1529     {
1530       undoMenuItem.setEnabled(true);
1531       CommandI command = viewport.getHistoryList().peek();
1532       undoMenuItem.setText(MessageManager
1533               .formatMessage("label.undo_command", new Object[]
1534               { command.getDescription() }));
1535     }
1536     else
1537     {
1538       undoMenuItem.setEnabled(false);
1539       undoMenuItem.setText(MessageManager.getString("action.undo"));
1540     }
1541
1542     if (viewport.getRedoList().size() > 0)
1543     {
1544       redoMenuItem.setEnabled(true);
1545
1546       CommandI command = viewport.getRedoList().peek();
1547       redoMenuItem.setText(MessageManager
1548               .formatMessage("label.redo_command", new Object[]
1549               { command.getDescription() }));
1550     }
1551     else
1552     {
1553       redoMenuItem.setEnabled(false);
1554       redoMenuItem.setText(MessageManager.getString("action.redo"));
1555     }
1556   }
1557
1558   @Override
1559   public void addHistoryItem(CommandI command)
1560   {
1561     if (command.getSize() > 0)
1562     {
1563       viewport.addToHistoryList(command);
1564       viewport.clearRedoList();
1565       updateEditMenuBar();
1566       viewport.updateHiddenColumns();
1567       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1568       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1569       // viewport.getColumnSelection()
1570       // .getHiddenColumns().size() > 0);
1571     }
1572   }
1573
1574   /**
1575    *
1576    * @return alignment objects for all views
1577    */
1578   AlignmentI[] getViewAlignments()
1579   {
1580     if (alignPanels != null)
1581     {
1582       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1583       int i = 0;
1584       for (AlignmentPanel ap : alignPanels)
1585       {
1586         als[i++] = ap.av.getAlignment();
1587       }
1588       return als;
1589     }
1590     if (viewport != null)
1591     {
1592       return new AlignmentI[] { viewport.getAlignment() };
1593     }
1594     return null;
1595   }
1596
1597   /**
1598    * DOCUMENT ME!
1599    *
1600    * @param e
1601    *          DOCUMENT ME!
1602    */
1603   @Override
1604   protected void undoMenuItem_actionPerformed(ActionEvent e)
1605   {
1606     if (viewport.getHistoryList().isEmpty())
1607     {
1608       return;
1609     }
1610     CommandI command = viewport.getHistoryList().pop();
1611     viewport.addToRedoList(command);
1612     command.undoCommand(getViewAlignments());
1613
1614     AlignmentViewport originalSource = getOriginatingSource(command);
1615     updateEditMenuBar();
1616
1617     if (originalSource != null)
1618     {
1619       if (originalSource != viewport)
1620       {
1621         Cache.log.warn(
1622                 "Implementation worry: mismatch of viewport origin for undo");
1623       }
1624       originalSource.updateHiddenColumns();
1625       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1626       // null
1627       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1628       // viewport.getColumnSelection()
1629       // .getHiddenColumns().size() > 0);
1630       originalSource.firePropertyChange("alignment", null,
1631               originalSource.getAlignment().getSequences());
1632     }
1633   }
1634
1635   /**
1636    * DOCUMENT ME!
1637    *
1638    * @param e
1639    *          DOCUMENT ME!
1640    */
1641   @Override
1642   protected void redoMenuItem_actionPerformed(ActionEvent e)
1643   {
1644     if (viewport.getRedoList().size() < 1)
1645     {
1646       return;
1647     }
1648
1649     CommandI command = viewport.getRedoList().pop();
1650     viewport.addToHistoryList(command);
1651     command.doCommand(getViewAlignments());
1652
1653     AlignmentViewport originalSource = getOriginatingSource(command);
1654     updateEditMenuBar();
1655
1656     if (originalSource != null)
1657     {
1658
1659       if (originalSource != viewport)
1660       {
1661         Cache.log.warn(
1662                 "Implementation worry: mismatch of viewport origin for redo");
1663       }
1664       originalSource.updateHiddenColumns();
1665       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666       // null
1667       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1668       // viewport.getColumnSelection()
1669       // .getHiddenColumns().size() > 0);
1670       originalSource.firePropertyChange("alignment", null,
1671               originalSource.getAlignment().getSequences());
1672     }
1673   }
1674
1675   AlignmentViewport getOriginatingSource(CommandI command)
1676   {
1677     AlignmentViewport originalSource = null;
1678     // For sequence removal and addition, we need to fire
1679     // the property change event FROM the viewport where the
1680     // original alignment was altered
1681     AlignmentI al = null;
1682     if (command instanceof EditCommand)
1683     {
1684       EditCommand editCommand = (EditCommand) command;
1685       al = editCommand.getAlignment();
1686       List<Component> comps = PaintRefresher.components
1687               .get(viewport.getSequenceSetId());
1688
1689       for (Component comp : comps)
1690       {
1691         if (comp instanceof AlignmentPanel)
1692         {
1693           if (al == ((AlignmentPanel) comp).av.getAlignment())
1694           {
1695             originalSource = ((AlignmentPanel) comp).av;
1696             break;
1697           }
1698         }
1699       }
1700     }
1701
1702     if (originalSource == null)
1703     {
1704       // The original view is closed, we must validate
1705       // the current view against the closed view first
1706       if (al != null)
1707       {
1708         PaintRefresher.validateSequences(al, viewport.getAlignment());
1709       }
1710
1711       originalSource = viewport;
1712     }
1713
1714     return originalSource;
1715   }
1716
1717   /**
1718    * DOCUMENT ME!
1719    *
1720    * @param up
1721    *          DOCUMENT ME!
1722    */
1723   public void moveSelectedSequences(boolean up)
1724   {
1725     SequenceGroup sg = viewport.getSelectionGroup();
1726
1727     if (sg == null)
1728     {
1729       return;
1730     }
1731     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1732             viewport.getHiddenRepSequences(), up);
1733     alignPanel.paintAlignment(true, false);
1734   }
1735
1736   synchronized void slideSequences(boolean right, int size)
1737   {
1738     List<SequenceI> sg = new ArrayList<>();
1739     if (viewport.cursorMode)
1740     {
1741       sg.add(viewport.getAlignment()
1742               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1743     }
1744     else if (viewport.getSelectionGroup() != null
1745             && viewport.getSelectionGroup().getSize() != viewport
1746                     .getAlignment().getHeight())
1747     {
1748       sg = viewport.getSelectionGroup()
1749               .getSequences(viewport.getHiddenRepSequences());
1750     }
1751
1752     if (sg.size() < 1)
1753     {
1754       return;
1755     }
1756
1757     List<SequenceI> invertGroup = new ArrayList<>();
1758
1759     for (SequenceI seq : viewport.getAlignment().getSequences())
1760     {
1761       if (!sg.contains(seq))
1762       {
1763         invertGroup.add(seq);
1764       }
1765     }
1766
1767     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1768
1769     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1770     for (int i = 0; i < invertGroup.size(); i++)
1771     {
1772       seqs2[i] = invertGroup.get(i);
1773     }
1774
1775     SlideSequencesCommand ssc;
1776     if (right)
1777     {
1778       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1779               viewport.getGapCharacter());
1780     }
1781     else
1782     {
1783       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1784               viewport.getGapCharacter());
1785     }
1786
1787     int groupAdjustment = 0;
1788     if (ssc.getGapsInsertedBegin() && right)
1789     {
1790       if (viewport.cursorMode)
1791       {
1792         alignPanel.getSeqPanel().moveCursor(size, 0);
1793       }
1794       else
1795       {
1796         groupAdjustment = size;
1797       }
1798     }
1799     else if (!ssc.getGapsInsertedBegin() && !right)
1800     {
1801       if (viewport.cursorMode)
1802       {
1803         alignPanel.getSeqPanel().moveCursor(-size, 0);
1804       }
1805       else
1806       {
1807         groupAdjustment = -size;
1808       }
1809     }
1810
1811     if (groupAdjustment != 0)
1812     {
1813       viewport.getSelectionGroup().setStartRes(
1814               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1815       viewport.getSelectionGroup().setEndRes(
1816               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817     }
1818
1819     /*
1820      * just extend the last slide command if compatible; but not if in
1821      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1822      */
1823     boolean appendHistoryItem = false;
1824     Deque<CommandI> historyList = viewport.getHistoryList();
1825     boolean inSplitFrame = getSplitViewContainer() != null;
1826     if (!inSplitFrame && historyList != null && historyList.size() > 0
1827             && historyList.peek() instanceof SlideSequencesCommand)
1828     {
1829       appendHistoryItem = ssc.appendSlideCommand(
1830               (SlideSequencesCommand) historyList.peek());
1831     }
1832
1833     if (!appendHistoryItem)
1834     {
1835       addHistoryItem(ssc);
1836     }
1837
1838     repaint();
1839   }
1840
1841   /**
1842    * DOCUMENT ME!
1843    *
1844    * @param e
1845    *          DOCUMENT ME!
1846    */
1847   @Override
1848   protected void copy_actionPerformed(ActionEvent e)
1849   {
1850     if (viewport.getSelectionGroup() == null)
1851     {
1852       return;
1853     }
1854     // TODO: preserve the ordering of displayed alignment annotation in any
1855     // internal paste (particularly sequence associated annotation)
1856     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1857     String[] omitHidden = null;
1858
1859     if (viewport.hasHiddenColumns())
1860     {
1861       omitHidden = viewport.getViewAsString(true);
1862     }
1863
1864     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1865             seqs, omitHidden, null);
1866
1867     StringSelection ss = new StringSelection(output);
1868
1869     try
1870     {
1871       jalview.gui.Desktop.internalCopy = true;
1872       // Its really worth setting the clipboard contents
1873       // to empty before setting the large StringSelection!!
1874       Toolkit.getDefaultToolkit().getSystemClipboard()
1875               .setContents(new StringSelection(""), null);
1876
1877       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1878               Desktop.instance);
1879     } catch (OutOfMemoryError er)
1880     {
1881       new OOMWarning("copying region", er);
1882       return;
1883     }
1884
1885     HiddenColumns hiddenColumns = null;
1886     if (viewport.hasHiddenColumns())
1887     {
1888       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1889       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1890
1891       // create new HiddenColumns object with copy of hidden regions
1892       // between startRes and endRes, offset by startRes
1893       hiddenColumns = new HiddenColumns(
1894               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1895               hiddenCutoff, hiddenOffset);
1896     }
1897
1898     Desktop.jalviewClipboard = new Object[] { seqs,
1899         viewport.getAlignment().getDataset(), hiddenColumns };
1900     statusBar.setText(MessageManager.formatMessage(
1901             "label.copied_sequences_to_clipboard", new Object[]
1902             { Integer.valueOf(seqs.length).toString() }));
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void pasteNew_actionPerformed(ActionEvent e)
1913   {
1914     paste(true);
1915   }
1916
1917   /**
1918    * DOCUMENT ME!
1919    *
1920    * @param e
1921    *          DOCUMENT ME!
1922    */
1923   @Override
1924   protected void pasteThis_actionPerformed(ActionEvent e)
1925   {
1926     paste(false);
1927   }
1928
1929   /**
1930    * Paste contents of Jalview clipboard
1931    *
1932    * @param newAlignment
1933    *          true to paste to a new alignment, otherwise add to this.
1934    */
1935   void paste(boolean newAlignment)
1936   {
1937     boolean externalPaste = true;
1938     try
1939     {
1940       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1941       Transferable contents = c.getContents(this);
1942
1943       if (contents == null)
1944       {
1945         return;
1946       }
1947
1948       String str;
1949       FileFormatI format;
1950       try
1951       {
1952         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1953         if (str.length() < 1)
1954         {
1955           return;
1956         }
1957
1958         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1959
1960       } catch (OutOfMemoryError er)
1961       {
1962         new OOMWarning("Out of memory pasting sequences!!", er);
1963         return;
1964       }
1965
1966       SequenceI[] sequences;
1967       boolean annotationAdded = false;
1968       AlignmentI alignment = null;
1969
1970       if (Desktop.jalviewClipboard != null)
1971       {
1972         // The clipboard was filled from within Jalview, we must use the
1973         // sequences
1974         // And dataset from the copied alignment
1975         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1976         // be doubly sure that we create *new* sequence objects.
1977         sequences = new SequenceI[newseq.length];
1978         for (int i = 0; i < newseq.length; i++)
1979         {
1980           sequences[i] = new Sequence(newseq[i]);
1981         }
1982         alignment = new Alignment(sequences);
1983         externalPaste = false;
1984       }
1985       else
1986       {
1987         // parse the clipboard as an alignment.
1988         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1989                 format);
1990         sequences = alignment.getSequencesArray();
1991       }
1992
1993       int alwidth = 0;
1994       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1995       int fgroup = -1;
1996
1997       if (newAlignment)
1998       {
1999
2000         if (Desktop.jalviewClipboard != null)
2001         {
2002           // dataset is inherited
2003           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2004         }
2005         else
2006         {
2007           // new dataset is constructed
2008           alignment.setDataset(null);
2009         }
2010         alwidth = alignment.getWidth() + 1;
2011       }
2012       else
2013       {
2014         AlignmentI pastedal = alignment; // preserve pasted alignment object
2015         // Add pasted sequences and dataset into existing alignment.
2016         alignment = viewport.getAlignment();
2017         alwidth = alignment.getWidth() + 1;
2018         // decide if we need to import sequences from an existing dataset
2019         boolean importDs = Desktop.jalviewClipboard != null
2020                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2021         // importDs==true instructs us to copy over new dataset sequences from
2022         // an existing alignment
2023         Vector newDs = (importDs) ? new Vector() : null; // used to create
2024         // minimum dataset set
2025
2026         for (int i = 0; i < sequences.length; i++)
2027         {
2028           if (importDs)
2029           {
2030             newDs.addElement(null);
2031           }
2032           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2033           // paste
2034           if (importDs && ds != null)
2035           {
2036             if (!newDs.contains(ds))
2037             {
2038               newDs.setElementAt(ds, i);
2039               ds = new Sequence(ds);
2040               // update with new dataset sequence
2041               sequences[i].setDatasetSequence(ds);
2042             }
2043             else
2044             {
2045               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2046             }
2047           }
2048           else
2049           {
2050             // copy and derive new dataset sequence
2051             sequences[i] = sequences[i].deriveSequence();
2052             alignment.getDataset()
2053                     .addSequence(sequences[i].getDatasetSequence());
2054             // TODO: avoid creation of duplicate dataset sequences with a
2055             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2056           }
2057           alignment.addSequence(sequences[i]); // merges dataset
2058         }
2059         if (newDs != null)
2060         {
2061           newDs.clear(); // tidy up
2062         }
2063         if (alignment.getAlignmentAnnotation() != null)
2064         {
2065           for (AlignmentAnnotation alan : alignment
2066                   .getAlignmentAnnotation())
2067           {
2068             if (alan.graphGroup > fgroup)
2069             {
2070               fgroup = alan.graphGroup;
2071             }
2072           }
2073         }
2074         if (pastedal.getAlignmentAnnotation() != null)
2075         {
2076           // Add any annotation attached to alignment.
