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.HMMFile;
  76 import jalview.io.HtmlSvgOutput;
  77 import jalview.io.IdentifyFile;
  78 import jalview.io.JPredFile;
  79 import jalview.io.JalviewFileChooser;
  80 import jalview.io.JalviewFileView;
  81 import jalview.io.JnetAnnotationMaker;
  82 import jalview.io.NewickFile;
  83 import jalview.io.ScoreMatrixFile;
  84 import jalview.io.TCoffeeScoreFile;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.MessageManager;
  91 import jalview.viewmodel.AlignmentViewport;
  92 import jalview.viewmodel.ViewportRanges;
  93 import jalview.ws.DBRefFetcher;
  94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  95 import jalview.ws.jws1.Discoverer;
  96 import jalview.ws.jws2.Jws2Discoverer;
  97 import jalview.ws.jws2.jabaws2.Jws2Instance;
  98 import jalview.ws.seqfetcher.DbSourceProxy;
  99
 100 import java.awt.BorderLayout;
 101 import java.awt.Component;
 102 import java.awt.Rectangle;
 103 import java.awt.Toolkit;
 104 import java.awt.datatransfer.Clipboard;
 105 import java.awt.datatransfer.DataFlavor;
 106 import java.awt.datatransfer.StringSelection;
 107 import java.awt.datatransfer.Transferable;
 108 import java.awt.dnd.DnDConstants;
 109 import java.awt.dnd.DropTargetDragEvent;
 110 import java.awt.dnd.DropTargetDropEvent;
 111 import java.awt.dnd.DropTargetEvent;
 112 import java.awt.dnd.DropTargetListener;
 113 import java.awt.event.ActionEvent;
 114 import java.awt.event.ActionListener;
 115 import java.awt.event.FocusAdapter;
 116 import java.awt.event.FocusEvent;
 117 import java.awt.event.ItemEvent;
 118 import java.awt.event.ItemListener;
 119 import java.awt.event.KeyAdapter;
 120 import java.awt.event.KeyEvent;
 121 import java.awt.event.MouseEvent;
 122 import java.awt.print.PageFormat;
 123 import java.awt.print.PrinterJob;
 124 import java.beans.PropertyChangeEvent;
 125 import java.io.File;
 126 import java.io.FileWriter;
 127 import java.io.PrintWriter;
 128 import java.net.URL;
 129 import java.util.ArrayList;
 130 import java.util.Arrays;
 131 import java.util.Deque;
 132 import java.util.Enumeration;
 133 import java.util.Hashtable;
 134 import java.util.List;
 135 import java.util.Vector;
 136
 137 import javax.swing.JCheckBoxMenuItem;
 138 import javax.swing.JEditorPane;
 139 import javax.swing.JInternalFrame;
 140 import javax.swing.JLayeredPane;
 141 import javax.swing.JMenu;
 142 import javax.swing.JMenuItem;
 143 import javax.swing.JScrollPane;
 144 import javax.swing.SwingUtilities;
 145
 146 /**
 147  * DOCUMENT ME!
 148  *
 149  * @author $author$
 150  * @version $Revision$
 151  */
 152 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 153         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 154 {
 155
 156   public static final int DEFAULT_WIDTH = 700;
 157
 158   public static final int DEFAULT_HEIGHT = 500;
 159
 160   /*
 161    * The currently displayed panel (selected tabbed view if more than one)
 162    */
 163   public AlignmentPanel alignPanel;
 164
 165   AlignViewport viewport;
 166
 167   ViewportRanges vpRanges;
 168
 169   public AlignViewControllerI avc;
 170
 171   List<AlignmentPanel> alignPanels = new ArrayList<>();
 172
 173   /**
 174    * Last format used to load or save alignments in this window
 175    */
 176   FileFormatI currentFileFormat = null;
 177
 178   /**
 179    * Current filename for this alignment
 180    */
 181   String fileName = null;
 182
 183   /**
 184    * Creates a new AlignFrame object with specific width and height.
 185    *
 186    * @param al
 187    * @param width
 188    * @param height
 189    */
 190   public AlignFrame(AlignmentI al, int width, int height)
 191   {
 192     this(al, null, width, height);
 193   }
 194
 195   /**
 196    * Creates a new AlignFrame object with specific width, height and
 197    * sequenceSetId
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    * @param sequenceSetId
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height,
 205           String sequenceSetId)
 206   {
 207     this(al, null, width, height, sequenceSetId);
 208   }
 209
 210   /**
 211    * Creates a new AlignFrame object with specific width, height and
 212    * sequenceSetId
 213    *
 214    * @param al
 215    * @param width
 216    * @param height
 217    * @param sequenceSetId
 218    * @param viewId
 219    */
 220   public AlignFrame(AlignmentI al, int width, int height,
 221           String sequenceSetId, String viewId)
 222   {
 223     this(al, null, width, height, sequenceSetId, viewId);
 224   }
 225
 226   /**
 227    * new alignment window with hidden columns
 228    *
 229    * @param al
 230    *          AlignmentI
 231    * @param hiddenColumns
 232    *          ColumnSelection or null
 233    * @param width
 234    *          Width of alignment frame
 235    * @param height
 236    *          height of frame.
 237    */
 238   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 239           int width, int height)
 240   {
 241     this(al, hiddenColumns, width, height, null);
 242   }
 243
 244   /**
 245    * Create alignment frame for al with hiddenColumns, a specific width and
 246    * height, and specific sequenceId
 247    *
 248    * @param al
 249    * @param hiddenColumns
 250    * @param width
 251    * @param height
 252    * @param sequenceSetId
 253    *          (may be null)
 254    */
 255   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 256           int width, int height, String sequenceSetId)
 257   {
 258     this(al, hiddenColumns, width, height, sequenceSetId, null);
 259   }
 260
 261   /**
 262    * Create alignment frame for al with hiddenColumns, a specific width and
 263    * height, and specific sequenceId
 264    *
 265    * @param al
 266    * @param hiddenColumns
 267    * @param width
 268    * @param height
 269    * @param sequenceSetId
 270    *          (may be null)
 271    * @param viewId
 272    *          (may be null)
 273    */
 274   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 275           int width, int height, String sequenceSetId, String viewId)
 276   {
 277     setSize(width, height);
 278
 279     if (al.getDataset() == null)
 280     {
 281       al.setDataset(null);
 282     }
 283
 284     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 285
 286     alignPanel = new AlignmentPanel(this, viewport);
 287
 288     addAlignmentPanel(alignPanel, true);
 289     init();
 290   }
 291
 292   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 293           HiddenColumns hiddenColumns, int width, int height)
 294   {
 295     setSize(width, height);
 296
 297     if (al.getDataset() == null)
 298     {
 299       al.setDataset(null);
 300     }
 301
 302     viewport = new AlignViewport(al, hiddenColumns);
 303
 304     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 305     {
 306       viewport.hideSequence(hiddenSeqs);
 307     }
 308     alignPanel = new AlignmentPanel(this, viewport);
 309     addAlignmentPanel(alignPanel, true);
 310     init();
 311   }
 312
 313   /**
 314    * Make a new AlignFrame from existing alignmentPanels
 315    *
 316    * @param ap
 317    *          AlignmentPanel
 318    * @param av
 319    *          AlignViewport
 320    */
 321   public AlignFrame(AlignmentPanel ap)
 322   {
 323     viewport = ap.av;
 324     alignPanel = ap;
 325     addAlignmentPanel(ap, false);
 326     init();
 327   }
 328
 329   /**
 330    * initalise the alignframe from the underlying viewport data and the
 331    * configurations
 332    */
 333   void init()
 334   {
 335     if (!Jalview.isHeadlessMode())
 336     {
 337       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 338     }
 339
 340     vpRanges = viewport.getRanges();
 341     avc = new jalview.controller.AlignViewController(this, viewport,
 342             alignPanel);
 343     if (viewport.getAlignmentConservationAnnotation() == null)
 344     {
 345       // BLOSUM62Colour.setEnabled(false);
 346       conservationMenuItem.setEnabled(false);
 347       modifyConservation.setEnabled(false);
 348       // PIDColour.setEnabled(false);
 349       // abovePIDThreshold.setEnabled(false);
 350       // modifyPID.setEnabled(false);
 351     }
 352
 353     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 354             "No sort");
 355
 356     if (sortby.equals("Id"))
 357     {
 358       sortIDMenuItem_actionPerformed(null);
 359     }
 360     else if (sortby.equals("Pairwise Identity"))
 361     {
 362       sortPairwiseMenuItem_actionPerformed(null);
 363     }
 364
 365     this.alignPanel.av
 366             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 367
 368     setMenusFromViewport(viewport);
 369     buildSortByAnnotationScoresMenu();
 370     calculateTree.addActionListener(new ActionListener()
 371     {
 372
 373       @Override
 374       public void actionPerformed(ActionEvent e)
 375       {
 376         openTreePcaDialog();
 377       }
 378     });
 379     buildColourMenu();
 380
 381     if (Desktop.desktop != null)
 382     {
 383       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 384       addServiceListeners();
 385       setGUINucleotide();
 386     }
 387
 388     if (viewport.getWrapAlignment())
 389     {
 390       wrapMenuItem_actionPerformed(null);
 391     }
 392
 393     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 394     {
 395       this.overviewMenuItem_actionPerformed(null);
 396     }
 397
 398     addKeyListener();
 399
 400     final List<AlignmentPanel> selviews = new ArrayList<>();
 401     final List<AlignmentPanel> origview = new ArrayList<>();
 402     final String menuLabel = MessageManager
 403             .getString("label.copy_format_from");
 404     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 405             new ViewSetProvider()
 406             {
 407
 408               @Override
 409               public AlignmentPanel[] getAllAlignmentPanels()
 410               {
 411                 origview.clear();
 412                 origview.add(alignPanel);
 413                 // make an array of all alignment panels except for this one
 414                 List<AlignmentPanel> aps = new ArrayList<>(
 415                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 416                 aps.remove(AlignFrame.this.alignPanel);
 417                 return aps.toArray(new AlignmentPanel[aps.size()]);
 418               }
 419             }, selviews, new ItemListener()
 420             {
 421
 422               @Override
 423               public void itemStateChanged(ItemEvent e)
 424               {
 425                 if (origview.size() > 0)
 426                 {
 427                   final AlignmentPanel ap = origview.get(0);
 428
 429                   /*
 430                    * Copy the ViewStyle of the selected panel to 'this one'.
 431                    * Don't change value of 'scaleProteinAsCdna' unless copying
 432                    * from a SplitFrame.
 433                    */
 434                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 435                           .getViewStyle();
 436                   boolean fromSplitFrame = selviews.get(0)
 437                           .getAlignViewport().getCodingComplement() != null;
 438                   if (!fromSplitFrame)
 439                   {
 440                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 441                             .getViewStyle().isScaleProteinAsCdna());
 442                   }
 443                   ap.getAlignViewport().setViewStyle(vs);
 444
 445                   /*
 446                    * Also rescale ViewStyle of SplitFrame complement if there is
 447                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 448                    * the whole ViewStyle (allow cDNA protein to have different
 449                    * fonts)
 450                    */
 451                   AlignViewportI complement = ap.getAlignViewport()
 452                           .getCodingComplement();
 453                   if (complement != null && vs.isScaleProteinAsCdna())
 454                   {
 455                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 456                     ((SplitFrame) af.getSplitViewContainer())
 457                             .adjustLayout();
 458                     af.setMenusForViewport();
 459                   }
 460
 461                   ap.updateLayout();
 462                   ap.setSelected(true);
 463                   ap.alignFrame.setMenusForViewport();
 464
 465                 }
 466               }
 467             });
 468     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 469             .indexOf("devel") > -1
 470             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 471                     .indexOf("test") > -1)
 472     {
 473       formatMenu.add(vsel);
 474     }
 475     addFocusListener(new FocusAdapter()
 476     {
 477       @Override
 478       public void focusGained(FocusEvent e)
 479       {
 480         Jalview.setCurrentAlignFrame(AlignFrame.this);
 481       }
 482     });
 483
 484   }
 485
 486   /**
 487    * Change the filename and format for the alignment, and enable the 'reload'
 488    * button functionality.
