src/jalview/gui/AlignFrame.java

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