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.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.io.vcf.VCFLoader;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.MessageManager;
  91 import jalview.viewmodel.AlignmentViewport;
  92 import jalview.viewmodel.ViewportRanges;
  93 import jalview.ws.DBRefFetcher;
  94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  95 import jalview.ws.jws1.Discoverer;
  96 import jalview.ws.jws2.Jws2Discoverer;
  97 import jalview.ws.jws2.jabaws2.Jws2Instance;
  98 import jalview.ws.seqfetcher.DbSourceProxy;
  99
 100 import java.awt.BorderLayout;
 101 import java.awt.Component;
 102 import java.awt.Rectangle;
 103 import java.awt.Toolkit;
 104 import java.awt.datatransfer.Clipboard;
 105 import java.awt.datatransfer.DataFlavor;
 106 import java.awt.datatransfer.StringSelection;
 107 import java.awt.datatransfer.Transferable;
 108 import java.awt.dnd.DnDConstants;
 109 import java.awt.dnd.DropTargetDragEvent;
 110 import java.awt.dnd.DropTargetDropEvent;
 111 import java.awt.dnd.DropTargetEvent;
 112 import java.awt.dnd.DropTargetListener;
 113 import java.awt.event.ActionEvent;
 114 import java.awt.event.ActionListener;
 115 import java.awt.event.FocusAdapter;
 116 import java.awt.event.FocusEvent;
 117 import java.awt.event.ItemEvent;
 118 import java.awt.event.ItemListener;
 119 import java.awt.event.KeyAdapter;
 120 import java.awt.event.KeyEvent;
 121 import java.awt.event.MouseEvent;
 122 import java.awt.print.PageFormat;
 123 import java.awt.print.PrinterJob;
 124 import java.beans.PropertyChangeEvent;
 125 import java.io.File;
 126 import java.io.FileWriter;
 127 import java.io.PrintWriter;
 128 import java.net.URL;
 129 import java.util.ArrayList;
 130 import java.util.Arrays;
 131 import java.util.Deque;
 132 import java.util.Enumeration;
 133 import java.util.Hashtable;
 134 import java.util.List;
 135 import java.util.Vector;
 136
 137 import javax.swing.JCheckBoxMenuItem;
 138 import javax.swing.JEditorPane;
 139 import javax.swing.JInternalFrame;
 140 import javax.swing.JLayeredPane;
 141 import javax.swing.JMenu;
 142 import javax.swing.JMenuItem;
 143 import javax.swing.JScrollPane;
 144 import javax.swing.SwingUtilities;
 145
 146 /**
 147  * DOCUMENT ME!
 148  *
 149  * @author $author$
 150  * @version $Revision$
 151  */
 152 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 153         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 154 {
 155
 156   public static final int DEFAULT_WIDTH = 700;
 157
 158   public static final int DEFAULT_HEIGHT = 500;
 159
 160   /*
 161    * The currently displayed panel (selected tabbed view if more than one)
 162    */
 163   public AlignmentPanel alignPanel;
 164
 165   AlignViewport viewport;
 166
 167   public AlignViewControllerI avc;
 168
 169   List<AlignmentPanel> alignPanels = new ArrayList<>();
 170
 171   /**
 172    * Last format used to load or save alignments in this window
 173    */
 174   FileFormatI currentFileFormat = null;
 175
 176   /**
 177    * Current filename for this alignment
 178    */
 179   String fileName = null;
 180
 181   /**
 182    * Creates a new AlignFrame object with specific width and height.
 183    *
 184    * @param al
 185    * @param width
 186    * @param height
 187    */
 188   public AlignFrame(AlignmentI al, int width, int height)
 189   {
 190     this(al, null, width, height);
 191   }
 192
 193   /**
 194    * Creates a new AlignFrame object with specific width, height and
 195    * sequenceSetId
 196    *
 197    * @param al
 198    * @param width
 199    * @param height
 200    * @param sequenceSetId
 201    */
 202   public AlignFrame(AlignmentI al, int width, int height,
 203           String sequenceSetId)
 204   {
 205     this(al, null, width, height, sequenceSetId);
 206   }
 207
 208   /**
 209    * Creates a new AlignFrame object with specific width, height and
 210    * sequenceSetId
 211    *
 212    * @param al
 213    * @param width
 214    * @param height
 215    * @param sequenceSetId
 216    * @param viewId
 217    */
 218   public AlignFrame(AlignmentI al, int width, int height,
 219           String sequenceSetId, String viewId)
 220   {
 221     this(al, null, width, height, sequenceSetId, viewId);
 222   }
 223
 224   /**
 225    * new alignment window with hidden columns
 226    *
 227    * @param al
 228    *          AlignmentI
 229    * @param hiddenColumns
 230    *          ColumnSelection or null
 231    * @param width
 232    *          Width of alignment frame
 233    * @param height
 234    *          height of frame.
 235    */
 236   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 237           int height)
 238   {
 239     this(al, hiddenColumns, width, height, null);
 240   }
 241
 242   /**
 243    * Create alignment frame for al with hiddenColumns, a specific width and
 244    * height, and specific sequenceId
 245    *
 246    * @param al
 247    * @param hiddenColumns
 248    * @param width
 249    * @param height
 250    * @param sequenceSetId
 251    *          (may be null)
 252    */
 253   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 254           int height, String sequenceSetId)
 255   {
 256     this(al, hiddenColumns, width, height, sequenceSetId, null);
 257   }
 258
 259   /**
 260    * Create alignment frame for al with hiddenColumns, a specific width and
 261    * height, and specific sequenceId
 262    *
 263    * @param al
 264    * @param hiddenColumns
 265    * @param width
 266    * @param height
 267    * @param sequenceSetId
 268    *          (may be null)
 269    * @param viewId
 270    *          (may be null)
 271    */
 272   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 273           int height, String sequenceSetId, String viewId)
 274   {
 275     setSize(width, height);
 276
 277     if (al.getDataset() == null)
 278     {
 279       al.setDataset(null);
 280     }
 281
 282     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 283
 284     alignPanel = new AlignmentPanel(this, viewport);
 285
 286     addAlignmentPanel(alignPanel, true);
 287     init();
 288   }
 289
 290   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 291           HiddenColumns hiddenColumns, int width, int height)
 292   {
 293     setSize(width, height);
 294
 295     if (al.getDataset() == null)
 296     {
 297       al.setDataset(null);
 298     }
 299
 300     viewport = new AlignViewport(al, hiddenColumns);
 301
 302     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 303     {
 304       viewport.hideSequence(hiddenSeqs);
 305     }
 306     alignPanel = new AlignmentPanel(this, viewport);
 307     addAlignmentPanel(alignPanel, true);
 308     init();
 309   }
 310
 311   /**
 312    * Make a new AlignFrame from existing alignmentPanels
 313    *
 314    * @param ap
 315    *          AlignmentPanel
 316    * @param av
 317    *          AlignViewport
 318    */
 319   public AlignFrame(AlignmentPanel ap)
 320   {
 321     viewport = ap.av;
 322     alignPanel = ap;
 323     addAlignmentPanel(ap, false);
 324     init();
 325   }
 326
 327   /**
 328    * initalise the alignframe from the underlying viewport data and the
 329    * configurations
 330    */
 331   void init()
 332   {
 333     if (!Jalview.isHeadlessMode())
 334     {
 335       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 336     }
 337
 338     avc = new jalview.controller.AlignViewController(this, viewport,
 339             alignPanel);
 340     if (viewport.getAlignmentConservationAnnotation() == null)
 341     {
 342       // BLOSUM62Colour.setEnabled(false);
 343       conservationMenuItem.setEnabled(false);
 344       modifyConservation.setEnabled(false);
 345       // PIDColour.setEnabled(false);
 346       // abovePIDThreshold.setEnabled(false);
 347       // modifyPID.setEnabled(false);
 348     }
 349
 350     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 351             "No sort");
 352
 353     if (sortby.equals("Id"))
 354     {
 355       sortIDMenuItem_actionPerformed(null);
 356     }
 357     else if (sortby.equals("Pairwise Identity"))
 358     {
 359       sortPairwiseMenuItem_actionPerformed(null);
 360     }
 361
 362     this.alignPanel.av
 363             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 364
 365     setMenusFromViewport(viewport);
 366     buildSortByAnnotationScoresMenu();
 367     calculateTree.addActionListener(new ActionListener()
 368     {
 369
 370       @Override
 371       public void actionPerformed(ActionEvent e)
 372       {
 373         openTreePcaDialog();
 374       }
 375     });
 376     buildColourMenu();
 377
 378     if (Desktop.desktop != null)
 379     {
 380       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 381       /**
 382        * BH 2018 ignore service listeners
 383        *
 384        * @j2sNative
 385        *
 386        */
 387       {
 388       addServiceListeners();
 389       }
 390       setGUINucleotide();
 391     }
 392
 393     if (viewport.getWrapAlignment())
 394     {
 395       wrapMenuItem_actionPerformed(null);
 396     }
 397
 398     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 399     {
 400       this.overviewMenuItem_actionPerformed(null);
 401     }
 402
 403     addKeyListener();
 404
 405     final List<AlignmentPanel> selviews = new ArrayList<>();
 406     final List<AlignmentPanel> origview = new ArrayList<>();
 407     final String menuLabel = MessageManager
 408             .getString("label.copy_format_from");
 409     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 410             new ViewSetProvider()
 411             {
 412
 413               @Override
 414               public AlignmentPanel[] getAllAlignmentPanels()
 415               {
 416                 origview.clear();
 417                 origview.add(alignPanel);
 418                 // make an array of all alignment panels except for this one
 419                 List<AlignmentPanel> aps = new ArrayList<>(
 420                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 421                 aps.remove(AlignFrame.this.alignPanel);
 422                 return aps.toArray(new AlignmentPanel[aps.size()]);
 423               }
 424             }, selviews, new ItemListener()
 425             {
 426
 427               @Override
 428               public void itemStateChanged(ItemEvent e)
 429               {
 430                 if (origview.size() > 0)
 431                 {
 432                   final AlignmentPanel ap = origview.get(0);
 433
 434                   /*
 435                    * Copy the ViewStyle of the selected panel to 'this one'.
 436                    * Don't change value of 'scaleProteinAsCdna' unless copying
 437                    * from a SplitFrame.
 438                    */
 439                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 440                           .getViewStyle();
 441                   boolean fromSplitFrame = selviews.get(0)
 442                           .getAlignViewport().getCodingComplement() != null;
 443                   if (!fromSplitFrame)
 444                   {
 445                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 446                             .getViewStyle().isScaleProteinAsCdna());
 447                   }
 448                   ap.getAlignViewport().setViewStyle(vs);
 449
 450                   /*
 451                    * Also rescale ViewStyle of SplitFrame complement if there is
 452                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 453                    * the whole ViewStyle (allow cDNA protein to have different
 454                    * fonts)
 455                    */
 456                   AlignViewportI complement = ap.getAlignViewport()
 457                           .getCodingComplement();
 458                   if (complement != null && vs.isScaleProteinAsCdna())
 459                   {
 460                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 461                     ((SplitFrame) af.getSplitViewContainer())
 462                             .adjustLayout();
 463                     af.setMenusForViewport();
 464                   }
 465
 466                   ap.updateLayout();
 467                   ap.setSelected(true);
 468                   ap.alignFrame.setMenusForViewport();
 469
 470                 }
 471               }
 472             });
 473     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 474             .indexOf("devel") > -1
 475             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 476                     .indexOf("test") > -1)
 477     {
 478       formatMenu.add(vsel);
 479     }
 480     addFocusListener(new FocusAdapter()
 481     {
 482       @Override
 483       public void focusGained(FocusEvent e)
 484       {
 485         Jalview.setCurrentAlignFrame(AlignFrame.this);
 486       }
 487     });
 488
 489   }
 490
 491   /**
 492    * Change the filename and format for the alignment, and enable the 'reload'
 493    * button functionality.
 494    *
 495    * @param file
 496    *          valid filename
 497    * @param format
 498    *          format of file
 499    */
 500   public void setFileName(String file, FileFormatI format)
 501   {
 502     fileName = file;
 503     setFileFormat(format);
 504     reload.setEnabled(true);
 505   }
 506
 507   /**
 508    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 509    * events
 510    */
 511   void addKeyListener()
 512   {
 513     addKeyListener(new KeyAdapter()
 514     {
 515       @Override
 516       public void keyPressed(KeyEvent evt)
 517       {
 518         if (viewport.cursorMode
 519                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 520                         && evt.getKeyCode() <= KeyEvent.VK_9)
 521                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 522                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 523                 && Character.isDigit(evt.getKeyChar()))
 524         {
 525           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 526         }
 527
 528         switch (evt.getKeyCode())
 529         {
 530
 531         case 27: // escape key
 532           deselectAllSequenceMenuItem_actionPerformed(null);
 533
 534           break;
 535
 536         case KeyEvent.VK_DOWN:
 537           if (evt.isAltDown() || !viewport.cursorMode)
 538           {
 539             moveSelectedSequences(false);
 540           }
 541           if (viewport.cursorMode)
 542           {
 543             alignPanel.getSeqPanel().moveCursor(0, 1);
 544           }
 545           break;
 546
 547         case KeyEvent.VK_UP:
 548           if (evt.isAltDown() || !viewport.cursorMode)
 549           {
 550             moveSelectedSequences(true);
 551           }
 552           if (viewport.cursorMode)
 553           {
 554             alignPanel.getSeqPanel().moveCursor(0, -1);
 555           }
 556
 557           break;
 558
 559         case KeyEvent.VK_LEFT:
 560           if (evt.isAltDown() || !viewport.cursorMode)
 561           {
 562             slideSequences(false,
 563                     alignPanel.getSeqPanel().getKeyboardNo1());
 564           }
 565           else
 566           {
 567             alignPanel.getSeqPanel().moveCursor(-1, 0);
 568           }
 569
 570           break;
 571
 572         case KeyEvent.VK_RIGHT:
 573           if (evt.isAltDown() || !viewport.cursorMode)
 574           {
 575             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 576           }
 577           else
 578           {
 579             alignPanel.getSeqPanel().moveCursor(1, 0);
 580           }
 581           break;
 582
 583         case KeyEvent.VK_SPACE:
 584           if (viewport.cursorMode)
 585           {
 586             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 587                     || evt.isShiftDown() || evt.isAltDown());
 588           }
 589           break;
 590
 591         // case KeyEvent.VK_A:
 592         // if (viewport.cursorMode)
 593         // {
 594         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 595         // //System.out.println("A");
 596         // }
 597         // break;
 598         /*
 599          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 600          * System.out.println("closing bracket"); } break;
 601          */
 602         case KeyEvent.VK_DELETE:
 603         case KeyEvent.VK_BACK_SPACE:
 604           if (!viewport.cursorMode)
 605           {
 606             cut_actionPerformed(null);
 607           }
 608           else
 609           {
 610             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 611                     || evt.isShiftDown() || evt.isAltDown());
 612           }
 613
 614           break;
 615
 616         case KeyEvent.VK_S:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorRow();
 620           }
 621           break;
 622         case KeyEvent.VK_C:
 623           if (viewport.cursorMode && !evt.isControlDown())
 624           {
 625             alignPanel.getSeqPanel().setCursorColumn();
 626           }
 627           break;
 628         case KeyEvent.VK_P:
 629           if (viewport.cursorMode)
 630           {
 631             alignPanel.getSeqPanel().setCursorPosition();
 632           }
 633           break;
 634
 635         case KeyEvent.VK_ENTER:
 636         case KeyEvent.VK_COMMA:
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().setCursorRowAndColumn();
 640           }
 641           break;
 642
 643         case KeyEvent.VK_Q:
 644           if (viewport.cursorMode)
 645           {
 646             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 647           }
 648           break;
 649         case KeyEvent.VK_M:
 650           if (viewport.cursorMode)
 651           {
 652             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 653           }
 654           break;
 655
 656         case KeyEvent.VK_F2:
 657           viewport.cursorMode = !viewport.cursorMode;
 658           statusBar.setText(MessageManager
 659                   .formatMessage("label.keyboard_editing_mode", new String[]
 660                   { (viewport.cursorMode ? "on" : "off") }));
 661           if (viewport.cursorMode)
 662           {
 663             ViewportRanges ranges = viewport.getRanges();
 664             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 665                     .getStartRes();
 666             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 667                     .getStartSeq();
 668           }
 669           alignPanel.getSeqPanel().seqCanvas.repaint();
 670           break;
 671
 672         case KeyEvent.VK_F1:
 673           try
 674           {
 675             Help.showHelpWindow();
 676           } catch (Exception ex)
 677           {
 678             ex.printStackTrace();
 679           }
 680           break;
 681         case KeyEvent.VK_H:
 682         {
 683           boolean toggleSeqs = !evt.isControlDown();
 684           boolean toggleCols = !evt.isShiftDown();
 685           toggleHiddenRegions(toggleSeqs, toggleCols);
 686           break;
 687         }
 688         case KeyEvent.VK_B:
 689         {
 690           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 691           boolean modifyExisting = true; // always modify, don't clear
 692                                          // evt.isShiftDown();
 693           boolean invertHighlighted = evt.isAltDown();
 694           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 695                   toggleSel);
 696           break;
 697         }
 698         case KeyEvent.VK_PAGE_UP:
 699           viewport.getRanges().pageUp();
 700           break;
 701         case KeyEvent.VK_PAGE_DOWN:
 702           viewport.getRanges().pageDown();
 703           break;
 704         }
 705       }
 706
 707       @Override
 708       public void keyReleased(KeyEvent evt)
 709       {
 710         switch (evt.getKeyCode())
 711         {
 712         case KeyEvent.VK_LEFT:
 713           if (evt.isAltDown() || !viewport.cursorMode)
 714           {
 715             viewport.firePropertyChange("alignment", null,
 716                     viewport.getAlignment().getSequences());
 717           }
 718           break;
 719
 720         case KeyEvent.VK_RIGHT:
 721           if (evt.isAltDown() || !viewport.cursorMode)
 722           {
 723             viewport.firePropertyChange("alignment", null,
 724                     viewport.getAlignment().getSequences());
 725           }
 726           break;
 727         }
 728       }
 729     });
 730   }
 731
 732   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 733   {
 734     ap.alignFrame = this;
 735     avc = new jalview.controller.AlignViewController(this, viewport,
 736             alignPanel);
 737
 738     alignPanels.add(ap);
 739
 740     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 741
 742     int aSize = alignPanels.size();
 743
 744     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 745
 746     if (aSize == 1 && ap.av.viewName == null)
 747     {
 748       this.getContentPane().add(ap, BorderLayout.CENTER);
 749     }
 750     else
 751     {
 752       if (aSize == 2)
 753       {
 754         setInitialTabVisible();
 755       }
 756
 757       expandViews.setEnabled(true);
 758       gatherViews.setEnabled(true);
 759       tabbedPane.addTab(ap.av.viewName, ap);
 760
 761       ap.setVisible(false);
 762     }
 763
 764     if (newPanel)
 765     {
 766       if (ap.av.isPadGaps())
 767       {
 768         ap.av.getAlignment().padGaps();
 769       }
 770       ap.av.updateConservation(ap);
 771       ap.av.updateConsensus(ap);
 772       ap.av.updateStrucConsensus(ap);
 773     }
 774   }
 775
 776   public void setInitialTabVisible()
 777   {
 778     expandViews.setEnabled(true);
 779     gatherViews.setEnabled(true);
 780     tabbedPane.setVisible(true);
 781     AlignmentPanel first = alignPanels.get(0);
 782     tabbedPane.addTab(first.av.viewName, first);
 783     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 784   }
 785
 786   public AlignViewport getViewport()
 787   {
 788     return viewport;
 789   }
 790
 791   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 792   private void addServiceListeners()
 793   {
 794     final java.beans.PropertyChangeListener thisListener;
 795     Desktop.instance.addJalviewPropertyChangeListener("services",
 796             thisListener = new java.beans.PropertyChangeListener()
 797             {
 798               @Override
 799               public void propertyChange(PropertyChangeEvent evt)
 800               {
 801                 // // System.out.println("Discoverer property change.");
 802                 // if (evt.getPropertyName().equals("services"))
 803                 {
 804                   SwingUtilities.invokeLater(new Runnable()
 805                   {
 806
 807                     @Override
 808                     public void run()
 809                     {
 810                       System.err.println(
 811                               "Rebuild WS Menu for service change");
 812                       BuildWebServiceMenu();
 813                     }
 814
 815                   });
 816                 }
 817               }
 818             });
 819     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 820     {
 821       @Override
 822       public void internalFrameClosed(
 823               javax.swing.event.InternalFrameEvent evt)
 824       {
 825         // System.out.println("deregistering discoverer listener");
 826         Desktop.instance.removeJalviewPropertyChangeListener("services",
 827                 thisListener);
 828         closeMenuItem_actionPerformed(true);
 829       };
 830     });
 831     // Finally, build the menu once to get current service state
 832     new Thread(new Runnable()
 833     {
 834       @Override
 835       public void run()
 836       {
 837         BuildWebServiceMenu();
 838       }
 839     }).start();
 840   }
 841
 842   /**
 843    * Configure menu items that vary according to whether the alignment is
 844    * nucleotide or protein
 845    */
 846   public void setGUINucleotide()
 847   {
 848     AlignmentI al = getViewport().getAlignment();
 849     boolean nucleotide = al.isNucleotide();
 850
 851     loadVcf.setVisible(nucleotide);
 852     showTranslation.setVisible(nucleotide);
 853     showReverse.setVisible(nucleotide);
 854     showReverseComplement.setVisible(nucleotide);
 855     conservationMenuItem.setEnabled(!nucleotide);
 856     modifyConservation
 857             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 858     showGroupConservation.setEnabled(!nucleotide);
 859
 860     showComplementMenuItem
 861             .setText(nucleotide ? MessageManager.getString("label.protein")
 862                     : MessageManager.getString("label.nucleotide"));
 863   }
 864
 865   /**
 866    * set up menus for the current viewport. This may be called after any
 867    * operation that affects the data in the current view (selection changed,
 868    * etc) to update the menus to reflect the new state.
