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