 489    *
 490    * @param file
 491    *          valid filename
 492    * @param format
 493    *          format of file
 494    */
 495   public void setFileName(String file, FileFormatI format)
 496   {
 497     fileName = file;
 498     setFileFormat(format);
 499     reload.setEnabled(true);
 500   }
 501
 502   /**
 503    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 504    * events
 505    */
 506   void addKeyListener()
 507   {
 508     addKeyListener(new KeyAdapter()
 509     {
 510       @Override
 511       public void keyPressed(KeyEvent evt)
 512       {
 513         if (viewport.cursorMode
 514                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 515                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 516                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 517                 && Character.isDigit(evt.getKeyChar()))
 518         {
 519           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 520         }
 521
 522         switch (evt.getKeyCode())
 523         {
 524
 525         case 27: // escape key
 526           deselectAllSequenceMenuItem_actionPerformed(null);
 527
 528           break;
 529
 530         case KeyEvent.VK_DOWN:
 531           if (evt.isAltDown() || !viewport.cursorMode)
 532           {
 533             moveSelectedSequences(false);
 534           }
 535           if (viewport.cursorMode)
 536           {
 537             alignPanel.getSeqPanel().moveCursor(0, 1);
 538           }
 539           break;
 540
 541         case KeyEvent.VK_UP:
 542           if (evt.isAltDown() || !viewport.cursorMode)
 543           {
 544             moveSelectedSequences(true);
 545           }
 546           if (viewport.cursorMode)
 547           {
 548             alignPanel.getSeqPanel().moveCursor(0, -1);
 549           }
 550
 551           break;
 552
 553         case KeyEvent.VK_LEFT:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555           {
 556             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 557           }
 558           else
 559           {
 560             alignPanel.getSeqPanel().moveCursor(-1, 0);
 561           }
 562
 563           break;
 564
 565         case KeyEvent.VK_RIGHT:
 566           if (evt.isAltDown() || !viewport.cursorMode)
 567           {
 568             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 569           }
 570           else
 571           {
 572             alignPanel.getSeqPanel().moveCursor(1, 0);
 573           }
 574           break;
 575
 576         case KeyEvent.VK_SPACE:
 577           if (viewport.cursorMode)
 578           {
 579             alignPanel.getSeqPanel().insertGapAtCursor(
 580                     evt.isControlDown() || evt.isShiftDown()
 581                             || evt.isAltDown());
 582           }
 583           break;
 584
 585         // case KeyEvent.VK_A:
 586         // if (viewport.cursorMode)
 587         // {
 588         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 589         // //System.out.println("A");
 590         // }
 591         // break;
 592         /*
 593          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 594          * System.out.println("closing bracket"); } break;
 595          */
 596         case KeyEvent.VK_DELETE:
 597         case KeyEvent.VK_BACK_SPACE:
 598           if (!viewport.cursorMode)
 599           {
 600             cut_actionPerformed(null);
 601           }
 602           else
 603           {
 604             alignPanel.getSeqPanel().deleteGapAtCursor(
 605                     evt.isControlDown() || evt.isShiftDown()
 606                             || evt.isAltDown());
 607           }
 608
 609           break;
 610
 611         case KeyEvent.VK_S:
 612           if (viewport.cursorMode)
 613           {
 614             alignPanel.getSeqPanel().setCursorRow();
 615           }
 616           break;
 617         case KeyEvent.VK_C:
 618           if (viewport.cursorMode && !evt.isControlDown())
 619           {
 620             alignPanel.getSeqPanel().setCursorColumn();
 621           }
 622           break;
 623         case KeyEvent.VK_P:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setCursorPosition();
 627           }
 628           break;
 629
 630         case KeyEvent.VK_ENTER:
 631         case KeyEvent.VK_COMMA:
 632           if (viewport.cursorMode)
 633           {
 634             alignPanel.getSeqPanel().setCursorRowAndColumn();
 635           }
 636           break;
 637
 638         case KeyEvent.VK_Q:
 639           if (viewport.cursorMode)
 640           {
 641             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 642           }
 643           break;
 644         case KeyEvent.VK_M:
 645           if (viewport.cursorMode)
 646           {
 647             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 648           }
 649           break;
 650
 651         case KeyEvent.VK_F2:
 652           viewport.cursorMode = !viewport.cursorMode;
 653           statusBar.setText(MessageManager.formatMessage(
 654                   "label.keyboard_editing_mode",
 655                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 656           if (viewport.cursorMode)
 657           {
 658             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 659                     .getStartRes();
 660             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 661                     .getStartSeq();
 662           }
 663           alignPanel.getSeqPanel().seqCanvas.repaint();
 664           break;
 665
 666         case KeyEvent.VK_F1:
 667           try
 668           {
 669             Help.showHelpWindow();
 670           } catch (Exception ex)
 671           {
 672             ex.printStackTrace();
 673           }
 674           break;
 675         case KeyEvent.VK_H:
 676         {
 677           boolean toggleSeqs = !evt.isControlDown();
 678           boolean toggleCols = !evt.isShiftDown();
 679           toggleHiddenRegions(toggleSeqs, toggleCols);
 680           break;
 681         }
 682         case KeyEvent.VK_B:
 683         {
 684           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 685           boolean modifyExisting = true; // always modify, don't clear
 686                                          // evt.isShiftDown();
 687           boolean invertHighlighted = evt.isAltDown();
 688           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 689                   toggleSel);
 690           break;
 691         }
 692         case KeyEvent.VK_PAGE_UP:
 693           if (viewport.getWrapAlignment())
 694           {
 695             vpRanges.scrollUp(true);
 696           }
 697           else
 698           {
 699             vpRanges.pageUp();
 700           }
 701           break;
 702         case KeyEvent.VK_PAGE_DOWN:
 703           if (viewport.getWrapAlignment())
 704           {
 705             vpRanges.scrollUp(false);
 706           }
 707           else
 708           {
 709             vpRanges.pageDown();
 710           }
 711           break;
 712         }
 713       }
 714
 715       @Override
 716       public void keyReleased(KeyEvent evt)
 717       {
 718         switch (evt.getKeyCode())
 719         {
 720         case KeyEvent.VK_LEFT:
 721           if (evt.isAltDown() || !viewport.cursorMode)
 722           {
 723             viewport.firePropertyChange("alignment", null, viewport
 724                     .getAlignment().getSequences());
 725           }
 726           break;
 727
 728         case KeyEvent.VK_RIGHT:
 729           if (evt.isAltDown() || !viewport.cursorMode)
 730           {
 731             viewport.firePropertyChange("alignment", null, viewport
 732                     .getAlignment().getSequences());
 733           }
 734           break;
 735         }
 736       }
 737     });
 738   }
 739
 740   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 741   {
 742     ap.alignFrame = this;
 743     avc = new jalview.controller.AlignViewController(this, viewport,
 744             alignPanel);
 745
 746     alignPanels.add(ap);
 747
 748     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 749
 750     int aSize = alignPanels.size();
 751
 752     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 753
 754     if (aSize == 1 && ap.av.viewName == null)
 755     {
 756       this.getContentPane().add(ap, BorderLayout.CENTER);
 757     }
 758     else
 759     {
 760       if (aSize == 2)
 761       {
 762         setInitialTabVisible();
 763       }
 764
 765       expandViews.setEnabled(true);
 766       gatherViews.setEnabled(true);
 767       tabbedPane.addTab(ap.av.viewName, ap);
 768
 769       ap.setVisible(false);
 770     }
 771
 772     if (newPanel)
 773     {
 774       if (ap.av.isPadGaps())
 775       {
 776         ap.av.getAlignment().padGaps();
 777       }
 778       ap.av.updateConservation(ap);
 779       ap.av.updateConsensus(ap);
 780       ap.av.updateStrucConsensus(ap);
 781     }
 782   }
 783
 784   public void setInitialTabVisible()
 785   {
 786     expandViews.setEnabled(true);
 787     gatherViews.setEnabled(true);
 788     tabbedPane.setVisible(true);
 789     AlignmentPanel first = alignPanels.get(0);
 790     tabbedPane.addTab(first.av.viewName, first);
 791     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 792   }
 793
 794   public AlignViewport getViewport()
 795   {
 796     return viewport;
 797   }
 798
 799   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 800   private void addServiceListeners()
 801   {
 802     final java.beans.PropertyChangeListener thisListener;
 803     Desktop.instance.addJalviewPropertyChangeListener("services",
 804             thisListener = new java.beans.PropertyChangeListener()
 805             {
 806               @Override
 807               public void propertyChange(PropertyChangeEvent evt)
 808               {
 809                 // // System.out.println("Discoverer property change.");
 810                 // if (evt.getPropertyName().equals("services"))
 811                 {
 812                   SwingUtilities.invokeLater(new Runnable()
 813                   {
 814
 815                     @Override
 816                     public void run()
 817                     {
 818                       System.err
 819                               .println("Rebuild WS Menu for service change");
 820                       BuildWebServiceMenu();
 821                     }
 822
 823                   });
 824                 }
 825               }
 826             });
 827     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 828     {
 829       @Override
 830       public void internalFrameClosed(
 831               javax.swing.event.InternalFrameEvent evt)
 832       {
 833         // System.out.println("deregistering discoverer listener");
 834         Desktop.instance.removeJalviewPropertyChangeListener("services",
 835                 thisListener);
 836         closeMenuItem_actionPerformed(true);
 837       };
 838     });
 839     // Finally, build the menu once to get current service state
 840     new Thread(new Runnable()
 841     {
 842       @Override
 843       public void run()
 844       {
 845         BuildWebServiceMenu();
 846       }
 847     }).start();
 848   }
 849
 850   /**
 851    * Configure menu items that vary according to whether the alignment is
 852    * nucleotide or protein
 853    */
 854   public void setGUINucleotide()
 855   {
 856     AlignmentI al = getViewport().getAlignment();
 857     boolean nucleotide = al.isNucleotide();
 858
 859     showTranslation.setVisible(nucleotide);
 860     showReverse.setVisible(nucleotide);
 861     showReverseComplement.setVisible(nucleotide);
 862     conservationMenuItem.setEnabled(!nucleotide);
 863     modifyConservation.setEnabled(!nucleotide
 864             && conservationMenuItem.isSelected());
 865     showGroupConservation.setEnabled(!nucleotide);
 866
 867     showComplementMenuItem.setText(nucleotide ? MessageManager
 868             .getString("label.protein") : MessageManager
 869             .getString("label.nucleotide"));
 870   }
 871
 872   /**
 873    * set up menus for the current viewport. This may be called after any
 874    * operation that affects the data in the current view (selection changed,
 875    * etc) to update the menus to reflect the new state.