 869    */
 870   @Override
 871   public void setMenusForViewport()
 872   {
 873     setMenusFromViewport(viewport);
 874   }
 875
 876   /**
 877    * Need to call this method when tabs are selected for multiple views, or when
 878    * loading from Jalview2XML.java
 879    *
 880    * @param av
 881    *          AlignViewport
 882    */
 883   void setMenusFromViewport(AlignViewport av)
 884   {
 885     padGapsMenuitem.setSelected(av.isPadGaps());
 886     colourTextMenuItem.setSelected(av.isShowColourText());
 887     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 888     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 889     conservationMenuItem.setSelected(av.getConservationSelected());
 890     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 891     seqLimits.setSelected(av.getShowJVSuffix());
 892     idRightAlign.setSelected(av.isRightAlignIds());
 893     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 894     renderGapsMenuItem.setSelected(av.isRenderGaps());
 895     wrapMenuItem.setSelected(av.getWrapAlignment());
 896     scaleAbove.setVisible(av.getWrapAlignment());
 897     scaleLeft.setVisible(av.getWrapAlignment());
 898     scaleRight.setVisible(av.getWrapAlignment());
 899     annotationPanelMenuItem.setState(av.isShowAnnotation());
 900     /*
 901      * Show/hide annotations only enabled if annotation panel is shown
 902      */
 903     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 905     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 906     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 907     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 908     viewTextMenuItem.setSelected(av.getShowText());
 909     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 910     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 911     showGroupConservation.setSelected(av.isShowGroupConservation());
 912     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 913     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 914     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 915
 916     ColourMenuHelper.setColourSelected(colourMenu,
 917             av.getGlobalColourScheme());
 918
 919     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 920     hiddenMarkers.setState(av.getShowHiddenMarkers());
 921     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 922     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 923     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 924     autoCalculate.setSelected(av.autoCalculateConsensus);
 925     sortByTree.setSelected(av.sortByTree);
 926     listenToViewSelections.setSelected(av.followSelection);
 927
 928     showProducts.setEnabled(canShowProducts());
 929     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 930
 931     updateEditMenuBar();
 932   }
 933
 934   /**
 935    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 936    *
 937    * @param b
 938    */
 939   public void setGroovyEnabled(boolean b)
 940   {
 941     runGroovy.setEnabled(b);
 942   }
 943
 944   private IProgressIndicator progressBar;
 945
 946   /*
 947    * (non-Javadoc)
 948    *
 949    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 950    */
 951   @Override
 952   public void setProgressBar(String message, long id)
 953   {
 954     progressBar.setProgressBar(message, id);
 955   }
 956
 957   @Override
 958   public void registerHandler(final long id,
 959           final IProgressIndicatorHandler handler)
 960   {
 961     progressBar.registerHandler(id, handler);
 962   }
 963
 964   /**
 965    *
 966    * @return true if any progress bars are still active
 967    */
 968   @Override
 969   public boolean operationInProgress()
 970   {
 971     return progressBar.operationInProgress();
 972   }
 973
 974   @Override
 975   public void setStatus(String text)
 976   {
 977     statusBar.setText(text);
 978   }
 979
 980   /*
 981    * Added so Castor Mapping file can obtain Jalview Version
 982    */
 983   public String getVersion()
 984   {
 985     return jalview.bin.Cache.getProperty("VERSION");
 986   }
 987
 988   public FeatureRenderer getFeatureRenderer()
 989   {
 990     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 991   }
 992
 993   @Override
 994   public void fetchSequence_actionPerformed(ActionEvent e)
 995   {
 996     new jalview.gui.SequenceFetcher(this);
 997   }
 998
 999   @Override
1000   public void addFromFile_actionPerformed(ActionEvent e)
1001   {
1002     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1003   }
1004
1005   @Override
1006   public void reload_actionPerformed(ActionEvent e)
1007   {
1008     if (fileName != null)
1009     {
1010       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1011       // originating file's format
1012       // TODO: work out how to recover feature settings for correct view(s) when
1013       // file is reloaded.
1014       if (FileFormat.Jalview.equals(currentFileFormat))
1015       {
1016         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1017         for (int i = 0; i < frames.length; i++)
1018         {
1019           if (frames[i] instanceof AlignFrame && frames[i] != this
1020                   && ((AlignFrame) frames[i]).fileName != null
1021                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1022           {
1023             try
1024             {
1025               frames[i].setSelected(true);
1026               Desktop.instance.closeAssociatedWindows();
1027             } catch (java.beans.PropertyVetoException ex)
1028             {
1029             }
1030           }
1031
1032         }
1033         Desktop.instance.closeAssociatedWindows();
1034
1035         FileLoader loader = new FileLoader();
1036         DataSourceType protocol = fileName.startsWith("http:")
1037                 ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1040       }
1041       else
1042       {
1043         Rectangle bounds = this.getBounds();
1044
1045         FileLoader loader = new FileLoader();
1046         DataSourceType protocol = fileName.startsWith("http:")
1047                 ? DataSourceType.URL
1048                 : DataSourceType.FILE;
1049         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1050                 protocol, currentFileFormat);
1051
1052         newframe.setBounds(bounds);
1053         if (featureSettings != null && featureSettings.isShowing())
1054         {
1055           final Rectangle fspos = featureSettings.frame.getBounds();
1056           // TODO: need a 'show feature settings' function that takes bounds -
1057           // need to refactor Desktop.addFrame
1058           newframe.featureSettings_actionPerformed(null);
1059           final FeatureSettings nfs = newframe.featureSettings;
1060           SwingUtilities.invokeLater(new Runnable()
1061           {
1062             @Override
1063             public void run()
1064             {
1065               nfs.frame.setBounds(fspos);
1066             }
1067           });
1068           this.featureSettings.close();
1069           this.featureSettings = null;
1070         }
1071         this.closeMenuItem_actionPerformed(true);
1072       }
1073     }
1074   }
1075
1076   @Override
1077   public void addFromText_actionPerformed(ActionEvent e)
1078   {
1079     Desktop.instance
1080             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1081   }
1082
1083   @Override
1084   public void addFromURL_actionPerformed(ActionEvent e)
1085   {
1086     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1087   }
1088
1089   @Override
1090   public void save_actionPerformed(ActionEvent e)
1091   {
1092     if (fileName == null || (currentFileFormat == null)
1093             || fileName.startsWith("http"))
1094     {
1095       saveAs_actionPerformed(null);
1096     }
1097     else
1098     {
1099       saveAlignment(fileName, currentFileFormat);
1100     }
1101   }
1102
1103   /**
1104    * DOCUMENT ME!
1105    *
1106    * @param e
1107    *          DOCUMENT ME!
1108    */
1109   @Override
1110   public void saveAs_actionPerformed(ActionEvent e)
1111   {
1112     String format = currentFileFormat == null ? null
1113             : currentFileFormat.getName();
1114     JalviewFileChooser chooser = JalviewFileChooser
1115             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1116
1117     chooser.setFileView(new JalviewFileView());
1118     chooser.setDialogTitle(
1119             MessageManager.getString("label.save_alignment_to_file"));
1120     chooser.setToolTipText(MessageManager.getString("action.save"));
1121
1122     int value = chooser.showSaveDialog(this);
1123
1124     if (value == JalviewFileChooser.APPROVE_OPTION)
1125     {
1126       currentFileFormat = chooser.getSelectedFormat();
1127       while (currentFileFormat == null)
1128       {
1129         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1130                 MessageManager.getString(
1131                         "label.select_file_format_before_saving"),
1132                 MessageManager.getString("label.file_format_not_specified"),
1133                 JvOptionPane.WARNING_MESSAGE);
1134         currentFileFormat = chooser.getSelectedFormat();
1135         value = chooser.showSaveDialog(this);
1136         if (value != JalviewFileChooser.APPROVE_OPTION)
1137         {
1138           return;
1139         }
1140       }
1141
1142       fileName = chooser.getSelectedFile().getPath();
1143
1144       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1145
1146       Cache.setProperty("LAST_DIRECTORY", fileName);
1147       saveAlignment(fileName, currentFileFormat);
1148     }
1149   }
1150
1151   public boolean saveAlignment(String file, FileFormatI format)
1152   {
1153     boolean success = true;
1154
1155     if (FileFormat.Jalview.equals(format))
1156     {
1157       String shortName = title;
1158
1159       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160       {
1161         shortName = shortName.substring(
1162                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1163       }
1164
1165       success = new Jalview2XML().saveAlignment(this, file, shortName);
1166
1167       statusBar.setText(MessageManager.formatMessage(
1168               "label.successfully_saved_to_file_in_format", new Object[]
1169               { fileName, format }));
1170
1171     }
1172     else
1173     {
1174       AlignmentExportData exportData = getAlignmentForExport(format,
1175               viewport, null);
1176       if (exportData.getSettings().isCancelled())
1177       {
1178         return false;
1179       }
1180       FormatAdapter f = new FormatAdapter(alignPanel,
1181               exportData.getSettings());
1182       String output = f.formatSequences(format, exportData.getAlignment(), // class
1183                                                                            // cast
1184                                                                            // exceptions
1185                                                                            // will
1186               // occur in the distant future
1187               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1188               f.getCacheSuffixDefault(format),
1189               viewport.getAlignment().getHiddenColumns());
1190
1191       if (output == null)
1192       {
1193         success = false;
1194       }
1195       else
1196       {
1197         try
1198         {
1199           PrintWriter out = new PrintWriter(new FileWriter(file));
1200
1201           out.print(output);
1202           out.close();
1203           this.setTitle(file);
1204           statusBar.setText(MessageManager.formatMessage(
1205                   "label.successfully_saved_to_file_in_format", new Object[]
1206                   { fileName, format.getName() }));
1207         } catch (Exception ex)
1208         {
1209           success = false;
1210           ex.printStackTrace();
1211         }
1212       }
1213     }
1214
1215     if (!success)
1216     {
1217       JvOptionPane.showInternalMessageDialog(this, MessageManager
1218               .formatMessage("label.couldnt_save_file", new Object[]
1219               { fileName }),
1220               MessageManager.getString("label.error_saving_file"),
1221               JvOptionPane.WARNING_MESSAGE);
1222     }
1223
1224     return success;
1225   }
1226
1227   private void warningMessage(String warning, String title)
1228   {
1229     if (new jalview.util.Platform().isHeadless())
1230     {
1231       System.err.println("Warning: " + title + "\nWarning: " + warning);
1232
1233     }
1234     else
1235     {
1236       JvOptionPane.showInternalMessageDialog(this, warning, title,
1237               JvOptionPane.WARNING_MESSAGE);
1238     }
1239     return;
1240   }
1241
1242   /**
1243    * DOCUMENT ME!
1244    *
1245    * @param e
1246    *          DOCUMENT ME!
1247    */
1248   @Override
1249   protected void outputText_actionPerformed(ActionEvent e)
1250   {
1251     FileFormatI fileFormat = FileFormats.getInstance()
1252             .forName(e.getActionCommand());
1253     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1254             viewport, null);
1255     if (exportData.getSettings().isCancelled())
1256     {
1257       return;
1258     }
1259     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1260     cap.setForInput(null);
1261     try
1262     {
1263       FileFormatI format = fileFormat;
1264       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1265               .formatSequences(format, exportData.getAlignment(),
1266                       exportData.getOmitHidden(),
1267                       exportData.getStartEndPostions(),
1268                       viewport.getAlignment().getHiddenColumns()));
1269       Desktop.addInternalFrame(cap, MessageManager
1270               .formatMessage("label.alignment_output_command", new Object[]
1271               { e.getActionCommand() }), 600, 500);
1272     } catch (OutOfMemoryError oom)
1273     {
1274       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1275               oom);
1276       cap.dispose();
1277     }
1278
1279   }
1280
1281   public static AlignmentExportData getAlignmentForExport(
1282           FileFormatI format, AlignViewportI viewport,
1283           AlignExportSettingI exportSettings)
1284   {
1285     AlignmentI alignmentToExport = null;
1286     AlignExportSettingI settings = exportSettings;
1287     String[] omitHidden = null;
1288
1289     HiddenSequences hiddenSeqs = viewport.getAlignment()
1290             .getHiddenSequences();
1291
1292     alignmentToExport = viewport.getAlignment();
1293
1294     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1295     if (settings == null)
1296     {
1297       settings = new AlignExportSettings(hasHiddenSeqs,
1298               viewport.hasHiddenColumns(), format);
1299     }
1300     // settings.isExportAnnotations();
1301
1302     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1303     {
1304       omitHidden = viewport.getViewAsString(false,
1305               settings.isExportHiddenSequences());
1306     }
1307
1308     int[] alignmentStartEnd = new int[2];
1309     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1310     {
1311       alignmentToExport = hiddenSeqs.getFullAlignment();
1312     }
1313     else
1314     {
1315       alignmentToExport = viewport.getAlignment();
1316     }
1317     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1318             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1319     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1320             omitHidden, alignmentStartEnd, settings);
1321     return ed;
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    *
1327    * @param e
1328    *          DOCUMENT ME!
1329    */
1330   @Override
1331   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1332   {
1333     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1334     htmlSVG.exportHTML(null);
1335   }
1336
1337   @Override
1338   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1339   {
1340     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1341     bjs.exportHTML(null);
1342   }
1343
1344   public void createImageMap(File file, String image)
1345   {
1346     alignPanel.makePNGImageMap(file, image);
1347   }
1348
1349   /**
1350    * DOCUMENT ME!
1351    *
1352    * @param e
1353    *          DOCUMENT ME!
1354    */
1355   @Override
1356   public void createPNG(File f)
1357   {
1358     alignPanel.makePNG(f);
1359   }
1360
1361   /**
1362    * DOCUMENT ME!
1363    *
1364    * @param e
1365    *          DOCUMENT ME!
1366    */
1367   @Override
1368   public void createEPS(File f)
1369   {
1370     alignPanel.makeEPS(f);
1371   }
1372
1373   @Override
1374   public void createSVG(File f)
1375   {
1376     alignPanel.makeSVG(f);
1377   }
1378
1379   @Override
1380   public void pageSetup_actionPerformed(ActionEvent e)
1381   {
1382     PrinterJob printJob = PrinterJob.getPrinterJob();
1383     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1384   }
1385
1386   /**
1387    * DOCUMENT ME!
1388    *
1389    * @param e
1390    *          DOCUMENT ME!
