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