2077           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2078           for (int i = 0; i < alann.length; i++)
2079           {
2080             annotationAdded = true;
2081             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2082             {
2083               AlignmentAnnotation newann = new AlignmentAnnotation(
2084                       alann[i]);
2085               if (newann.graphGroup > -1)
2086               {
2087                 if (newGraphGroups.size() <= newann.graphGroup
2088                         || newGraphGroups.get(newann.graphGroup) == null)
2089                 {
2090                   for (int q = newGraphGroups
2091                           .size(); q <= newann.graphGroup; q++)
2092                   {
2093                     newGraphGroups.add(q, null);
2094                   }
2095                   newGraphGroups.set(newann.graphGroup,
2096                           Integer.valueOf(++fgroup));
2097                 }
2098                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2099                         .intValue();
2100               }
2101
2102               newann.padAnnotation(alwidth);
2103               alignment.addAnnotation(newann);
2104             }
2105           }
2106         }
2107       }
2108       if (!newAlignment)
2109       {
2110         // /////
2111         // ADD HISTORY ITEM
2112         //
2113         addHistoryItem(new EditCommand(
2114                 MessageManager.getString("label.add_sequences"),
2115                 Action.PASTE, sequences, 0, alignment.getWidth(),
2116                 alignment));
2117       }
2118       // Add any annotations attached to sequences
2119       for (int i = 0; i < sequences.length; i++)
2120       {
2121         if (sequences[i].getAnnotation() != null)
2122         {
2123           AlignmentAnnotation newann;
2124           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125           {
2126             annotationAdded = true;
2127             newann = sequences[i].getAnnotation()[a];
2128             newann.adjustForAlignment();
2129             newann.padAnnotation(alwidth);
2130             if (newann.graphGroup > -1)
2131             {
2132               if (newann.graphGroup > -1)
2133               {
2134                 if (newGraphGroups.size() <= newann.graphGroup
2135                         || newGraphGroups.get(newann.graphGroup) == null)
2136                 {
2137                   for (int q = newGraphGroups
2138                           .size(); q <= newann.graphGroup; q++)
2139                   {
2140                     newGraphGroups.add(q, null);
2141                   }
2142                   newGraphGroups.set(newann.graphGroup,
2143                           Integer.valueOf(++fgroup));
2144                 }
2145                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2146                         .intValue();
2147               }
2148             }
2149             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2150             // was
2151             // duplicated
2152             // earlier
2153             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2154                     a);
2155           }
2156         }
2157       }
2158       if (!newAlignment)
2159       {
2160
2161         // propagate alignment changed.
2162         viewport.getRanges().setEndSeq(alignment.getHeight());
2163         if (annotationAdded)
2164         {
2165           // Duplicate sequence annotation in all views.
2166           AlignmentI[] alview = this.getViewAlignments();
2167           for (int i = 0; i < sequences.length; i++)
2168           {
2169             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2170             if (sann == null)
2171             {
2172               continue;
2173             }
2174             for (int avnum = 0; avnum < alview.length; avnum++)
2175             {
2176               if (alview[avnum] != alignment)
2177               {
2178                 // duplicate in a view other than the one with input focus
2179                 int avwidth = alview[avnum].getWidth() + 1;
2180                 // this relies on sann being preserved after we
2181                 // modify the sequence's annotation array for each duplication
2182                 for (int a = 0; a < sann.length; a++)
2183                 {
2184                   AlignmentAnnotation newann = new AlignmentAnnotation(
2185                           sann[a]);
2186                   sequences[i].addAlignmentAnnotation(newann);
2187                   newann.padAnnotation(avwidth);
2188                   alview[avnum].addAnnotation(newann); // annotation was
2189                   // duplicated earlier
2190                   // TODO JAL-1145 graphGroups are not updated for sequence
2191                   // annotation added to several views. This may cause
2192                   // strangeness
2193                   alview[avnum].setAnnotationIndex(newann, a);
2194                 }
2195               }
2196             }
2197           }
2198           buildSortByAnnotationScoresMenu();
2199         }
2200         viewport.firePropertyChange("alignment", null,
2201                 alignment.getSequences());
2202         if (alignPanels != null)
2203         {
2204           for (AlignmentPanel ap : alignPanels)
2205           {
2206             ap.validateAnnotationDimensions(false);
2207           }
2208         }
2209         else
2210         {
2211           alignPanel.validateAnnotationDimensions(false);
2212         }
2213
2214       }
2215       else
2216       {
2217         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2218                 DEFAULT_HEIGHT);
2219         String newtitle = new String("Copied sequences");
2220
2221         if (Desktop.jalviewClipboard != null
2222                 && Desktop.jalviewClipboard[2] != null)
2223         {
2224           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2225           af.viewport.setHiddenColumns(hc);
2226         }
2227
2228         // >>>This is a fix for the moment, until a better solution is
2229         // found!!<<<
2230         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2231                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2232                         .getFeatureRenderer());
2233
2234         // TODO: maintain provenance of an alignment, rather than just make the
2235         // title a concatenation of operations.
2236         if (!externalPaste)
2237         {
2238           if (title.startsWith("Copied sequences"))
2239           {
2240             newtitle = title;
2241           }
2242           else
2243           {
2244             newtitle = newtitle.concat("- from " + title);
2245           }
2246         }
2247         else
2248         {
2249           newtitle = new String("Pasted sequences");
2250         }
2251
2252         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2253                 DEFAULT_HEIGHT);
2254
2255       }
2256
2257     } catch (Exception ex)
2258     {
2259       ex.printStackTrace();
2260       System.out.println("Exception whilst pasting: " + ex);
2261       // could be anything being pasted in here
2262     }
2263
2264   }
2265
2266   @Override
2267   protected void expand_newalign(ActionEvent e)
2268   {
2269     try
2270     {
2271       AlignmentI alignment = AlignmentUtils
2272               .expandContext(getViewport().getAlignment(), -1);
2273       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2274               DEFAULT_HEIGHT);
2275       String newtitle = new String("Flanking alignment");
2276
2277       if (Desktop.jalviewClipboard != null
2278               && Desktop.jalviewClipboard[2] != null)
2279       {
2280         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2281         af.viewport.setHiddenColumns(hc);
2282       }
2283
2284       // >>>This is a fix for the moment, until a better solution is
2285       // found!!<<<
2286       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2287               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2288                       .getFeatureRenderer());
2289
2290       // TODO: maintain provenance of an alignment, rather than just make the
2291       // title a concatenation of operations.
2292       {
2293         if (title.startsWith("Copied sequences"))
2294         {
2295           newtitle = title;
2296         }
2297         else
2298         {
2299           newtitle = newtitle.concat("- from " + title);
2300         }
2301       }
2302
2303       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2304
2305     } catch (Exception ex)
2306     {
2307       ex.printStackTrace();
2308       System.out.println("Exception whilst pasting: " + ex);
2309       // could be anything being pasted in here
2310     } catch (OutOfMemoryError oom)
2311     {
2312       new OOMWarning("Viewing flanking region of alignment", oom);
2313     }
2314   }
2315
2316   /**
2317    * DOCUMENT ME!
2318    *
2319    * @param e
2320    *          DOCUMENT ME!
2321    */
2322   @Override
2323   protected void cut_actionPerformed(ActionEvent e)
2324   {
2325     copy_actionPerformed(null);
2326     delete_actionPerformed(null);
2327   }
2328
2329   /**
2330    * DOCUMENT ME!
2331    *
2332    * @param e
2333    *          DOCUMENT ME!
2334    */
2335   @Override
2336   protected void delete_actionPerformed(ActionEvent evt)
2337   {
2338
2339     SequenceGroup sg = viewport.getSelectionGroup();
2340     if (sg == null)
2341     {
2342       return;
2343     }
2344
2345     /*
2346      * If the cut affects all sequences, warn, remove highlighted columns
2347      */
2348     if (sg.getSize() == viewport.getAlignment().getHeight())
2349     {
2350       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2351               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2352       if (isEntireAlignWidth)
2353       {
2354         int confirm = JvOptionPane.showConfirmDialog(this,
2355                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2356                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2357                 JvOptionPane.OK_CANCEL_OPTION);
2358
2359         if (confirm == JvOptionPane.CANCEL_OPTION
2360                 || confirm == JvOptionPane.CLOSED_OPTION)
2361         {
2362           return;
2363         }
2364       }
2365       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2366               sg.getEndRes() + 1);
2367     }
2368     SequenceI[] cut = sg.getSequences()
2369             .toArray(new SequenceI[sg.getSize()]);
2370
2371     addHistoryItem(new EditCommand(
2372             MessageManager.getString("label.cut_sequences"), Action.CUT,
2373             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2374             viewport.getAlignment()));
2375
2376     viewport.setSelectionGroup(null);
2377     viewport.sendSelection();
2378     viewport.getAlignment().deleteGroup(sg);
2379
2380     viewport.firePropertyChange("alignment", null,
2381             viewport.getAlignment().getSequences());
2382     if (viewport.getAlignment().getHeight() < 1)
2383     {
2384       try
2385       {
2386         this.setClosed(true);
2387       } catch (Exception ex)
2388       {
2389       }
2390     }
2391   }
2392
2393   /**
2394    * DOCUMENT ME!
2395    *
2396    * @param e
2397    *          DOCUMENT ME!
2398    */
2399   @Override
2400   protected void deleteGroups_actionPerformed(ActionEvent e)
2401   {
2402     if (avc.deleteGroups())
2403     {
2404       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2405       alignPanel.updateAnnotation();
2406       alignPanel.paintAlignment(true, true);
2407     }
2408   }
2409
2410   /**
2411    * DOCUMENT ME!
2412    *
2413    * @param e
2414    *          DOCUMENT ME!
2415    */
2416   @Override
2417   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2418   {
2419     SequenceGroup sg = new SequenceGroup(
2420             viewport.getAlignment().getSequences());
2421
2422     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2423     viewport.setSelectionGroup(sg);
2424     viewport.isSelectionGroupChanged(true);
2425     viewport.sendSelection();
2426     // JAL-2034 - should delegate to
2427     // alignPanel to decide if overview needs
2428     // updating.
2429     alignPanel.paintAlignment(false, false);
2430     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2431   }
2432
2433   /**
2434    * DOCUMENT ME!
2435    *
2436    * @param e
2437    *          DOCUMENT ME!
2438    */
2439   @Override
2440   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441   {
2442     if (viewport.cursorMode)
2443     {
2444       alignPanel.getSeqPanel().keyboardNo1 = null;
2445       alignPanel.getSeqPanel().keyboardNo2 = null;
2446     }
2447     viewport.setSelectionGroup(null);
2448     viewport.getColumnSelection().clear();
2449     viewport.setSelectionGroup(null);
2450     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2451     // JAL-2034 - should delegate to
2452     // alignPanel to decide if overview needs
2453     // updating.
2454     alignPanel.paintAlignment(false, false);
2455     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2456     viewport.sendSelection();
2457   }
2458
2459   /**
2460    * DOCUMENT ME!
2461    *
2462    * @param e
2463    *          DOCUMENT ME!
2464    */
2465   @Override
2466   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2467   {
2468     SequenceGroup sg = viewport.getSelectionGroup();
2469
2470     if (sg == null)
2471     {
2472       selectAllSequenceMenuItem_actionPerformed(null);
2473
2474       return;
2475     }
2476
2477     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2478     {
2479       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2480     }
2481     // JAL-2034 - should delegate to
2482     // alignPanel to decide if overview needs
2483     // updating.
2484
2485     alignPanel.paintAlignment(true, false);
2486     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2487     viewport.sendSelection();
2488   }
2489
2490   @Override
2491   public void invertColSel_actionPerformed(ActionEvent e)
2492   {
2493     viewport.invertColumnSelection();
2494     alignPanel.paintAlignment(true, false);
2495     viewport.sendSelection();
2496   }
2497
2498   /**
2499    * DOCUMENT ME!
2500    *
2501    * @param e
2502    *          DOCUMENT ME!
2503    */
2504   @Override
2505   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506   {
2507     trimAlignment(true);
2508   }
2509
2510   /**
2511    * DOCUMENT ME!
2512    *
2513    * @param e
2514    *          DOCUMENT ME!
2515    */
2516   @Override
2517   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518   {
2519     trimAlignment(false);
2520   }
2521
2522   void trimAlignment(boolean trimLeft)
2523   {
2524     ColumnSelection colSel = viewport.getColumnSelection();
2525     int column;
2526
2527     if (!colSel.isEmpty())
2528     {
2529       if (trimLeft)
2530       {
2531         column = colSel.getMin();
2532       }
2533       else
2534       {
2535         column = colSel.getMax();
2536       }
2537
2538       SequenceI[] seqs;
2539       if (viewport.getSelectionGroup() != null)
2540       {
2541         seqs = viewport.getSelectionGroup()
2542                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2543       }
2544       else
2545       {
2546         seqs = viewport.getAlignment().getSequencesArray();
2547       }
2548
2549       TrimRegionCommand trimRegion;
2550       if (trimLeft)
2551       {
2552         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2553                 column, viewport.getAlignment());
2554         viewport.getRanges().setStartRes(0);
2555       }
2556       else
2557       {
2558         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2559                 column, viewport.getAlignment());
2560       }
2561
2562       statusBar.setText(MessageManager
2563               .formatMessage("label.removed_columns", new String[]
2564               { Integer.valueOf(trimRegion.getSize()).toString() }));
2565
2566       addHistoryItem(trimRegion);
2567
2568       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2569       {
2570         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2571                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2572         {
2573           viewport.getAlignment().deleteGroup(sg);
2574         }
2575       }
2576
2577       viewport.firePropertyChange("alignment", null,
2578               viewport.getAlignment().getSequences());
2579     }
2580   }
2581
2582   /**
2583    * DOCUMENT ME!
2584    *
2585    * @param e
2586    *          DOCUMENT ME!