1391    */
1392   @Override
1393   public void printMenuItem_actionPerformed(ActionEvent e)
1394   {
1395     // Putting in a thread avoids Swing painting problems
1396     PrintThread thread = new PrintThread(alignPanel);
1397     thread.start();
1398   }
1399
1400   @Override
1401   public void exportFeatures_actionPerformed(ActionEvent e)
1402   {
1403     new AnnotationExporter(alignPanel).exportFeatures();
1404   }
1405
1406   @Override
1407   public void exportAnnotations_actionPerformed(ActionEvent e)
1408   {
1409     new AnnotationExporter(alignPanel).exportAnnotations();
1410   }
1411
1412   @Override
1413   public void associatedData_actionPerformed(ActionEvent e)
1414   {
1415     // Pick the tree file
1416     JalviewFileChooser chooser = new JalviewFileChooser(
1417             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1418     chooser.setFileView(new JalviewFileView());
1419     chooser.setDialogTitle(
1420             MessageManager.getString("label.load_jalview_annotations"));
1421     chooser.setToolTipText(
1422             MessageManager.getString("label.load_jalview_annotations"));
1423
1424     int value = chooser.showOpenDialog(null);
1425
1426     if (value == JalviewFileChooser.APPROVE_OPTION)
1427     {
1428       String choice = chooser.getSelectedFile().getPath();
1429       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1430       loadJalviewDataFile(choice, null, null, null);
1431     }
1432
1433   }
1434
1435   /**
1436    * Close the current view or all views in the alignment frame. If the frame
1437    * only contains one view then the alignment will be removed from memory.
1438    *
1439    * @param closeAllTabs
1440    */
1441   @Override
1442   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1443   {
1444     if (alignPanels != null && alignPanels.size() < 2)
1445     {
1446       closeAllTabs = true;
1447     }
1448
1449     try
1450     {
1451       if (alignPanels != null)
1452       {
1453         if (closeAllTabs)
1454         {
1455           if (this.isClosed())
1456           {
1457             // really close all the windows - otherwise wait till
1458             // setClosed(true) is called
1459             for (int i = 0; i < alignPanels.size(); i++)
1460             {
1461               AlignmentPanel ap = alignPanels.get(i);
1462               ap.closePanel();
1463             }
1464           }
1465         }
1466         else
1467         {
1468           closeView(alignPanel);
1469         }
1470       }
1471
1472       if (closeAllTabs)
1473       {
1474         /*
1475          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1476          * be called recursively, with the frame now in 'closed' state
1477          */
1478         this.setClosed(true);
1479       }
1480     } catch (Exception ex)
1481     {
1482       ex.printStackTrace();
1483     }
1484   }
1485
1486   /**
1487    * Close the specified panel and close up tabs appropriately.
1488    *
1489    * @param panelToClose
1490    */
1491   public void closeView(AlignmentPanel panelToClose)
1492   {
1493     int index = tabbedPane.getSelectedIndex();
1494     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1495     alignPanels.remove(panelToClose);
1496     panelToClose.closePanel();
1497     panelToClose = null;
1498
1499     tabbedPane.removeTabAt(closedindex);
1500     tabbedPane.validate();
1501
1502     if (index > closedindex || index == tabbedPane.getTabCount())
1503     {
1504       // modify currently selected tab index if necessary.
1505       index--;
1506     }
1507
1508     this.tabSelectionChanged(index);
1509   }
1510
1511   /**
1512    * DOCUMENT ME!
1513    */
1514   void updateEditMenuBar()
1515   {
1516
1517     if (viewport.getHistoryList().size() > 0)
1518     {
1519       undoMenuItem.setEnabled(true);
1520       CommandI command = viewport.getHistoryList().peek();
1521       undoMenuItem.setText(MessageManager
1522               .formatMessage("label.undo_command", new Object[]
1523               { command.getDescription() }));
1524     }
1525     else
1526     {
1527       undoMenuItem.setEnabled(false);
1528       undoMenuItem.setText(MessageManager.getString("action.undo"));
1529     }
1530
1531     if (viewport.getRedoList().size() > 0)
1532     {
1533       redoMenuItem.setEnabled(true);
1534
1535       CommandI command = viewport.getRedoList().peek();
1536       redoMenuItem.setText(MessageManager
1537               .formatMessage("label.redo_command", new Object[]
1538               { command.getDescription() }));
1539     }
1540     else
1541     {
1542       redoMenuItem.setEnabled(false);
1543       redoMenuItem.setText(MessageManager.getString("action.redo"));
1544     }
1545   }
1546
1547   @Override
1548   public void addHistoryItem(CommandI command)
1549   {
1550     if (command.getSize() > 0)
1551     {
1552       viewport.addToHistoryList(command);
1553       viewport.clearRedoList();
1554       updateEditMenuBar();
1555       viewport.updateHiddenColumns();
1556       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1557       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1558       // viewport.getColumnSelection()
1559       // .getHiddenColumns().size() > 0);
1560     }
1561   }
1562
1563   /**
1564    *
1565    * @return alignment objects for all views
1566    */
1567   AlignmentI[] getViewAlignments()
1568   {
1569     if (alignPanels != null)
1570     {
1571       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1572       int i = 0;
1573       for (AlignmentPanel ap : alignPanels)
1574       {
1575         als[i++] = ap.av.getAlignment();
1576       }
1577       return als;
1578     }
1579     if (viewport != null)
1580     {
1581       return new AlignmentI[] { viewport.getAlignment() };
1582     }
1583     return null;
1584   }
1585
1586   /**
1587    * DOCUMENT ME!
1588    *
1589    * @param e
1590    *          DOCUMENT ME!
1591    */
1592   @Override
1593   protected void undoMenuItem_actionPerformed(ActionEvent e)
1594   {
1595     if (viewport.getHistoryList().isEmpty())
1596     {
1597       return;
1598     }
1599     CommandI command = viewport.getHistoryList().pop();
1600     viewport.addToRedoList(command);
1601     command.undoCommand(getViewAlignments());
1602
1603     AlignmentViewport originalSource = getOriginatingSource(command);
1604     updateEditMenuBar();
1605
1606     if (originalSource != null)
1607     {
1608       if (originalSource != viewport)
1609       {
1610         Cache.log.warn(
1611                 "Implementation worry: mismatch of viewport origin for undo");
1612       }
1613       originalSource.updateHiddenColumns();
1614       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1615       // null
1616       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1617       // viewport.getColumnSelection()
1618       // .getHiddenColumns().size() > 0);
1619       originalSource.firePropertyChange("alignment", null,
1620               originalSource.getAlignment().getSequences());
1621     }
1622   }
1623
1624   /**
1625    * DOCUMENT ME!
1626    *
1627    * @param e
1628    *          DOCUMENT ME!
1629    */
1630   @Override
1631   protected void redoMenuItem_actionPerformed(ActionEvent e)
1632   {
1633     if (viewport.getRedoList().size() < 1)
1634     {
1635       return;
1636     }
1637
1638     CommandI command = viewport.getRedoList().pop();
1639     viewport.addToHistoryList(command);
1640     command.doCommand(getViewAlignments());
1641
1642     AlignmentViewport originalSource = getOriginatingSource(command);
1643     updateEditMenuBar();
1644
1645     if (originalSource != null)
1646     {
1647
1648       if (originalSource != viewport)
1649       {
1650         Cache.log.warn(
1651                 "Implementation worry: mismatch of viewport origin for redo");
1652       }
1653       originalSource.updateHiddenColumns();
1654       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655       // null
1656       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657       // viewport.getColumnSelection()
1658       // .getHiddenColumns().size() > 0);
1659       originalSource.firePropertyChange("alignment", null,
1660               originalSource.getAlignment().getSequences());
1661     }
1662   }
1663
1664   AlignmentViewport getOriginatingSource(CommandI command)
1665   {
1666     AlignmentViewport originalSource = null;
1667     // For sequence removal and addition, we need to fire
1668     // the property change event FROM the viewport where the
1669     // original alignment was altered
1670     AlignmentI al = null;
1671     if (command instanceof EditCommand)
1672     {
1673       EditCommand editCommand = (EditCommand) command;
1674       al = editCommand.getAlignment();
1675       List<Component> comps = PaintRefresher.components
1676               .get(viewport.getSequenceSetId());
1677
1678       for (Component comp : comps)
1679       {
1680         if (comp instanceof AlignmentPanel)
1681         {
1682           if (al == ((AlignmentPanel) comp).av.getAlignment())
1683           {
1684             originalSource = ((AlignmentPanel) comp).av;
1685             break;
1686           }
1687         }
1688       }
1689     }
1690
1691     if (originalSource == null)
1692     {
1693       // The original view is closed, we must validate
1694       // the current view against the closed view first
1695       if (al != null)
1696       {
1697         PaintRefresher.validateSequences(al, viewport.getAlignment());
1698       }
1699
1700       originalSource = viewport;
1701     }
1702
1703     return originalSource;
1704   }
1705
1706   /**
1707    * DOCUMENT ME!
1708    *
1709    * @param up
1710    *          DOCUMENT ME!
1711    */
1712   public void moveSelectedSequences(boolean up)
1713   {
1714     SequenceGroup sg = viewport.getSelectionGroup();
1715
1716     if (sg == null)
1717     {
1718       return;
1719     }
1720     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1721             viewport.getHiddenRepSequences(), up);
1722     alignPanel.paintAlignment(true, false);
1723   }
1724
1725   synchronized void slideSequences(boolean right, int size)
1726   {
1727     List<SequenceI> sg = new ArrayList<>();
1728     if (viewport.cursorMode)
1729     {
1730       sg.add(viewport.getAlignment()
1731               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1732     }
1733     else if (viewport.getSelectionGroup() != null
1734             && viewport.getSelectionGroup().getSize() != viewport
1735                     .getAlignment().getHeight())
1736     {
1737       sg = viewport.getSelectionGroup()
1738               .getSequences(viewport.getHiddenRepSequences());
1739     }
1740
1741     if (sg.size() < 1)
1742     {
1743       return;
1744     }
1745
1746     List<SequenceI> invertGroup = new ArrayList<>();
1747
1748     for (SequenceI seq : viewport.getAlignment().getSequences())
1749     {
1750       if (!sg.contains(seq))
1751       {
1752         invertGroup.add(seq);
1753       }
1754     }
1755
1756     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1757
1758     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1759     for (int i = 0; i < invertGroup.size(); i++)
1760     {
1761       seqs2[i] = invertGroup.get(i);
1762     }
1763
1764     SlideSequencesCommand ssc;
1765     if (right)
1766     {
1767       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1768               viewport.getGapCharacter());
1769     }
1770     else
1771     {
1772       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1773               viewport.getGapCharacter());
1774     }
1775
1776     int groupAdjustment = 0;
1777     if (ssc.getGapsInsertedBegin() && right)
1778     {
1779       if (viewport.cursorMode)
1780       {
1781         alignPanel.getSeqPanel().moveCursor(size, 0);
1782       }
1783       else
1784       {
1785         groupAdjustment = size;
1786       }
1787     }
1788     else if (!ssc.getGapsInsertedBegin() && !right)
1789     {
1790       if (viewport.cursorMode)
1791       {
1792         alignPanel.getSeqPanel().moveCursor(-size, 0);
1793       }
1794       else
1795       {
1796         groupAdjustment = -size;
1797       }
1798     }
1799
1800     if (groupAdjustment != 0)
1801     {
1802       viewport.getSelectionGroup().setStartRes(
1803               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804       viewport.getSelectionGroup().setEndRes(
1805               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1806     }
1807
1808     /*
1809      * just extend the last slide command if compatible; but not if in
1810      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1811      */
1812     boolean appendHistoryItem = false;
1813     Deque<CommandI> historyList = viewport.getHistoryList();
1814     boolean inSplitFrame = getSplitViewContainer() != null;
1815     if (!inSplitFrame && historyList != null && historyList.size() > 0
1816             && historyList.peek() instanceof SlideSequencesCommand)
1817     {
1818       appendHistoryItem = ssc.appendSlideCommand(
1819               (SlideSequencesCommand) historyList.peek());
1820     }
1821
1822     if (!appendHistoryItem)
1823     {
1824       addHistoryItem(ssc);
1825     }
1826
1827     repaint();
1828   }
1829
1830   /**
1831    * DOCUMENT ME!
1832    *
1833    * @param e
1834    *          DOCUMENT ME!
1835    */
1836   @Override
1837   protected void copy_actionPerformed(ActionEvent e)
1838   {
1839     if (viewport.getSelectionGroup() == null)
1840     {
1841       return;
1842     }
1843     // TODO: preserve the ordering of displayed alignment annotation in any
1844     // internal paste (particularly sequence associated annotation)
1845     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1846     String[] omitHidden = null;
1847
1848     if (viewport.hasHiddenColumns())
1849     {
1850       omitHidden = viewport.getViewAsString(true);
1851     }
1852
1853     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1854             seqs, omitHidden, null);
1855
1856     StringSelection ss = new StringSelection(output);
1857
1858     try
1859     {
1860       jalview.gui.Desktop.internalCopy = true;
1861       // Its really worth setting the clipboard contents
1862       // to empty before setting the large StringSelection!!
1863       Toolkit.getDefaultToolkit().getSystemClipboard()
1864               .setContents(new StringSelection(""), null);
1865
1866       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1867               Desktop.instance);
1868     } catch (OutOfMemoryError er)
1869     {
1870       new OOMWarning("copying region", er);
1871       return;
1872     }
1873
1874     HiddenColumns hiddenColumns = null;
1875     if (viewport.hasHiddenColumns())
1876     {
1877       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1878       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1879
1880       // create new HiddenColumns object with copy of hidden regions
1881       // between startRes and endRes, offset by startRes
1882       hiddenColumns = new HiddenColumns(
1883               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1884               hiddenCutoff, hiddenOffset);
1885     }
1886
1887     Desktop.jalviewClipboard = new Object[] { seqs,
1888         viewport.getAlignment().getDataset(), hiddenColumns };
1889     statusBar.setText(MessageManager.formatMessage(
1890             "label.copied_sequences_to_clipboard", new Object[]
1891             { Integer.valueOf(seqs.length).toString() }));
1892   }
1893
1894   /**
1895    * DOCUMENT ME!
1896    *
1897    * @param e
1898    *          DOCUMENT ME!
1899    */
1900   @Override
1901   protected void pasteNew_actionPerformed(ActionEvent e)
1902   {
1903     paste(true);
1904   }
1905
1906   /**
1907    * DOCUMENT ME!
1908    *
1909    * @param e
1910    *          DOCUMENT ME!
1911    */
1912   @Override
1913   protected void pasteThis_actionPerformed(ActionEvent e)
1914   {
1915     paste(false);
1916   }
1917
1918   /**
1919    * Paste contents of Jalview clipboard
1920    *
1921    * @param newAlignment
1922    *          true to paste to a new alignment, otherwise add to this.
1923    */
1924   void paste(boolean newAlignment)
1925   {
1926     boolean externalPaste = true;
1927     try
1928     {
1929       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1930       Transferable contents = c.getContents(this);
1931
1932       if (contents == null)
1933       {
1934         return;
1935       }
1936
1937       String str;
1938       FileFormatI format;
1939       try
1940       {
1941         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1942         if (str.length() < 1)
1943         {
1944           return;
1945         }
1946
1947         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1948
1949       } catch (OutOfMemoryError er)
1950       {
1951         new OOMWarning("Out of memory pasting sequences!!", er);
1952         return;
1953       }
1954
1955       SequenceI[] sequences;
1956       boolean annotationAdded = false;
1957       AlignmentI alignment = null;
1958
1959       if (Desktop.jalviewClipboard != null)
1960       {
1961         // The clipboard was filled from within Jalview, we must use the
1962         // sequences
1963         // And dataset from the copied alignment
1964         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1965         // be doubly sure that we create *new* sequence objects.
1966         sequences = new SequenceI[newseq.length];
1967         for (int i = 0; i < newseq.length; i++)
1968         {
1969           sequences[i] = new Sequence(newseq[i]);
1970         }
1971         alignment = new Alignment(sequences);
1972         externalPaste = false;
1973       }
1974       else
1975       {
1976         // parse the clipboard as an alignment.
1977         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1978                 format);
1979         sequences = alignment.getSequencesArray();
1980       }
1981
1982       int alwidth = 0;
1983       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1984       int fgroup = -1;
1985
1986       if (newAlignment)
1987       {
1988
1989         if (Desktop.jalviewClipboard != null)
1990         {
1991           // dataset is inherited
1992           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1993         }
1994         else
1995         {
1996           // new dataset is constructed
1997           alignment.setDataset(null);
1998         }
1999         alwidth = alignment.getWidth() + 1;
2000       }
2001       else
2002       {
2003         AlignmentI pastedal = alignment; // preserve pasted alignment object
2004         // Add pasted sequences and dataset into existing alignment.
2005         alignment = viewport.getAlignment();
2006         alwidth = alignment.getWidth() + 1;
2007         // decide if we need to import sequences from an existing dataset
2008         boolean importDs = Desktop.jalviewClipboard != null
2009                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2010         // importDs==true instructs us to copy over new dataset sequences from
2011         // an existing alignment
2012         Vector newDs = (importDs) ? new Vector() : null; // used to create
2013         // minimum dataset set
2014
2015         for (int i = 0; i < sequences.length; i++)
2016         {
2017           if (importDs)
2018           {
2019             newDs.addElement(null);
2020           }
2021           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2022           // paste
2023           if (importDs && ds != null)
2024           {
2025             if (!newDs.contains(ds))
2026             {
2027               newDs.setElementAt(ds, i);
2028               ds = new Sequence(ds);
2029               // update with new dataset sequence
2030               sequences[i].setDatasetSequence(ds);
2031             }
2032             else
2033             {
2034               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2035             }
2036           }
2037           else
2038           {
2039             // copy and derive new dataset sequence
2040             sequences[i] = sequences[i].deriveSequence();
2041             alignment.getDataset()
2042                     .addSequence(sequences[i].getDatasetSequence());
2043             // TODO: avoid creation of duplicate dataset sequences with a
2044             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2045           }
2046           alignment.addSequence(sequences[i]); // merges dataset
2047         }
2048         if (newDs != null)
2049         {
2050           newDs.clear(); // tidy up
2051         }
2052         if (alignment.getAlignmentAnnotation() != null)
2053         {
2054           for (AlignmentAnnotation alan : alignment
2055                   .getAlignmentAnnotation())
2056           {
2057             if (alan.graphGroup > fgroup)
2058             {
2059               fgroup = alan.graphGroup;
2060             }
2061           }
2062         }
2063         if (pastedal.getAlignmentAnnotation() != null)
2064         {
2065           // Add any annotation attached to alignment.