 876    */
 877   @Override
 878   public void setMenusForViewport()
 879   {
 880     setMenusFromViewport(viewport);
 881   }
 882
 883   /**
 884    * Need to call this method when tabs are selected for multiple views, or when
 885    * loading from Jalview2XML.java
 886    *
 887    * @param av
 888    *          AlignViewport
 889    */
 890   void setMenusFromViewport(AlignViewport av)
 891   {
 892     padGapsMenuitem.setSelected(av.isPadGaps());
 893     colourTextMenuItem.setSelected(av.isShowColourText());
 894     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 895     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 896     conservationMenuItem.setSelected(av.getConservationSelected());
 897     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 898     seqLimits.setSelected(av.getShowJVSuffix());
 899     idRightAlign.setSelected(av.isRightAlignIds());
 900     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 901     renderGapsMenuItem.setSelected(av.isRenderGaps());
 902     wrapMenuItem.setSelected(av.getWrapAlignment());
 903     scaleAbove.setVisible(av.getWrapAlignment());
 904     scaleLeft.setVisible(av.getWrapAlignment());
 905     scaleRight.setVisible(av.getWrapAlignment());
 906     annotationPanelMenuItem.setState(av.isShowAnnotation());
 907     /*
 908      * Show/hide annotations only enabled if annotation panel is shown
 909      */
 910     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 911     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 912     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 913     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 914     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 915     viewTextMenuItem.setSelected(av.getShowText());
 916     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 917     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 918     showGroupConservation.setSelected(av.isShowGroupConservation());
 919     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 920     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 921     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 922
 923     ColourMenuHelper.setColourSelected(colourMenu,
 924             av.getGlobalColourScheme());
 925
 926     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 927     hiddenMarkers.setState(av.getShowHiddenMarkers());
 928     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 929     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 930     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 931     autoCalculate.setSelected(av.autoCalculateConsensus);
 932     sortByTree.setSelected(av.sortByTree);
 933     listenToViewSelections.setSelected(av.followSelection);
 934
 935     showProducts.setEnabled(canShowProducts());
 936     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 937
 938     updateEditMenuBar();
 939   }
 940
 941   /**
 942    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 943    *
 944    * @param b
 945    */
 946   public void setGroovyEnabled(boolean b)
 947   {
 948     runGroovy.setEnabled(b);
 949   }
 950
 951   private IProgressIndicator progressBar;
 952
 953   /*
 954    * (non-Javadoc)
 955    *
 956    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 957    */
 958   @Override
 959   public void setProgressBar(String message, long id)
 960   {
 961     progressBar.setProgressBar(message, id);
 962   }
 963
 964   @Override
 965   public void registerHandler(final long id,
 966           final IProgressIndicatorHandler handler)
 967   {
 968     progressBar.registerHandler(id, handler);
 969   }
 970
 971   /**
 972    *
 973    * @return true if any progress bars are still active
 974    */
 975   @Override
 976   public boolean operationInProgress()
 977   {
 978     return progressBar.operationInProgress();
 979   }
 980
 981   @Override
 982   public void setStatus(String text)
 983   {
 984     statusBar.setText(text);
 985   }
 986
 987   /*
 988    * Added so Castor Mapping file can obtain Jalview Version
 989    */
 990   public String getVersion()
 991   {
 992     return jalview.bin.Cache.getProperty("VERSION");
 993   }
 994
 995   public FeatureRenderer getFeatureRenderer()
 996   {
 997     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 998   }
 999
1000   @Override
1001   public void fetchSequence_actionPerformed(ActionEvent e)
1002   {
1003     new jalview.gui.SequenceFetcher(this);
1004   }
1005
1006   @Override
1007   public void addFromFile_actionPerformed(ActionEvent e)
1008   {
1009     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1010   }
1011
1012   @Override
1013   public void reload_actionPerformed(ActionEvent e)
1014   {
1015     if (fileName != null)
1016     {
1017       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1018       // originating file's format
1019       // TODO: work out how to recover feature settings for correct view(s) when
1020       // file is reloaded.
1021       if (FileFormat.Jalview.equals(currentFileFormat))
1022       {
1023         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1024         for (int i = 0; i < frames.length; i++)
1025         {
1026           if (frames[i] instanceof AlignFrame && frames[i] != this
1027                   && ((AlignFrame) frames[i]).fileName != null
1028                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1029           {
1030             try
1031             {
1032               frames[i].setSelected(true);
1033               Desktop.instance.closeAssociatedWindows();
1034             } catch (java.beans.PropertyVetoException ex)
1035             {
1036             }
1037           }
1038
1039         }
1040         Desktop.instance.closeAssociatedWindows();
1041
1042         FileLoader loader = new FileLoader();
1043         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1044                 : DataSourceType.FILE;
1045         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1046       }
1047       else
1048       {
1049         Rectangle bounds = this.getBounds();
1050
1051         FileLoader loader = new FileLoader();
1052         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1053                 : DataSourceType.FILE;
1054         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1055                 protocol, currentFileFormat);
1056
1057         newframe.setBounds(bounds);
1058         if (featureSettings != null && featureSettings.isShowing())
1059         {
1060           final Rectangle fspos = featureSettings.frame.getBounds();
1061           // TODO: need a 'show feature settings' function that takes bounds -
1062           // need to refactor Desktop.addFrame
1063           newframe.featureSettings_actionPerformed(null);
1064           final FeatureSettings nfs = newframe.featureSettings;
1065           SwingUtilities.invokeLater(new Runnable()
1066           {
1067             @Override
1068             public void run()
1069             {
1070               nfs.frame.setBounds(fspos);
1071             }
1072           });
1073           this.featureSettings.close();
1074           this.featureSettings = null;
1075         }
1076         this.closeMenuItem_actionPerformed(true);
1077       }
1078     }
1079   }
1080
1081   @Override
1082   public void addFromText_actionPerformed(ActionEvent e)
1083   {
1084     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1085             .getAlignPanel());
1086   }
1087
1088   @Override
1089   public void addFromURL_actionPerformed(ActionEvent e)
1090   {
1091     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1092   }
1093
1094   @Override
1095   public void save_actionPerformed(ActionEvent e)
1096   {
1097     if (fileName == null || (currentFileFormat == null)
1098             || fileName.startsWith("http"))
1099     {
1100       saveAs_actionPerformed(null);
1101     }
1102     else
1103     {
1104       saveAlignment(fileName, currentFileFormat);
1105     }
1106   }
1107
1108   /**
1109    * DOCUMENT ME!
1110    *
1111    * @param e
1112    *          DOCUMENT ME!
1113    */
1114   @Override
1115   public void saveAs_actionPerformed(ActionEvent e)
1116   {
1117     String format = currentFileFormat == null ? null : currentFileFormat
1118             .getName();
1119     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1120             Cache.getProperty("LAST_DIRECTORY"), format);
1121
1122     chooser.setFileView(new JalviewFileView());
1123     chooser.setDialogTitle(MessageManager
1124             .getString("label.save_alignment_to_file"));
1125     chooser.setToolTipText(MessageManager.getString("action.save"));
1126
1127     int value = chooser.showSaveDialog(this);
1128
1129     if (value == JalviewFileChooser.APPROVE_OPTION)
1130     {
1131       currentFileFormat = chooser.getSelectedFormat();
1132       while (currentFileFormat == null)
1133       {
1134         JvOptionPane
1135                 .showInternalMessageDialog(
1136                         Desktop.desktop,
1137                         MessageManager
1138                                 .getString("label.select_file_format_before_saving"),
1139                         MessageManager
1140                                 .getString("label.file_format_not_specified"),
1141                         JvOptionPane.WARNING_MESSAGE);
1142         currentFileFormat = chooser.getSelectedFormat();
1143         value = chooser.showSaveDialog(this);
1144         if (value != JalviewFileChooser.APPROVE_OPTION)
1145         {
1146           return;
1147         }
1148       }
1149
1150       fileName = chooser.getSelectedFile().getPath();
1151
1152       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1153
1154       Cache.setProperty("LAST_DIRECTORY", fileName);
1155       saveAlignment(fileName, currentFileFormat);
1156     }
1157   }
1158
1159   public boolean saveAlignment(String file, FileFormatI format)
1160   {
1161     boolean success = true;
1162
1163     if (FileFormat.Jalview.equals(format))
1164     {
1165       String shortName = title;
1166
1167       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1168       {
1169         shortName = shortName.substring(shortName
1170                 .lastIndexOf(java.io.File.separatorChar) + 1);
1171       }
1172
1173       success = new Jalview2XML().saveAlignment(this, file, shortName);
1174
1175       statusBar.setText(MessageManager.formatMessage(
1176               "label.successfully_saved_to_file_in_format", new Object[] {
1177                   fileName, format }));
1178
1179     }
1180     else
1181     {
1182       AlignmentExportData exportData = getAlignmentForExport(format,
1183               viewport, null);
1184       if (exportData.getSettings().isCancelled())
1185       {
1186         return false;
1187       }
1188       FormatAdapter f = new FormatAdapter(alignPanel,
1189               exportData.getSettings());
1190       String output = f.formatSequences(
1191               format,
1192               exportData.getAlignment(), // class cast exceptions will
1193               // occur in the distant future
1194               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1195               f.getCacheSuffixDefault(format), viewport.getAlignment()
1196                       .getHiddenColumns());
1197
1198       if (output == null)
1199       {
1200         success = false;
1201       }
1202       else
1203       {
1204         try
1205         {
1206           PrintWriter out = new PrintWriter(new FileWriter(file));
1207
1208           out.print(output);
1209           out.close();
1210           this.setTitle(file);
1211           statusBar.setText(MessageManager.formatMessage(
1212                   "label.successfully_saved_to_file_in_format",
1213                   new Object[] { fileName, format.getName() }));
1214         } catch (Exception ex)
1215         {
1216           success = false;
1217           ex.printStackTrace();
1218         }
1219       }
1220     }
1221
1222     if (!success)
1223     {
1224       JvOptionPane.showInternalMessageDialog(this, MessageManager
1225               .formatMessage("label.couldnt_save_file",
1226                       new Object[] { fileName }), MessageManager
1227               .getString("label.error_saving_file"),
1228               JvOptionPane.WARNING_MESSAGE);
1229     }
1230
1231     return success;
1232   }
1233
1234   private void warningMessage(String warning, String title)
1235   {
1236     if (new jalview.util.Platform().isHeadless())
1237     {
1238       System.err.println("Warning: " + title + "\nWarning: " + warning);
1239
1240     }
1241     else
1242     {
1243       JvOptionPane.showInternalMessageDialog(this, warning, title,
1244               JvOptionPane.WARNING_MESSAGE);
1245     }
1246     return;
1247   }
1248
1249   /**
1250    * DOCUMENT ME!
1251    *
1252    * @param e
1253    *          DOCUMENT ME!