2587    */
2588   @Override
2589   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2590   {
2591     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2592
2593     SequenceI[] seqs;
2594     if (viewport.getSelectionGroup() != null)
2595     {
2596       seqs = viewport.getSelectionGroup()
2597               .getSequencesAsArray(viewport.getHiddenRepSequences());
2598       start = viewport.getSelectionGroup().getStartRes();
2599       end = viewport.getSelectionGroup().getEndRes();
2600     }
2601     else
2602     {
2603       seqs = viewport.getAlignment().getSequencesArray();
2604     }
2605
2606     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2607             "Remove Gapped Columns", seqs, start, end,
2608             viewport.getAlignment());
2609
2610     addHistoryItem(removeGapCols);
2611
2612     statusBar.setText(MessageManager
2613             .formatMessage("label.removed_empty_columns", new Object[]
2614             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2615
2616     // This is to maintain viewport position on first residue
2617     // of first sequence
2618     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2619     ViewportRanges ranges = viewport.getRanges();
2620     int startRes = seq.findPosition(ranges.getStartRes());
2621     // ShiftList shifts;
2622     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2623     // edit.alColumnChanges=shifts.getInverse();
2624     // if (viewport.hasHiddenColumns)
2625     // viewport.getColumnSelection().compensateForEdits(shifts);
2626     ranges.setStartRes(seq.findIndex(startRes) - 1);
2627     viewport.firePropertyChange("alignment", null,
2628             viewport.getAlignment().getSequences());
2629
2630   }
2631
2632   /**
2633    * DOCUMENT ME!
2634    *
2635    * @param e
2636    *          DOCUMENT ME!
2637    */
2638   @Override
2639   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2640   {
2641     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2642
2643     SequenceI[] seqs;
2644     if (viewport.getSelectionGroup() != null)
2645     {
2646       seqs = viewport.getSelectionGroup()
2647               .getSequencesAsArray(viewport.getHiddenRepSequences());
2648       start = viewport.getSelectionGroup().getStartRes();
2649       end = viewport.getSelectionGroup().getEndRes();
2650     }
2651     else
2652     {
2653       seqs = viewport.getAlignment().getSequencesArray();
2654     }
2655
2656     // This is to maintain viewport position on first residue
2657     // of first sequence
2658     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2659     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2660
2661     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2662             viewport.getAlignment()));
2663
2664     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2665
2666     viewport.firePropertyChange("alignment", null,
2667             viewport.getAlignment().getSequences());
2668
2669   }
2670
2671   /**
2672    * DOCUMENT ME!
2673    *
2674    * @param e
2675    *          DOCUMENT ME!
2676    */
2677   @Override
2678   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2679   {
2680     viewport.setPadGaps(padGapsMenuitem.isSelected());
2681     viewport.firePropertyChange("alignment", null,
2682             viewport.getAlignment().getSequences());
2683   }
2684
2685   /**
2686    * DOCUMENT ME!
2687    *
2688    * @param e
2689    *          DOCUMENT ME!
2690    */
2691   @Override
2692   public void findMenuItem_actionPerformed(ActionEvent e)
2693   {
2694     new Finder();
2695   }
2696
2697   /**
2698    * Create a new view of the current alignment.
2699    */
2700   @Override
2701   public void newView_actionPerformed(ActionEvent e)
2702   {
2703     newView(null, true);
2704   }
2705
2706   /**
2707    * Creates and shows a new view of the current alignment.
2708    *
2709    * @param viewTitle
2710    *          title of newly created view; if null, one will be generated
2711    * @param copyAnnotation
2712    *          if true then duplicate all annnotation, groups and settings
2713    * @return new alignment panel, already displayed.
2714    */
2715   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2716   {
2717     /*
2718      * Create a new AlignmentPanel (with its own, new Viewport)
2719      */
2720     AlignmentPanel newap = new jalview.project.Jalview2XML()
2721             .copyAlignPanel(alignPanel);
2722     if (!copyAnnotation)
2723     {
2724       /*
2725        * remove all groups and annotation except for the automatic stuff
2726        */
2727       newap.av.getAlignment().deleteAllGroups();
2728       newap.av.getAlignment().deleteAllAnnotations(false);
2729     }
2730
2731     newap.av.setGatherViewsHere(false);
2732
2733     if (viewport.getViewName() == null)
2734     {
2735       viewport.setViewName(MessageManager
2736               .getString("label.view_name_original"));
2737     }
2738
2739     /*
2740      * Views share the same edits undo and redo stacks
2741      */
2742     newap.av.setHistoryList(viewport.getHistoryList());
2743     newap.av.setRedoList(viewport.getRedoList());
2744
2745     /*
2746      * copy any visualisation settings that are not saved in the project
2747      */
2748     newap.av.setColourAppliesToAllGroups(
2749             viewport.getColourAppliesToAllGroups());
2750
2751     /*
2752      * Views share the same mappings; need to deregister any new mappings
2753      * created by copyAlignPanel, and register the new reference to the shared
2754      * mappings
2755      */
2756     newap.av.replaceMappings(viewport.getAlignment());
2757
2758     /*
2759      * start up cDNA consensus (if applicable) now mappings are in place
2760      */
2761     if (newap.av.initComplementConsensus())
2762     {
2763       newap.refresh(true); // adjust layout of annotations
2764     }
2765
2766     newap.av.setViewName(getNewViewName(viewTitle));
2767
2768     addAlignmentPanel(newap, true);
2769     newap.alignmentChanged();
2770
2771     if (alignPanels.size() == 2)
2772     {
2773       viewport.setGatherViewsHere(true);
2774     }
2775     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2776     return newap;
2777   }
2778
2779   /**
2780    * Make a new name for the view, ensuring it is unique within the current
2781    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2782    * these now use viewId. Unique view names are still desirable for usability.)
2783    *
2784    * @param viewTitle
2785    * @return
2786    */
2787   protected String getNewViewName(String viewTitle)
2788   {
2789     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2790     boolean addFirstIndex = false;
2791     if (viewTitle == null || viewTitle.trim().length() == 0)
2792     {
2793       viewTitle = MessageManager.getString("action.view");
2794       addFirstIndex = true;
2795     }
2796     else
2797     {
2798       index = 1;// we count from 1 if given a specific name
2799     }
2800     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2801
2802     List<Component> comps = PaintRefresher.components
2803             .get(viewport.getSequenceSetId());
2804
2805     List<String> existingNames = getExistingViewNames(comps);
2806
2807     while (existingNames.contains(newViewName))
2808     {
2809       newViewName = viewTitle + " " + (++index);
2810     }
2811     return newViewName;
2812   }
2813
2814   /**
2815    * Returns a list of distinct view names found in the given list of
2816    * components. View names are held on the viewport of an AlignmentPanel.
2817    *
2818    * @param comps
2819    * @return
2820    */
2821   protected List<String> getExistingViewNames(List<Component> comps)
2822   {
2823     List<String> existingNames = new ArrayList<>();
2824     for (Component comp : comps)
2825     {
2826       if (comp instanceof AlignmentPanel)
2827       {
2828         AlignmentPanel ap = (AlignmentPanel) comp;
2829         if (!existingNames.contains(ap.av.getViewName()))
2830         {
2831           existingNames.add(ap.av.getViewName());
2832         }
2833       }
2834     }
2835     return existingNames;
2836   }
2837
2838   /**
2839    * Explode tabbed views into separate windows.
2840    */
2841   @Override
2842   public void expandViews_actionPerformed(ActionEvent e)
2843   {
2844     Desktop.explodeViews(this);
2845   }
2846
2847   /**
2848    * Gather views in separate windows back into a tabbed presentation.
2849    */
2850   @Override
2851   public void gatherViews_actionPerformed(ActionEvent e)
2852   {
2853     Desktop.instance.gatherViews(this);
2854   }
2855
2856   /**
2857    * DOCUMENT ME!
2858    *
2859    * @param e
2860    *          DOCUMENT ME!
2861    */
2862   @Override
2863   public void font_actionPerformed(ActionEvent e)
2864   {
2865     new FontChooser(alignPanel);
2866   }
2867
2868   /**
2869    * DOCUMENT ME!
2870    *
2871    * @param e
2872    *          DOCUMENT ME!
2873    */
2874   @Override
2875   protected void seqLimit_actionPerformed(ActionEvent e)
2876   {
2877     viewport.setShowJVSuffix(seqLimits.isSelected());
2878
2879     alignPanel.getIdPanel().getIdCanvas()
2880             .setPreferredSize(alignPanel.calculateIdWidth());
2881     alignPanel.paintAlignment(true, false);
2882   }
2883
2884   @Override
2885   public void idRightAlign_actionPerformed(ActionEvent e)
2886   {
2887     viewport.setRightAlignIds(idRightAlign.isSelected());
2888     alignPanel.paintAlignment(false, false);
2889   }
2890
2891   @Override
2892   public void centreColumnLabels_actionPerformed(ActionEvent e)
2893   {
2894     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2895     alignPanel.paintAlignment(false, false);
2896   }
2897
2898   /*
2899    * (non-Javadoc)
2900    *
2901    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2902    */
2903   @Override
2904   protected void followHighlight_actionPerformed()
2905   {
2906     /*
2907      * Set the 'follow' flag on the Viewport (and scroll to position if now
2908      * true).
2909      */
2910     final boolean state = this.followHighlightMenuItem.getState();
2911     viewport.setFollowHighlight(state);
2912     if (state)
2913     {
2914       alignPanel.scrollToPosition(viewport.getSearchResults());
2915     }
2916   }
2917
2918   /**
2919    * DOCUMENT ME!
2920    *
2921    * @param e
2922    *          DOCUMENT ME!
2923    */
2924   @Override
2925   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2926   {
2927     viewport.setColourText(colourTextMenuItem.isSelected());
2928     alignPanel.paintAlignment(false, false);
2929   }
2930
2931   /**
2932    * DOCUMENT ME!
2933    *
2934    * @param e
2935    *          DOCUMENT ME!
2936    */
2937   @Override
2938   public void wrapMenuItem_actionPerformed(ActionEvent e)
2939   {
2940     scaleAbove.setVisible(wrapMenuItem.isSelected());
2941     scaleLeft.setVisible(wrapMenuItem.isSelected());
2942     scaleRight.setVisible(wrapMenuItem.isSelected());
2943     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2944     alignPanel.updateLayout();
2945   }
2946
2947   @Override
2948   public void showAllSeqs_actionPerformed(ActionEvent e)
2949   {
2950     viewport.showAllHiddenSeqs();
2951   }
2952
2953   @Override
2954   public void showAllColumns_actionPerformed(ActionEvent e)
2955   {
2956     viewport.showAllHiddenColumns();
2957     alignPanel.paintAlignment(true, true);
2958     viewport.sendSelection();
2959   }
2960
2961   @Override
2962   public void hideSelSequences_actionPerformed(ActionEvent e)
2963   {
2964     viewport.hideAllSelectedSeqs();
2965   }
2966
2967   /**
2968    * called by key handler and the hide all/show all menu items
2969    *
2970    * @param toggleSeqs
2971    * @param toggleCols
2972    */
2973   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2974   {
2975
2976     boolean hide = false;
2977     SequenceGroup sg = viewport.getSelectionGroup();
2978     if (!toggleSeqs && !toggleCols)
2979     {
2980       // Hide everything by the current selection - this is a hack - we do the
2981       // invert and then hide
2982       // first check that there will be visible columns after the invert.
2983       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2984               && sg.getStartRes() <= sg.getEndRes()))
2985       {
2986         // now invert the sequence set, if required - empty selection implies
2987         // that no hiding is required.
2988         if (sg != null)
2989         {
2990           invertSequenceMenuItem_actionPerformed(null);
2991           sg = viewport.getSelectionGroup();
2992           toggleSeqs = true;
2993
2994         }
2995         viewport.expandColSelection(sg, true);
2996         // finally invert the column selection and get the new sequence
2997         // selection.
2998         invertColSel_actionPerformed(null);
2999         toggleCols = true;
3000       }
3001     }
3002
3003     if (toggleSeqs)
3004     {
3005       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3006       {
3007         hideSelSequences_actionPerformed(null);
3008         hide = true;
3009       }
3010       else if (!(toggleCols && viewport.hasSelectedColumns()))
3011       {
3012         showAllSeqs_actionPerformed(null);
3013       }
3014     }
3015
3016     if (toggleCols)
3017     {
3018       if (viewport.hasSelectedColumns())
3019       {
3020         hideSelColumns_actionPerformed(null);
3021         if (!toggleSeqs)
3022         {
3023           viewport.setSelectionGroup(sg);
3024         }
3025       }
3026       else if (!hide)
3027       {
3028         showAllColumns_actionPerformed(null);
3029       }
3030     }
3031   }
3032
3033   /*
3034    * (non-Javadoc)
3035    *
3036    * @see
3037    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3038    * event.ActionEvent)
3039    */
3040   @Override
3041   public void hideAllButSelection_actionPerformed(ActionEvent e)
3042   {
3043     toggleHiddenRegions(false, false);
3044     viewport.sendSelection();
3045   }
3046
3047   /*
3048    * (non-Javadoc)
3049    *
3050    * @see
3051    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3052    * .ActionEvent)
3053    */
3054   @Override
3055   public void hideAllSelection_actionPerformed(ActionEvent e)
3056   {
3057     SequenceGroup sg = viewport.getSelectionGroup();
3058     viewport.expandColSelection(sg, false);
3059     viewport.hideAllSelectedSeqs();
3060     viewport.hideSelectedColumns();
3061     alignPanel.updateLayout();
3062     alignPanel.paintAlignment(true, true);
3063     viewport.sendSelection();
3064   }
3065
3066   /*
3067    * (non-Javadoc)
3068    *
3069    * @see
3070    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3071    * ActionEvent)
3072    */
3073   @Override
3074   public void showAllhidden_actionPerformed(ActionEvent e)
3075   {
3076     viewport.showAllHiddenColumns();
3077     viewport.showAllHiddenSeqs();
3078     alignPanel.paintAlignment(true, true);
3079     viewport.sendSelection();
3080   }
3081
3082   @Override
3083   public void hideSelColumns_actionPerformed(ActionEvent e)
3084   {
3085     viewport.hideSelectedColumns();
3086     alignPanel.updateLayout();
3087     alignPanel.paintAlignment(true, true);
3088     viewport.sendSelection();
3089   }
3090
3091   @Override
3092   public void hiddenMarkers_actionPerformed(ActionEvent e)
3093   {
3094     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3095     repaint();
3096   }
3097
3098   /**
3099    * DOCUMENT ME!
3100    *
3101    * @param e
3102    *          DOCUMENT ME!
3103    */
3104   @Override
3105   protected void scaleAbove_actionPerformed(ActionEvent e)
3106   {
3107     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3108     alignPanel.updateLayout();
3109     alignPanel.paintAlignment(true, false);
3110   }
3111
3112   /**
3113    * DOCUMENT ME!
3114    *
3115    * @param e
3116    *          DOCUMENT ME!
3117    */
3118   @Override
3119   protected void scaleLeft_actionPerformed(ActionEvent e)
3120   {
3121     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3122     alignPanel.updateLayout();
3123     alignPanel.paintAlignment(true, false);
3124   }
3125
3126   /**
3127    * DOCUMENT ME!
3128    *
3129    * @param e
3130    *          DOCUMENT ME!