2066           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2067           for (int i = 0; i < alann.length; i++)
2068           {
2069             annotationAdded = true;
2070             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2071             {
2072               AlignmentAnnotation newann = new AlignmentAnnotation(
2073                       alann[i]);
2074               if (newann.graphGroup > -1)
2075               {
2076                 if (newGraphGroups.size() <= newann.graphGroup
2077                         || newGraphGroups.get(newann.graphGroup) == null)
2078                 {
2079                   for (int q = newGraphGroups
2080                           .size(); q <= newann.graphGroup; q++)
2081                   {
2082                     newGraphGroups.add(q, null);
2083                   }
2084                   newGraphGroups.set(newann.graphGroup,
2085                           new Integer(++fgroup));
2086                 }
2087                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2088                         .intValue();
2089               }
2090
2091               newann.padAnnotation(alwidth);
2092               alignment.addAnnotation(newann);
2093             }
2094           }
2095         }
2096       }
2097       if (!newAlignment)
2098       {
2099         // /////
2100         // ADD HISTORY ITEM
2101         //
2102         addHistoryItem(new EditCommand(
2103                 MessageManager.getString("label.add_sequences"),
2104                 Action.PASTE, sequences, 0, alignment.getWidth(),
2105                 alignment));
2106       }
2107       // Add any annotations attached to sequences
2108       for (int i = 0; i < sequences.length; i++)
2109       {
2110         if (sequences[i].getAnnotation() != null)
2111         {
2112           AlignmentAnnotation newann;
2113           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2114           {
2115             annotationAdded = true;
2116             newann = sequences[i].getAnnotation()[a];
2117             newann.adjustForAlignment();
2118             newann.padAnnotation(alwidth);
2119             if (newann.graphGroup > -1)
2120             {
2121               if (newann.graphGroup > -1)
2122               {
2123                 if (newGraphGroups.size() <= newann.graphGroup
2124                         || newGraphGroups.get(newann.graphGroup) == null)
2125                 {
2126                   for (int q = newGraphGroups
2127                           .size(); q <= newann.graphGroup; q++)
2128                   {
2129                     newGraphGroups.add(q, null);
2130                   }
2131                   newGraphGroups.set(newann.graphGroup,
2132                           new Integer(++fgroup));
2133                 }
2134                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2135                         .intValue();
2136               }
2137             }
2138             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2139             // was
2140             // duplicated
2141             // earlier
2142             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2143                     a);
2144           }
2145         }
2146       }
2147       if (!newAlignment)
2148       {
2149
2150         // propagate alignment changed.
2151         viewport.getRanges().setEndSeq(alignment.getHeight());
2152         if (annotationAdded)
2153         {
2154           // Duplicate sequence annotation in all views.
2155           AlignmentI[] alview = this.getViewAlignments();
2156           for (int i = 0; i < sequences.length; i++)
2157           {
2158             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2159             if (sann == null)
2160             {
2161               continue;
2162             }
2163             for (int avnum = 0; avnum < alview.length; avnum++)
2164             {
2165               if (alview[avnum] != alignment)
2166               {
2167                 // duplicate in a view other than the one with input focus
2168                 int avwidth = alview[avnum].getWidth() + 1;
2169                 // this relies on sann being preserved after we
2170                 // modify the sequence's annotation array for each duplication
2171                 for (int a = 0; a < sann.length; a++)
2172                 {
2173                   AlignmentAnnotation newann = new AlignmentAnnotation(
2174                           sann[a]);
2175                   sequences[i].addAlignmentAnnotation(newann);
2176                   newann.padAnnotation(avwidth);
2177                   alview[avnum].addAnnotation(newann); // annotation was
2178                   // duplicated earlier
2179                   // TODO JAL-1145 graphGroups are not updated for sequence
2180                   // annotation added to several views. This may cause
2181                   // strangeness
2182                   alview[avnum].setAnnotationIndex(newann, a);
2183                 }
2184               }
2185             }
2186           }
2187           buildSortByAnnotationScoresMenu();
2188         }
2189         viewport.firePropertyChange("alignment", null,
2190                 alignment.getSequences());
2191         if (alignPanels != null)
2192         {
2193           for (AlignmentPanel ap : alignPanels)
2194           {
2195             ap.validateAnnotationDimensions(false);
2196           }
2197         }
2198         else
2199         {
2200           alignPanel.validateAnnotationDimensions(false);
2201         }
2202
2203       }
2204       else
2205       {
2206         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2207                 DEFAULT_HEIGHT);
2208         String newtitle = new String("Copied sequences");
2209
2210         if (Desktop.jalviewClipboard != null
2211                 && Desktop.jalviewClipboard[2] != null)
2212         {
2213           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2214           af.viewport.setHiddenColumns(hc);
2215         }
2216
2217         // >>>This is a fix for the moment, until a better solution is
2218         // found!!<<<
2219         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2220                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2221                         .getFeatureRenderer());
2222
2223         // TODO: maintain provenance of an alignment, rather than just make the
2224         // title a concatenation of operations.
2225         if (!externalPaste)
2226         {
2227           if (title.startsWith("Copied sequences"))
2228           {
2229             newtitle = title;
2230           }
2231           else
2232           {
2233             newtitle = newtitle.concat("- from " + title);
2234           }
2235         }
2236         else
2237         {
2238           newtitle = new String("Pasted sequences");
2239         }
2240
2241         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2242                 DEFAULT_HEIGHT);
2243
2244       }
2245
2246     } catch (Exception ex)
2247     {
2248       ex.printStackTrace();
2249       System.out.println("Exception whilst pasting: " + ex);
2250       // could be anything being pasted in here
2251     }
2252
2253   }
2254
2255   @Override
2256   protected void expand_newalign(ActionEvent e)
2257   {
2258     try
2259     {
2260       AlignmentI alignment = AlignmentUtils
2261               .expandContext(getViewport().getAlignment(), -1);
2262       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2263               DEFAULT_HEIGHT);
2264       String newtitle = new String("Flanking alignment");
2265
2266       if (Desktop.jalviewClipboard != null
2267               && Desktop.jalviewClipboard[2] != null)
2268       {
2269         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2270         af.viewport.setHiddenColumns(hc);
2271       }
2272
2273       // >>>This is a fix for the moment, until a better solution is
2274       // found!!<<<
2275       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2276               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2277                       .getFeatureRenderer());
2278
2279       // TODO: maintain provenance of an alignment, rather than just make the
2280       // title a concatenation of operations.
2281       {
2282         if (title.startsWith("Copied sequences"))
2283         {
2284           newtitle = title;
2285         }
2286         else
2287         {
2288           newtitle = newtitle.concat("- from " + title);
2289         }
2290       }
2291
2292       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2293
2294     } catch (Exception ex)
2295     {
2296       ex.printStackTrace();
2297       System.out.println("Exception whilst pasting: " + ex);
2298       // could be anything being pasted in here
2299     } catch (OutOfMemoryError oom)
2300     {
2301       new OOMWarning("Viewing flanking region of alignment", oom);
2302     }
2303   }
2304
2305   /**
2306    * DOCUMENT ME!
2307    *
2308    * @param e
2309    *          DOCUMENT ME!
2310    */
2311   @Override
2312   protected void cut_actionPerformed(ActionEvent e)
2313   {
2314     copy_actionPerformed(null);
2315     delete_actionPerformed(null);
2316   }
2317
2318   /**
2319    * DOCUMENT ME!
2320    *
2321    * @param e
2322    *          DOCUMENT ME!
2323    */
2324   @Override
2325   protected void delete_actionPerformed(ActionEvent evt)
2326   {
2327
2328     SequenceGroup sg = viewport.getSelectionGroup();
2329     if (sg == null)
2330     {
2331       return;
2332     }
2333
2334     /*
2335      * If the cut affects all sequences, warn, remove highlighted columns
2336      */
2337     if (sg.getSize() == viewport.getAlignment().getHeight())
2338     {
2339       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2340               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2341       if (isEntireAlignWidth)
2342       {
2343         int confirm = JvOptionPane.showConfirmDialog(this,
2344                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2345                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2346                 JvOptionPane.OK_CANCEL_OPTION);
2347
2348         if (confirm == JvOptionPane.CANCEL_OPTION
2349                 || confirm == JvOptionPane.CLOSED_OPTION)
2350         {
2351           return;
2352         }
2353       }
2354       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2355               sg.getEndRes() + 1);
2356     }
2357     SequenceI[] cut = sg.getSequences()
2358             .toArray(new SequenceI[sg.getSize()]);
2359
2360     addHistoryItem(new EditCommand(
2361             MessageManager.getString("label.cut_sequences"), Action.CUT,
2362             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2363             viewport.getAlignment()));
2364
2365     viewport.setSelectionGroup(null);
2366     viewport.sendSelection();
2367     viewport.getAlignment().deleteGroup(sg);
2368
2369     viewport.firePropertyChange("alignment", null,
2370             viewport.getAlignment().getSequences());
2371     if (viewport.getAlignment().getHeight() < 1)
2372     {
2373       try
2374       {
2375         this.setClosed(true);
2376       } catch (Exception ex)
2377       {
2378       }
2379     }
2380   }
2381
2382   /**
2383    * DOCUMENT ME!
2384    *
2385    * @param e
2386    *          DOCUMENT ME!
2387    */
2388   @Override
2389   protected void deleteGroups_actionPerformed(ActionEvent e)
2390   {
2391     if (avc.deleteGroups())
2392     {
2393       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2394       alignPanel.updateAnnotation();
2395       alignPanel.paintAlignment(true, true);
2396     }
2397   }
2398
2399   /**
2400    * DOCUMENT ME!
2401    *
2402    * @param e
2403    *          DOCUMENT ME!
2404    */
2405   @Override
2406   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2407   {
2408     SequenceGroup sg = new SequenceGroup();
2409
2410     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2411     {
2412       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2413     }
2414
2415     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2416     viewport.setSelectionGroup(sg);
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 Jalview2XML().copyAlignPanel(alignPanel);
2713     if (!copyAnnotation)
2714     {
2715       /*
2716        * remove all groups and annotation except for the automatic stuff
2717        */
2718       newap.av.getAlignment().deleteAllGroups();
2719       newap.av.getAlignment().deleteAllAnnotations(false);
2720     }
2721
2722     newap.av.setGatherViewsHere(false);
2723
2724     if (viewport.viewName == null)
2725     {
2726       viewport.viewName = MessageManager
2727               .getString("label.view_name_original");
2728     }
2729
2730     /*
2731      * Views share the same edits undo and redo stacks
2732      */
2733     newap.av.setHistoryList(viewport.getHistoryList());
2734     newap.av.setRedoList(viewport.getRedoList());
2735
2736     /*
2737      * Views share the same mappings; need to deregister any new mappings
2738      * created by copyAlignPanel, and register the new reference to the shared
2739      * mappings
2740      */
2741     newap.av.replaceMappings(viewport.getAlignment());
2742
2743     /*
2744      * start up cDNA consensus (if applicable) now mappings are in place
2745      */
2746     if (newap.av.initComplementConsensus())
2747     {
2748       newap.refresh(true); // adjust layout of annotations
2749     }
2750
2751     newap.av.viewName = getNewViewName(viewTitle);
2752
2753     addAlignmentPanel(newap, true);
2754     newap.alignmentChanged();
2755
2756     if (alignPanels.size() == 2)
2757     {
2758       viewport.setGatherViewsHere(true);
2759     }
2760     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2761     return newap;
2762   }
2763
2764   /**
2765    * Make a new name for the view, ensuring it is unique within the current
2766    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2767    * these now use viewId. Unique view names are still desirable for usability.)
2768    *
2769    * @param viewTitle
2770    * @return
2771    */
2772   protected String getNewViewName(String viewTitle)
2773   {
2774     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2775     boolean addFirstIndex = false;
2776     if (viewTitle == null || viewTitle.trim().length() == 0)
2777     {
2778       viewTitle = MessageManager.getString("action.view");
2779       addFirstIndex = true;
2780     }
2781     else
2782     {
2783       index = 1;// we count from 1 if given a specific name
2784     }
2785     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2786
2787     List<Component> comps = PaintRefresher.components
2788             .get(viewport.getSequenceSetId());
2789
2790     List<String> existingNames = getExistingViewNames(comps);
2791
2792     while (existingNames.contains(newViewName))
2793     {
2794       newViewName = viewTitle + " " + (++index);
2795     }
2796     return newViewName;
2797   }
2798
2799   /**
2800    * Returns a list of distinct view names found in the given list of
2801    * components. View names are held on the viewport of an AlignmentPanel.
2802    *
2803    * @param comps
2804    * @return
2805    */
2806   protected List<String> getExistingViewNames(List<Component> comps)
2807   {
2808     List<String> existingNames = new ArrayList<>();
2809     for (Component comp : comps)
2810     {
2811       if (comp instanceof AlignmentPanel)
2812       {
2813         AlignmentPanel ap = (AlignmentPanel) comp;
2814         if (!existingNames.contains(ap.av.viewName))
2815         {
2816           existingNames.add(ap.av.viewName);
2817         }
2818       }
2819     }
2820     return existingNames;
2821   }
2822
2823   /**
2824    * Explode tabbed views into separate windows.
2825    */
2826   @Override
2827   public void expandViews_actionPerformed(ActionEvent e)
2828   {
2829     Desktop.explodeViews(this);
2830   }
2831
2832   /**
2833    * Gather views in separate windows back into a tabbed presentation.
2834    */
2835   @Override
2836   public void gatherViews_actionPerformed(ActionEvent e)
2837   {
2838     Desktop.instance.gatherViews(this);
2839   }
2840
2841   /**
2842    * DOCUMENT ME!
2843    *
2844    * @param e
2845    *          DOCUMENT ME!
2846    */
2847   @Override
2848   public void font_actionPerformed(ActionEvent e)
2849   {
2850     new FontChooser(alignPanel);
2851   }
2852
2853   /**
2854    * DOCUMENT ME!
2855    *
2856    * @param e
2857    *          DOCUMENT ME!
2858    */
2859   @Override
2860   protected void seqLimit_actionPerformed(ActionEvent e)
2861   {
2862     viewport.setShowJVSuffix(seqLimits.isSelected());
2863
2864     alignPanel.getIdPanel().getIdCanvas()
2865             .setPreferredSize(alignPanel.calculateIdWidth());
2866     alignPanel.paintAlignment(true, false);
2867   }
2868
2869   @Override
2870   public void idRightAlign_actionPerformed(ActionEvent e)
2871   {
2872     viewport.setRightAlignIds(idRightAlign.isSelected());
2873     alignPanel.paintAlignment(false, false);
2874   }
2875
2876   @Override
2877   public void centreColumnLabels_actionPerformed(ActionEvent e)
2878   {
2879     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2880     alignPanel.paintAlignment(false, false);
2881   }
2882
2883   /*
2884    * (non-Javadoc)
2885    *
2886    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2887    */
2888   @Override
2889   protected void followHighlight_actionPerformed()
2890   {
2891     /*
2892      * Set the 'follow' flag on the Viewport (and scroll to position if now
2893      * true).
2894      */
2895     final boolean state = this.followHighlightMenuItem.getState();
2896     viewport.setFollowHighlight(state);
2897     if (state)
2898     {
2899       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2900     }
2901   }
2902
2903   /**
2904    * DOCUMENT ME!
2905    *
2906    * @param e
2907    *          DOCUMENT ME!
2908    */
2909   @Override
2910   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2911   {
2912     viewport.setColourText(colourTextMenuItem.isSelected());
2913     alignPanel.paintAlignment(false, false);
2914   }
2915
2916   /**
2917    * DOCUMENT ME!
2918    *
2919    * @param e
2920    *          DOCUMENT ME!
2921    */
2922   @Override
2923   public void wrapMenuItem_actionPerformed(ActionEvent e)
2924   {
2925     scaleAbove.setVisible(wrapMenuItem.isSelected());
2926     scaleLeft.setVisible(wrapMenuItem.isSelected());
2927     scaleRight.setVisible(wrapMenuItem.isSelected());
2928     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2929     alignPanel.updateLayout();
2930   }
2931
2932   @Override
2933   public void showAllSeqs_actionPerformed(ActionEvent e)
2934   {
2935     viewport.showAllHiddenSeqs();
2936   }
2937
2938   @Override
2939   public void showAllColumns_actionPerformed(ActionEvent e)
2940   {
2941     viewport.showAllHiddenColumns();
2942     alignPanel.paintAlignment(true, true);
2943     viewport.sendSelection();
2944   }
2945
2946   @Override
2947   public void hideSelSequences_actionPerformed(ActionEvent e)
2948   {
2949     viewport.hideAllSelectedSeqs();
2950   }
2951
2952   /**
2953    * called by key handler and the hide all/show all menu items
2954    *
2955    * @param toggleSeqs
2956    * @param toggleCols
2957    */
2958   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2959   {
2960
2961     boolean hide = false;
2962     SequenceGroup sg = viewport.getSelectionGroup();
2963     if (!toggleSeqs && !toggleCols)
2964     {
2965       // Hide everything by the current selection - this is a hack - we do the
2966       // invert and then hide
2967       // first check that there will be visible columns after the invert.
2968       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2969               && sg.getStartRes() <= sg.getEndRes()))
2970       {
2971         // now invert the sequence set, if required - empty selection implies
2972         // that no hiding is required.
2973         if (sg != null)
2974         {
2975           invertSequenceMenuItem_actionPerformed(null);
2976           sg = viewport.getSelectionGroup();
2977           toggleSeqs = true;
2978
2979         }
2980         viewport.expandColSelection(sg, true);
2981         // finally invert the column selection and get the new sequence
2982         // selection.
2983         invertColSel_actionPerformed(null);
2984         toggleCols = true;
2985       }
2986     }
2987
2988     if (toggleSeqs)
2989     {
2990       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2991       {
2992         hideSelSequences_actionPerformed(null);
2993         hide = true;
2994       }
2995       else if (!(toggleCols && viewport.hasSelectedColumns()))
2996       {
2997         showAllSeqs_actionPerformed(null);
2998       }
2999     }
3000
3001     if (toggleCols)
3002     {
3003       if (viewport.hasSelectedColumns())
3004       {
3005         hideSelColumns_actionPerformed(null);
3006         if (!toggleSeqs)
3007         {
3008           viewport.setSelectionGroup(sg);
3009         }
3010       }
3011       else if (!hide)
3012       {
3013         showAllColumns_actionPerformed(null);
3014       }
3015     }
3016   }
3017
3018   /*
3019    * (non-Javadoc)
3020    *
3021    * @see
3022    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3023    * event.ActionEvent)
3024    */
3025   @Override
3026   public void hideAllButSelection_actionPerformed(ActionEvent e)
3027   {
3028     toggleHiddenRegions(false, false);
3029     viewport.sendSelection();
3030   }
3031
3032   /*
3033    * (non-Javadoc)
3034    *
3035    * @see
3036    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3037    * .ActionEvent)
3038    */
3039   @Override
3040   public void hideAllSelection_actionPerformed(ActionEvent e)
3041   {
3042     SequenceGroup sg = viewport.getSelectionGroup();
3043     viewport.expandColSelection(sg, false);
3044     viewport.hideAllSelectedSeqs();
3045     viewport.hideSelectedColumns();
3046     alignPanel.paintAlignment(true, true);
3047     viewport.sendSelection();
3048   }
3049
3050   /*
3051    * (non-Javadoc)
3052    *
3053    * @see
3054    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3055    * ActionEvent)
3056    */
3057   @Override
3058   public void showAllhidden_actionPerformed(ActionEvent e)
3059   {
3060     viewport.showAllHiddenColumns();
3061     viewport.showAllHiddenSeqs();
3062     alignPanel.paintAlignment(true, true);
3063     viewport.sendSelection();
3064   }
3065
3066   @Override
3067   public void hideSelColumns_actionPerformed(ActionEvent e)
3068   {
3069     viewport.hideSelectedColumns();
3070     alignPanel.paintAlignment(true, true);
3071     viewport.sendSelection();
3072   }
3073
3074   @Override
3075   public void hiddenMarkers_actionPerformed(ActionEvent e)
3076   {
3077     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3078     repaint();
3079   }
3080
3081   /**
3082    * DOCUMENT ME!