1254    */
1255   @Override
1256   protected void outputText_actionPerformed(ActionEvent e)
1257   {
1258     FileFormatI fileFormat = FileFormats.getInstance().forName(
1259             e.getActionCommand());
1260     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1261             viewport, null);
1262     if (exportData.getSettings().isCancelled())
1263     {
1264       return;
1265     }
1266     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1267     cap.setForInput(null);
1268     try
1269     {
1270       FileFormatI format = fileFormat;
1271       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1272               .formatSequences(format, exportData.getAlignment(),
1273                       exportData.getOmitHidden(),
1274  exportData
1275                               .getStartEndPostions(), viewport
1276                               .getAlignment().getHiddenColumns()));
1277       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1278               "label.alignment_output_command",
1279               new Object[] { e.getActionCommand() }), 600, 500);
1280     } catch (OutOfMemoryError oom)
1281     {
1282       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1283       cap.dispose();
1284     }
1285
1286   }
1287
1288   public static AlignmentExportData getAlignmentForExport(
1289           FileFormatI format, AlignViewportI viewport,
1290           AlignExportSettingI exportSettings)
1291   {
1292     AlignmentI alignmentToExport = null;
1293     AlignExportSettingI settings = exportSettings;
1294     String[] omitHidden = null;
1295
1296     HiddenSequences hiddenSeqs = viewport.getAlignment()
1297             .getHiddenSequences();
1298
1299     alignmentToExport = viewport.getAlignment();
1300
1301     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1302     if (settings == null)
1303     {
1304       settings = new AlignExportSettings(hasHiddenSeqs,
1305               viewport.hasHiddenColumns(), format);
1306     }
1307     // settings.isExportAnnotations();
1308
1309     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1310     {
1311       omitHidden = viewport.getViewAsString(false,
1312               settings.isExportHiddenSequences());
1313     }
1314
1315     int[] alignmentStartEnd = new int[2];
1316     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1317     {
1318       alignmentToExport = hiddenSeqs.getFullAlignment();
1319     }
1320     else
1321     {
1322       alignmentToExport = viewport.getAlignment();
1323     }
1324     alignmentStartEnd = alignmentToExport
1325             .getVisibleStartAndEndIndex(viewport.getAlignment()
1326                     .getHiddenColumns()
1327                     .getHiddenRegions());
1328     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1329             omitHidden, alignmentStartEnd, settings);
1330     return ed;
1331   }
1332
1333   /**
1334    * DOCUMENT ME!
1335    *
1336    * @param e
1337    *          DOCUMENT ME!
1338    */
1339   @Override
1340   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1341   {
1342     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1343     htmlSVG.exportHTML(null);
1344   }
1345
1346   @Override
1347   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348   {
1349     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1350     bjs.exportHTML(null);
1351   }
1352
1353   public void createImageMap(File file, String image)
1354   {
1355     alignPanel.makePNGImageMap(file, image);
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *          DOCUMENT ME!
1363    */
1364   @Override
1365   public void createPNG(File f)
1366   {
1367     alignPanel.makePNG(f);
1368   }
1369
1370   /**
1371    * DOCUMENT ME!
1372    *
1373    * @param e
1374    *          DOCUMENT ME!
1375    */
1376   @Override
1377   public void createEPS(File f)
1378   {
1379     alignPanel.makeEPS(f);
1380   }
1381
1382   @Override
1383   public void createSVG(File f)
1384   {
1385     alignPanel.makeSVG(f);
1386   }
1387
1388   @Override
1389   public void pageSetup_actionPerformed(ActionEvent e)
1390   {
1391     PrinterJob printJob = PrinterJob.getPrinterJob();
1392     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1393   }
1394
1395   /**
1396    * DOCUMENT ME!
1397    *
1398    * @param e
1399    *          DOCUMENT ME!
1400    */
1401   @Override
1402   public void printMenuItem_actionPerformed(ActionEvent e)
1403   {
1404     // Putting in a thread avoids Swing painting problems
1405     PrintThread thread = new PrintThread(alignPanel);
1406     thread.start();
1407   }
1408
1409   @Override
1410   public void exportFeatures_actionPerformed(ActionEvent e)
1411   {
1412     new AnnotationExporter().exportFeatures(alignPanel);
1413   }
1414
1415   @Override
1416   public void exportAnnotations_actionPerformed(ActionEvent e)
1417   {
1418     new AnnotationExporter().exportAnnotations(alignPanel);
1419   }
1420
1421   @Override
1422   public void associatedData_actionPerformed(ActionEvent e)
1423   {
1424     // Pick the tree file
1425     JalviewFileChooser chooser = new JalviewFileChooser(
1426             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427     chooser.setFileView(new JalviewFileView());
1428     chooser.setDialogTitle(MessageManager
1429             .getString("label.load_jalview_annotations"));
1430     chooser.setToolTipText(MessageManager
1431             .getString("label.load_jalview_annotations"));
1432
1433     int value = chooser.showOpenDialog(null);
1434
1435     if (value == JalviewFileChooser.APPROVE_OPTION)
1436     {
1437       String choice = chooser.getSelectedFile().getPath();
1438       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439       loadJalviewDataFile(choice, null, null, null);
1440     }
1441
1442   }
1443
1444   /**
1445    * Close the current view or all views in the alignment frame. If the frame
1446    * only contains one view then the alignment will be removed from memory.
1447    *
1448    * @param closeAllTabs
1449    */
1450   @Override
1451   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452   {
1453     if (alignPanels != null && alignPanels.size() < 2)
1454     {
1455       closeAllTabs = true;
1456     }
1457
1458     try
1459     {
1460       if (alignPanels != null)
1461       {
1462         if (closeAllTabs)
1463         {
1464           if (this.isClosed())
1465           {
1466             // really close all the windows - otherwise wait till
1467             // setClosed(true) is called
1468             for (int i = 0; i < alignPanels.size(); i++)
1469             {
1470               AlignmentPanel ap = alignPanels.get(i);
1471               ap.closePanel();
1472             }
1473           }
1474         }
1475         else
1476         {
1477           closeView(alignPanel);
1478         }
1479       }
1480
1481       if (closeAllTabs)
1482       {
1483         /*
1484          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485          * be called recursively, with the frame now in 'closed' state
1486          */
1487         this.setClosed(true);
1488       }
1489     } catch (Exception ex)
1490     {
1491       ex.printStackTrace();
1492     }
1493   }
1494
1495   /**
1496    * Close the specified panel and close up tabs appropriately.
1497    *
1498    * @param panelToClose
1499    */
1500   public void closeView(AlignmentPanel panelToClose)
1501   {
1502     int index = tabbedPane.getSelectedIndex();
1503     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504     alignPanels.remove(panelToClose);
1505     panelToClose.closePanel();
1506     panelToClose = null;
1507
1508     tabbedPane.removeTabAt(closedindex);
1509     tabbedPane.validate();
1510
1511     if (index > closedindex || index == tabbedPane.getTabCount())
1512     {
1513       // modify currently selected tab index if necessary.
1514       index--;
1515     }
1516
1517     this.tabSelectionChanged(index);
1518   }
1519
1520   /**
1521    * DOCUMENT ME!
1522    */
1523   void updateEditMenuBar()
1524   {
1525
1526     if (viewport.getHistoryList().size() > 0)
1527     {
1528       undoMenuItem.setEnabled(true);
1529       CommandI command = viewport.getHistoryList().peek();
1530       undoMenuItem.setText(MessageManager.formatMessage(
1531               "label.undo_command",
1532               new Object[] { command.getDescription() }));
1533     }
1534     else
1535     {
1536       undoMenuItem.setEnabled(false);
1537       undoMenuItem.setText(MessageManager.getString("action.undo"));
1538     }
1539
1540     if (viewport.getRedoList().size() > 0)
1541     {
1542       redoMenuItem.setEnabled(true);
1543
1544       CommandI command = viewport.getRedoList().peek();
1545       redoMenuItem.setText(MessageManager.formatMessage(
1546               "label.redo_command",
1547               new Object[] { command.getDescription() }));
1548     }
1549     else
1550     {
1551       redoMenuItem.setEnabled(false);
1552       redoMenuItem.setText(MessageManager.getString("action.redo"));
1553     }
1554   }
1555
1556   @Override
1557   public void addHistoryItem(CommandI command)
1558   {
1559     if (command.getSize() > 0)
1560     {
1561       viewport.addToHistoryList(command);
1562       viewport.clearRedoList();
1563       updateEditMenuBar();
1564       viewport.updateHiddenColumns();
1565       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567       // viewport.getColumnSelection()
1568       // .getHiddenColumns().size() > 0);
1569     }
1570   }
1571
1572   /**
1573    *
1574    * @return alignment objects for all views
1575    */
1576   AlignmentI[] getViewAlignments()
1577   {
1578     if (alignPanels != null)
1579     {
1580       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581       int i = 0;
1582       for (AlignmentPanel ap : alignPanels)
1583       {
1584         als[i++] = ap.av.getAlignment();
1585       }
1586       return als;
1587     }
1588     if (viewport != null)
1589     {
1590       return new AlignmentI[] { viewport.getAlignment() };
1591     }
1592     return null;
1593   }
1594
1595   /**
1596    * DOCUMENT ME!
1597    *
1598    * @param e
1599    *          DOCUMENT ME!
1600    */
1601   @Override
1602   protected void undoMenuItem_actionPerformed(ActionEvent e)
1603   {
1604     if (viewport.getHistoryList().isEmpty())
1605     {
1606       return;
1607     }
1608     CommandI command = viewport.getHistoryList().pop();
1609     viewport.addToRedoList(command);
1610     command.undoCommand(getViewAlignments());
1611
1612     AlignmentViewport originalSource = getOriginatingSource(command);
1613     updateEditMenuBar();
1614
1615     if (originalSource != null)
1616     {
1617       if (originalSource != viewport)
1618       {
1619         Cache.log
1620                 .warn("Implementation worry: mismatch of viewport origin for undo");
1621       }
1622       originalSource.updateHiddenColumns();
1623       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624       // null
1625       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626       // viewport.getColumnSelection()
1627       // .getHiddenColumns().size() > 0);
1628       originalSource.firePropertyChange("alignment", null, originalSource
1629               .getAlignment().getSequences());
1630     }
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   @Override
1640   protected void redoMenuItem_actionPerformed(ActionEvent e)
1641   {
1642     if (viewport.getRedoList().size() < 1)
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getRedoList().pop();
1648     viewport.addToHistoryList(command);
1649     command.doCommand(getViewAlignments());
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     updateEditMenuBar();
1653
1654     if (originalSource != null)
1655     {
1656
1657       if (originalSource != viewport)
1658       {
1659         Cache.log
1660                 .warn("Implementation worry: mismatch of viewport origin for redo");
1661       }
1662       originalSource.updateHiddenColumns();
1663       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664       // null
1665       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666       // viewport.getColumnSelection()
1667       // .getHiddenColumns().size() > 0);
1668       originalSource.firePropertyChange("alignment", null, originalSource
1669               .getAlignment().getSequences());
1670     }
1671   }
1672
1673   AlignmentViewport getOriginatingSource(CommandI command)
1674   {
1675     AlignmentViewport originalSource = null;
1676     // For sequence removal and addition, we need to fire
1677     // the property change event FROM the viewport where the
1678     // original alignment was altered
1679     AlignmentI al = null;
1680     if (command instanceof EditCommand)
1681     {
1682       EditCommand editCommand = (EditCommand) command;
1683       al = editCommand.getAlignment();
1684       List<Component> comps = PaintRefresher.components.get(viewport
1685               .getSequenceSetId());
1686
1687       for (Component comp : comps)
1688       {
1689         if (comp instanceof AlignmentPanel)
1690         {
1691           if (al == ((AlignmentPanel) comp).av.getAlignment())
1692           {
1693             originalSource = ((AlignmentPanel) comp).av;
1694             break;
1695           }
1696         }
1697       }
1698     }
1699
1700     if (originalSource == null)
1701     {
1702       // The original view is closed, we must validate
1703       // the current view against the closed view first
1704       if (al != null)
1705       {
1706         PaintRefresher.validateSequences(al, viewport.getAlignment());
1707       }
1708
1709       originalSource = viewport;
1710     }
1711
1712     return originalSource;
1713   }
1714
1715   /**
1716    * DOCUMENT ME!
1717    *
1718    * @param up
1719    *          DOCUMENT ME!