3131    */
3132   @Override
3133   protected void scaleRight_actionPerformed(ActionEvent e)
3134   {
3135     viewport.setScaleRightWrapped(scaleRight.isSelected());
3136     alignPanel.updateLayout();
3137     alignPanel.paintAlignment(true, false);
3138   }
3139
3140   /**
3141    * DOCUMENT ME!
3142    *
3143    * @param e
3144    *          DOCUMENT ME!
3145    */
3146   @Override
3147   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3148   {
3149     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3150     alignPanel.paintAlignment(false, false);
3151   }
3152
3153   /**
3154    * DOCUMENT ME!
3155    *
3156    * @param e
3157    *          DOCUMENT ME!
3158    */
3159   @Override
3160   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3161   {
3162     viewport.setShowText(viewTextMenuItem.isSelected());
3163     alignPanel.paintAlignment(false, false);
3164   }
3165
3166   /**
3167    * DOCUMENT ME!
3168    *
3169    * @param e
3170    *          DOCUMENT ME!
3171    */
3172   @Override
3173   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3174   {
3175     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3176     alignPanel.paintAlignment(false, false);
3177   }
3178
3179   public FeatureSettings featureSettings;
3180
3181   @Override
3182   public FeatureSettingsControllerI getFeatureSettingsUI()
3183   {
3184     return featureSettings;
3185   }
3186
3187   @Override
3188   public void featureSettings_actionPerformed(ActionEvent e)
3189   {
3190     showFeatureSettingsUI();
3191   }
3192
3193   @Override
3194   public FeatureSettingsControllerI showFeatureSettingsUI()
3195   {
3196     if (featureSettings != null)
3197     {
3198       featureSettings.closeOldSettings();
3199       featureSettings = null;
3200     }
3201     if (!showSeqFeatures.isSelected())
3202     {
3203       // make sure features are actually displayed
3204       showSeqFeatures.setSelected(true);
3205       showSeqFeatures_actionPerformed(null);
3206     }
3207     featureSettings = new FeatureSettings(this);
3208     return featureSettings;
3209   }
3210
3211   /**
3212    * Set or clear 'Show Sequence Features'
3213    *
3214    * @param evt
3215    *          DOCUMENT ME!
3216    */
3217   @Override
3218   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3219   {
3220     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3221     alignPanel.paintAlignment(true, true);
3222   }
3223
3224   /**
3225    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3226    * the annotations panel as a whole.
3227    *
3228    * The options to show/hide all annotations should be enabled when the panel
3229    * is shown, and disabled when the panel is hidden.
3230    *
3231    * @param e
3232    */
3233   @Override
3234   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3235   {
3236     final boolean setVisible = annotationPanelMenuItem.isSelected();
3237     viewport.setShowAnnotation(setVisible);
3238     this.showAllSeqAnnotations.setEnabled(setVisible);
3239     this.hideAllSeqAnnotations.setEnabled(setVisible);
3240     this.showAllAlAnnotations.setEnabled(setVisible);
3241     this.hideAllAlAnnotations.setEnabled(setVisible);
3242     alignPanel.updateLayout();
3243   }
3244
3245   @Override
3246   public void alignmentProperties()
3247   {
3248     JEditorPane editPane = new JEditorPane("text/html", "");
3249     editPane.setEditable(false);
3250     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3251             .formatAsHtml();
3252     editPane.setText(
3253             MessageManager.formatMessage("label.html_content", new Object[]
3254             { contents.toString() }));
3255     JInternalFrame frame = new JInternalFrame();
3256     frame.getContentPane().add(new JScrollPane(editPane));
3257
3258     Desktop.addInternalFrame(frame, MessageManager
3259             .formatMessage("label.alignment_properties", new Object[]
3260             { getTitle() }), 500, 400);
3261   }
3262
3263   /**
3264    * DOCUMENT ME!
3265    *
3266    * @param e
3267    *          DOCUMENT ME!
3268    */
3269   @Override
3270   public void overviewMenuItem_actionPerformed(ActionEvent e)
3271   {
3272     if (alignPanel.overviewPanel != null)
3273     {
3274       return;
3275     }
3276
3277     JInternalFrame frame = new JInternalFrame();
3278     final OverviewPanel overview = new OverviewPanel(alignPanel);
3279     frame.setContentPane(overview);
3280     Desktop.addInternalFrame(frame, MessageManager
3281             .formatMessage("label.overview_params", new Object[]
3282             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3283             true, true);
3284     frame.pack();
3285     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3286     frame.addInternalFrameListener(
3287             new javax.swing.event.InternalFrameAdapter()
3288             {
3289               @Override
3290               public void internalFrameClosed(
3291                       javax.swing.event.InternalFrameEvent evt)
3292               {
3293                 overview.dispose();
3294                 alignPanel.setOverviewPanel(null);
3295               };
3296             });
3297     if (getKeyListeners().length > 0)
3298     {
3299       frame.addKeyListener(getKeyListeners()[0]);
3300     }
3301
3302     alignPanel.setOverviewPanel(overview);
3303   }
3304
3305   @Override
3306   public void textColour_actionPerformed()
3307   {
3308     new TextColourChooser().chooseColour(alignPanel, null);
3309   }
3310
3311   /*
3312    * public void covariationColour_actionPerformed() {
3313    * changeColour(new
3314    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3315    * ()[0])); }
3316    */
3317   @Override
3318   public void annotationColour_actionPerformed()
3319   {
3320     new AnnotationColourChooser(viewport, alignPanel);
3321   }
3322
3323   @Override
3324   public void annotationColumn_actionPerformed(ActionEvent e)
3325   {
3326     new AnnotationColumnChooser(viewport, alignPanel);
3327   }
3328
3329   /**
3330    * Action on the user checking or unchecking the option to apply the selected
3331    * colour scheme to all groups. If unchecked, groups may have their own
3332    * independent colour schemes.
3333    *
3334    * @param selected
3335    */
3336   @Override
3337   public void applyToAllGroups_actionPerformed(boolean selected)
3338   {
3339     viewport.setColourAppliesToAllGroups(selected);
3340   }
3341
3342   /**
3343    * Action on user selecting a colour from the colour menu
3344    *
3345    * @param name
3346    *          the name (not the menu item label!) of the colour scheme
3347    */
3348   @Override
3349   public void changeColour_actionPerformed(String name)
3350   {
3351     /*
3352      * 'User Defined' opens a panel to configure or load a
3353      * user-defined colour scheme
3354      */
3355     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3356     {
3357       new UserDefinedColours(alignPanel);
3358       return;
3359     }
3360
3361     /*
3362      * otherwise set the chosen colour scheme (or null for 'None')
3363      */
3364     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3365             viewport,
3366             viewport.getAlignment(), viewport.getHiddenRepSequences());
3367     changeColour(cs);
3368   }
3369
3370   /**
3371    * Actions on setting or changing the alignment colour scheme
3372    *
3373    * @param cs
3374    */
3375   @Override
3376   public void changeColour(ColourSchemeI cs)
3377   {
3378     // TODO: pull up to controller method
3379     ColourMenuHelper.setColourSelected(colourMenu, cs);
3380
3381     viewport.setGlobalColourScheme(cs);
3382
3383     alignPanel.paintAlignment(true, true);
3384   }
3385
3386   /**
3387    * Show the PID threshold slider panel
3388    */
3389   @Override
3390   protected void modifyPID_actionPerformed()
3391   {
3392     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3393             alignPanel.getViewName());
3394     SliderPanel.showPIDSlider();
3395   }
3396
3397   /**
3398    * Show the Conservation slider panel
3399    */
3400   @Override
3401   protected void modifyConservation_actionPerformed()
3402   {
3403     SliderPanel.setConservationSlider(alignPanel,
3404             viewport.getResidueShading(), alignPanel.getViewName());
3405     SliderPanel.showConservationSlider();
3406   }
3407
3408   /**
3409    * Action on selecting or deselecting (Colour) By Conservation
3410    */
3411   @Override
3412   public void conservationMenuItem_actionPerformed(boolean selected)
3413   {
3414     modifyConservation.setEnabled(selected);
3415     viewport.setConservationSelected(selected);
3416     viewport.getResidueShading().setConservationApplied(selected);
3417
3418     changeColour(viewport.getGlobalColourScheme());
3419     if (selected)
3420     {
3421       modifyConservation_actionPerformed();
3422     }
3423     else
3424     {
3425       SliderPanel.hideConservationSlider();
3426     }
3427   }
3428
3429   /**
3430    * Action on selecting or deselecting (Colour) Above PID Threshold
3431    */
3432   @Override
3433   public void abovePIDThreshold_actionPerformed(boolean selected)
3434   {
3435     modifyPID.setEnabled(selected);
3436     viewport.setAbovePIDThreshold(selected);
3437     if (!selected)
3438     {
3439       viewport.getResidueShading().setThreshold(0,
3440               viewport.isIgnoreGapsConsensus());
3441     }
3442
3443     changeColour(viewport.getGlobalColourScheme());
3444     if (selected)
3445     {
3446       modifyPID_actionPerformed();
3447     }
3448     else
3449     {
3450       SliderPanel.hidePIDSlider();
3451     }
3452   }
3453
3454   /**
3455    * DOCUMENT ME!
3456    *
3457    * @param e
3458    *          DOCUMENT ME!
3459    */
3460   @Override
3461   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3462   {
3463     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3464     AlignmentSorter.sortByPID(viewport.getAlignment(),
3465             viewport.getAlignment().getSequenceAt(0));
3466     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3467             viewport.getAlignment()));
3468     alignPanel.paintAlignment(true, false);
3469   }
3470
3471   /**
3472    * DOCUMENT ME!
3473    *
3474    * @param e
3475    *          DOCUMENT ME!
3476    */
3477   @Override
3478   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3479   {
3480     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3481     AlignmentSorter.sortByID(viewport.getAlignment());
3482     addHistoryItem(
3483             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3484     alignPanel.paintAlignment(true, false);
3485   }
3486
3487   /**
3488    * DOCUMENT ME!
3489    *
3490    * @param e
3491    *          DOCUMENT ME!
3492    */
3493   @Override
3494   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3495   {
3496     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3497     AlignmentSorter.sortByLength(viewport.getAlignment());
3498     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3499             viewport.getAlignment()));
3500     alignPanel.paintAlignment(true, false);
3501   }
3502
3503   /**
3504    * DOCUMENT ME!
3505    *
3506    * @param e
3507    *          DOCUMENT ME!
3508    */
3509   @Override
3510   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3511   {
3512     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3513     AlignmentSorter.sortByGroup(viewport.getAlignment());
3514     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3515             viewport.getAlignment()));
3516
3517     alignPanel.paintAlignment(true, false);
3518   }
3519
3520   /**
3521    * DOCUMENT ME!
3522    *
3523    * @param e
3524    *          DOCUMENT ME!
3525    */
3526   @Override
3527   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3528   {
3529     new RedundancyPanel(alignPanel, this);
3530   }
3531
3532   /**
3533    * DOCUMENT ME!
3534    *
3535    * @param e
3536    *          DOCUMENT ME!
3537    */
3538   @Override
3539   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3540   {
3541     if ((viewport.getSelectionGroup() == null)
3542             || (viewport.getSelectionGroup().getSize() < 2))
3543     {
3544       JvOptionPane.showInternalMessageDialog(this,
3545               MessageManager.getString(
3546                       "label.you_must_select_least_two_sequences"),
3547               MessageManager.getString("label.invalid_selection"),
3548               JvOptionPane.WARNING_MESSAGE);
3549     }
3550     else
3551     {
3552       JInternalFrame frame = new JInternalFrame();
3553       frame.setContentPane(new PairwiseAlignPanel(viewport));
3554       Desktop.addInternalFrame(frame,
3555               MessageManager.getString("action.pairwise_alignment"), 600,
3556               500);
3557     }
3558   }
3559
3560   @Override
3561   public void autoCalculate_actionPerformed(ActionEvent e)
3562   {
3563     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3564     if (viewport.autoCalculateConsensus)
3565     {
3566       viewport.firePropertyChange("alignment", null,
3567               viewport.getAlignment().getSequences());
3568     }
3569   }
3570
3571   @Override
3572   public void sortByTreeOption_actionPerformed(ActionEvent e)
3573   {
3574     viewport.sortByTree = sortByTree.isSelected();
3575   }
3576
3577   @Override
3578   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3579   {
3580     viewport.followSelection = listenToViewSelections.isSelected();
3581   }
3582
3583   /**
3584    * Constructs a tree panel and adds it to the desktop
3585    *
3586    * @param type
3587    *          tree type (NJ or AV)
3588    * @param modelName
3589    *          name of score model used to compute the tree
3590    * @param options
3591    *          parameters for the distance or similarity calculation
3592    */
3593   void newTreePanel(String type, String modelName,
3594           SimilarityParamsI options)
3595   {
3596     String frameTitle = "";
3597     TreePanel tp;
3598
3599     boolean onSelection = false;
3600     if (viewport.getSelectionGroup() != null
3601             && viewport.getSelectionGroup().getSize() > 0)
3602     {
3603       SequenceGroup sg = viewport.getSelectionGroup();
3604
3605       /* Decide if the selection is a column region */
3606       for (SequenceI _s : sg.getSequences())
3607       {
3608         if (_s.getLength() < sg.getEndRes())
3609         {
3610           JvOptionPane.showMessageDialog(Desktop.desktop,
3611                   MessageManager.getString(
3612                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3613                   MessageManager.getString(
3614                           "label.sequences_selection_not_aligned"),
3615                   JvOptionPane.WARNING_MESSAGE);
3616
3617           return;
3618         }
3619       }
3620       onSelection = true;
3621     }
3622     else
3623     {
3624       if (viewport.getAlignment().getHeight() < 2)
3625       {
3626         return;
3627       }
3628     }
3629
3630     tp = new TreePanel(alignPanel, type, modelName, options);
3631     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3632
3633     frameTitle += " from ";
3634
3635     if (viewport.getViewName() != null)
3636     {
3637       frameTitle += viewport.getViewName() + " of ";
3638     }
3639
3640     frameTitle += this.title;
3641
3642     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3643   }
3644
3645   /**
3646    * DOCUMENT ME!
3647    *
3648    * @param title
3649    *          DOCUMENT ME!
3650    * @param order
3651    *          DOCUMENT ME!