3083    *
3084    * @param e
3085    *          DOCUMENT ME!
3086    */
3087   @Override
3088   protected void scaleAbove_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3091     // TODO: do we actually need to update overview for scale above change ?
3092     alignPanel.paintAlignment(true, false);
3093   }
3094
3095   /**
3096    * DOCUMENT ME!
3097    *
3098    * @param e
3099    *          DOCUMENT ME!
3100    */
3101   @Override
3102   protected void scaleLeft_actionPerformed(ActionEvent e)
3103   {
3104     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3105     alignPanel.paintAlignment(true, false);
3106   }
3107
3108   /**
3109    * DOCUMENT ME!
3110    *
3111    * @param e
3112    *          DOCUMENT ME!
3113    */
3114   @Override
3115   protected void scaleRight_actionPerformed(ActionEvent e)
3116   {
3117     viewport.setScaleRightWrapped(scaleRight.isSelected());
3118     alignPanel.paintAlignment(true, false);
3119   }
3120
3121   /**
3122    * DOCUMENT ME!
3123    *
3124    * @param e
3125    *          DOCUMENT ME!
3126    */
3127   @Override
3128   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3129   {
3130     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3131     alignPanel.paintAlignment(false, false);
3132   }
3133
3134   /**
3135    * DOCUMENT ME!
3136    *
3137    * @param e
3138    *          DOCUMENT ME!
3139    */
3140   @Override
3141   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3142   {
3143     viewport.setShowText(viewTextMenuItem.isSelected());
3144     alignPanel.paintAlignment(false, false);
3145   }
3146
3147   /**
3148    * DOCUMENT ME!
3149    *
3150    * @param e
3151    *          DOCUMENT ME!
3152    */
3153   @Override
3154   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3155   {
3156     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3157     alignPanel.paintAlignment(false, false);
3158   }
3159
3160   public FeatureSettings featureSettings;
3161
3162   @Override
3163   public FeatureSettingsControllerI getFeatureSettingsUI()
3164   {
3165     return featureSettings;
3166   }
3167
3168   @Override
3169   public void featureSettings_actionPerformed(ActionEvent e)
3170   {
3171     if (featureSettings != null)
3172     {
3173       featureSettings.close();
3174       featureSettings = null;
3175     }
3176     if (!showSeqFeatures.isSelected())
3177     {
3178       // make sure features are actually displayed
3179       showSeqFeatures.setSelected(true);
3180       showSeqFeatures_actionPerformed(null);
3181     }
3182     featureSettings = new FeatureSettings(this);
3183   }
3184
3185   /**
3186    * Set or clear 'Show Sequence Features'
3187    *
3188    * @param evt
3189    *          DOCUMENT ME!
3190    */
3191   @Override
3192   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3193   {
3194     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3195     alignPanel.paintAlignment(true, true);
3196   }
3197
3198   /**
3199    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3200    * the annotations panel as a whole.
3201    *
3202    * The options to show/hide all annotations should be enabled when the panel
3203    * is shown, and disabled when the panel is hidden.
3204    *
3205    * @param e
3206    */
3207   @Override
3208   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3209   {
3210     final boolean setVisible = annotationPanelMenuItem.isSelected();
3211     viewport.setShowAnnotation(setVisible);
3212     this.showAllSeqAnnotations.setEnabled(setVisible);
3213     this.hideAllSeqAnnotations.setEnabled(setVisible);
3214     this.showAllAlAnnotations.setEnabled(setVisible);
3215     this.hideAllAlAnnotations.setEnabled(setVisible);
3216     alignPanel.updateLayout();
3217   }
3218
3219   @Override
3220   public void alignmentProperties()
3221   {
3222     JEditorPane editPane = new JEditorPane("text/html", "");
3223     editPane.setEditable(false);
3224     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3225             .formatAsHtml();
3226     editPane.setText(
3227             MessageManager.formatMessage("label.html_content", new Object[]
3228             { contents.toString() }));
3229     JInternalFrame frame = new JInternalFrame();
3230     frame.getContentPane().add(new JScrollPane(editPane));
3231
3232     Desktop.addInternalFrame(frame, MessageManager
3233             .formatMessage("label.alignment_properties", new Object[]
3234             { getTitle() }), 500, 400);
3235   }
3236
3237   /**
3238    * DOCUMENT ME!
3239    *
3240    * @param e
3241    *          DOCUMENT ME!
3242    */
3243   @Override
3244   public void overviewMenuItem_actionPerformed(ActionEvent e)
3245   {
3246     if (alignPanel.overviewPanel != null)
3247     {
3248       return;
3249     }
3250
3251     JInternalFrame frame = new JInternalFrame();
3252     final OverviewPanel overview = new OverviewPanel(alignPanel);
3253     frame.setContentPane(overview);
3254     Desktop.addInternalFrame(frame, MessageManager
3255             .formatMessage("label.overview_params", new Object[]
3256             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3257             true, true);
3258     frame.pack();
3259     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3260     frame.addInternalFrameListener(
3261             new javax.swing.event.InternalFrameAdapter()
3262             {
3263               @Override
3264               public void internalFrameClosed(
3265                       javax.swing.event.InternalFrameEvent evt)
3266               {
3267                 overview.dispose();
3268                 alignPanel.setOverviewPanel(null);
3269               };
3270             });
3271     if (getKeyListeners().length > 0)
3272     {
3273       frame.addKeyListener(getKeyListeners()[0]);
3274     }
3275
3276     alignPanel.setOverviewPanel(overview);
3277   }
3278
3279   @Override
3280   public void textColour_actionPerformed()
3281   {
3282     new TextColourChooser().chooseColour(alignPanel, null);
3283   }
3284
3285   /*
3286    * public void covariationColour_actionPerformed() {
3287    * changeColour(new
3288    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3289    * ()[0])); }
3290    */
3291   @Override
3292   public void annotationColour_actionPerformed()
3293   {
3294     new AnnotationColourChooser(viewport, alignPanel);
3295   }
3296
3297   @Override
3298   public void annotationColumn_actionPerformed(ActionEvent e)
3299   {
3300     new AnnotationColumnChooser(viewport, alignPanel);
3301   }
3302
3303   /**
3304    * Action on the user checking or unchecking the option to apply the selected
3305    * colour scheme to all groups. If unchecked, groups may have their own
3306    * independent colour schemes.
3307    *
3308    * @param selected
3309    */
3310   @Override
3311   public void applyToAllGroups_actionPerformed(boolean selected)
3312   {
3313     viewport.setColourAppliesToAllGroups(selected);
3314   }
3315
3316   /**
3317    * Action on user selecting a colour from the colour menu
3318    *
3319    * @param name
3320    *          the name (not the menu item label!) of the colour scheme
3321    */
3322   @Override
3323   public void changeColour_actionPerformed(String name)
3324   {
3325     /*
3326      * 'User Defined' opens a panel to configure or load a
3327      * user-defined colour scheme
3328      */
3329     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3330     {
3331       new UserDefinedColours(alignPanel);
3332       return;
3333     }
3334
3335     /*
3336      * otherwise set the chosen colour scheme (or null for 'None')
3337      */
3338     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3339             viewport.getAlignment(), viewport.getHiddenRepSequences());
3340     changeColour(cs);
3341   }
3342
3343   /**
3344    * Actions on setting or changing the alignment colour scheme
3345    *
3346    * @param cs
3347    */
3348   @Override
3349   public void changeColour(ColourSchemeI cs)
3350   {
3351     // TODO: pull up to controller method
3352     ColourMenuHelper.setColourSelected(colourMenu, cs);
3353
3354     viewport.setGlobalColourScheme(cs);
3355
3356     alignPanel.paintAlignment(true, true);
3357   }
3358
3359   /**
3360    * Show the PID threshold slider panel
3361    */
3362   @Override
3363   protected void modifyPID_actionPerformed()
3364   {
3365     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3366             alignPanel.getViewName());
3367     SliderPanel.showPIDSlider();
3368   }
3369
3370   /**
3371    * Show the Conservation slider panel
3372    */
3373   @Override
3374   protected void modifyConservation_actionPerformed()
3375   {
3376     SliderPanel.setConservationSlider(alignPanel,
3377             viewport.getResidueShading(), alignPanel.getViewName());
3378     SliderPanel.showConservationSlider();
3379   }
3380
3381   /**
3382    * Action on selecting or deselecting (Colour) By Conservation
3383    */
3384   @Override
3385   public void conservationMenuItem_actionPerformed(boolean selected)
3386   {
3387     modifyConservation.setEnabled(selected);
3388     viewport.setConservationSelected(selected);
3389     viewport.getResidueShading().setConservationApplied(selected);
3390
3391     changeColour(viewport.getGlobalColourScheme());
3392     if (selected)
3393     {
3394       modifyConservation_actionPerformed();
3395     }
3396     else
3397     {
3398       SliderPanel.hideConservationSlider();
3399     }
3400   }
3401
3402   /**
3403    * Action on selecting or deselecting (Colour) Above PID Threshold
3404    */
3405   @Override
3406   public void abovePIDThreshold_actionPerformed(boolean selected)
3407   {
3408     modifyPID.setEnabled(selected);
3409     viewport.setAbovePIDThreshold(selected);
3410     if (!selected)
3411     {
3412       viewport.getResidueShading().setThreshold(0,
3413               viewport.isIgnoreGapsConsensus());
3414     }
3415
3416     changeColour(viewport.getGlobalColourScheme());
3417     if (selected)
3418     {
3419       modifyPID_actionPerformed();
3420     }
3421     else
3422     {
3423       SliderPanel.hidePIDSlider();
3424     }
3425   }
3426
3427   /**
3428    * DOCUMENT ME!
3429    *
3430    * @param e
3431    *          DOCUMENT ME!
3432    */
3433   @Override
3434   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3435   {
3436     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3437     AlignmentSorter.sortByPID(viewport.getAlignment(),
3438             viewport.getAlignment().getSequenceAt(0));
3439     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3440             viewport.getAlignment()));
3441     alignPanel.paintAlignment(true, false);
3442   }
3443
3444   /**
3445    * DOCUMENT ME!
3446    *
3447    * @param e
3448    *          DOCUMENT ME!
3449    */
3450   @Override
3451   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3452   {
3453     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454     AlignmentSorter.sortByID(viewport.getAlignment());
3455     addHistoryItem(
3456             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3457     alignPanel.paintAlignment(true, false);
3458   }
3459
3460   /**
3461    * DOCUMENT ME!
3462    *
3463    * @param e
3464    *          DOCUMENT ME!
3465    */
3466   @Override
3467   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3468   {
3469     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470     AlignmentSorter.sortByLength(viewport.getAlignment());
3471     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3472             viewport.getAlignment()));
3473     alignPanel.paintAlignment(true, false);
3474   }
3475
3476   /**
3477    * DOCUMENT ME!
3478    *
3479    * @param e
3480    *          DOCUMENT ME!
3481    */
3482   @Override
3483   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3484   {
3485     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486     AlignmentSorter.sortByGroup(viewport.getAlignment());
3487     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3488             viewport.getAlignment()));
3489
3490     alignPanel.paintAlignment(true, false);
3491   }
3492
3493   /**
3494    * DOCUMENT ME!
3495    *
3496    * @param e
3497    *          DOCUMENT ME!
3498    */
3499   @Override
3500   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3501   {
3502     new RedundancyPanel(alignPanel, this);
3503   }
3504
3505   /**
3506    * DOCUMENT ME!
3507    *
3508    * @param e
3509    *          DOCUMENT ME!
3510    */
3511   @Override
3512   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3513   {
3514     if ((viewport.getSelectionGroup() == null)
3515             || (viewport.getSelectionGroup().getSize() < 2))
3516     {
3517       JvOptionPane.showInternalMessageDialog(this,
3518               MessageManager.getString(
3519                       "label.you_must_select_least_two_sequences"),
3520               MessageManager.getString("label.invalid_selection"),
3521               JvOptionPane.WARNING_MESSAGE);
3522     }
3523     else
3524     {
3525       JInternalFrame frame = new JInternalFrame();
3526       frame.setContentPane(new PairwiseAlignPanel(viewport));
3527       Desktop.addInternalFrame(frame,
3528               MessageManager.getString("action.pairwise_alignment"), 600,
3529               500);
3530     }
3531   }
3532
3533   @Override
3534   public void autoCalculate_actionPerformed(ActionEvent e)
3535   {
3536     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3537     if (viewport.autoCalculateConsensus)
3538     {
3539       viewport.firePropertyChange("alignment", null,
3540               viewport.getAlignment().getSequences());
3541     }
3542   }
3543
3544   @Override
3545   public void sortByTreeOption_actionPerformed(ActionEvent e)
3546   {
3547     viewport.sortByTree = sortByTree.isSelected();
3548   }
3549
3550   @Override
3551   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3552   {
3553     viewport.followSelection = listenToViewSelections.isSelected();
3554   }
3555
3556   /**
3557    * Constructs a tree panel and adds it to the desktop
3558    *
3559    * @param type
3560    *          tree type (NJ or AV)
3561    * @param modelName
3562    *          name of score model used to compute the tree
3563    * @param options
3564    *          parameters for the distance or similarity calculation
3565    */
3566   void newTreePanel(String type, String modelName,
3567           SimilarityParamsI options)
3568   {
3569     String frameTitle = "";
3570     TreePanel tp;
3571
3572     boolean onSelection = false;
3573     if (viewport.getSelectionGroup() != null
3574             && viewport.getSelectionGroup().getSize() > 0)
3575     {
3576       SequenceGroup sg = viewport.getSelectionGroup();
3577
3578       /* Decide if the selection is a column region */
3579       for (SequenceI _s : sg.getSequences())
3580       {
3581         if (_s.getLength() < sg.getEndRes())
3582         {
3583           JvOptionPane.showMessageDialog(Desktop.desktop,
3584                   MessageManager.getString(
3585                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3586                   MessageManager.getString(
3587                           "label.sequences_selection_not_aligned"),
3588                   JvOptionPane.WARNING_MESSAGE);
3589
3590           return;
3591         }
3592       }
3593       onSelection = true;
3594     }
3595     else
3596     {
3597       if (viewport.getAlignment().getHeight() < 2)
3598       {
3599         return;
3600       }
3601     }
3602
3603     tp = new TreePanel(alignPanel, type, modelName, options);
3604     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3605
3606     frameTitle += " from ";
3607
3608     if (viewport.viewName != null)
3609     {
3610       frameTitle += viewport.viewName + " of ";
3611     }
3612
3613     frameTitle += this.title;
3614
3615     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3616   }
3617
3618   /**
3619    * DOCUMENT ME!
3620    *
3621    * @param title
3622    *          DOCUMENT ME!
3623    * @param order
3624    *          DOCUMENT ME!
3625    */
3626   public void addSortByOrderMenuItem(String title,
3627           final AlignmentOrder order)
3628   {
3629     final JMenuItem item = new JMenuItem(MessageManager
3630             .formatMessage("action.by_title_param", new Object[]
3631             { title }));
3632     sort.add(item);
3633     item.addActionListener(new java.awt.event.ActionListener()
3634     {
3635       @Override
3636       public void actionPerformed(ActionEvent e)
3637       {
3638         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3639
3640         // TODO: JBPNote - have to map order entries to curent SequenceI
3641         // pointers
3642         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3643
3644         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3645                 viewport.getAlignment()));
3646
3647         alignPanel.paintAlignment(true, false);
3648       }
3649     });
3650   }
3651
3652   /**
3653    * Add a new sort by annotation score menu item
3654    *
3655    * @param sort
3656    *          the menu to add the option to
3657    * @param scoreLabel
3658    *          the label used to retrieve scores for each sequence on the
3659    *          alignment
3660    */
3661   public void addSortByAnnotScoreMenuItem(JMenu sort,
3662           final String scoreLabel)
3663   {
3664     final JMenuItem item = new JMenuItem(scoreLabel);
3665     sort.add(item);
3666     item.addActionListener(new java.awt.event.ActionListener()
3667     {
3668       @Override
3669       public void actionPerformed(ActionEvent e)
3670       {
3671         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3672         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3673                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3674         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3675                 viewport.getAlignment()));
3676         alignPanel.paintAlignment(true, false);
3677       }
3678     });
3679   }
3680
3681   /**
3682    * last hash for alignment's annotation array - used to minimise cost of
3683    * rebuild.
3684    */
3685   protected int _annotationScoreVectorHash;
3686
3687   /**
3688    * search the alignment and rebuild the sort by annotation score submenu the
3689    * last alignment annotation vector hash is stored to minimize cost of
3690    * rebuilding in subsequence calls.
3691    *
3692    */
3693   @Override
3694   public void buildSortByAnnotationScoresMenu()
3695   {
3696     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3697     {
3698       return;
3699     }
3700
3701     if (viewport.getAlignment().getAlignmentAnnotation()
3702             .hashCode() != _annotationScoreVectorHash)
3703     {
3704       sortByAnnotScore.removeAll();
3705       // almost certainly a quicker way to do this - but we keep it simple
3706       Hashtable scoreSorts = new Hashtable();
3707       AlignmentAnnotation aann[];
3708       for (SequenceI sqa : viewport.getAlignment().getSequences())
3709       {
3710         aann = sqa.getAnnotation();
3711         for (int i = 0; aann != null && i < aann.length; i++)
3712         {
3713           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3714           {
3715             scoreSorts.put(aann[i].label, aann[i].label);
3716           }
3717         }
3718       }
3719       Enumeration labels = scoreSorts.keys();
3720       while (labels.hasMoreElements())
3721       {
3722         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3723                 (String) labels.nextElement());
3724       }
3725       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3726       scoreSorts.clear();
3727
3728       _annotationScoreVectorHash = viewport.getAlignment()
3729               .getAlignmentAnnotation().hashCode();
3730     }
3731   }
3732
3733   /**
3734    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3735    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3736    * call. Listeners are added to remove the menu item when the treePanel is
3737    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3738    * modified.