1720    */
1721   public void moveSelectedSequences(boolean up)
1722   {
1723     SequenceGroup sg = viewport.getSelectionGroup();
1724
1725     if (sg == null)
1726     {
1727       return;
1728     }
1729     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730             viewport.getHiddenRepSequences(), up);
1731     alignPanel.paintAlignment(true);
1732   }
1733
1734   synchronized void slideSequences(boolean right, int size)
1735   {
1736     List<SequenceI> sg = new ArrayList<>();
1737     if (viewport.cursorMode)
1738     {
1739       sg.add(viewport.getAlignment().getSequenceAt(
1740               alignPanel.getSeqPanel().seqCanvas.cursorY));
1741     }
1742     else if (viewport.getSelectionGroup() != null
1743             && viewport.getSelectionGroup().getSize() != viewport
1744                     .getAlignment().getHeight())
1745     {
1746       sg = viewport.getSelectionGroup().getSequences(
1747               viewport.getHiddenRepSequences());
1748     }
1749
1750     if (sg.size() < 1)
1751     {
1752       return;
1753     }
1754
1755     List<SequenceI> invertGroup = new ArrayList<>();
1756
1757     for (SequenceI seq : viewport.getAlignment().getSequences())
1758     {
1759       if (!sg.contains(seq))
1760       {
1761         invertGroup.add(seq);
1762       }
1763     }
1764
1765     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766
1767     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768     for (int i = 0; i < invertGroup.size(); i++)
1769     {
1770       seqs2[i] = invertGroup.get(i);
1771     }
1772
1773     SlideSequencesCommand ssc;
1774     if (right)
1775     {
1776       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1777               size, viewport.getGapCharacter());
1778     }
1779     else
1780     {
1781       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1782               size, viewport.getGapCharacter());
1783     }
1784
1785     int groupAdjustment = 0;
1786     if (ssc.getGapsInsertedBegin() && right)
1787     {
1788       if (viewport.cursorMode)
1789       {
1790         alignPanel.getSeqPanel().moveCursor(size, 0);
1791       }
1792       else
1793       {
1794         groupAdjustment = size;
1795       }
1796     }
1797     else if (!ssc.getGapsInsertedBegin() && !right)
1798     {
1799       if (viewport.cursorMode)
1800       {
1801         alignPanel.getSeqPanel().moveCursor(-size, 0);
1802       }
1803       else
1804       {
1805         groupAdjustment = -size;
1806       }
1807     }
1808
1809     if (groupAdjustment != 0)
1810     {
1811       viewport.getSelectionGroup().setStartRes(
1812               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813       viewport.getSelectionGroup().setEndRes(
1814               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1815     }
1816
1817     /*
1818      * just extend the last slide command if compatible; but not if in
1819      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820      */
1821     boolean appendHistoryItem = false;
1822     Deque<CommandI> historyList = viewport.getHistoryList();
1823     boolean inSplitFrame = getSplitViewContainer() != null;
1824     if (!inSplitFrame && historyList != null && historyList.size() > 0
1825             && historyList.peek() instanceof SlideSequencesCommand)
1826     {
1827       appendHistoryItem = ssc
1828               .appendSlideCommand((SlideSequencesCommand) historyList
1829                       .peek());
1830     }
1831
1832     if (!appendHistoryItem)
1833     {
1834       addHistoryItem(ssc);
1835     }
1836
1837     repaint();
1838   }
1839
1840   /**
1841    * DOCUMENT ME!
1842    *
1843    * @param e
1844    *          DOCUMENT ME!
1845    */
1846   @Override
1847   protected void copy_actionPerformed(ActionEvent e)
1848   {
1849     System.gc();
1850     if (viewport.getSelectionGroup() == null)
1851     {
1852       return;
1853     }
1854     // TODO: preserve the ordering of displayed alignment annotation in any
1855     // internal paste (particularly sequence associated annotation)
1856     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1857     String[] omitHidden = null;
1858
1859     if (viewport.hasHiddenColumns())
1860     {
1861       omitHidden = viewport.getViewAsString(true);
1862     }
1863
1864     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1865             seqs, omitHidden, null);
1866
1867     StringSelection ss = new StringSelection(output);
1868
1869     try
1870     {
1871       jalview.gui.Desktop.internalCopy = true;
1872       // Its really worth setting the clipboard contents
1873       // to empty before setting the large StringSelection!!
1874       Toolkit.getDefaultToolkit().getSystemClipboard()
1875               .setContents(new StringSelection(""), null);
1876
1877       Toolkit.getDefaultToolkit().getSystemClipboard()
1878               .setContents(ss, Desktop.instance);
1879     } catch (OutOfMemoryError er)
1880     {
1881       new OOMWarning("copying region", er);
1882       return;
1883     }
1884
1885     ArrayList<int[]> hiddenColumns = null;
1886     if (viewport.hasHiddenColumns())
1887     {
1888       hiddenColumns = new ArrayList<>();
1889       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1890               .getSelectionGroup().getEndRes();
1891       for (int[] region : viewport.getAlignment().getHiddenColumns()
1892               .getHiddenRegions())
1893       {
1894         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1895         {
1896           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1897               region[1] - hiddenOffset });
1898         }
1899       }
1900     }
1901
1902     Desktop.jalviewClipboard = new Object[] { seqs,
1903         viewport.getAlignment().getDataset(), hiddenColumns };
1904     statusBar.setText(MessageManager.formatMessage(
1905             "label.copied_sequences_to_clipboard", new Object[] { Integer
1906                     .valueOf(seqs.length).toString() }));
1907   }
1908
1909   /**
1910    * DOCUMENT ME!
1911    *
1912    * @param e
1913    *          DOCUMENT ME!
1914    */
1915   @Override
1916   protected void pasteNew_actionPerformed(ActionEvent e)
1917   {
1918     paste(true);
1919   }
1920
1921   /**
1922    * DOCUMENT ME!
1923    *
1924    * @param e
1925    *          DOCUMENT ME!
1926    */
1927   @Override
1928   protected void pasteThis_actionPerformed(ActionEvent e)
1929   {
1930     paste(false);
1931   }
1932
1933   /**
1934    * Paste contents of Jalview clipboard
1935    *
1936    * @param newAlignment
1937    *          true to paste to a new alignment, otherwise add to this.
1938    */
1939   void paste(boolean newAlignment)
1940   {
1941     boolean externalPaste = true;
1942     try
1943     {
1944       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1945       Transferable contents = c.getContents(this);
1946
1947       if (contents == null)
1948       {
1949         return;
1950       }
1951
1952       String str;
1953       FileFormatI format;
1954       try
1955       {
1956         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957         if (str.length() < 1)
1958         {
1959           return;
1960         }
1961
1962         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1963
1964       } catch (OutOfMemoryError er)
1965       {
1966         new OOMWarning("Out of memory pasting sequences!!", er);
1967         return;
1968       }
1969
1970       SequenceI[] sequences;
1971       boolean annotationAdded = false;
1972       AlignmentI alignment = null;
1973
1974       if (Desktop.jalviewClipboard != null)
1975       {
1976         // The clipboard was filled from within Jalview, we must use the
1977         // sequences
1978         // And dataset from the copied alignment
1979         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980         // be doubly sure that we create *new* sequence objects.
1981         sequences = new SequenceI[newseq.length];
1982         for (int i = 0; i < newseq.length; i++)
1983         {
1984           sequences[i] = new Sequence(newseq[i]);
1985         }
1986         alignment = new Alignment(sequences);
1987         externalPaste = false;
1988       }
1989       else
1990       {
1991         // parse the clipboard as an alignment.
1992         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1993                 format);
1994         sequences = alignment.getSequencesArray();
1995       }
1996
1997       int alwidth = 0;
1998       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1999       int fgroup = -1;
2000
2001       if (newAlignment)
2002       {
2003
2004         if (Desktop.jalviewClipboard != null)
2005         {
2006           // dataset is inherited
2007           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2008         }
2009         else
2010         {
2011           // new dataset is constructed
2012           alignment.setDataset(null);
2013         }
2014         alwidth = alignment.getWidth() + 1;
2015       }
2016       else
2017       {
2018         AlignmentI pastedal = alignment; // preserve pasted alignment object
2019         // Add pasted sequences and dataset into existing alignment.
2020         alignment = viewport.getAlignment();
2021         alwidth = alignment.getWidth() + 1;
2022         // decide if we need to import sequences from an existing dataset
2023         boolean importDs = Desktop.jalviewClipboard != null
2024                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2025         // importDs==true instructs us to copy over new dataset sequences from
2026         // an existing alignment
2027         Vector newDs = (importDs) ? new Vector() : null; // used to create
2028         // minimum dataset set
2029
2030         for (int i = 0; i < sequences.length; i++)
2031         {
2032           if (importDs)
2033           {
2034             newDs.addElement(null);
2035           }
2036           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2037           // paste
2038           if (importDs && ds != null)
2039           {
2040             if (!newDs.contains(ds))
2041             {
2042               newDs.setElementAt(ds, i);
2043               ds = new Sequence(ds);
2044               // update with new dataset sequence
2045               sequences[i].setDatasetSequence(ds);
2046             }
2047             else
2048             {
2049               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2050             }
2051           }
2052           else
2053           {
2054             // copy and derive new dataset sequence
2055             sequences[i] = sequences[i].deriveSequence();
2056             alignment.getDataset().addSequence(
2057                     sequences[i].getDatasetSequence());
2058             // TODO: avoid creation of duplicate dataset sequences with a
2059             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2060           }
2061           alignment.addSequence(sequences[i]); // merges dataset
2062         }
2063         if (newDs != null)
2064         {
2065           newDs.clear(); // tidy up
2066         }
2067         if (alignment.getAlignmentAnnotation() != null)
2068         {
2069           for (AlignmentAnnotation alan : alignment
2070                   .getAlignmentAnnotation())
2071           {
2072             if (alan.graphGroup > fgroup)
2073             {
2074               fgroup = alan.graphGroup;
2075             }
2076           }
2077         }
2078         if (pastedal.getAlignmentAnnotation() != null)
2079         {
2080           // Add any annotation attached to alignment.
2081           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2082           for (int i = 0; i < alann.length; i++)
2083           {
2084             annotationAdded = true;
2085             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2086             {
2087               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2088               if (newann.graphGroup > -1)
2089               {
2090                 if (newGraphGroups.size() <= newann.graphGroup
2091                         || newGraphGroups.get(newann.graphGroup) == null)
2092                 {
2093                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2094                   {
2095                     newGraphGroups.add(q, null);
2096                   }
2097                   newGraphGroups.set(newann.graphGroup, new Integer(
2098                           ++fgroup));
2099                 }
2100                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2101                         .intValue();
2102               }
2103
2104               newann.padAnnotation(alwidth);
2105               alignment.addAnnotation(newann);
2106             }
2107           }
2108         }
2109       }
2110       if (!newAlignment)
2111       {
2112         // /////
2113         // ADD HISTORY ITEM
2114         //
2115         addHistoryItem(new EditCommand(
2116                 MessageManager.getString("label.add_sequences"),
2117                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2118       }
2119       // Add any annotations attached to sequences
2120       for (int i = 0; i < sequences.length; i++)
2121       {
2122         if (sequences[i].getAnnotation() != null)
2123         {
2124           AlignmentAnnotation newann;
2125           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2126           {
2127             annotationAdded = true;
2128             newann = sequences[i].getAnnotation()[a];
2129             newann.adjustForAlignment();
2130             newann.padAnnotation(alwidth);
2131             if (newann.graphGroup > -1)
2132             {
2133               if (newann.graphGroup > -1)
2134               {
2135                 if (newGraphGroups.size() <= newann.graphGroup
2136                         || newGraphGroups.get(newann.graphGroup) == null)
2137                 {
2138                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2139                   {
2140                     newGraphGroups.add(q, null);
2141                   }
2142                   newGraphGroups.set(newann.graphGroup, new Integer(
2143                           ++fgroup));
2144                 }
2145                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2146                         .intValue();
2147               }
2148             }
2149             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2150             // was
2151             // duplicated
2152             // earlier
2153             alignment
2154                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2155           }
2156         }
2157       }
2158       if (!newAlignment)
2159       {
2160
2161         // propagate alignment changed.