3652    */
3653   public void addSortByOrderMenuItem(String title,
3654           final AlignmentOrder order)
3655   {
3656     final JMenuItem item = new JMenuItem(MessageManager
3657             .formatMessage("action.by_title_param", new Object[]
3658             { title }));
3659     sort.add(item);
3660     item.addActionListener(new java.awt.event.ActionListener()
3661     {
3662       @Override
3663       public void actionPerformed(ActionEvent e)
3664       {
3665         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3666
3667         // TODO: JBPNote - have to map order entries to curent SequenceI
3668         // pointers
3669         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3670
3671         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3672                 viewport.getAlignment()));
3673
3674         alignPanel.paintAlignment(true, false);
3675       }
3676     });
3677   }
3678
3679   /**
3680    * Add a new sort by annotation score menu item
3681    *
3682    * @param sort
3683    *          the menu to add the option to
3684    * @param scoreLabel
3685    *          the label used to retrieve scores for each sequence on the
3686    *          alignment
3687    */
3688   public void addSortByAnnotScoreMenuItem(JMenu sort,
3689           final String scoreLabel)
3690   {
3691     final JMenuItem item = new JMenuItem(scoreLabel);
3692     sort.add(item);
3693     item.addActionListener(new java.awt.event.ActionListener()
3694     {
3695       @Override
3696       public void actionPerformed(ActionEvent e)
3697       {
3698         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3699         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3700                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3701         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3702                 viewport.getAlignment()));
3703         alignPanel.paintAlignment(true, false);
3704       }
3705     });
3706   }
3707
3708   /**
3709    * last hash for alignment's annotation array - used to minimise cost of
3710    * rebuild.
3711    */
3712   protected int _annotationScoreVectorHash;
3713
3714   /**
3715    * search the alignment and rebuild the sort by annotation score submenu the
3716    * last alignment annotation vector hash is stored to minimize cost of
3717    * rebuilding in subsequence calls.
3718    *
3719    */
3720   @Override
3721   public void buildSortByAnnotationScoresMenu()
3722   {
3723     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3724     {
3725       return;
3726     }
3727
3728     if (viewport.getAlignment().getAlignmentAnnotation()
3729             .hashCode() != _annotationScoreVectorHash)
3730     {
3731       sortByAnnotScore.removeAll();
3732       // almost certainly a quicker way to do this - but we keep it simple
3733       Hashtable scoreSorts = new Hashtable();
3734       AlignmentAnnotation aann[];
3735       for (SequenceI sqa : viewport.getAlignment().getSequences())
3736       {
3737         aann = sqa.getAnnotation();
3738         for (int i = 0; aann != null && i < aann.length; i++)
3739         {
3740           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3741           {
3742             scoreSorts.put(aann[i].label, aann[i].label);
3743           }
3744         }
3745       }
3746       Enumeration labels = scoreSorts.keys();
3747       while (labels.hasMoreElements())
3748       {
3749         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3750                 (String) labels.nextElement());
3751       }
3752       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3753       scoreSorts.clear();
3754
3755       _annotationScoreVectorHash = viewport.getAlignment()
3756               .getAlignmentAnnotation().hashCode();
3757     }
3758   }
3759
3760   /**
3761    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3762    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3763    * call. Listeners are added to remove the menu item when the treePanel is
3764    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3765    * modified.
3766    */
3767   @Override
3768   public void buildTreeSortMenu()
3769   {
3770     sortByTreeMenu.removeAll();
3771
3772     List<Component> comps = PaintRefresher.components
3773             .get(viewport.getSequenceSetId());
3774     List<TreePanel> treePanels = new ArrayList<>();
3775     for (Component comp : comps)
3776     {
3777       if (comp instanceof TreePanel)
3778       {
3779         treePanels.add((TreePanel) comp);
3780       }
3781     }
3782
3783     if (treePanels.size() < 1)
3784     {
3785       sortByTreeMenu.setVisible(false);
3786       return;
3787     }
3788
3789     sortByTreeMenu.setVisible(true);
3790
3791     for (final TreePanel tp : treePanels)
3792     {
3793       final JMenuItem item = new JMenuItem(tp.getTitle());
3794       item.addActionListener(new java.awt.event.ActionListener()
3795       {
3796         @Override
3797         public void actionPerformed(ActionEvent e)
3798         {
3799           tp.sortByTree_actionPerformed();
3800           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3801
3802         }
3803       });
3804
3805       sortByTreeMenu.add(item);
3806     }
3807   }
3808
3809   public boolean sortBy(AlignmentOrder alorder, String undoname)
3810   {
3811     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3812     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3813     if (undoname != null)
3814     {
3815       addHistoryItem(new OrderCommand(undoname, oldOrder,
3816               viewport.getAlignment()));
3817     }
3818     alignPanel.paintAlignment(true, false);
3819     return true;
3820   }
3821
3822   /**
3823    * Work out whether the whole set of sequences or just the selected set will
3824    * be submitted for multiple alignment.
3825    *
3826    */
3827   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3828   {
3829     // Now, check we have enough sequences
3830     AlignmentView msa = null;
3831
3832     if ((viewport.getSelectionGroup() != null)
3833             && (viewport.getSelectionGroup().getSize() > 1))
3834     {
3835       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3836       // some common interface!
3837       /*
3838        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3839        * SequenceI[sz = seqs.getSize(false)];
3840        *
3841        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3842        * seqs.getSequenceAt(i); }
3843        */
3844       msa = viewport.getAlignmentView(true);
3845     }
3846     else if (viewport.getSelectionGroup() != null
3847             && viewport.getSelectionGroup().getSize() == 1)
3848     {
3849       int option = JvOptionPane.showConfirmDialog(this,
3850               MessageManager.getString("warn.oneseq_msainput_selection"),
3851               MessageManager.getString("label.invalid_selection"),
3852               JvOptionPane.OK_CANCEL_OPTION);
3853       if (option == JvOptionPane.OK_OPTION)
3854       {
3855         msa = viewport.getAlignmentView(false);
3856       }
3857     }
3858     else
3859     {
3860       msa = viewport.getAlignmentView(false);
3861     }
3862     return msa;
3863   }
3864
3865   /**
3866    * Decides what is submitted to a secondary structure prediction service: the
3867    * first sequence in the alignment, or in the current selection, or, if the
3868    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3869    * region or the whole alignment. (where the first sequence in the set is the
3870    * one that the prediction will be for).
3871    */
3872   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3873   {
3874     AlignmentView seqs = null;
3875
3876     if ((viewport.getSelectionGroup() != null)
3877             && (viewport.getSelectionGroup().getSize() > 0))
3878     {
3879       seqs = viewport.getAlignmentView(true);
3880     }
3881     else
3882     {
3883       seqs = viewport.getAlignmentView(false);
3884     }
3885     // limit sequences - JBPNote in future - could spawn multiple prediction
3886     // jobs
3887     // TODO: viewport.getAlignment().isAligned is a global state - the local
3888     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3889     if (!viewport.getAlignment().isAligned(false))
3890     {
3891       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3892       // TODO: if seqs.getSequences().length>1 then should really have warned
3893       // user!
3894
3895     }
3896     return seqs;
3897   }
3898
3899   /**
3900    * DOCUMENT ME!
3901    *
3902    * @param e
3903    *          DOCUMENT ME!
3904    */
3905   @Override
3906   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3907   {
3908     // Pick the tree file
3909     JalviewFileChooser chooser = new JalviewFileChooser(
3910             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3911     chooser.setFileView(new JalviewFileView());
3912     chooser.setDialogTitle(
3913             MessageManager.getString("label.select_newick_like_tree_file"));
3914     chooser.setToolTipText(
3915             MessageManager.getString("label.load_tree_file"));
3916
3917     int value = chooser.showOpenDialog(null);
3918
3919     if (value == JalviewFileChooser.APPROVE_OPTION)
3920     {
3921       String filePath = chooser.getSelectedFile().getPath();
3922       Cache.setProperty("LAST_DIRECTORY", filePath);
3923       NewickFile fin = null;
3924       try
3925       {
3926         fin = new NewickFile(filePath, DataSourceType.FILE);
3927         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3928       } catch (Exception ex)
3929       {
3930         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3931                 MessageManager.getString("label.problem_reading_tree_file"),
3932                 JvOptionPane.WARNING_MESSAGE);
3933         ex.printStackTrace();
3934       }
3935       if (fin != null && fin.hasWarningMessage())
3936       {
3937         JvOptionPane.showMessageDialog(Desktop.desktop,
3938                 fin.getWarningMessage(),
3939                 MessageManager
3940                         .getString("label.possible_problem_with_tree_file"),
3941                 JvOptionPane.WARNING_MESSAGE);
3942       }
3943     }
3944   }
3945
3946   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3947   {
3948     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3949   }
3950
3951   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3952           int h, int x, int y)
3953   {
3954     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3955   }
3956
3957   /**
3958    * Add a treeviewer for the tree extracted from a Newick file object to the
3959    * current alignment view
3960    *
3961    * @param nf
3962    *          the tree
3963    * @param title
3964    *          tree viewer title
3965    * @param input
3966    *          Associated alignment input data (or null)
3967    * @param w
3968    *          width
3969    * @param h
3970    *          height
3971    * @param x
3972    *          position
3973    * @param y
3974    *          position
3975    * @return TreePanel handle
3976    */
3977   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3978           AlignmentView input, int w, int h, int x, int y)
3979   {
3980     TreePanel tp = null;
3981
3982     try
3983     {
3984       nf.parse();
3985
3986       if (nf.getTree() != null)
3987       {
3988         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3989
3990         tp.setSize(w, h);
3991
3992         if (x > 0 && y > 0)
3993         {
3994           tp.setLocation(x, y);
3995         }
3996
3997         Desktop.addInternalFrame(tp, treeTitle, w, h);
3998       }
3999     } catch (Exception ex)
4000     {
4001       ex.printStackTrace();
4002     }
4003
4004     return tp;
4005   }
4006
4007   private boolean buildingMenu = false;
4008
4009   /**
4010    * Generates menu items and listener event actions for web service clients
4011    *
4012    */
4013   public void BuildWebServiceMenu()
4014   {
4015     while (buildingMenu)
4016     {
4017       try
4018       {
4019         System.err.println("Waiting for building menu to finish.");
4020         Thread.sleep(10);
4021       } catch (Exception e)
4022       {
4023       }
4024     }
4025     final AlignFrame me = this;
4026     buildingMenu = true;
4027     new Thread(new Runnable()
4028     {
4029       @Override
4030       public void run()
4031       {
4032         final List<JMenuItem> legacyItems = new ArrayList<>();
4033         try
4034         {
4035           // System.err.println("Building ws menu again "
4036           // + Thread.currentThread());
4037           // TODO: add support for context dependent disabling of services based
4038           // on
4039           // alignment and current selection
4040           // TODO: add additional serviceHandle parameter to specify abstract
4041           // handler
4042           // class independently of AbstractName
4043           // TODO: add in rediscovery GUI function to restart discoverer
4044           // TODO: group services by location as well as function and/or
4045           // introduce
4046           // object broker mechanism.
4047           final Vector<JMenu> wsmenu = new Vector<>();
4048           final IProgressIndicator af = me;
4049
4050           /*
4051            * do not i18n these strings - they are hard-coded in class
4052            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4053            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4054            */
4055           final JMenu msawsmenu = new JMenu("Alignment");
4056           final JMenu secstrmenu = new JMenu(
4057                   "Secondary Structure Prediction");
4058           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4059           final JMenu analymenu = new JMenu("Analysis");
4060           final JMenu dismenu = new JMenu("Protein Disorder");
4061           // JAL-940 - only show secondary structure prediction services from
4062           // the legacy server
4063           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4064               // &&
4065           Discoverer.services != null && (Discoverer.services.size() > 0))
4066           {
4067             // TODO: refactor to allow list of AbstractName/Handler bindings to
4068             // be
4069             // stored or retrieved from elsewhere
4070             // No MSAWS used any more:
4071             // Vector msaws = null; // (Vector)
4072             // Discoverer.services.get("MsaWS");
4073             Vector secstrpr = (Vector) Discoverer.services
4074                     .get("SecStrPred");
4075             if (secstrpr != null)
4076             {
4077               // Add any secondary structure prediction services
4078               for (int i = 0, j = secstrpr.size(); i < j; i++)
4079               {
4080                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4081                         .get(i);
4082                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4083                         .getServiceClient(sh);
4084                 int p = secstrmenu.getItemCount();
4085                 impl.attachWSMenuEntry(secstrmenu, me);
4086                 int q = secstrmenu.getItemCount();
4087                 for (int litm = p; litm < q; litm++)
4088                 {
4089                   legacyItems.add(secstrmenu.getItem(litm));
4090                 }
4091               }
4092             }
4093           }
4094
4095           // Add all submenus in the order they should appear on the web
4096           // services menu
4097           wsmenu.add(msawsmenu);
4098           wsmenu.add(secstrmenu);
4099           wsmenu.add(dismenu);
4100           wsmenu.add(analymenu);
4101           // No search services yet
4102           // wsmenu.add(seqsrchmenu);
4103
4104           javax.swing.SwingUtilities.invokeLater(new Runnable()
4105           {
4106             @Override
4107             public void run()
4108             {
4109               try
4110               {
4111                 webService.removeAll();
4112                 // first, add discovered services onto the webservices menu
4113                 if (wsmenu.size() > 0)
4114                 {
4115                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4116                   {
4117                     webService.add(wsmenu.get(i));
4118                   }
4119                 }
4120                 else
4121                 {
4122                   webService.add(me.webServiceNoServices);
4123                 }
4124                 // TODO: move into separate menu builder class.
4125                 boolean new_sspred = false;
4126                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4127                 {
4128                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4129                   if (jws2servs != null)
4130                   {
4131                     if (jws2servs.hasServices())
4132                     {
4133                       jws2servs.attachWSMenuEntry(webService, me);
4134                       for (Jws2Instance sv : jws2servs.getServices())
4135                       {
4136                         if (sv.description.toLowerCase().contains("jpred"))
4137                         {
4138                           for (JMenuItem jmi : legacyItems)
4139                           {
4140                             jmi.setVisible(false);
4141                           }
4142                         }
4143                       }
4144
4145                     }
4146                     if (jws2servs.isRunning())
4147                     {
4148                       JMenuItem tm = new JMenuItem(
4149                               "Still discovering JABA Services");
4150                       tm.setEnabled(false);
4151                       webService.add(tm);
4152                     }
4153                   }
4154                 }
4155                 build_urlServiceMenu(me.webService);
4156                 build_fetchdbmenu(webService);
4157                 for (JMenu item : wsmenu)
4158                 {
4159                   if (item.getItemCount() == 0)
4160                   {
4161                     item.setEnabled(false);
4162                   }
4163                   else
4164                   {
4165                     item.setEnabled(true);
4166                   }
4167                 }
4168               } catch (Exception e)
4169               {
4170                 Cache.log.debug(
4171                         "Exception during web service menu building process.",
4172                         e);
4173               }
4174             }
4175           });
4176         } catch (Exception e)
4177         {
4178         }
4179         buildingMenu = false;
4180       }
4181     }).start();
4182
4183   }
4184
4185   /**
4186    * construct any groupURL type service menu entries.