3739    */
3740   @Override
3741   public void buildTreeSortMenu()
3742   {
3743     sortByTreeMenu.removeAll();
3744
3745     List<Component> comps = PaintRefresher.components
3746             .get(viewport.getSequenceSetId());
3747     List<TreePanel> treePanels = new ArrayList<>();
3748     for (Component comp : comps)
3749     {
3750       if (comp instanceof TreePanel)
3751       {
3752         treePanels.add((TreePanel) comp);
3753       }
3754     }
3755
3756     if (treePanels.size() < 1)
3757     {
3758       sortByTreeMenu.setVisible(false);
3759       return;
3760     }
3761
3762     sortByTreeMenu.setVisible(true);
3763
3764     for (final TreePanel tp : treePanels)
3765     {
3766       final JMenuItem item = new JMenuItem(tp.getTitle());
3767       item.addActionListener(new java.awt.event.ActionListener()
3768       {
3769         @Override
3770         public void actionPerformed(ActionEvent e)
3771         {
3772           tp.sortByTree_actionPerformed();
3773           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3774
3775         }
3776       });
3777
3778       sortByTreeMenu.add(item);
3779     }
3780   }
3781
3782   public boolean sortBy(AlignmentOrder alorder, String undoname)
3783   {
3784     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3785     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3786     if (undoname != null)
3787     {
3788       addHistoryItem(new OrderCommand(undoname, oldOrder,
3789               viewport.getAlignment()));
3790     }
3791     alignPanel.paintAlignment(true, false);
3792     return true;
3793   }
3794
3795   /**
3796    * Work out whether the whole set of sequences or just the selected set will
3797    * be submitted for multiple alignment.
3798    *
3799    */
3800   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3801   {
3802     // Now, check we have enough sequences
3803     AlignmentView msa = null;
3804
3805     if ((viewport.getSelectionGroup() != null)
3806             && (viewport.getSelectionGroup().getSize() > 1))
3807     {
3808       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3809       // some common interface!
3810       /*
3811        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3812        * SequenceI[sz = seqs.getSize(false)];
3813        *
3814        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3815        * seqs.getSequenceAt(i); }
3816        */
3817       msa = viewport.getAlignmentView(true);
3818     }
3819     else if (viewport.getSelectionGroup() != null
3820             && viewport.getSelectionGroup().getSize() == 1)
3821     {
3822       int option = JvOptionPane.showConfirmDialog(this,
3823               MessageManager.getString("warn.oneseq_msainput_selection"),
3824               MessageManager.getString("label.invalid_selection"),
3825               JvOptionPane.OK_CANCEL_OPTION);
3826       if (option == JvOptionPane.OK_OPTION)
3827       {
3828         msa = viewport.getAlignmentView(false);
3829       }
3830     }
3831     else
3832     {
3833       msa = viewport.getAlignmentView(false);
3834     }
3835     return msa;
3836   }
3837
3838   /**
3839    * Decides what is submitted to a secondary structure prediction service: the
3840    * first sequence in the alignment, or in the current selection, or, if the
3841    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3842    * region or the whole alignment. (where the first sequence in the set is the
3843    * one that the prediction will be for).
3844    */
3845   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3846   {
3847     AlignmentView seqs = null;
3848
3849     if ((viewport.getSelectionGroup() != null)
3850             && (viewport.getSelectionGroup().getSize() > 0))
3851     {
3852       seqs = viewport.getAlignmentView(true);
3853     }
3854     else
3855     {
3856       seqs = viewport.getAlignmentView(false);
3857     }
3858     // limit sequences - JBPNote in future - could spawn multiple prediction
3859     // jobs
3860     // TODO: viewport.getAlignment().isAligned is a global state - the local
3861     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3862     if (!viewport.getAlignment().isAligned(false))
3863     {
3864       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3865       // TODO: if seqs.getSequences().length>1 then should really have warned
3866       // user!
3867
3868     }
3869     return seqs;
3870   }
3871
3872   /**
3873    * DOCUMENT ME!
3874    *
3875    * @param e
3876    *          DOCUMENT ME!
3877    */
3878   @Override
3879   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3880   {
3881     // Pick the tree file
3882     JalviewFileChooser chooser = new JalviewFileChooser(
3883             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3884     chooser.setFileView(new JalviewFileView());
3885     chooser.setDialogTitle(
3886             MessageManager.getString("label.select_newick_like_tree_file"));
3887     chooser.setToolTipText(
3888             MessageManager.getString("label.load_tree_file"));
3889
3890     int value = chooser.showOpenDialog(null);
3891
3892     if (value == JalviewFileChooser.APPROVE_OPTION)
3893     {
3894       String filePath = chooser.getSelectedFile().getPath();
3895       Cache.setProperty("LAST_DIRECTORY", filePath);
3896       NewickFile fin = null;
3897       try
3898       {
3899         fin = new NewickFile(filePath, DataSourceType.FILE);
3900         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3901       } catch (Exception ex)
3902       {
3903         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3904                 MessageManager.getString("label.problem_reading_tree_file"),
3905                 JvOptionPane.WARNING_MESSAGE);
3906         ex.printStackTrace();
3907       }
3908       if (fin != null && fin.hasWarningMessage())
3909       {
3910         JvOptionPane.showMessageDialog(Desktop.desktop,
3911                 fin.getWarningMessage(),
3912                 MessageManager
3913                         .getString("label.possible_problem_with_tree_file"),
3914                 JvOptionPane.WARNING_MESSAGE);
3915       }
3916     }
3917   }
3918
3919   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3920   {
3921     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3922   }
3923
3924   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3925           int h, int x, int y)
3926   {
3927     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3928   }
3929
3930   /**
3931    * Add a treeviewer for the tree extracted from a Newick file object to the
3932    * current alignment view
3933    *
3934    * @param nf
3935    *          the tree
3936    * @param title
3937    *          tree viewer title
3938    * @param input
3939    *          Associated alignment input data (or null)
3940    * @param w
3941    *          width
3942    * @param h
3943    *          height
3944    * @param x
3945    *          position
3946    * @param y
3947    *          position
3948    * @return TreePanel handle
3949    */
3950   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3951           AlignmentView input, int w, int h, int x, int y)
3952   {
3953     TreePanel tp = null;
3954
3955     try
3956     {
3957       nf.parse();
3958
3959       if (nf.getTree() != null)
3960       {
3961         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3962
3963         tp.setSize(w, h);
3964
3965         if (x > 0 && y > 0)
3966         {
3967           tp.setLocation(x, y);
3968         }
3969
3970         Desktop.addInternalFrame(tp, treeTitle, w, h);
3971       }
3972     } catch (Exception ex)
3973     {
3974       ex.printStackTrace();
3975     }
3976
3977     return tp;
3978   }
3979
3980   private boolean buildingMenu = false;
3981
3982   /**
3983    * Generates menu items and listener event actions for web service clients
3984    *
3985    */
3986   public void BuildWebServiceMenu()
3987   {
3988     while (buildingMenu)
3989     {
3990       try
3991       {
3992         System.err.println("Waiting for building menu to finish.");
3993         Thread.sleep(10);
3994       } catch (Exception e)
3995       {
3996       }
3997     }
3998     final AlignFrame me = this;
3999     buildingMenu = true;
4000     new Thread(new Runnable()
4001     {
4002       @Override
4003       public void run()
4004       {
4005         final List<JMenuItem> legacyItems = new ArrayList<>();
4006         try
4007         {
4008           // System.err.println("Building ws menu again "
4009           // + Thread.currentThread());
4010           // TODO: add support for context dependent disabling of services based
4011           // on
4012           // alignment and current selection
4013           // TODO: add additional serviceHandle parameter to specify abstract
4014           // handler
4015           // class independently of AbstractName
4016           // TODO: add in rediscovery GUI function to restart discoverer
4017           // TODO: group services by location as well as function and/or
4018           // introduce
4019           // object broker mechanism.
4020           final Vector<JMenu> wsmenu = new Vector<>();
4021           final IProgressIndicator af = me;
4022
4023           /*
4024            * do not i18n these strings - they are hard-coded in class
4025            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4026            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4027            */
4028           final JMenu msawsmenu = new JMenu("Alignment");
4029           final JMenu secstrmenu = new JMenu(
4030                   "Secondary Structure Prediction");
4031           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4032           final JMenu analymenu = new JMenu("Analysis");
4033           final JMenu dismenu = new JMenu("Protein Disorder");
4034           // JAL-940 - only show secondary structure prediction services from
4035           // the legacy server
4036           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4037               // &&
4038           Discoverer.services != null && (Discoverer.services.size() > 0))
4039           {
4040             // TODO: refactor to allow list of AbstractName/Handler bindings to
4041             // be
4042             // stored or retrieved from elsewhere
4043             // No MSAWS used any more:
4044             // Vector msaws = null; // (Vector)
4045             // Discoverer.services.get("MsaWS");
4046             Vector secstrpr = (Vector) Discoverer.services
4047                     .get("SecStrPred");
4048             if (secstrpr != null)
4049             {
4050               // Add any secondary structure prediction services
4051               for (int i = 0, j = secstrpr.size(); i < j; i++)
4052               {
4053                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4054                         .get(i);
4055                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4056                         .getServiceClient(sh);
4057                 int p = secstrmenu.getItemCount();
4058                 impl.attachWSMenuEntry(secstrmenu, me);
4059                 int q = secstrmenu.getItemCount();
4060                 for (int litm = p; litm < q; litm++)
4061                 {
4062                   legacyItems.add(secstrmenu.getItem(litm));
4063                 }
4064               }
4065             }
4066           }
4067
4068           // Add all submenus in the order they should appear on the web
4069           // services menu
4070           wsmenu.add(msawsmenu);
4071           wsmenu.add(secstrmenu);
4072           wsmenu.add(dismenu);
4073           wsmenu.add(analymenu);
4074           // No search services yet
4075           // wsmenu.add(seqsrchmenu);
4076
4077           javax.swing.SwingUtilities.invokeLater(new Runnable()
4078           {
4079             @Override
4080             public void run()
4081             {
4082               try
4083               {
4084                 webService.removeAll();
4085                 // first, add discovered services onto the webservices menu
4086                 if (wsmenu.size() > 0)
4087                 {
4088                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4089                   {
4090                     webService.add(wsmenu.get(i));
4091                   }
4092                 }
4093                 else
4094                 {
4095                   webService.add(me.webServiceNoServices);
4096                 }
4097                 // TODO: move into separate menu builder class.
4098                 boolean new_sspred = false;
4099                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4100                 {
4101                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4102                   if (jws2servs != null)
4103                   {
4104                     if (jws2servs.hasServices())
4105                     {
4106                       jws2servs.attachWSMenuEntry(webService, me);
4107                       for (Jws2Instance sv : jws2servs.getServices())
4108                       {
4109                         if (sv.description.toLowerCase().contains("jpred"))
4110                         {
4111                           for (JMenuItem jmi : legacyItems)
4112                           {
4113                             jmi.setVisible(false);
4114                           }
4115                         }
4116                       }
4117
4118                     }
4119                     if (jws2servs.isRunning())
4120                     {
4121                       JMenuItem tm = new JMenuItem(
4122                               "Still discovering JABA Services");
4123                       tm.setEnabled(false);
4124                       webService.add(tm);
4125                     }
4126                   }
4127                 }
4128                 build_urlServiceMenu(me.webService);
4129                 build_fetchdbmenu(webService);
4130                 for (JMenu item : wsmenu)
4131                 {
4132                   if (item.getItemCount() == 0)
4133                   {
4134                     item.setEnabled(false);
4135                   }
4136                   else
4137                   {
4138                     item.setEnabled(true);
4139                   }
4140                 }
4141               } catch (Exception e)
4142               {
4143                 Cache.log.debug(
4144                         "Exception during web service menu building process.",
4145                         e);
4146               }
4147             }
4148           });
4149         } catch (Exception e)
4150         {
4151         }
4152         buildingMenu = false;
4153       }
4154     }).start();
4155
4156   }
4157
4158   /**
4159    * construct any groupURL type service menu entries.
4160    *
4161    * @param webService
4162    */
4163   private void build_urlServiceMenu(JMenu webService)
4164   {
4165     // TODO: remove this code when 2.7 is released
4166     // DEBUG - alignmentView
4167     /*
4168      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4169      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4170      *
4171      * @Override public void actionPerformed(ActionEvent e) {
4172      * jalview.datamodel.AlignmentView
4173      * .testSelectionViews(af.viewport.getAlignment(),
4174      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4175      *
4176      * }); webService.add(testAlView);
4177      */
4178     // TODO: refactor to RestClient discoverer and merge menu entries for
4179     // rest-style services with other types of analysis/calculation service
4180     // SHmmr test client - still being implemented.
4181     // DEBUG - alignmentView
4182
4183     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4184             .getRestClients())
4185     {
4186       client.attachWSMenuEntry(
4187               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4188               this);
4189     }
4190   }
4191
4192   /**
4193    * Searches the alignment sequences for xRefs and builds the Show
4194    * Cross-References menu (formerly called Show Products), with database
4195    * sources for which cross-references are found (protein sources for a
4196    * nucleotide alignment and vice versa)
4197    *
4198    * @return true if Show Cross-references menu should be enabled
4199    */
4200   public boolean canShowProducts()
4201   {
4202     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4203     AlignmentI dataset = viewport.getAlignment().getDataset();
4204
4205     showProducts.removeAll();
4206     final boolean dna = viewport.getAlignment().isNucleotide();
4207
4208     if (seqs == null || seqs.length == 0)
4209     {
4210       // nothing to see here.
4211       return false;
4212     }
4213
4214     boolean showp = false;
4215     try
4216     {
4217       List<String> ptypes = new CrossRef(seqs, dataset)
4218               .findXrefSourcesForSequences(dna);
4219
4220       for (final String source : ptypes)
4221       {
4222         showp = true;
4223         final AlignFrame af = this;
4224         JMenuItem xtype = new JMenuItem(source);
4225         xtype.addActionListener(new ActionListener()
4226         {
4227           @Override
4228           public void actionPerformed(ActionEvent e)
4229           {
4230             showProductsFor(af.viewport.getSequenceSelection(), dna,
4231                     source);
4232           }
4233         });
4234         showProducts.add(xtype);
4235       }
4236       showProducts.setVisible(showp);
4237       showProducts.setEnabled(showp);
4238     } catch (Exception e)
4239     {
4240       Cache.log.warn(
4241               "canShowProducts threw an exception - please report to help@jalview.org",
4242               e);
4243       return false;
4244     }
4245     return showp;
4246   }
4247
4248   /**
4249    * Finds and displays cross-references for the selected sequences (protein
4250    * products for nucleotide sequences, dna coding sequences for peptides).
4251    *
4252    * @param sel
4253    *          the sequences to show cross-references for
4254    * @param dna
4255    *          true if from a nucleotide alignment (so showing proteins)
4256    * @param source
4257    *          the database to show cross-references for
4258    */
4259   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4260           final String source)
4261   {
4262     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4263             .start();
4264   }
4265
4266   /**
4267    * Construct and display a new frame containing the translation of this
4268    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4269    */
4270   @Override
4271   public void showTranslation_actionPerformed(ActionEvent e)
4272   {
4273     AlignmentI al = null;
4274     try
4275     {
4276       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4277
4278       al = dna.translateCdna();
4279     } catch (Exception ex)
4280     {
4281       jalview.bin.Cache.log.error(
4282               "Exception during translation. Please report this !", ex);
4283       final String msg = MessageManager.getString(
4284               "label.error_when_translating_sequences_submit_bug_report");
4285       final String errorTitle = MessageManager
4286               .getString("label.implementation_error")
4287               + MessageManager.getString("label.translation_failed");
4288       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4289               JvOptionPane.ERROR_MESSAGE);
4290       return;
4291     }
4292     if (al == null || al.getHeight() == 0)
4293     {
4294       final String msg = MessageManager.getString(
4295               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4296       final String errorTitle = MessageManager
4297               .getString("label.translation_failed");
4298       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4299               JvOptionPane.WARNING_MESSAGE);
4300     }
4301     else
4302     {
4303       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4304       af.setFileFormat(this.currentFileFormat);
4305       final String newTitle = MessageManager
4306               .formatMessage("label.translation_of_params", new Object[]
4307               { this.getTitle() });
4308       af.setTitle(newTitle);
4309       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4310       {
4311         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4312         viewport.openSplitFrame(af, new Alignment(seqs));
4313       }
4314       else
4315       {
4316         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4317                 DEFAULT_HEIGHT);
4318       }
4319     }
4320   }
4321
4322   /**
4323    * Set the file format
4324    *
4325    * @param format
4326    */
4327   public void setFileFormat(FileFormatI format)
4328   {
4329     this.currentFileFormat = format;
4330   }
4331
4332   /**
4333    * Try to load a features file onto the alignment.
4334    *
4335    * @param file
4336    *          contents or path to retrieve file
4337    * @param sourceType
4338    *          access mode of file (see jalview.io.AlignFile)
4339    * @return true if features file was parsed correctly.