2162         vpRanges.setEndSeq(alignment.getHeight());
2163         if (annotationAdded)
2164         {
2165           // Duplicate sequence annotation in all views.
2166           AlignmentI[] alview = this.getViewAlignments();
2167           for (int i = 0; i < sequences.length; i++)
2168           {
2169             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2170             if (sann == null)
2171             {
2172               continue;
2173             }
2174             for (int avnum = 0; avnum < alview.length; avnum++)
2175             {
2176               if (alview[avnum] != alignment)
2177               {
2178                 // duplicate in a view other than the one with input focus
2179                 int avwidth = alview[avnum].getWidth() + 1;
2180                 // this relies on sann being preserved after we
2181                 // modify the sequence's annotation array for each duplication
2182                 for (int a = 0; a < sann.length; a++)
2183                 {
2184                   AlignmentAnnotation newann = new AlignmentAnnotation(
2185                           sann[a]);
2186                   sequences[i].addAlignmentAnnotation(newann);
2187                   newann.padAnnotation(avwidth);
2188                   alview[avnum].addAnnotation(newann); // annotation was
2189                   // duplicated earlier
2190                   // TODO JAL-1145 graphGroups are not updated for sequence
2191                   // annotation added to several views. This may cause
2192                   // strangeness
2193                   alview[avnum].setAnnotationIndex(newann, a);
2194                 }
2195               }
2196             }
2197           }
2198           buildSortByAnnotationScoresMenu();
2199         }
2200         viewport.firePropertyChange("alignment", null,
2201                 alignment.getSequences());
2202         if (alignPanels != null)
2203         {
2204           for (AlignmentPanel ap : alignPanels)
2205           {
2206             ap.validateAnnotationDimensions(false);
2207           }
2208         }
2209         else
2210         {
2211           alignPanel.validateAnnotationDimensions(false);
2212         }
2213
2214       }
2215       else
2216       {
2217         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2218                 DEFAULT_HEIGHT);
2219         String newtitle = new String("Copied sequences");
2220
2221         if (Desktop.jalviewClipboard != null
2222                 && Desktop.jalviewClipboard[2] != null)
2223         {
2224           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2225           for (int[] region : hc)
2226           {
2227             af.viewport.hideColumns(region[0], region[1]);
2228           }
2229         }
2230
2231         // >>>This is a fix for the moment, until a better solution is
2232         // found!!<<<
2233         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2234                 .transferSettings(
2235                         alignPanel.getSeqPanel().seqCanvas
2236                                 .getFeatureRenderer());
2237
2238         // TODO: maintain provenance of an alignment, rather than just make the
2239         // title a concatenation of operations.
2240         if (!externalPaste)
2241         {
2242           if (title.startsWith("Copied sequences"))
2243           {
2244             newtitle = title;
2245           }
2246           else
2247           {
2248             newtitle = newtitle.concat("- from " + title);
2249           }
2250         }
2251         else
2252         {
2253           newtitle = new String("Pasted sequences");
2254         }
2255
2256         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2257                 DEFAULT_HEIGHT);
2258
2259       }
2260
2261     } catch (Exception ex)
2262     {
2263       ex.printStackTrace();
2264       System.out.println("Exception whilst pasting: " + ex);
2265       // could be anything being pasted in here
2266     }
2267
2268   }
2269
2270   @Override
2271   protected void expand_newalign(ActionEvent e)
2272   {
2273     try
2274     {
2275       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2276               .getAlignment(), -1);
2277       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2278               DEFAULT_HEIGHT);
2279       String newtitle = new String("Flanking alignment");
2280
2281       if (Desktop.jalviewClipboard != null
2282               && Desktop.jalviewClipboard[2] != null)
2283       {
2284         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2285         for (int region[] : hc)
2286         {
2287           af.viewport.hideColumns(region[0], region[1]);
2288         }
2289       }
2290
2291       // >>>This is a fix for the moment, until a better solution is
2292       // found!!<<<
2293       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2294               .transferSettings(
2295                       alignPanel.getSeqPanel().seqCanvas
2296                               .getFeatureRenderer());
2297
2298       // TODO: maintain provenance of an alignment, rather than just make the
2299       // title a concatenation of operations.
2300       {
2301         if (title.startsWith("Copied sequences"))
2302         {
2303           newtitle = title;
2304         }
2305         else
2306         {
2307           newtitle = newtitle.concat("- from " + title);
2308         }
2309       }
2310
2311       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2312
2313     } catch (Exception ex)
2314     {
2315       ex.printStackTrace();
2316       System.out.println("Exception whilst pasting: " + ex);
2317       // could be anything being pasted in here
2318     } catch (OutOfMemoryError oom)
2319     {
2320       new OOMWarning("Viewing flanking region of alignment", oom);
2321     }
2322   }
2323
2324   /**
2325    * DOCUMENT ME!
2326    *
2327    * @param e
2328    *          DOCUMENT ME!
2329    */
2330   @Override
2331   protected void cut_actionPerformed(ActionEvent e)
2332   {
2333     copy_actionPerformed(null);
2334     delete_actionPerformed(null);
2335   }
2336
2337   /**
2338    * DOCUMENT ME!
2339    *
2340    * @param e
2341    *          DOCUMENT ME!
2342    */
2343   @Override
2344   protected void delete_actionPerformed(ActionEvent evt)
2345   {
2346
2347     SequenceGroup sg = viewport.getSelectionGroup();
2348     if (sg == null)
2349     {
2350       return;
2351     }
2352
2353     /*
2354      * If the cut affects all sequences, warn, remove highlighted columns
2355      */
2356     if (sg.getSize() == viewport.getAlignment().getHeight())
2357     {
2358       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2359               .getAlignment().getWidth()) ? true : false;
2360       if (isEntireAlignWidth)
2361       {
2362         int confirm = JvOptionPane.showConfirmDialog(this,
2363                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2364                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2365                 JvOptionPane.OK_CANCEL_OPTION);
2366
2367         if (confirm == JvOptionPane.CANCEL_OPTION
2368                 || confirm == JvOptionPane.CLOSED_OPTION)
2369         {
2370           return;
2371         }
2372       }
2373       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2374               sg.getEndRes() + 1);
2375     }
2376     SequenceI[] cut = sg.getSequences()
2377             .toArray(new SequenceI[sg.getSize()]);
2378
2379     addHistoryItem(new EditCommand(
2380             MessageManager.getString("label.cut_sequences"), Action.CUT,
2381             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2382             viewport.getAlignment()));
2383
2384     viewport.setSelectionGroup(null);
2385     viewport.sendSelection();
2386     viewport.getAlignment().deleteGroup(sg);
2387
2388     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2389             .getSequences());
2390     if (viewport.getAlignment().getHeight() < 1)
2391     {
2392       try
2393       {
2394         this.setClosed(true);
2395       } catch (Exception ex)
2396       {
2397       }
2398     }
2399   }
2400
2401   /**
2402    * DOCUMENT ME!
2403    *
2404    * @param e
2405    *          DOCUMENT ME!
2406    */
2407   @Override
2408   protected void deleteGroups_actionPerformed(ActionEvent e)
2409   {
2410     if (avc.deleteGroups())
2411     {
2412       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2413       alignPanel.updateAnnotation();
2414       alignPanel.paintAlignment(true);
2415     }
2416   }
2417
2418   /**
2419    * DOCUMENT ME!
2420    *
2421    * @param e
2422    *          DOCUMENT ME!
2423    */
2424   @Override
2425   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426   {
2427     SequenceGroup sg = new SequenceGroup();
2428
2429     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2430     {
2431       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2432     }
2433
2434     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2435     viewport.setSelectionGroup(sg);
2436     viewport.sendSelection();
2437     // JAL-2034 - should delegate to
2438     // alignPanel to decide if overview needs
2439     // updating.
2440     alignPanel.paintAlignment(false);
2441     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2442   }
2443
2444   /**
2445    * DOCUMENT ME!
2446    *
2447    * @param e
2448    *          DOCUMENT ME!
2449    */
2450   @Override
2451   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2452   {
2453     if (viewport.cursorMode)
2454     {
2455       alignPanel.getSeqPanel().keyboardNo1 = null;
2456       alignPanel.getSeqPanel().keyboardNo2 = null;
2457     }
2458     viewport.setSelectionGroup(null);
2459     viewport.getColumnSelection().clear();
2460     viewport.setSelectionGroup(null);
2461     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2462     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2463     // JAL-2034 - should delegate to
2464     // alignPanel to decide if overview needs
2465     // updating.
2466     alignPanel.paintAlignment(false);
2467     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2468     viewport.sendSelection();
2469   }
2470
2471   /**
2472    * DOCUMENT ME!
2473    *
2474    * @param e
2475    *          DOCUMENT ME!
2476    */
2477   @Override
2478   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2479   {
2480     SequenceGroup sg = viewport.getSelectionGroup();
2481
2482     if (sg == null)
2483     {
2484       selectAllSequenceMenuItem_actionPerformed(null);
2485
2486       return;
2487     }
2488
2489     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2490     {
2491       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2492     }
2493     // JAL-2034 - should delegate to
2494     // alignPanel to decide if overview needs
2495     // updating.
2496
2497     alignPanel.paintAlignment(true);
2498     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2499     viewport.sendSelection();
2500   }
2501
2502   @Override
2503   public void invertColSel_actionPerformed(ActionEvent e)
2504   {
2505     viewport.invertColumnSelection();
2506     alignPanel.paintAlignment(true);
2507     viewport.sendSelection();
2508   }
2509
2510   /**
2511    * DOCUMENT ME!
2512    *
2513    * @param e
2514    *          DOCUMENT ME!
2515    */
2516   @Override
2517   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2518   {
2519     trimAlignment(true);
2520   }
2521
2522   /**
2523    * DOCUMENT ME!
2524    *
2525    * @param e
2526    *          DOCUMENT ME!
2527    */
2528   @Override
2529   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2530   {
2531     trimAlignment(false);
2532   }
2533
2534   void trimAlignment(boolean trimLeft)
2535   {
2536     ColumnSelection colSel = viewport.getColumnSelection();
2537     int column;
2538
2539     if (!colSel.isEmpty())
2540     {
2541       if (trimLeft)
2542       {
2543         column = colSel.getMin();
2544       }
2545       else
2546       {
2547         column = colSel.getMax();
2548       }
2549
2550       SequenceI[] seqs;
2551       if (viewport.getSelectionGroup() != null)
2552       {
2553         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2554                 viewport.getHiddenRepSequences());
2555       }
2556       else
2557       {
2558         seqs = viewport.getAlignment().getSequencesArray();
2559       }
2560
2561       TrimRegionCommand trimRegion;
2562       if (trimLeft)
2563       {
2564         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2565                 column, viewport.getAlignment());
2566         vpRanges.setStartRes(0);
2567       }
2568       else
2569       {
2570         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2571                 column, viewport.getAlignment());
2572       }
2573
2574       statusBar.setText(MessageManager.formatMessage(
2575               "label.removed_columns",
2576               new String[] { Integer.valueOf(trimRegion.getSize())
2577                       .toString() }));
2578
2579       addHistoryItem(trimRegion);
2580
2581       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2582       {
2583         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2584                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2585         {
2586           viewport.getAlignment().deleteGroup(sg);
2587         }
2588       }
2589
2590       viewport.firePropertyChange("alignment", null, viewport
2591               .getAlignment().getSequences());
2592     }
2593   }
2594
2595   /**
2596    * DOCUMENT ME!