4187    *
4188    * @param webService
4189    */
4190   private void build_urlServiceMenu(JMenu webService)
4191   {
4192     // TODO: remove this code when 2.7 is released
4193     // DEBUG - alignmentView
4194     /*
4195      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4196      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4197      *
4198      * @Override public void actionPerformed(ActionEvent e) {
4199      * jalview.datamodel.AlignmentView
4200      * .testSelectionViews(af.viewport.getAlignment(),
4201      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4202      *
4203      * }); webService.add(testAlView);
4204      */
4205     // TODO: refactor to RestClient discoverer and merge menu entries for
4206     // rest-style services with other types of analysis/calculation service
4207     // SHmmr test client - still being implemented.
4208     // DEBUG - alignmentView
4209
4210     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4211             .getRestClients())
4212     {
4213       client.attachWSMenuEntry(
4214               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4215               this);
4216     }
4217   }
4218
4219   /**
4220    * Searches the alignment sequences for xRefs and builds the Show
4221    * Cross-References menu (formerly called Show Products), with database
4222    * sources for which cross-references are found (protein sources for a
4223    * nucleotide alignment and vice versa)
4224    *
4225    * @return true if Show Cross-references menu should be enabled
4226    */
4227   public boolean canShowProducts()
4228   {
4229     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4230     AlignmentI dataset = viewport.getAlignment().getDataset();
4231
4232     showProducts.removeAll();
4233     final boolean dna = viewport.getAlignment().isNucleotide();
4234
4235     if (seqs == null || seqs.length == 0)
4236     {
4237       // nothing to see here.
4238       return false;
4239     }
4240
4241     boolean showp = false;
4242     try
4243     {
4244       List<String> ptypes = new CrossRef(seqs, dataset)
4245               .findXrefSourcesForSequences(dna);
4246
4247       for (final String source : ptypes)
4248       {
4249         showp = true;
4250         final AlignFrame af = this;
4251         JMenuItem xtype = new JMenuItem(source);
4252         xtype.addActionListener(new ActionListener()
4253         {
4254           @Override
4255           public void actionPerformed(ActionEvent e)
4256           {
4257             showProductsFor(af.viewport.getSequenceSelection(), dna,
4258                     source);
4259           }
4260         });
4261         showProducts.add(xtype);
4262       }
4263       showProducts.setVisible(showp);
4264       showProducts.setEnabled(showp);
4265     } catch (Exception e)
4266     {
4267       Cache.log.warn(
4268               "canShowProducts threw an exception - please report to help@jalview.org",
4269               e);
4270       return false;
4271     }
4272     return showp;
4273   }
4274
4275   /**
4276    * Finds and displays cross-references for the selected sequences (protein
4277    * products for nucleotide sequences, dna coding sequences for peptides).
4278    *
4279    * @param sel
4280    *          the sequences to show cross-references for
4281    * @param dna
4282    *          true if from a nucleotide alignment (so showing proteins)
4283    * @param source
4284    *          the database to show cross-references for
4285    */
4286   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4287           final String source)
4288   {
4289     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4290             .start();
4291   }
4292
4293   /**
4294    * Construct and display a new frame containing the translation of this
4295    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4296    */
4297   @Override
4298   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4299   {
4300     AlignmentI al = null;
4301     try
4302     {
4303       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4304
4305       al = dna.translateCdna(codeTable);
4306     } catch (Exception ex)
4307     {
4308       jalview.bin.Cache.log.error(
4309               "Exception during translation. Please report this !", ex);
4310       final String msg = MessageManager.getString(
4311               "label.error_when_translating_sequences_submit_bug_report");
4312       final String errorTitle = MessageManager
4313               .getString("label.implementation_error")
4314               + MessageManager.getString("label.translation_failed");
4315       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4316               JvOptionPane.ERROR_MESSAGE);
4317       return;
4318     }
4319     if (al == null || al.getHeight() == 0)
4320     {
4321       final String msg = MessageManager.getString(
4322               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4323       final String errorTitle = MessageManager
4324               .getString("label.translation_failed");
4325       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4326               JvOptionPane.WARNING_MESSAGE);
4327     }
4328     else
4329     {
4330       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4331       af.setFileFormat(this.currentFileFormat);
4332       final String newTitle = MessageManager
4333               .formatMessage("label.translation_of_params", new Object[]
4334               { this.getTitle(), codeTable.getId() });
4335       af.setTitle(newTitle);
4336       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4337       {
4338         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4339         viewport.openSplitFrame(af, new Alignment(seqs));
4340       }
4341       else
4342       {
4343         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4344                 DEFAULT_HEIGHT);
4345       }
4346     }
4347   }
4348
4349   /**
4350    * Set the file format
4351    *
4352    * @param format
4353    */
4354   public void setFileFormat(FileFormatI format)
4355   {
4356     this.currentFileFormat = format;
4357   }
4358
4359   /**
4360    * Try to load a features file onto the alignment.
4361    *
4362    * @param file
4363    *          contents or path to retrieve file
4364    * @param sourceType
4365    *          access mode of file (see jalview.io.AlignFile)
4366    * @return true if features file was parsed correctly.
4367    */
4368   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4369   {
4370     return avc.parseFeaturesFile(file, sourceType,
4371             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4372
4373   }
4374
4375   @Override
4376   public void refreshFeatureUI(boolean enableIfNecessary)
4377   {
4378     // note - currently this is only still here rather than in the controller
4379     // because of the featureSettings hard reference that is yet to be
4380     // abstracted
4381     if (enableIfNecessary)
4382     {
4383       viewport.setShowSequenceFeatures(true);
4384       showSeqFeatures.setSelected(true);
4385     }
4386
4387   }
4388
4389   @Override
4390   public void dragEnter(DropTargetDragEvent evt)
4391   {
4392   }
4393
4394   @Override
4395   public void dragExit(DropTargetEvent evt)
4396   {
4397   }
4398
4399   @Override
4400   public void dragOver(DropTargetDragEvent evt)
4401   {
4402   }
4403
4404   @Override
4405   public void dropActionChanged(DropTargetDragEvent evt)
4406   {
4407   }
4408
4409   @Override
4410   public void drop(DropTargetDropEvent evt)
4411   {
4412     // JAL-1552 - acceptDrop required before getTransferable call for
4413     // Java's Transferable for native dnd
4414     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4415     Transferable t = evt.getTransferable();
4416     final AlignFrame thisaf = this;
4417     final List<String> files = new ArrayList<>();
4418     List<DataSourceType> protocols = new ArrayList<>();
4419
4420     try
4421     {
4422       Desktop.transferFromDropTarget(files, protocols, evt, t);
4423     } catch (Exception e)
4424     {
4425       e.printStackTrace();
4426     }
4427     if (files != null)
4428     {
4429       new Thread(new Runnable()
4430       {
4431         @Override
4432         public void run()
4433         {
4434           try
4435           {
4436             // check to see if any of these files have names matching sequences
4437             // in
4438             // the alignment
4439             SequenceIdMatcher idm = new SequenceIdMatcher(
4440                     viewport.getAlignment().getSequencesArray());
4441             /**
4442              * Object[] { String,SequenceI}
4443              */
4444             ArrayList<Object[]> filesmatched = new ArrayList<>();
4445             ArrayList<String> filesnotmatched = new ArrayList<>();
4446             for (int i = 0; i < files.size(); i++)
4447             {
4448               String file = files.get(i).toString();
4449               String pdbfn = "";
4450               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4451               if (protocol == DataSourceType.FILE)
4452               {
4453                 File fl = new File(file);
4454                 pdbfn = fl.getName();
4455               }
4456               else if (protocol == DataSourceType.URL)
4457               {
4458                 URL url = new URL(file);
4459                 pdbfn = url.getFile();
4460               }
4461               if (pdbfn.length() > 0)
4462               {
4463                 // attempt to find a match in the alignment
4464                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4465                 int l = 0, c = pdbfn.indexOf(".");
4466                 while (mtch == null && c != -1)
4467                 {
4468                   do
4469                   {
4470                     l = c;
4471                   } while ((c = pdbfn.indexOf(".", l)) > l);
4472                   if (l > -1)
4473                   {
4474                     pdbfn = pdbfn.substring(0, l);
4475                   }
4476                   mtch = idm.findAllIdMatches(pdbfn);
4477                 }
4478                 if (mtch != null)
4479                 {
4480                   FileFormatI type = null;
4481                   try
4482                   {
4483                     type = new IdentifyFile().identify(file, protocol);
4484                   } catch (Exception ex)
4485                   {
4486                     type = null;
4487                   }
4488                   if (type != null && type.isStructureFile())
4489                   {
4490                     filesmatched.add(new Object[] { file, protocol, mtch });
4491                     continue;
4492                   }
4493                 }
4494                 // File wasn't named like one of the sequences or wasn't a PDB
4495                 // file.
4496                 filesnotmatched.add(file);
4497               }
4498             }
4499             int assocfiles = 0;
4500             if (filesmatched.size() > 0)
4501             {
4502               boolean autoAssociate = Cache
4503                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4504               if (!autoAssociate)
4505               {
4506                 String msg = MessageManager.formatMessage(
4507                         "label.automatically_associate_structure_files_with_sequences_same_name",
4508                         new Object[]
4509                         { Integer.valueOf(filesmatched.size())
4510                                 .toString() });
4511                 String ttl = MessageManager.getString(
4512                         "label.automatically_associate_structure_files_by_name");
4513                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4514                         ttl, JvOptionPane.YES_NO_OPTION);
4515                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4516               }
4517               if (autoAssociate)
4518               {
4519                 for (Object[] fm : filesmatched)
4520                 {
4521                   // try and associate
4522                   // TODO: may want to set a standard ID naming formalism for
4523                   // associating PDB files which have no IDs.
4524                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4525                   {
4526                     PDBEntry pe = new AssociatePdbFileWithSeq()
4527                             .associatePdbWithSeq((String) fm[0],
4528                                     (DataSourceType) fm[1], toassoc, false,
4529                                     Desktop.instance);
4530                     if (pe != null)
4531                     {
4532                       System.err.println("Associated file : "
4533                               + ((String) fm[0]) + " with "
4534                               + toassoc.getDisplayId(true));
4535                       assocfiles++;
4536                     }
4537                   }
4538                   // TODO: do we need to update overview ? only if features are
4539                   // shown I guess
4540                   alignPanel.paintAlignment(true, false);
4541                 }
4542               }
4543               else
4544               {
4545                 /*
4546                  * add declined structures as sequences
4547                  */
4548                 for (Object[] o : filesmatched)
4549                 {
4550                   filesnotmatched.add((String) o[0]);
4551                 }
4552               }
4553             }
4554             if (filesnotmatched.size() > 0)
4555             {
4556               if (assocfiles > 0 && (Cache.getDefault(
4557                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4558                       || JvOptionPane.showConfirmDialog(thisaf,
4559                               "<html>" + MessageManager.formatMessage(
4560                                       "label.ignore_unmatched_dropped_files_info",
4561                                       new Object[]
4562                                       { Integer.valueOf(
4563                                               filesnotmatched.size())
4564                                               .toString() })
4565                                       + "</html>",
4566                               MessageManager.getString(
4567                                       "label.ignore_unmatched_dropped_files"),
4568                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4569               {
4570                 return;
4571               }
4572               for (String fn : filesnotmatched)
4573               {
4574                 loadJalviewDataFile(fn, null, null, null);
4575               }
4576
4577             }
4578           } catch (Exception ex)
4579           {
4580             ex.printStackTrace();
4581           }
4582         }
4583       }).start();
4584     }
4585   }
4586
4587   /**
4588    * Attempt to load a "dropped" file or URL string, by testing in turn for
4589    * <ul>
4590    * <li>an Annotation file</li>
4591    * <li>a JNet file</li>
4592    * <li>a features file</li>
4593    * <li>else try to interpret as an alignment file</li>
4594    * </ul>
4595    *
4596    * @param file
4597    *          either a filename or a URL string.
4598    */
4599   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4600           FileFormatI format, SequenceI assocSeq)
4601   {
4602     try
4603     {
4604       if (sourceType == null)
4605       {
4606         sourceType = FormatAdapter.checkProtocol(file);
4607       }
4608       // if the file isn't identified, or not positively identified as some
4609       // other filetype (PFAM is default unidentified alignment file type) then
4610       // try to parse as annotation.
4611       boolean isAnnotation = (format == null
4612               || FileFormat.Pfam.equals(format))
4613                       ? new AnnotationFile().annotateAlignmentView(viewport,
4614                               file, sourceType)
4615                       : false;
4616
4617       if (!isAnnotation)
4618       {
4619         // first see if its a T-COFFEE score file
4620         TCoffeeScoreFile tcf = null;
4621         try
4622         {
4623           tcf = new TCoffeeScoreFile(file, sourceType);
4624           if (tcf.isValid())
4625           {
4626             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4627             {
4628               buildColourMenu();
4629               changeColour(
4630                       new TCoffeeColourScheme(viewport.getAlignment()));
4631               isAnnotation = true;
4632               statusBar.setText(MessageManager.getString(
4633                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4634             }
4635             else
4636             {
4637               // some problem - if no warning its probable that the ID matching
4638               // process didn't work
4639               JvOptionPane.showMessageDialog(Desktop.desktop,
4640                       tcf.getWarningMessage() == null
4641                               ? MessageManager.getString(
4642                                       "label.check_file_matches_sequence_ids_alignment")
4643                               : tcf.getWarningMessage(),
4644                       MessageManager.getString(
4645                               "label.problem_reading_tcoffee_score_file"),
4646                       JvOptionPane.WARNING_MESSAGE);
4647             }
4648           }
4649           else
4650           {
4651             tcf = null;
4652           }
4653         } catch (Exception x)
4654         {
4655           Cache.log.debug(
4656                   "Exception when processing data source as T-COFFEE score file",
4657                   x);
4658           tcf = null;
4659         }
4660         if (tcf == null)
4661         {
4662           // try to see if its a JNet 'concise' style annotation file *before*
4663           // we
4664           // try to parse it as a features file
4665           if (format == null)
4666           {
4667             format = new IdentifyFile().identify(file, sourceType);
4668           }
4669           if (FileFormat.ScoreMatrix == format)
4670           {
4671             ScoreMatrixFile sm = new ScoreMatrixFile(
4672                     new FileParse(file, sourceType));
4673             sm.parse();
4674             // todo: i18n this message
4675             statusBar.setText(MessageManager.formatMessage(
4676                     "label.successfully_loaded_matrix",
4677                     sm.getMatrixName()));
4678           }
4679           else if (FileFormat.Jnet.equals(format))
4680           {
4681             JPredFile predictions = new JPredFile(file, sourceType);
4682             new JnetAnnotationMaker();
4683             JnetAnnotationMaker.add_annotation(predictions,
4684                     viewport.getAlignment(), 0, false);
4685             viewport.getAlignment().setupJPredAlignment();
4686             isAnnotation = true;
4687           }
4688           // else if (IdentifyFile.FeaturesFile.equals(format))
4689           else if (FileFormat.Features.equals(format))
4690           {
4691             if (parseFeaturesFile(file, sourceType))
4692             {
4693               alignPanel.paintAlignment(true, true);
4694             }
4695           }
4696           else
4697           {
4698             new FileLoader().LoadFile(viewport, file, sourceType, format);
4699           }
4700         }
4701       }
4702       if (isAnnotation)
4703       {
4704
4705         alignPanel.adjustAnnotationHeight();
4706         viewport.updateSequenceIdColours();
4707         buildSortByAnnotationScoresMenu();
4708         alignPanel.paintAlignment(true, true);
4709       }
4710     } catch (Exception ex)
4711     {
4712       ex.printStackTrace();
4713     } catch (OutOfMemoryError oom)
4714     {
4715       try
4716       {
4717         System.gc();
4718       } catch (Exception x)
4719       {
4720       }
4721       new OOMWarning(
4722               "loading data "
4723                       + (sourceType != null
4724                               ? (sourceType == DataSourceType.PASTE
4725                                       ? "from clipboard."
