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