2597    *
2598    * @param e
2599    *          DOCUMENT ME!
2600    */
2601   @Override
2602   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2603   {
2604     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2605
2606     SequenceI[] seqs;
2607     if (viewport.getSelectionGroup() != null)
2608     {
2609       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2610               viewport.getHiddenRepSequences());
2611       start = viewport.getSelectionGroup().getStartRes();
2612       end = viewport.getSelectionGroup().getEndRes();
2613     }
2614     else
2615     {
2616       seqs = viewport.getAlignment().getSequencesArray();
2617     }
2618
2619     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2620             "Remove Gapped Columns", seqs, start, end,
2621             viewport.getAlignment());
2622
2623     addHistoryItem(removeGapCols);
2624
2625     statusBar.setText(MessageManager.formatMessage(
2626             "label.removed_empty_columns",
2627             new Object[] { Integer.valueOf(removeGapCols.getSize())
2628                     .toString() }));
2629
2630     // This is to maintain viewport position on first residue
2631     // of first sequence
2632     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2633     int startRes = seq.findPosition(vpRanges.getStartRes());
2634     // ShiftList shifts;
2635     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2636     // edit.alColumnChanges=shifts.getInverse();
2637     // if (viewport.hasHiddenColumns)
2638     // viewport.getColumnSelection().compensateForEdits(shifts);
2639     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2640     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2641             .getSequences());
2642
2643   }
2644
2645   /**
2646    * DOCUMENT ME!
2647    *
2648    * @param e
2649    *          DOCUMENT ME!
2650    */
2651   @Override
2652   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2653   {
2654     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2655
2656     SequenceI[] seqs;
2657     if (viewport.getSelectionGroup() != null)
2658     {
2659       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2660               viewport.getHiddenRepSequences());
2661       start = viewport.getSelectionGroup().getStartRes();
2662       end = viewport.getSelectionGroup().getEndRes();
2663     }
2664     else
2665     {
2666       seqs = viewport.getAlignment().getSequencesArray();
2667     }
2668
2669     // This is to maintain viewport position on first residue
2670     // of first sequence
2671     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672     int startRes = seq.findPosition(vpRanges.getStartRes());
2673
2674     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2675             viewport.getAlignment()));
2676
2677     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2678
2679     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2680             .getSequences());
2681
2682   }
2683
2684   /**
2685    * DOCUMENT ME!
2686    *
2687    * @param e
2688    *          DOCUMENT ME!
2689    */
2690   @Override
2691   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2692   {
2693     viewport.setPadGaps(padGapsMenuitem.isSelected());
2694     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2695             .getSequences());
2696   }
2697
2698   /**
2699    * DOCUMENT ME!
2700    *
2701    * @param e
2702    *          DOCUMENT ME!
2703    */
2704   @Override
2705   public void findMenuItem_actionPerformed(ActionEvent e)
2706   {
2707     new Finder();
2708   }
2709
2710   /**
2711    * Create a new view of the current alignment.
2712    */
2713   @Override
2714   public void newView_actionPerformed(ActionEvent e)
2715   {
2716     newView(null, true);
2717   }
2718
2719   /**
2720    * Creates and shows a new view of the current alignment.
2721    *
2722    * @param viewTitle
2723    *          title of newly created view; if null, one will be generated
2724    * @param copyAnnotation
2725    *          if true then duplicate all annnotation, groups and settings
2726    * @return new alignment panel, already displayed.
2727    */
2728   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2729   {
2730     /*
2731      * Create a new AlignmentPanel (with its own, new Viewport)
2732      */
2733     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2734             true);
2735     if (!copyAnnotation)
2736     {
2737       /*
2738        * remove all groups and annotation except for the automatic stuff
2739        */
2740       newap.av.getAlignment().deleteAllGroups();
2741       newap.av.getAlignment().deleteAllAnnotations(false);
2742     }
2743
2744     newap.av.setGatherViewsHere(false);
2745
2746     if (viewport.viewName == null)
2747     {
2748       viewport.viewName = MessageManager
2749               .getString("label.view_name_original");
2750     }
2751
2752     /*
2753      * Views share the same edits undo and redo stacks
2754      */
2755     newap.av.setHistoryList(viewport.getHistoryList());
2756     newap.av.setRedoList(viewport.getRedoList());
2757
2758     /*
2759      * Views share the same mappings; need to deregister any new mappings
2760      * created by copyAlignPanel, and register the new reference to the shared
2761      * mappings
2762      */
2763     newap.av.replaceMappings(viewport.getAlignment());
2764
2765     /*
2766      * start up cDNA consensus (if applicable) now mappings are in place
2767      */
2768     if (newap.av.initComplementConsensus())
2769     {
2770       newap.refresh(true); // adjust layout of annotations
2771     }
2772
2773     newap.av.viewName = getNewViewName(viewTitle);
2774
2775     addAlignmentPanel(newap, true);
2776     newap.alignmentChanged();
2777
2778     if (alignPanels.size() == 2)
2779     {
2780       viewport.setGatherViewsHere(true);
2781     }
2782     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2783     return newap;
2784   }
2785
2786   /**
2787    * Make a new name for the view, ensuring it is unique within the current
2788    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2789    * these now use viewId. Unique view names are still desirable for usability.)
2790    *
2791    * @param viewTitle
2792    * @return
2793    */
2794   protected String getNewViewName(String viewTitle)
2795   {
2796     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2797     boolean addFirstIndex = false;
2798     if (viewTitle == null || viewTitle.trim().length() == 0)
2799     {
2800       viewTitle = MessageManager.getString("action.view");
2801       addFirstIndex = true;
2802     }
2803     else
2804     {
2805       index = 1;// we count from 1 if given a specific name
2806     }
2807     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2808
2809     List<Component> comps = PaintRefresher.components.get(viewport
2810             .getSequenceSetId());
2811
2812     List<String> existingNames = getExistingViewNames(comps);
2813
2814     while (existingNames.contains(newViewName))
2815     {
2816       newViewName = viewTitle + " " + (++index);
2817     }
2818     return newViewName;
2819   }
2820
2821   /**
2822    * Returns a list of distinct view names found in the given list of
2823    * components. View names are held on the viewport of an AlignmentPanel.
2824    *
2825    * @param comps
2826    * @return
2827    */
2828   protected List<String> getExistingViewNames(List<Component> comps)
2829   {
2830     List<String> existingNames = new ArrayList<>();
2831     for (Component comp : comps)
2832     {
2833       if (comp instanceof AlignmentPanel)
2834       {
2835         AlignmentPanel ap = (AlignmentPanel) comp;
2836         if (!existingNames.contains(ap.av.viewName))
2837         {
2838           existingNames.add(ap.av.viewName);
2839         }
2840       }
2841     }
2842     return existingNames;
2843   }
2844
2845   /**
2846    * Explode tabbed views into separate windows.
2847    */
2848   @Override
2849   public void expandViews_actionPerformed(ActionEvent e)
2850   {
2851     Desktop.explodeViews(this);
2852   }
2853
2854   /**
2855    * Gather views in separate windows back into a tabbed presentation.
2856    */
2857   @Override
2858   public void gatherViews_actionPerformed(ActionEvent e)
2859   {
2860     Desktop.instance.gatherViews(this);
2861   }
2862
2863   /**
2864    * DOCUMENT ME!
2865    *
2866    * @param e
2867    *          DOCUMENT ME!
2868    */
2869   @Override
2870   public void font_actionPerformed(ActionEvent e)
2871   {
2872     new FontChooser(alignPanel);
2873   }
2874
2875   /**
2876    * DOCUMENT ME!
2877    *
2878    * @param e
2879    *          DOCUMENT ME!
2880    */
2881   @Override
2882   protected void seqLimit_actionPerformed(ActionEvent e)
2883   {
2884     viewport.setShowJVSuffix(seqLimits.isSelected());
2885
2886     alignPanel.getIdPanel().getIdCanvas()
2887             .setPreferredSize(alignPanel.calculateIdWidth());
2888     alignPanel.paintAlignment(true);
2889   }
2890
2891   @Override
2892   public void idRightAlign_actionPerformed(ActionEvent e)
2893   {
2894     viewport.setRightAlignIds(idRightAlign.isSelected());
2895     alignPanel.paintAlignment(true);
2896   }
2897
2898   @Override
2899   public void centreColumnLabels_actionPerformed(ActionEvent e)
2900   {
2901     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2902     alignPanel.paintAlignment(true);
2903   }
2904
2905   /*
2906    * (non-Javadoc)
2907    *
2908    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2909    */
2910   @Override
2911   protected void followHighlight_actionPerformed()
2912   {
2913     /*
2914      * Set the 'follow' flag on the Viewport (and scroll to position if now
2915      * true).
2916      */
2917     final boolean state = this.followHighlightMenuItem.getState();
2918     viewport.setFollowHighlight(state);
2919     if (state)
2920     {
2921       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2922     }
2923   }
2924
2925   /**
2926    * DOCUMENT ME!
2927    *
2928    * @param e
2929    *          DOCUMENT ME!
2930    */
2931   @Override
2932   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2933   {
2934     viewport.setColourText(colourTextMenuItem.isSelected());
2935     alignPanel.paintAlignment(true);
2936   }
2937
2938   /**
2939    * DOCUMENT ME!
2940    *
2941    * @param e
2942    *          DOCUMENT ME!
2943    */
2944   @Override
2945   public void wrapMenuItem_actionPerformed(ActionEvent e)
2946   {
2947     scaleAbove.setVisible(wrapMenuItem.isSelected());
2948     scaleLeft.setVisible(wrapMenuItem.isSelected());
2949     scaleRight.setVisible(wrapMenuItem.isSelected());
2950     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2951     alignPanel.updateLayout();
2952   }
2953
2954   @Override
2955   public void showAllSeqs_actionPerformed(ActionEvent e)
2956   {
2957     viewport.showAllHiddenSeqs();
2958   }
2959
2960   @Override
2961   public void showAllColumns_actionPerformed(ActionEvent e)
2962   {
2963     viewport.showAllHiddenColumns();
2964     repaint();
2965     viewport.sendSelection();
2966   }
2967
2968   @Override
2969   public void hideSelSequences_actionPerformed(ActionEvent e)
2970   {
2971     viewport.hideAllSelectedSeqs();
2972     // alignPanel.paintAlignment(true);
2973   }
2974
2975   /**
2976    * called by key handler and the hide all/show all menu items
2977    *
2978    * @param toggleSeqs
2979    * @param toggleCols
2980    */
2981   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2982   {
2983
2984     boolean hide = false;
2985     SequenceGroup sg = viewport.getSelectionGroup();
2986     if (!toggleSeqs && !toggleCols)
2987     {
2988       // Hide everything by the current selection - this is a hack - we do the
2989       // invert and then hide
2990       // first check that there will be visible columns after the invert.
2991       if (viewport.hasSelectedColumns()
2992               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2993                       .getEndRes()))
2994       {
2995         // now invert the sequence set, if required - empty selection implies
2996         // that no hiding is required.
2997         if (sg != null)
2998         {
2999           invertSequenceMenuItem_actionPerformed(null);
3000           sg = viewport.getSelectionGroup();
3001           toggleSeqs = true;
3002
3003         }
3004         viewport.expandColSelection(sg, true);
3005         // finally invert the column selection and get the new sequence
3006         // selection.