4340    */
4341   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4342   {
4343     return avc.parseFeaturesFile(file, sourceType,
4344             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4345
4346   }
4347
4348   @Override
4349   public void refreshFeatureUI(boolean enableIfNecessary)
4350   {
4351     // note - currently this is only still here rather than in the controller
4352     // because of the featureSettings hard reference that is yet to be
4353     // abstracted
4354     if (enableIfNecessary)
4355     {
4356       viewport.setShowSequenceFeatures(true);
4357       showSeqFeatures.setSelected(true);
4358     }
4359
4360   }
4361
4362   @Override
4363   public void dragEnter(DropTargetDragEvent evt)
4364   {
4365   }
4366
4367   @Override
4368   public void dragExit(DropTargetEvent evt)
4369   {
4370   }
4371
4372   @Override
4373   public void dragOver(DropTargetDragEvent evt)
4374   {
4375   }
4376
4377   @Override
4378   public void dropActionChanged(DropTargetDragEvent evt)
4379   {
4380   }
4381
4382   @Override
4383   public void drop(DropTargetDropEvent evt)
4384   {
4385     // JAL-1552 - acceptDrop required before getTransferable call for
4386     // Java's Transferable for native dnd
4387     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4388     Transferable t = evt.getTransferable();
4389     final AlignFrame thisaf = this;
4390     final List<String> files = new ArrayList<>();
4391     List<DataSourceType> protocols = new ArrayList<>();
4392
4393     try
4394     {
4395       Desktop.transferFromDropTarget(files, protocols, evt, t);
4396     } catch (Exception e)
4397     {
4398       e.printStackTrace();
4399     }
4400     if (files != null)
4401     {
4402       new Thread(new Runnable()
4403       {
4404         @Override
4405         public void run()
4406         {
4407           try
4408           {
4409             // check to see if any of these files have names matching sequences
4410             // in
4411             // the alignment
4412             SequenceIdMatcher idm = new SequenceIdMatcher(
4413                     viewport.getAlignment().getSequencesArray());
4414             /**
4415              * Object[] { String,SequenceI}
4416              */
4417             ArrayList<Object[]> filesmatched = new ArrayList<>();
4418             ArrayList<String> filesnotmatched = new ArrayList<>();
4419             for (int i = 0; i < files.size(); i++)
4420             {
4421               String file = files.get(i).toString();
4422               String pdbfn = "";
4423               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4424               if (protocol == DataSourceType.FILE)
4425               {
4426                 File fl = new File(file);
4427                 pdbfn = fl.getName();
4428               }
4429               else if (protocol == DataSourceType.URL)
4430               {
4431                 URL url = new URL(file);
4432                 pdbfn = url.getFile();
4433               }
4434               if (pdbfn.length() > 0)
4435               {
4436                 // attempt to find a match in the alignment
4437                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4438                 int l = 0, c = pdbfn.indexOf(".");
4439                 while (mtch == null && c != -1)
4440                 {
4441                   do
4442                   {
4443                     l = c;
4444                   } while ((c = pdbfn.indexOf(".", l)) > l);
4445                   if (l > -1)
4446                   {
4447                     pdbfn = pdbfn.substring(0, l);
4448                   }
4449                   mtch = idm.findAllIdMatches(pdbfn);
4450                 }
4451                 if (mtch != null)
4452                 {
4453                   FileFormatI type = null;
4454                   try
4455                   {
4456                     type = new IdentifyFile().identify(file, protocol);
4457                   } catch (Exception ex)
4458                   {
4459                     type = null;
4460                   }
4461                   if (type != null && type.isStructureFile())
4462                   {
4463                     filesmatched.add(new Object[] { file, protocol, mtch });
4464                     continue;
4465                   }
4466                 }
4467                 // File wasn't named like one of the sequences or wasn't a PDB
4468                 // file.
4469                 filesnotmatched.add(file);
4470               }
4471             }
4472             int assocfiles = 0;
4473             if (filesmatched.size() > 0)
4474             {
4475               boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4476               if (!autoAssociate)
4477               {
4478                 String msg = MessageManager.formatMessage(
4479                         "label.automatically_associate_structure_files_with_sequences_same_name",
4480                         new Object[]
4481                         { Integer.valueOf(filesmatched.size())
4482                                 .toString() });
4483                 String ttl = MessageManager.getString(
4484                         "label.automatically_associate_structure_files_by_name");
4485                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4486                         ttl, JvOptionPane.YES_NO_OPTION);
4487                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4488               }
4489               if (autoAssociate)
4490               {
4491                 for (Object[] fm : filesmatched)
4492                 {
4493                   // try and associate
4494                   // TODO: may want to set a standard ID naming formalism for
4495                   // associating PDB files which have no IDs.
4496                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4497                   {
4498                     PDBEntry pe = new AssociatePdbFileWithSeq()
4499                             .associatePdbWithSeq((String) fm[0],
4500                                     (DataSourceType) fm[1], toassoc, false,
4501                                     Desktop.instance);
4502                     if (pe != null)
4503                     {
4504                       System.err.println("Associated file : "
4505                               + ((String) fm[0]) + " with "
4506                               + toassoc.getDisplayId(true));
4507                       assocfiles++;
4508                     }
4509                   }
4510                   // TODO: do we need to update overview ? only if features are
4511                   // shown I guess
4512                   alignPanel.paintAlignment(true, false);
4513                 }
4514               }
4515               else
4516               {
4517                 /*
4518                  * add declined structures as sequences
4519                  */
4520                 for (Object[] o : filesmatched)
4521                 {
4522                   filesnotmatched.add((String) o[0]);
4523                 }
4524               }
4525             }
4526             if (filesnotmatched.size() > 0)
4527             {
4528               if (assocfiles > 0 && (Cache.getDefault(
4529                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4530                       || JvOptionPane.showConfirmDialog(thisaf,
4531                               "<html>" + MessageManager.formatMessage(
4532                                       "label.ignore_unmatched_dropped_files_info",
4533                                       new Object[]
4534                                       { Integer.valueOf(
4535                                               filesnotmatched.size())
4536                                               .toString() })
4537                                       + "</html>",
4538                               MessageManager.getString(
4539                                       "label.ignore_unmatched_dropped_files"),
4540                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4541               {
4542                 return;
4543               }
4544               for (String fn : filesnotmatched)
4545               {
4546                 loadJalviewDataFile(fn, null, null, null);
4547               }
4548
4549             }
4550           } catch (Exception ex)
4551           {
4552             ex.printStackTrace();
4553           }
4554         }
4555       }).start();
4556     }
4557   }
4558
4559   /**
4560    * Attempt to load a "dropped" file or URL string, by testing in turn for
4561    * <ul>
4562    * <li>an Annotation file</li>
4563    * <li>a JNet file</li>
4564    * <li>a features file</li>
4565    * <li>else try to interpret as an alignment file</li>
4566    * </ul>
4567    *
4568    * @param file
4569    *          either a filename or a URL string.
4570    */
4571   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4572           FileFormatI format, SequenceI assocSeq)
4573   {
4574     try
4575     {
4576       if (sourceType == null)
4577       {
4578         sourceType = FormatAdapter.checkProtocol(file);
4579       }
4580       // if the file isn't identified, or not positively identified as some
4581       // other filetype (PFAM is default unidentified alignment file type) then
4582       // try to parse as annotation.
4583       boolean isAnnotation = (format == null
4584               || FileFormat.Pfam.equals(format))
4585                       ? new AnnotationFile().annotateAlignmentView(viewport,
4586                               file, sourceType)
4587                       : false;
4588
4589       if (!isAnnotation)
4590       {
4591         // first see if its a T-COFFEE score file
4592         TCoffeeScoreFile tcf = null;
4593         try
4594         {
4595           tcf = new TCoffeeScoreFile(file, sourceType);
4596           if (tcf.isValid())
4597           {
4598             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4599             {
4600               buildColourMenu();
4601               changeColour(
4602                       new TCoffeeColourScheme(viewport.getAlignment()));
4603               isAnnotation = true;
4604               statusBar.setText(MessageManager.getString(
4605                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4606             }
4607             else
4608             {
4609               // some problem - if no warning its probable that the ID matching
4610               // process didn't work
4611               JvOptionPane.showMessageDialog(Desktop.desktop,
4612                       tcf.getWarningMessage() == null
4613                               ? MessageManager.getString(
4614                                       "label.check_file_matches_sequence_ids_alignment")
4615                               : tcf.getWarningMessage(),
4616                       MessageManager.getString(
4617                               "label.problem_reading_tcoffee_score_file"),
4618                       JvOptionPane.WARNING_MESSAGE);
4619             }
4620           }
4621           else
4622           {
4623             tcf = null;
4624           }
4625         } catch (Exception x)
4626         {
4627           Cache.log.debug(
4628                   "Exception when processing data source as T-COFFEE score file",
4629                   x);
4630           tcf = null;
4631         }
4632         if (tcf == null)
4633         {
4634           // try to see if its a JNet 'concise' style annotation file *before*
4635           // we
4636           // try to parse it as a features file
4637           if (format == null)
4638           {
4639             format = new IdentifyFile().identify(file, sourceType);
4640           }
4641           if (FileFormat.ScoreMatrix == format)
4642           {
4643             ScoreMatrixFile sm = new ScoreMatrixFile(
4644                     new FileParse(file, sourceType));
4645             sm.parse();
4646             // todo: i18n this message
4647             statusBar.setText(MessageManager.formatMessage(
4648                     "label.successfully_loaded_matrix",
4649                     sm.getMatrixName()));
4650           }
4651           else if (FileFormat.Jnet.equals(format))
4652           {
4653             JPredFile predictions = new JPredFile(file, sourceType);
4654             new JnetAnnotationMaker();
4655             JnetAnnotationMaker.add_annotation(predictions,
4656                     viewport.getAlignment(), 0, false);
4657             viewport.getAlignment().setupJPredAlignment();
4658             isAnnotation = true;
4659           }
4660           // else if (IdentifyFile.FeaturesFile.equals(format))
4661           else if (FileFormat.Features.equals(format))
4662           {
4663             if (parseFeaturesFile(file, sourceType))
4664             {
4665               alignPanel.paintAlignment(true, true);
4666             }
4667           }
4668           else
4669           {
4670             new FileLoader().LoadFile(viewport, file, sourceType, format);
4671           }
4672         }
4673       }
4674       if (isAnnotation)
4675       {
4676
4677         alignPanel.adjustAnnotationHeight();
4678         viewport.updateSequenceIdColours();
4679         buildSortByAnnotationScoresMenu();
4680         alignPanel.paintAlignment(true, true);
4681       }
4682     } catch (Exception ex)
4683     {
4684       ex.printStackTrace();
4685     } catch (OutOfMemoryError oom)
4686     {
4687       try
4688       {
4689         System.gc();
4690       } catch (Exception x)
4691       {
4692       }
4693       new OOMWarning(
4694               "loading data "
4695                       + (sourceType != null
4696                               ? (sourceType == DataSourceType.PASTE
4697                                       ? "from clipboard."
4698                                       : "using " + sourceType + " from "
4699                                               + file)
4700                               : ".")
4701                       + (format != null
4702                               ? "(parsing as '" + format + "' file)"
4703                               : ""),
4704               oom, Desktop.desktop);
4705     }
4706   }
4707
4708   /**
4709    * Method invoked by the ChangeListener on the tabbed pane, in other words
4710    * when a different tabbed pane is selected by the user or programmatically.
4711    */
4712   @Override
4713   public void tabSelectionChanged(int index)
4714   {
4715     if (index > -1)
4716     {
4717       alignPanel = alignPanels.get(index);
4718       viewport = alignPanel.av;
4719       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4720       setMenusFromViewport(viewport);
4721     }
4722
4723     /*
4724      * 'focus' any colour slider that is open to the selected viewport
4725      */
4726     if (viewport.getConservationSelected())
4727     {
4728       SliderPanel.setConservationSlider(alignPanel,
4729               viewport.getResidueShading(), alignPanel.getViewName());
4730     }
4731     else
4732     {
4733       SliderPanel.hideConservationSlider();
4734     }
4735     if (viewport.getAbovePIDThreshold())
4736     {
4737       SliderPanel.setPIDSliderSource(alignPanel,
4738               viewport.getResidueShading(), alignPanel.getViewName());
4739     }
4740     else
4741     {
4742       SliderPanel.hidePIDSlider();
4743     }
4744
4745     /*
4746      * If there is a frame linked to this one in a SplitPane, switch it to the
4747      * same view tab index. No infinite recursion of calls should happen, since
4748      * tabSelectionChanged() should not get invoked on setting the selected
4749      * index to an unchanged value. Guard against setting an invalid index
4750      * before the new view peer tab has been created.
4751      */
4752     final AlignViewportI peer = viewport.getCodingComplement();
4753     if (peer != null)
4754     {
4755       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4756               .getAlignPanel().alignFrame;
4757       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4758       {
4759         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4760       }
4761     }
4762   }
4763
4764   /**
4765    * On right mouse click on view tab, prompt for and set new view name.
4766    */
4767   @Override
4768   public void tabbedPane_mousePressed(MouseEvent e)
4769   {
4770     if (e.isPopupTrigger())
4771     {
4772       String msg = MessageManager.getString("label.enter_view_name");
4773       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4774               JvOptionPane.QUESTION_MESSAGE);
4775
4776       if (reply != null)
4777       {
4778         viewport.viewName = reply;
4779         // TODO warn if reply is in getExistingViewNames()?
4780         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4781       }
4782     }
4783   }
4784
4785   public AlignViewport getCurrentView()
4786   {
4787     return viewport;
4788   }
4789
4790   /**
4791    * Open the dialog for regex description parsing.
4792    */
4793   @Override
4794   protected void extractScores_actionPerformed(ActionEvent e)
4795   {
4796     ParseProperties pp = new jalview.analysis.ParseProperties(
4797             viewport.getAlignment());
4798     // TODO: verify regex and introduce GUI dialog for version 2.5
4799     // if (pp.getScoresFromDescription("col", "score column ",
4800     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4801     // true)>0)
4802     if (pp.getScoresFromDescription("description column",
4803             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4804     {
4805       buildSortByAnnotationScoresMenu();
4806     }
4807   }
4808
4809   /*
4810    * (non-Javadoc)
4811    *
4812    * @see
4813    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4814    * )
4815    */
4816   @Override
4817   protected void showDbRefs_actionPerformed(ActionEvent e)
4818   {
4819     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4820   }
4821
4822   /*
4823    * (non-Javadoc)
4824    *
4825    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4826    * ActionEvent)
4827    */
4828   @Override
4829   protected void showNpFeats_actionPerformed(ActionEvent e)
4830   {
4831     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4832   }
4833
4834   /**
4835    * find the viewport amongst the tabs in this alignment frame and close that
4836    * tab
4837    *
4838    * @param av
4839    */
4840   public boolean closeView(AlignViewportI av)
4841   {
4842     if (viewport == av)
4843     {
4844       this.closeMenuItem_actionPerformed(false);
4845       return true;
4846     }
4847     Component[] comp = tabbedPane.getComponents();
4848     for (int i = 0; comp != null && i < comp.length; i++)
4849     {
4850       if (comp[i] instanceof AlignmentPanel)
4851       {
4852         if (((AlignmentPanel) comp[i]).av == av)
4853         {
4854           // close the view.
4855           closeView((AlignmentPanel) comp[i]);
4856           return true;
4857         }
4858       }
4859     }
4860     return false;
4861   }
4862
4863   protected void build_fetchdbmenu(JMenu webService)
4864   {
4865     // Temporary hack - DBRef Fetcher always top level ws entry.
4866     // TODO We probably want to store a sequence database checklist in
4867     // preferences and have checkboxes.. rather than individual sources selected
4868     // here
4869     final JMenu rfetch = new JMenu(
4870             MessageManager.getString("action.fetch_db_references"));
4871     rfetch.setToolTipText(MessageManager.getString(
4872             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4873     webService.add(rfetch);
4874
4875     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4876             MessageManager.getString("option.trim_retrieved_seqs"));
4877     trimrs.setToolTipText(
4878             MessageManager.getString("label.trim_retrieved_sequences"));
4879     trimrs.setSelected(
4880             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4881     trimrs.addActionListener(new ActionListener()
4882     {
4883       @Override
4884       public void actionPerformed(ActionEvent e)
4885       {
4886         trimrs.setSelected(trimrs.isSelected());
4887         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4888                 Boolean.valueOf(trimrs.isSelected()).toString());
4889       };
4890     });
4891     rfetch.add(trimrs);
4892     JMenuItem fetchr = new JMenuItem(
4893             MessageManager.getString("label.standard_databases"));
4894     fetchr.setToolTipText(
4895             MessageManager.getString("label.fetch_embl_uniprot"));
4896     fetchr.addActionListener(new ActionListener()
4897     {
4898
4899       @Override
4900       public void actionPerformed(ActionEvent e)
4901       {
4902         new Thread(new Runnable()
4903         {
4904           @Override
4905           public void run()
4906           {
4907             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4908                     .getAlignment().isNucleotide();
4909             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4910                     alignPanel.av.getSequenceSelection(),
4911                     alignPanel.alignFrame, null,
4912                     alignPanel.alignFrame.featureSettings, isNucleotide);
4913             dbRefFetcher.addListener(new FetchFinishedListenerI()
4914             {
4915               @Override
4916               public void finished()
4917               {
4918                 AlignFrame.this.setMenusForViewport();
4919               }
4920             });
4921             dbRefFetcher.fetchDBRefs(false);
4922           }
4923         }).start();
4924
4925       }
4926
4927     });
4928     rfetch.add(fetchr);
4929     final AlignFrame me = this;
4930     new Thread(new Runnable()
4931     {
4932       @Override
4933       public void run()
4934       {
4935         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4936                 .getSequenceFetcherSingleton(me);
4937         javax.swing.SwingUtilities.invokeLater(new Runnable()
4938         {
4939           @Override
4940           public void run()
4941           {
4942             String[] dbclasses = sf.getOrderedSupportedSources();
4943             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4944             // jalview.util.QuickSort.sort(otherdb, otherdb);
4945             List<DbSourceProxy> otherdb;
4946             JMenu dfetch = new JMenu();
4947             JMenu ifetch = new JMenu();
4948             JMenuItem fetchr = null;
4949             int comp = 0, icomp = 0, mcomp = 15;
4950             String mname = null;
4951             int dbi = 0;
4952             for (String dbclass : dbclasses)
4953             {
4954               otherdb = sf.getSourceProxy(dbclass);
4955               // add a single entry for this class, or submenu allowing 'fetch
4956               // all' or pick one
4957               if (otherdb == null || otherdb.size() < 1)
4958               {
4959                 continue;
4960               }
4961               // List<DbSourceProxy> dbs=otherdb;
4962               // otherdb=new ArrayList<DbSourceProxy>();
4963               // for (DbSourceProxy db:dbs)
4964               // {
4965               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4966               // }
4967               if (mname == null)
4968               {
4969                 mname = "From " + dbclass;
4970               }
4971               if (otherdb.size() == 1)
4972               {
4973                 final DbSourceProxy[] dassource = otherdb
4974                         .toArray(new DbSourceProxy[0]);
4975                 DbSourceProxy src = otherdb.get(0);
4976                 fetchr = new JMenuItem(src.getDbSource());
4977                 fetchr.addActionListener(new ActionListener()
4978                 {
4979
4980                   @Override
4981                   public void actionPerformed(ActionEvent e)
4982                   {
4983                     new Thread(new Runnable()
4984                     {
4985
4986                       @Override
4987                       public void run()
4988                       {
4989                         boolean isNucleotide = alignPanel.alignFrame
4990                                 .getViewport().getAlignment()
4991                                 .isNucleotide();
4992                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4993                                 alignPanel.av.getSequenceSelection(),
4994                                 alignPanel.alignFrame, dassource,
4995                                 alignPanel.alignFrame.featureSettings,
4996                                 isNucleotide);
4997                         dbRefFetcher
4998                                 .addListener(new FetchFinishedListenerI()
4999                                 {
5000                                   @Override
5001                                   public void finished()
5002                                   {
5003                                     AlignFrame.this.setMenusForViewport();
5004                                   }
5005                                 });
5006                         dbRefFetcher.fetchDBRefs(false);
5007                       }
5008                     }).start();
5009                   }
5010
5011                 });
5012                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5013                         MessageManager.formatMessage(
5014                                 "label.fetch_retrieve_from", new Object[]
5015                                 { src.getDbName() })));
5016                 dfetch.add(fetchr);
5017                 comp++;
5018               }
5019               else
5020               {
5021                 final DbSourceProxy[] dassource = otherdb
5022                         .toArray(new DbSourceProxy[0]);
5023                 // fetch all entry
5024                 DbSourceProxy src = otherdb.get(0);
5025                 fetchr = new JMenuItem(MessageManager
5026                         .formatMessage("label.fetch_all_param", new Object[]
5027                         { src.getDbSource() }));
5028                 fetchr.addActionListener(new ActionListener()
5029                 {
5030                   @Override
5031                   public void actionPerformed(ActionEvent e)
5032                   {
5033                     new Thread(new Runnable()
5034                     {
5035
5036                       @Override
5037                       public void run()
5038                       {
5039                         boolean isNucleotide = alignPanel.alignFrame
5040                                 .getViewport().getAlignment()
5041                                 .isNucleotide();
5042                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5043                                 alignPanel.av.getSequenceSelection(),
5044                                 alignPanel.alignFrame, dassource,
5045                                 alignPanel.alignFrame.featureSettings,
5046                                 isNucleotide);
5047                         dbRefFetcher
5048                                 .addListener(new FetchFinishedListenerI()
5049                                 {
5050                                   @Override
5051                                   public void finished()
5052                                   {
5053                                     AlignFrame.this.setMenusForViewport();
5054                                   }
5055                                 });
5056                         dbRefFetcher.fetchDBRefs(false);
5057                       }
5058                     }).start();
5059                   }
5060                 });
5061
5062                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5063                         MessageManager.formatMessage(
5064                                 "label.fetch_retrieve_from_all_sources",
5065                                 new Object[]
5066                                 { Integer.valueOf(otherdb.size())
5067                                         .toString(),
5068                                     src.getDbSource(), src.getDbName() })));
5069                 dfetch.add(fetchr);
5070                 comp++;
5071                 // and then build the rest of the individual menus
5072                 ifetch = new JMenu(MessageManager.formatMessage(
5073                         "label.source_from_db_source", new Object[]
5074                         { src.getDbSource() }));
5075                 icomp = 0;
5076                 String imname = null;
5077                 int i = 0;
5078                 for (DbSourceProxy sproxy : otherdb)
5079                 {
5080                   String dbname = sproxy.getDbName();
5081                   String sname = dbname.length() > 5
5082                           ? dbname.substring(0, 5) + "..."