4726                                       : "using " + sourceType + " from "
4727                                               + file)
4728                               : ".")
4729                       + (format != null
4730                               ? "(parsing as '" + format + "' file)"
4731                               : ""),
4732               oom, Desktop.desktop);
4733     }
4734   }
4735
4736   /**
4737    * Method invoked by the ChangeListener on the tabbed pane, in other words
4738    * when a different tabbed pane is selected by the user or programmatically.
4739    */
4740   @Override
4741   public void tabSelectionChanged(int index)
4742   {
4743     if (index > -1)
4744     {
4745       alignPanel = alignPanels.get(index);
4746       viewport = alignPanel.av;
4747       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4748       setMenusFromViewport(viewport);
4749     }
4750
4751     /*
4752      * 'focus' any colour slider that is open to the selected viewport
4753      */
4754     if (viewport.getConservationSelected())
4755     {
4756       SliderPanel.setConservationSlider(alignPanel,
4757               viewport.getResidueShading(), alignPanel.getViewName());
4758     }
4759     else
4760     {
4761       SliderPanel.hideConservationSlider();
4762     }
4763     if (viewport.getAbovePIDThreshold())
4764     {
4765       SliderPanel.setPIDSliderSource(alignPanel,
4766               viewport.getResidueShading(), alignPanel.getViewName());
4767     }
4768     else
4769     {
4770       SliderPanel.hidePIDSlider();
4771     }
4772
4773     /*
4774      * If there is a frame linked to this one in a SplitPane, switch it to the
4775      * same view tab index. No infinite recursion of calls should happen, since
4776      * tabSelectionChanged() should not get invoked on setting the selected
4777      * index to an unchanged value. Guard against setting an invalid index
4778      * before the new view peer tab has been created.
4779      */
4780     final AlignViewportI peer = viewport.getCodingComplement();
4781     if (peer != null)
4782     {
4783       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4784               .getAlignPanel().alignFrame;
4785       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4786       {
4787         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4788       }
4789     }
4790   }
4791
4792   /**
4793    * On right mouse click on view tab, prompt for and set new view name.
4794    */
4795   @Override
4796   public void tabbedPane_mousePressed(MouseEvent e)
4797   {
4798     if (e.isPopupTrigger())
4799     {
4800       String msg = MessageManager.getString("label.enter_view_name");
4801       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4802               JvOptionPane.QUESTION_MESSAGE);
4803
4804       if (reply != null)
4805       {
4806         viewport.setViewName(reply);
4807         // TODO warn if reply is in getExistingViewNames()?
4808         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4809       }
4810     }
4811   }
4812
4813   public AlignViewport getCurrentView()
4814   {
4815     return viewport;
4816   }
4817
4818   /**
4819    * Open the dialog for regex description parsing.
4820    */
4821   @Override
4822   protected void extractScores_actionPerformed(ActionEvent e)
4823   {
4824     ParseProperties pp = new jalview.analysis.ParseProperties(
4825             viewport.getAlignment());
4826     // TODO: verify regex and introduce GUI dialog for version 2.5
4827     // if (pp.getScoresFromDescription("col", "score column ",
4828     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4829     // true)>0)
4830     if (pp.getScoresFromDescription("description column",
4831             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4832     {
4833       buildSortByAnnotationScoresMenu();
4834     }
4835   }
4836
4837   /*
4838    * (non-Javadoc)
4839    *
4840    * @see
4841    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4842    * )
4843    */
4844   @Override
4845   protected void showDbRefs_actionPerformed(ActionEvent e)
4846   {
4847     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4848   }
4849
4850   /*
4851    * (non-Javadoc)
4852    *
4853    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4854    * ActionEvent)
4855    */
4856   @Override
4857   protected void showNpFeats_actionPerformed(ActionEvent e)
4858   {
4859     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4860   }
4861
4862   /**
4863    * find the viewport amongst the tabs in this alignment frame and close that
4864    * tab
4865    *
4866    * @param av
4867    */
4868   public boolean closeView(AlignViewportI av)
4869   {
4870     if (viewport == av)
4871     {
4872       this.closeMenuItem_actionPerformed(false);
4873       return true;
4874     }
4875     Component[] comp = tabbedPane.getComponents();
4876     for (int i = 0; comp != null && i < comp.length; i++)
4877     {
4878       if (comp[i] instanceof AlignmentPanel)
4879       {
4880         if (((AlignmentPanel) comp[i]).av == av)
4881         {
4882           // close the view.
4883           closeView((AlignmentPanel) comp[i]);
4884           return true;
4885         }
4886       }
4887     }
4888     return false;
4889   }
4890
4891   protected void build_fetchdbmenu(JMenu webService)
4892   {
4893     // Temporary hack - DBRef Fetcher always top level ws entry.
4894     // TODO We probably want to store a sequence database checklist in
4895     // preferences and have checkboxes.. rather than individual sources selected
4896     // here
4897     final JMenu rfetch = new JMenu(
4898             MessageManager.getString("action.fetch_db_references"));
4899     rfetch.setToolTipText(MessageManager.getString(
4900             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4901     webService.add(rfetch);
4902
4903     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4904             MessageManager.getString("option.trim_retrieved_seqs"));
4905     trimrs.setToolTipText(
4906             MessageManager.getString("label.trim_retrieved_sequences"));
4907     trimrs.setSelected(
4908             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4909     trimrs.addActionListener(new ActionListener()
4910     {
4911       @Override
4912       public void actionPerformed(ActionEvent e)
4913       {
4914         trimrs.setSelected(trimrs.isSelected());
4915         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4916                 Boolean.valueOf(trimrs.isSelected()).toString());
4917       };
4918     });
4919     rfetch.add(trimrs);
4920     JMenuItem fetchr = new JMenuItem(
4921             MessageManager.getString("label.standard_databases"));
4922     fetchr.setToolTipText(
4923             MessageManager.getString("label.fetch_embl_uniprot"));
4924     fetchr.addActionListener(new ActionListener()
4925     {
4926
4927       @Override
4928       public void actionPerformed(ActionEvent e)
4929       {
4930         new Thread(new Runnable()
4931         {
4932           @Override
4933           public void run()
4934           {
4935             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4936                     .getAlignment().isNucleotide();
4937             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4938                     alignPanel.av.getSequenceSelection(),
4939                     alignPanel.alignFrame, null,
4940                     alignPanel.alignFrame.featureSettings, isNucleotide);
4941             dbRefFetcher.addListener(new FetchFinishedListenerI()
4942             {
4943               @Override
4944               public void finished()
4945               {
4946
4947                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
4948                         .getFeatureSettingsModels())
4949                 {
4950
4951                   alignPanel.av.mergeFeaturesStyle(srcSettings);
4952                 }
4953                 AlignFrame.this.setMenusForViewport();
4954               }
4955             });
4956             dbRefFetcher.fetchDBRefs(false);
4957           }
4958         }).start();
4959
4960       }
4961
4962     });
4963     rfetch.add(fetchr);
4964     final AlignFrame me = this;
4965     new Thread(new Runnable()
4966     {
4967       @Override
4968       public void run()
4969       {
4970         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4971                 .getSequenceFetcherSingleton(me);
4972         javax.swing.SwingUtilities.invokeLater(new Runnable()
4973         {
4974           @Override
4975           public void run()
4976           {
4977             String[] dbclasses = sf.getOrderedSupportedSources();
4978             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4979             // jalview.util.QuickSort.sort(otherdb, otherdb);
4980             List<DbSourceProxy> otherdb;
4981             JMenu dfetch = new JMenu();
4982             JMenu ifetch = new JMenu();
4983             JMenuItem fetchr = null;
4984             int comp = 0, icomp = 0, mcomp = 15;
4985             String mname = null;
4986             int dbi = 0;
4987             for (String dbclass : dbclasses)
4988             {
4989               otherdb = sf.getSourceProxy(dbclass);
4990               // add a single entry for this class, or submenu allowing 'fetch
4991               // all' or pick one
4992               if (otherdb == null || otherdb.size() < 1)
4993               {
4994                 continue;
4995               }
4996               // List<DbSourceProxy> dbs=otherdb;
4997               // otherdb=new ArrayList<DbSourceProxy>();
4998               // for (DbSourceProxy db:dbs)
4999               // {
5000               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5001               // }
5002               if (mname == null)
5003               {
5004                 mname = "From " + dbclass;
5005               }
5006               if (otherdb.size() == 1)
5007               {
5008                 final DbSourceProxy[] dassource = otherdb
5009                         .toArray(new DbSourceProxy[0]);
5010                 DbSourceProxy src = otherdb.get(0);
5011                 fetchr = new JMenuItem(src.getDbSource());
5012                 fetchr.addActionListener(new ActionListener()
5013                 {
5014
5015                   @Override
5016                   public void actionPerformed(ActionEvent e)
5017                   {
5018                     new Thread(new Runnable()
5019                     {
5020
5021                       @Override
5022                       public void run()
5023                       {
5024                         boolean isNucleotide = alignPanel.alignFrame
5025                                 .getViewport().getAlignment()
5026                                 .isNucleotide();
5027                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5028                                 alignPanel.av.getSequenceSelection(),
5029                                 alignPanel.alignFrame, dassource,
5030                                 alignPanel.alignFrame.featureSettings,
5031                                 isNucleotide);
5032                         dbRefFetcher
5033                                 .addListener(new FetchFinishedListenerI()
5034                                 {
5035                                   @Override
5036                                   public void finished()
5037                                   {
5038                                     FeatureSettingsModelI srcSettings = dassource[0]
5039                                             .getFeatureColourScheme();
5040                                     alignPanel.av.mergeFeaturesStyle(
5041                                             srcSettings);
5042                                     AlignFrame.this.setMenusForViewport();
5043                                   }
5044                                 });
5045                         dbRefFetcher.fetchDBRefs(false);
5046                       }
5047                     }).start();
5048                   }
5049
5050                 });
5051                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5052                         MessageManager.formatMessage(
5053                                 "label.fetch_retrieve_from", new Object[]
5054                                 { src.getDbName() })));
5055                 dfetch.add(fetchr);
5056                 comp++;
5057               }
5058               else
5059               {
5060                 final DbSourceProxy[] dassource = otherdb
5061                         .toArray(new DbSourceProxy[0]);
5062                 // fetch all entry
5063                 DbSourceProxy src = otherdb.get(0);
5064                 fetchr = new JMenuItem(MessageManager
5065                         .formatMessage("label.fetch_all_param", new Object[]
5066                         { src.getDbSource() }));
5067                 fetchr.addActionListener(new ActionListener()
5068                 {
5069                   @Override
5070                   public void actionPerformed(ActionEvent e)
5071                   {
5072                     new Thread(new Runnable()
5073                     {
5074
5075                       @Override
5076                       public void run()
5077                       {
5078                         boolean isNucleotide = alignPanel.alignFrame
5079                                 .getViewport().getAlignment()
5080                                 .isNucleotide();
5081                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5082                                 alignPanel.av.getSequenceSelection(),
5083                                 alignPanel.alignFrame, dassource,
5084                                 alignPanel.alignFrame.featureSettings,
5085                                 isNucleotide);
5086                         dbRefFetcher
5087                                 .addListener(new FetchFinishedListenerI()
5088                                 {
5089                                   @Override
5090                                   public void finished()
5091                                   {
5092                                     AlignFrame.this.setMenusForViewport();
5093                                   }
5094                                 });
5095                         dbRefFetcher.fetchDBRefs(false);
5096                       }
5097                     }).start();
5098                   }
5099                 });
5100
5101                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5102                         MessageManager.formatMessage(
5103                                 "label.fetch_retrieve_from_all_sources",
5104                                 new Object[]
5105                                 { Integer.valueOf(otherdb.size())
5106                                         .toString(),
5107                                     src.getDbSource(), src.getDbName() })));
5108                 dfetch.add(fetchr);
5109                 comp++;
5110                 // and then build the rest of the individual menus
5111                 ifetch = new JMenu(MessageManager.formatMessage(
5112                         "label.source_from_db_source", new Object[]
5113                         { src.getDbSource() }));
5114                 icomp = 0;
5115                 String imname = null;
5116                 int i = 0;
5117                 for (DbSourceProxy sproxy : otherdb)
5118                 {
5119                   String dbname = sproxy.getDbName();
5120                   String sname = dbname.length() > 5
5121                           ? dbname.substring(0, 5) + "..."
5122                           : dbname;
5123                   String msname = dbname.length() > 10
5124                           ? dbname.substring(0, 10) + "..."