5083                           : dbname;
5084                   String msname = dbname.length() > 10
5085                           ? dbname.substring(0, 10) + "..."
5086                           : dbname;
5087                   if (imname == null)
5088                   {
5089                     imname = MessageManager
5090                             .formatMessage("label.from_msname", new Object[]
5091                             { sname });
5092                   }
5093                   fetchr = new JMenuItem(msname);
5094                   final DbSourceProxy[] dassrc = { sproxy };
5095                   fetchr.addActionListener(new ActionListener()
5096                   {
5097
5098                     @Override
5099                     public void actionPerformed(ActionEvent e)
5100                     {
5101                       new Thread(new Runnable()
5102                       {
5103
5104                         @Override
5105                         public void run()
5106                         {
5107                           boolean isNucleotide = alignPanel.alignFrame
5108                                   .getViewport().getAlignment()
5109                                   .isNucleotide();
5110                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5111                                   alignPanel.av.getSequenceSelection(),
5112                                   alignPanel.alignFrame, dassrc,
5113                                   alignPanel.alignFrame.featureSettings,
5114                                   isNucleotide);
5115                           dbRefFetcher
5116                                   .addListener(new FetchFinishedListenerI()
5117                                   {
5118                                     @Override
5119                                     public void finished()
5120                                     {
5121                                       AlignFrame.this.setMenusForViewport();
5122                                     }
5123                                   });
5124                           dbRefFetcher.fetchDBRefs(false);
5125                         }
5126                       }).start();
5127                     }
5128
5129                   });
5130                   fetchr.setToolTipText(
5131                           "<html>" + MessageManager.formatMessage(
5132                                   "label.fetch_retrieve_from", new Object[]
5133                                   { dbname }));
5134                   ifetch.add(fetchr);
5135                   ++i;
5136                   if (++icomp >= mcomp || i == (otherdb.size()))
5137                   {
5138                     ifetch.setText(MessageManager.formatMessage(
5139                             "label.source_to_target", imname, sname));
5140                     dfetch.add(ifetch);
5141                     ifetch = new JMenu();
5142                     imname = null;
5143                     icomp = 0;
5144                     comp++;
5145                   }
5146                 }
5147               }
5148               ++dbi;
5149               if (comp >= mcomp || dbi >= (dbclasses.length))
5150               {
5151                 dfetch.setText(MessageManager.formatMessage(
5152                         "label.source_to_target", mname, dbclass));
5153                 rfetch.add(dfetch);
5154                 dfetch = new JMenu();
5155                 mname = null;
5156                 comp = 0;
5157               }
5158             }
5159           }
5160         });
5161       }
5162     }).start();
5163
5164   }
5165
5166   /**
5167    * Left justify the whole alignment.
5168    */
5169   @Override
5170   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5171   {
5172     AlignmentI al = viewport.getAlignment();
5173     al.justify(false);
5174     viewport.firePropertyChange("alignment", null, al);
5175   }
5176
5177   /**
5178    * Right justify the whole alignment.
5179    */
5180   @Override
5181   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5182   {
5183     AlignmentI al = viewport.getAlignment();
5184     al.justify(true);
5185     viewport.firePropertyChange("alignment", null, al);
5186   }
5187
5188   @Override
5189   public void setShowSeqFeatures(boolean b)
5190   {
5191     showSeqFeatures.setSelected(b);
5192     viewport.setShowSequenceFeatures(b);
5193   }
5194
5195   /*
5196    * (non-Javadoc)
5197    *
5198    * @see
5199    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5200    * awt.event.ActionEvent)
5201    */
5202   @Override
5203   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5204   {
5205     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5206     alignPanel.paintAlignment(false, false);
5207   }
5208
5209   /*
5210    * (non-Javadoc)
5211    *
5212    * @see
5213    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5214    * .ActionEvent)
5215    */
5216   @Override
5217   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5218   {
5219     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5220     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5221
5222   }
5223
5224   /*
5225    * (non-Javadoc)
5226    *
5227    * @see
5228    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5229    * .event.ActionEvent)
5230    */
5231   @Override
5232   protected void showGroupConservation_actionPerformed(ActionEvent e)
5233   {
5234     viewport.setShowGroupConservation(showGroupConservation.getState());
5235     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5236   }
5237
5238   /*
5239    * (non-Javadoc)
5240    *
5241    * @see
5242    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5243    * .event.ActionEvent)
5244    */
5245   @Override
5246   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5247   {
5248     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5249     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5250   }
5251
5252   /*
5253    * (non-Javadoc)
5254    *
5255    * @see
5256    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5257    * .event.ActionEvent)
5258    */
5259   @Override
5260   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5261   {
5262     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5263     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5264   }
5265
5266   @Override
5267   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5268   {
5269     showSequenceLogo.setState(true);
5270     viewport.setShowSequenceLogo(true);
5271     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5272     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5273   }
5274
5275   @Override
5276   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5277   {
5278     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5279   }
5280
5281   /*
5282    * (non-Javadoc)
5283    *
5284    * @see
5285    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5286    * .event.ActionEvent)
5287    */
5288   @Override
5289   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5290   {
5291     if (avc.makeGroupsFromSelection())
5292     {
5293       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5294       alignPanel.updateAnnotation();
5295       alignPanel.paintAlignment(true, true);
5296     }
5297   }
5298
5299   public void clearAlignmentSeqRep()
5300   {
5301     // TODO refactor alignmentseqrep to controller
5302     if (viewport.getAlignment().hasSeqrep())
5303     {
5304       viewport.getAlignment().setSeqrep(null);
5305       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5306       alignPanel.updateAnnotation();
5307       alignPanel.paintAlignment(true, true);
5308     }
5309   }
5310
5311   @Override
5312   protected void createGroup_actionPerformed(ActionEvent e)
5313   {
5314     if (avc.createGroup())
5315     {
5316       alignPanel.alignmentChanged();
5317     }
5318   }
5319
5320   @Override
5321   protected void unGroup_actionPerformed(ActionEvent e)
5322   {
5323     if (avc.unGroup())
5324     {
5325       alignPanel.alignmentChanged();
5326     }
5327   }
5328
5329   /**
5330    * make the given alignmentPanel the currently selected tab
5331    *
5332    * @param alignmentPanel
5333    */
5334   public void setDisplayedView(AlignmentPanel alignmentPanel)
5335   {
5336     if (!viewport.getSequenceSetId()
5337             .equals(alignmentPanel.av.getSequenceSetId()))
5338     {
5339       throw new Error(MessageManager.getString(
5340               "error.implementation_error_cannot_show_view_alignment_frame"));
5341     }
5342     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5343             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5344     {
5345       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5346     }
5347   }
5348
5349   /**
5350    * Action on selection of menu options to Show or Hide annotations.
5351    *
5352    * @param visible
5353    * @param forSequences
5354    *          update sequence-related annotations
5355    * @param forAlignment
5356    *          update non-sequence-related annotations
5357    */
5358   @Override
5359   protected void setAnnotationsVisibility(boolean visible,
5360           boolean forSequences, boolean forAlignment)
5361   {
5362     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5363             .getAlignmentAnnotation();
5364     if (anns == null)
5365     {
5366       return;
5367     }
5368     for (AlignmentAnnotation aa : anns)
5369     {
5370       /*
5371        * don't display non-positional annotations on an alignment
5372        */
5373       if (aa.annotations == null)
5374       {
5375         continue;
5376       }
5377       boolean apply = (aa.sequenceRef == null && forAlignment)
5378               || (aa.sequenceRef != null && forSequences);
5379       if (apply)
5380       {
5381         aa.visible = visible;
5382       }
5383     }
5384     alignPanel.validateAnnotationDimensions(true);
5385     alignPanel.alignmentChanged();
5386   }
5387
5388   /**
5389    * Store selected annotation sort order for the view and repaint.
5390    */
5391   @Override
5392   protected void sortAnnotations_actionPerformed()
5393   {
5394     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5395     this.alignPanel.av
5396             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5397     alignPanel.paintAlignment(false, false);
5398   }
5399
5400   /**
5401    *
5402    * @return alignment panels in this alignment frame
5403    */
5404   public List<? extends AlignmentViewPanel> getAlignPanels()
5405   {
5406     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5407   }
5408
5409   /**
5410    * Open a new alignment window, with the cDNA associated with this (protein)
5411    * alignment, aligned as is the protein.
5412    */
5413   protected void viewAsCdna_actionPerformed()
5414   {
5415     // TODO no longer a menu action - refactor as required
5416     final AlignmentI alignment = getViewport().getAlignment();
5417     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5418     if (mappings == null)
5419     {
5420       return;
5421     }
5422     List<SequenceI> cdnaSeqs = new ArrayList<>();
5423     for (SequenceI aaSeq : alignment.getSequences())
5424     {
5425       for (AlignedCodonFrame acf : mappings)
5426       {
5427         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5428         if (dnaSeq != null)
5429         {
5430           /*
5431            * There is a cDNA mapping for this protein sequence - add to new
5432            * alignment. It will share the same dataset sequence as other mapped
5433            * cDNA (no new mappings need to be created).
5434            */
5435           final Sequence newSeq = new Sequence(dnaSeq);
5436           newSeq.setDatasetSequence(dnaSeq);
5437           cdnaSeqs.add(newSeq);
5438         }
5439       }
5440     }
5441     if (cdnaSeqs.size() == 0)
5442     {
5443       // show a warning dialog no mapped cDNA
5444       return;
5445     }
5446     AlignmentI cdna = new Alignment(
5447             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5448     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5449             AlignFrame.DEFAULT_HEIGHT);
5450     cdna.alignAs(alignment);
5451     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5452             + this.title;
5453     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5454             AlignFrame.DEFAULT_HEIGHT);
5455   }
5456
5457   /**
5458    * Set visibility of dna/protein complement view (available when shown in a
5459    * split frame).
5460    *
5461    * @param show
5462    */
5463   @Override
5464   protected void showComplement_actionPerformed(boolean show)
5465   {
5466     SplitContainerI sf = getSplitViewContainer();
5467     if (sf != null)
5468     {
5469       sf.setComplementVisible(this, show);
5470     }
5471   }
5472
5473   /**
5474    * Generate the reverse (optionally complemented) of the selected sequences,
5475    * and add them to the alignment
5476    */
5477   @Override
5478   protected void showReverse_actionPerformed(boolean complement)
5479   {
5480     AlignmentI al = null;
5481     try
5482     {
5483       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5484       al = dna.reverseCdna(complement);
5485       viewport.addAlignment(al, "");
5486       addHistoryItem(new EditCommand(
5487               MessageManager.getString("label.add_sequences"), Action.PASTE,
5488               al.getSequencesArray(), 0, al.getWidth(),
5489               viewport.getAlignment()));
5490     } catch (Exception ex)
5491     {
5492       System.err.println(ex.getMessage());
5493       return;
5494     }
5495   }
5496
5497   /**
5498    * Try to run a script in the Groovy console, having first ensured that this
5499    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5500    * be targeted at this alignment.
5501    */
5502   @Override
5503   protected void runGroovy_actionPerformed()
5504   {
5505     Jalview.setCurrentAlignFrame(this);
5506     groovy.ui.Console console = Desktop.getGroovyConsole();
5507     if (console != null)
5508     {
5509       try
5510       {
5511         console.runScript();
5512       } catch (Exception ex)
5513       {
5514         System.err.println((ex.toString()));
5515         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5516                 MessageManager.getString("label.couldnt_run_groovy_script"),
5517                 MessageManager.getString("label.groovy_support_failed"),
5518                 JvOptionPane.ERROR_MESSAGE);
5519       }
5520     }
5521     else
5522     {
5523       System.err.println("Can't run Groovy script as console not found");
5524     }
5525   }
5526
5527   /**
5528    * Hides columns containing (or not containing) a specified feature, provided
5529    * that would not leave all columns hidden
5530    *
5531    * @param featureType
5532    * @param columnsContaining
5533    * @return
5534    */
5535   public boolean hideFeatureColumns(String featureType,
5536           boolean columnsContaining)
5537   {
5538     boolean notForHiding = avc.markColumnsContainingFeatures(
5539             columnsContaining, false, false, featureType);
5540     if (notForHiding)
5541     {
5542       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5543               false, featureType))
5544       {
5545         getViewport().hideSelectedColumns();
5546         return true;
5547       }
5548     }
5549     return false;
5550   }
5551
5552   @Override
5553   protected void selectHighlightedColumns_actionPerformed(
5554           ActionEvent actionEvent)
5555   {
5556     // include key modifier check in case user selects from menu
5557     avc.markHighlightedColumns(
5558             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5559             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5560                     | ActionEvent.CTRL_MASK)) != 0);
5561   }
5562
5563   /**
5564    * Rebuilds the Colour menu, including any user-defined colours which have
5565    * been loaded either on startup or during the session
5566    */
5567   public void buildColourMenu()
5568   {
5569     colourMenu.removeAll();
5570
5571     colourMenu.add(applyToAllGroups);
5572     colourMenu.add(textColour);
5573     colourMenu.addSeparator();
5574
5575     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5576             false);
5577
5578     colourMenu.addSeparator();
5579     colourMenu.add(conservationMenuItem);
5580     colourMenu.add(modifyConservation);
5581     colourMenu.add(abovePIDThreshold);
5582     colourMenu.add(modifyPID);
5583     colourMenu.add(annotationColour);
5584
5585     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5586     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5587   }
5588
5589   /**
5590    * Open a dialog (if not already open) that allows the user to select and
5591    * calculate PCA or Tree analysis
5592    */
5593   protected void openTreePcaDialog()
5594   {
5595     if (alignPanel.getCalculationDialog() == null)
5596     {
5597       new CalculationChooser(AlignFrame.this);
5598     }
5599   }
5600
5601   @Override
5602   protected void loadVcf_actionPerformed()
5603   {
5604     JalviewFileChooser chooser = new JalviewFileChooser(
5605             Cache.getProperty("LAST_DIRECTORY"));
5606     chooser.setFileView(new JalviewFileView());
5607     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5608     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5609
5610     int value = chooser.showOpenDialog(null);
5611
5612     if (value == JalviewFileChooser.APPROVE_OPTION)
5613     {
5614       String choice = chooser.getSelectedFile().getPath();
5615       Cache.setProperty("LAST_DIRECTORY", choice);
5616       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5617       new VCFLoader(choice).loadVCF(seqs, this);
5618     }
5619
5620   }
5621 }
5622
5623 class PrintThread extends Thread
5624 {
5625   AlignmentPanel ap;
5626
5627   public PrintThread(AlignmentPanel ap)
5628   {
5629     this.ap = ap;
5630   }
5631
5632   static PageFormat pf;
5633
5634   @Override
5635   public void run()
5636   {
5637     PrinterJob printJob = PrinterJob.getPrinterJob();
5638
5639     if (pf != null)
5640     {
5641       printJob.setPrintable(ap, pf);
5642     }
5643     else
5644     {
5645       printJob.setPrintable(ap);
5646     }
5647
5648     if (printJob.printDialog())
5649     {
5650       try
5651       {
5652         printJob.print();
5653       } catch (Exception PrintException)
5654       {
5655         PrintException.printStackTrace();
5656       }
5657     }
5658   }
5659 }