5125                           : dbname;
5126                   if (imname == null)
5127                   {
5128                     imname = MessageManager
5129                             .formatMessage("label.from_msname", new Object[]
5130                             { sname });
5131                   }
5132                   fetchr = new JMenuItem(msname);
5133                   final DbSourceProxy[] dassrc = { sproxy };
5134                   fetchr.addActionListener(new ActionListener()
5135                   {
5136
5137                     @Override
5138                     public void actionPerformed(ActionEvent e)
5139                     {
5140                       new Thread(new Runnable()
5141                       {
5142
5143                         @Override
5144                         public void run()
5145                         {
5146                           boolean isNucleotide = alignPanel.alignFrame
5147                                   .getViewport().getAlignment()
5148                                   .isNucleotide();
5149                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5150                                   alignPanel.av.getSequenceSelection(),
5151                                   alignPanel.alignFrame, dassrc,
5152                                   alignPanel.alignFrame.featureSettings,
5153                                   isNucleotide);
5154                           dbRefFetcher
5155                                   .addListener(new FetchFinishedListenerI()
5156                                   {
5157                                     @Override
5158                                     public void finished()
5159                                     {
5160                                       AlignFrame.this.setMenusForViewport();
5161                                     }
5162                                   });
5163                           dbRefFetcher.fetchDBRefs(false);
5164                         }
5165                       }).start();
5166                     }
5167
5168                   });
5169                   fetchr.setToolTipText(
5170                           "<html>" + MessageManager.formatMessage(
5171                                   "label.fetch_retrieve_from", new Object[]
5172                                   { dbname }));
5173                   ifetch.add(fetchr);
5174                   ++i;
5175                   if (++icomp >= mcomp || i == (otherdb.size()))
5176                   {
5177                     ifetch.setText(MessageManager.formatMessage(
5178                             "label.source_to_target", imname, sname));
5179                     dfetch.add(ifetch);
5180                     ifetch = new JMenu();
5181                     imname = null;
5182                     icomp = 0;
5183                     comp++;
5184                   }
5185                 }
5186               }
5187               ++dbi;
5188               if (comp >= mcomp || dbi >= (dbclasses.length))
5189               {
5190                 dfetch.setText(MessageManager.formatMessage(
5191                         "label.source_to_target", mname, dbclass));
5192                 rfetch.add(dfetch);
5193                 dfetch = new JMenu();
5194                 mname = null;
5195                 comp = 0;
5196               }
5197             }
5198           }
5199         });
5200       }
5201     }).start();
5202
5203   }
5204
5205   /**
5206    * Left justify the whole alignment.
5207    */
5208   @Override
5209   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5210   {
5211     AlignmentI al = viewport.getAlignment();
5212     al.justify(false);
5213     viewport.firePropertyChange("alignment", null, al);
5214   }
5215
5216   /**
5217    * Right justify the whole alignment.
5218    */
5219   @Override
5220   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5221   {
5222     AlignmentI al = viewport.getAlignment();
5223     al.justify(true);
5224     viewport.firePropertyChange("alignment", null, al);
5225   }
5226
5227   @Override
5228   public void setShowSeqFeatures(boolean b)
5229   {
5230     showSeqFeatures.setSelected(b);
5231     viewport.setShowSequenceFeatures(b);
5232   }
5233
5234   /*
5235    * (non-Javadoc)
5236    *
5237    * @see
5238    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5239    * awt.event.ActionEvent)
5240    */
5241   @Override
5242   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5243   {
5244     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5245     alignPanel.paintAlignment(false, false);
5246   }
5247
5248   /*
5249    * (non-Javadoc)
5250    *
5251    * @see
5252    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5253    * .ActionEvent)
5254    */
5255   @Override
5256   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5257   {
5258     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5259     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5260
5261   }
5262
5263   /*
5264    * (non-Javadoc)
5265    *
5266    * @see
5267    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5268    * .event.ActionEvent)
5269    */
5270   @Override
5271   protected void showGroupConservation_actionPerformed(ActionEvent e)
5272   {
5273     viewport.setShowGroupConservation(showGroupConservation.getState());
5274     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5275   }
5276
5277   /*
5278    * (non-Javadoc)
5279    *
5280    * @see
5281    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5282    * .event.ActionEvent)
5283    */
5284   @Override
5285   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5286   {
5287     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5288     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5289   }
5290
5291   /*
5292    * (non-Javadoc)
5293    *
5294    * @see
5295    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5296    * .event.ActionEvent)
5297    */
5298   @Override
5299   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5300   {
5301     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5302     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5303   }
5304
5305   @Override
5306   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5307   {
5308     showSequenceLogo.setState(true);
5309     viewport.setShowSequenceLogo(true);
5310     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5311     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5312   }
5313
5314   @Override
5315   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5316   {
5317     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5318   }
5319
5320   /*
5321    * (non-Javadoc)
5322    *
5323    * @see
5324    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5325    * .event.ActionEvent)
5326    */
5327   @Override
5328   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5329   {
5330     if (avc.makeGroupsFromSelection())
5331     {
5332       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5333       alignPanel.updateAnnotation();
5334       alignPanel.paintAlignment(true,
5335               viewport.needToUpdateStructureViews());
5336     }
5337   }
5338
5339   public void clearAlignmentSeqRep()
5340   {
5341     // TODO refactor alignmentseqrep to controller
5342     if (viewport.getAlignment().hasSeqrep())
5343     {
5344       viewport.getAlignment().setSeqrep(null);
5345       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5346       alignPanel.updateAnnotation();
5347       alignPanel.paintAlignment(true, true);
5348     }
5349   }
5350
5351   @Override
5352   protected void createGroup_actionPerformed(ActionEvent e)
5353   {
5354     if (avc.createGroup())
5355     {
5356       if (applyAutoAnnotationSettings.isSelected())
5357       {
5358         alignPanel.updateAnnotation(true, false);
5359       }
5360       alignPanel.alignmentChanged();
5361     }
5362   }
5363
5364   @Override
5365   protected void unGroup_actionPerformed(ActionEvent e)
5366   {
5367     if (avc.unGroup())
5368     {
5369       alignPanel.alignmentChanged();
5370     }
5371   }
5372
5373   /**
5374    * make the given alignmentPanel the currently selected tab
5375    *
5376    * @param alignmentPanel
5377    */
5378   public void setDisplayedView(AlignmentPanel alignmentPanel)
5379   {
5380     if (!viewport.getSequenceSetId()
5381             .equals(alignmentPanel.av.getSequenceSetId()))
5382     {
5383       throw new Error(MessageManager.getString(
5384               "error.implementation_error_cannot_show_view_alignment_frame"));
5385     }
5386     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5387             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5388     {
5389       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5390     }
5391   }
5392
5393   /**
5394    * Action on selection of menu options to Show or Hide annotations.
5395    *
5396    * @param visible
5397    * @param forSequences
5398    *          update sequence-related annotations
5399    * @param forAlignment
5400    *          update non-sequence-related annotations
5401    */
5402   @Override
5403   protected void setAnnotationsVisibility(boolean visible,
5404           boolean forSequences, boolean forAlignment)
5405   {
5406     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5407             .getAlignmentAnnotation();
5408     if (anns == null)
5409     {
5410       return;
5411     }
5412     for (AlignmentAnnotation aa : anns)
5413     {
5414       /*
5415        * don't display non-positional annotations on an alignment
5416        */
5417       if (aa.annotations == null)
5418       {
5419         continue;
5420       }
5421       boolean apply = (aa.sequenceRef == null && forAlignment)
5422               || (aa.sequenceRef != null && forSequences);
5423       if (apply)
5424       {
5425         aa.visible = visible;
5426       }
5427     }
5428     alignPanel.validateAnnotationDimensions(true);
5429     alignPanel.alignmentChanged();
5430   }
5431
5432   /**
5433    * Store selected annotation sort order for the view and repaint.
5434    */
5435   @Override
5436   protected void sortAnnotations_actionPerformed()
5437   {
5438     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5439     this.alignPanel.av
5440             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5441     alignPanel.paintAlignment(false, false);
5442   }
5443
5444   /**
5445    *
5446    * @return alignment panels in this alignment frame
5447    */
5448   public List<? extends AlignmentViewPanel> getAlignPanels()
5449   {
5450     // alignPanels is never null
5451     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5452     return alignPanels;
5453   }
5454
5455   /**
5456    * Open a new alignment window, with the cDNA associated with this (protein)
5457    * alignment, aligned as is the protein.
5458    */
5459   protected void viewAsCdna_actionPerformed()
5460   {
5461     // TODO no longer a menu action - refactor as required
5462     final AlignmentI alignment = getViewport().getAlignment();
5463     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5464     if (mappings == null)
5465     {
5466       return;
5467     }
5468     List<SequenceI> cdnaSeqs = new ArrayList<>();
5469     for (SequenceI aaSeq : alignment.getSequences())
5470     {
5471       for (AlignedCodonFrame acf : mappings)
5472       {
5473         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5474         if (dnaSeq != null)
5475         {
5476           /*
5477            * There is a cDNA mapping for this protein sequence - add to new
5478            * alignment. It will share the same dataset sequence as other mapped
5479            * cDNA (no new mappings need to be created).
5480            */
5481           final Sequence newSeq = new Sequence(dnaSeq);
5482           newSeq.setDatasetSequence(dnaSeq);
5483           cdnaSeqs.add(newSeq);
5484         }
5485       }
5486     }
5487     if (cdnaSeqs.size() == 0)
5488     {
5489       // show a warning dialog no mapped cDNA
5490       return;
5491     }
5492     AlignmentI cdna = new Alignment(
5493             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5494     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5495             AlignFrame.DEFAULT_HEIGHT);
5496     cdna.alignAs(alignment);
5497     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5498             + this.title;
5499     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5500             AlignFrame.DEFAULT_HEIGHT);
5501   }
5502
5503   /**
5504    * Set visibility of dna/protein complement view (available when shown in a
5505    * split frame).
5506    *
5507    * @param show
5508    */
5509   @Override
5510   protected void showComplement_actionPerformed(boolean show)
5511   {
5512     SplitContainerI sf = getSplitViewContainer();
5513     if (sf != null)
5514     {
5515       sf.setComplementVisible(this, show);
5516     }
5517   }
5518
5519   /**
5520    * Generate the reverse (optionally complemented) of the selected sequences,
5521    * and add them to the alignment
5522    */
5523   @Override
5524   protected void showReverse_actionPerformed(boolean complement)
5525   {
5526     AlignmentI al = null;
5527     try
5528     {
5529       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5530       al = dna.reverseCdna(complement);
5531       viewport.addAlignment(al, "");
5532       addHistoryItem(new EditCommand(
5533               MessageManager.getString("label.add_sequences"), Action.PASTE,
5534               al.getSequencesArray(), 0, al.getWidth(),
5535               viewport.getAlignment()));
5536     } catch (Exception ex)
5537     {
5538       System.err.println(ex.getMessage());
5539       return;
5540     }
5541   }
5542
5543   /**
5544    * Try to run a script in the Groovy console, having first ensured that this
5545    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5546    * be targeted at this alignment.
5547    */
5548   @Override
5549   protected void runGroovy_actionPerformed()
5550   {
5551     Jalview.setCurrentAlignFrame(this);
5552     groovy.ui.Console console = Desktop.getGroovyConsole();
5553     if (console != null)
5554     {
5555       try
5556       {
5557         console.runScript();
5558       } catch (Exception ex)
5559       {
5560         System.err.println((ex.toString()));
5561         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5562                 MessageManager.getString("label.couldnt_run_groovy_script"),
5563                 MessageManager.getString("label.groovy_support_failed"),
5564                 JvOptionPane.ERROR_MESSAGE);
5565       }
5566     }
5567     else
5568     {
5569       System.err.println("Can't run Groovy script as console not found");
5570     }
5571   }
5572
5573   /**
5574    * Hides columns containing (or not containing) a specified feature, provided
5575    * that would not leave all columns hidden
5576    *
5577    * @param featureType
5578    * @param columnsContaining
5579    * @return
5580    */
5581   public boolean hideFeatureColumns(String featureType,
5582           boolean columnsContaining)
5583   {
5584     boolean notForHiding = avc.markColumnsContainingFeatures(
5585             columnsContaining, false, false, featureType);
5586     if (notForHiding)
5587     {
5588       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5589               false, featureType))
5590       {
5591         getViewport().hideSelectedColumns();
5592         return true;
5593       }
5594     }
5595     return false;
5596   }
5597
5598   @Override
5599   protected void selectHighlightedColumns_actionPerformed(
5600           ActionEvent actionEvent)
5601   {
5602     // include key modifier check in case user selects from menu
5603     avc.markHighlightedColumns(
5604             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5605             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5606                     | ActionEvent.CTRL_MASK)) != 0);
5607   }
5608
5609   /**
5610    * Rebuilds the Colour menu, including any user-defined colours which have
5611    * been loaded either on startup or during the session
5612    */
5613   public void buildColourMenu()
5614   {
5615     colourMenu.removeAll();
5616
5617     colourMenu.add(applyToAllGroups);
5618     colourMenu.add(textColour);
5619     colourMenu.addSeparator();
5620
5621     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5622             viewport.getAlignment(), false);
5623
5624     colourMenu.add(annotationColour);
5625     bg.add(annotationColour);
5626     colourMenu.addSeparator();
5627     colourMenu.add(conservationMenuItem);
5628     colourMenu.add(modifyConservation);
5629     colourMenu.add(abovePIDThreshold);
5630     colourMenu.add(modifyPID);
5631
5632     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5633     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5634   }
5635
5636   /**
5637    * Open a dialog (if not already open) that allows the user to select and
5638    * calculate PCA or Tree analysis
5639    */
5640   protected void openTreePcaDialog()
5641   {
5642     if (alignPanel.getCalculationDialog() == null)
5643     {
5644       new CalculationChooser(AlignFrame.this);
5645     }
5646   }
5647
5648   @Override
5649   protected void loadVcf_actionPerformed()
5650   {
5651     JalviewFileChooser chooser = new JalviewFileChooser(
5652             Cache.getProperty("LAST_DIRECTORY"));
5653     chooser.setFileView(new JalviewFileView());
5654     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5655     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5656
5657     int value = chooser.showOpenDialog(null);
5658
5659     if (value == JalviewFileChooser.APPROVE_OPTION)
5660     {
5661       String choice = chooser.getSelectedFile().getPath();
5662       Cache.setProperty("LAST_DIRECTORY", choice);
5663       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5664       new VCFLoader(choice).loadVCF(seqs, this);
5665     }
5666
5667   }
5668
5669   private Rectangle lastFeatureSettingsBounds = null;
5670   @Override
5671   public void setFeatureSettingsGeometry(Rectangle bounds)
5672   {
5673     lastFeatureSettingsBounds = bounds;
5674   }
5675
5676   @Override
5677   public Rectangle getFeatureSettingsGeometry()
5678   {
5679     return lastFeatureSettingsBounds;
5680   }
5681 }
5682
5683 class PrintThread extends Thread
5684 {
5685   AlignmentPanel ap;
5686
5687   public PrintThread(AlignmentPanel ap)
5688   {
5689     this.ap = ap;
5690   }
5691
5692   static PageFormat pf;
5693
5694   @Override
5695   public void run()
5696   {
5697     PrinterJob printJob = PrinterJob.getPrinterJob();
5698
5699     if (pf != null)
5700     {
5701       printJob.setPrintable(ap, pf);
5702     }
5703     else
5704     {
5705       printJob.setPrintable(ap);
5706     }
5707
5708     if (printJob.printDialog())
5709     {
5710       try
5711       {
5712         printJob.print();
5713       } catch (Exception PrintException)
5714       {
5715         PrintException.printStackTrace();
5716       }
5717     }
5718   }
5719 }