3007         invertColSel_actionPerformed(null);
3008         toggleCols = true;
3009       }
3010     }
3011
3012     if (toggleSeqs)
3013     {
3014       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3015       {
3016         hideSelSequences_actionPerformed(null);
3017         hide = true;
3018       }
3019       else if (!(toggleCols && viewport.hasSelectedColumns()))
3020       {
3021         showAllSeqs_actionPerformed(null);
3022       }
3023     }
3024
3025     if (toggleCols)
3026     {
3027       if (viewport.hasSelectedColumns())
3028       {
3029         hideSelColumns_actionPerformed(null);
3030         if (!toggleSeqs)
3031         {
3032           viewport.setSelectionGroup(sg);
3033         }
3034       }
3035       else if (!hide)
3036       {
3037         showAllColumns_actionPerformed(null);
3038       }
3039     }
3040   }
3041
3042   /*
3043    * (non-Javadoc)
3044    *
3045    * @see
3046    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3047    * event.ActionEvent)
3048    */
3049   @Override
3050   public void hideAllButSelection_actionPerformed(ActionEvent e)
3051   {
3052     toggleHiddenRegions(false, false);
3053     viewport.sendSelection();
3054   }
3055
3056   /*
3057    * (non-Javadoc)
3058    *
3059    * @see
3060    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3061    * .ActionEvent)
3062    */
3063   @Override
3064   public void hideAllSelection_actionPerformed(ActionEvent e)
3065   {
3066     SequenceGroup sg = viewport.getSelectionGroup();
3067     viewport.expandColSelection(sg, false);
3068     viewport.hideAllSelectedSeqs();
3069     viewport.hideSelectedColumns();
3070     alignPanel.paintAlignment(true);
3071     viewport.sendSelection();
3072   }
3073
3074   /*
3075    * (non-Javadoc)
3076    *
3077    * @see
3078    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3079    * ActionEvent)
3080    */
3081   @Override
3082   public void showAllhidden_actionPerformed(ActionEvent e)
3083   {
3084     viewport.showAllHiddenColumns();
3085     viewport.showAllHiddenSeqs();
3086     alignPanel.paintAlignment(true);
3087     viewport.sendSelection();
3088   }
3089
3090   @Override
3091   public void hideSelColumns_actionPerformed(ActionEvent e)
3092   {
3093     viewport.hideSelectedColumns();
3094     alignPanel.paintAlignment(true);
3095     viewport.sendSelection();
3096   }
3097
3098   @Override
3099   public void hiddenMarkers_actionPerformed(ActionEvent e)
3100   {
3101     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3102     repaint();
3103   }
3104
3105   /**
3106    * DOCUMENT ME!
3107    *
3108    * @param e
3109    *          DOCUMENT ME!
3110    */
3111   @Override
3112   protected void scaleAbove_actionPerformed(ActionEvent e)
3113   {
3114     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3115     alignPanel.paintAlignment(true);
3116   }
3117
3118   /**
3119    * DOCUMENT ME!
3120    *
3121    * @param e
3122    *          DOCUMENT ME!
3123    */
3124   @Override
3125   protected void scaleLeft_actionPerformed(ActionEvent e)
3126   {
3127     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3128     alignPanel.paintAlignment(true);
3129   }
3130
3131   /**
3132    * DOCUMENT ME!
3133    *
3134    * @param e
3135    *          DOCUMENT ME!
3136    */
3137   @Override
3138   protected void scaleRight_actionPerformed(ActionEvent e)
3139   {
3140     viewport.setScaleRightWrapped(scaleRight.isSelected());
3141     alignPanel.paintAlignment(true);
3142   }
3143
3144   /**
3145    * DOCUMENT ME!
3146    *
3147    * @param e
3148    *          DOCUMENT ME!
3149    */
3150   @Override
3151   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3152   {
3153     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3154     alignPanel.paintAlignment(true);
3155   }
3156
3157   /**
3158    * DOCUMENT ME!
3159    *
3160    * @param e
3161    *          DOCUMENT ME!
3162    */
3163   @Override
3164   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3165   {
3166     viewport.setShowText(viewTextMenuItem.isSelected());
3167     alignPanel.paintAlignment(true);
3168   }
3169
3170   /**
3171    * DOCUMENT ME!
3172    *
3173    * @param e
3174    *          DOCUMENT ME!
3175    */
3176   @Override
3177   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3178   {
3179     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3180     alignPanel.paintAlignment(true);
3181   }
3182
3183   public FeatureSettings featureSettings;
3184
3185   @Override
3186   public FeatureSettingsControllerI getFeatureSettingsUI()
3187   {
3188     return featureSettings;
3189   }
3190
3191   @Override
3192   public void featureSettings_actionPerformed(ActionEvent e)
3193   {
3194     if (featureSettings != null)
3195     {
3196       featureSettings.close();
3197       featureSettings = null;
3198     }
3199     if (!showSeqFeatures.isSelected())
3200     {
3201       // make sure features are actually displayed
3202       showSeqFeatures.setSelected(true);
3203       showSeqFeatures_actionPerformed(null);
3204     }
3205     featureSettings = new FeatureSettings(this);
3206   }
3207
3208   /**
3209    * Set or clear 'Show Sequence Features'
3210    *
3211    * @param evt
3212    *          DOCUMENT ME!
3213    */
3214   @Override
3215   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3216   {
3217     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3218     alignPanel.paintAlignment(true);
3219     if (alignPanel.getOverviewPanel() != null)
3220     {
3221       alignPanel.getOverviewPanel().updateOverviewImage();
3222     }
3223   }
3224
3225   /**
3226    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3227    * the annotations panel as a whole.
3228    *
3229    * The options to show/hide all annotations should be enabled when the panel
3230    * is shown, and disabled when the panel is hidden.
3231    *
3232    * @param e
3233    */
3234   @Override
3235   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3236   {
3237     final boolean setVisible = annotationPanelMenuItem.isSelected();
3238     viewport.setShowAnnotation(setVisible);
3239     this.showAllSeqAnnotations.setEnabled(setVisible);
3240     this.hideAllSeqAnnotations.setEnabled(setVisible);
3241     this.showAllAlAnnotations.setEnabled(setVisible);
3242     this.hideAllAlAnnotations.setEnabled(setVisible);
3243     alignPanel.updateLayout();
3244   }
3245
3246   @Override
3247   public void alignmentProperties()
3248   {
3249     JEditorPane editPane = new JEditorPane("text/html", "");
3250     editPane.setEditable(false);
3251     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3252             .formatAsHtml();
3253     editPane.setText(MessageManager.formatMessage("label.html_content",
3254             new Object[] { contents.toString() }));
3255     JInternalFrame frame = new JInternalFrame();
3256     frame.getContentPane().add(new JScrollPane(editPane));
3257
3258     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3259             "label.alignment_properties", new Object[] { getTitle() }),
3260             500, 400);
3261   }
3262
3263   /**
3264    * DOCUMENT ME!
3265    *
3266    * @param e
3267    *          DOCUMENT ME!
3268    */
3269   @Override
3270   public void overviewMenuItem_actionPerformed(ActionEvent e)
3271   {
3272     if (alignPanel.overviewPanel != null)
3273     {
3274       return;
3275     }
3276
3277     JInternalFrame frame = new JInternalFrame();
3278     OverviewPanel overview = new OverviewPanel(alignPanel);
3279     frame.setContentPane(overview);
3280     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3281             "label.overview_params", new Object[] { this.getTitle() }),
3282             true, frame.getWidth(), frame.getHeight(), true, true);
3283     frame.pack();
3284     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3285     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3286     {
3287       @Override
3288       public void internalFrameClosed(
3289               javax.swing.event.InternalFrameEvent evt)
3290       {
3291         alignPanel.setOverviewPanel(null);
3292       };
3293     });
3294
3295     alignPanel.setOverviewPanel(overview);
3296   }
3297
3298   @Override
3299   public void textColour_actionPerformed()
3300   {
3301     new TextColourChooser().chooseColour(alignPanel, null);
3302   }
3303
3304   /*
3305    * public void covariationColour_actionPerformed() {
3306    * changeColour(new
3307    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3308    * ()[0])); }
3309    */
3310   @Override
3311   public void annotationColour_actionPerformed()
3312   {
3313     new AnnotationColourChooser(viewport, alignPanel);
3314   }
3315
3316   @Override
3317   public void annotationColumn_actionPerformed(ActionEvent e)
3318   {
3319     new AnnotationColumnChooser(viewport, alignPanel);
3320   }
3321
3322   /**
3323    * Action on the user checking or unchecking the option to apply the selected
3324    * colour scheme to all groups. If unchecked, groups may have their own
3325    * independent colour schemes.
3326    *
3327    * @param selected
3328    */
3329   @Override
3330   public void applyToAllGroups_actionPerformed(boolean selected)
3331   {
3332     viewport.setColourAppliesToAllGroups(selected);
3333   }
3334
3335   /**
3336    * Action on user selecting a colour from the colour menu
3337    *
3338    * @param name
3339    *          the name (not the menu item label!) of the colour scheme
3340    */
3341   @Override
3342   public void changeColour_actionPerformed(String name)
3343   {
3344     /*
3345      * 'User Defined' opens a panel to configure or load a
3346      * user-defined colour scheme
3347      */
3348     if (ResidueColourScheme.USER_DEFINED.equals(name))
3349     {
3350       new UserDefinedColours(alignPanel);
3351       return;
3352     }
3353
3354     /*
3355      * otherwise set the chosen colour scheme (or null for 'None')
3356      */
3357     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3358             viewport.getAlignment(), viewport.getHiddenRepSequences());
3359     changeColour(cs);
3360   }
3361
3362   /**
3363    * Actions on setting or changing the alignment colour scheme
3364    *
3365    * @param cs
3366    */
3367   @Override
3368   public void changeColour(ColourSchemeI cs)
3369   {
3370     // TODO: pull up to controller method
3371     ColourMenuHelper.setColourSelected(colourMenu, cs);
3372
3373     viewport.setGlobalColourScheme(cs);
3374
3375     alignPanel.paintAlignment(true);
3376   }
3377
3378   /**
3379    * Show the PID threshold slider panel
3380    */
3381   @Override
3382   protected void modifyPID_actionPerformed()
3383   {
3384     SliderPanel.setPIDSliderSource(alignPanel,
3385             viewport.getResidueShading(), alignPanel.getViewName());
3386     SliderPanel.showPIDSlider();
3387   }
3388
3389   /**
3390    * Show the Conservation slider panel
3391    */
3392   @Override
3393   protected void modifyConservation_actionPerformed()
3394   {
3395     SliderPanel.setConservationSlider(alignPanel,
3396             viewport.getResidueShading(), alignPanel.getViewName());
3397     SliderPanel.showConservationSlider();
3398   }
3399
3400   /**
3401    * Action on selecting or deselecting (Colour) By Conservation
3402    */
3403   @Override
3404   public void conservationMenuItem_actionPerformed(boolean selected)
3405   {
3406     modifyConservation.setEnabled(selected);
3407     viewport.setConservationSelected(selected);
3408     viewport.getResidueShading().setConservationApplied(selected);
3409
3410     changeColour(viewport.getGlobalColourScheme());
3411     if (selected)
3412     {
3413       modifyConservation_actionPerformed();
3414     }
3415     else
3416     {
3417       SliderPanel.hideConservationSlider();
3418     }
3419   }
3420
3421   /**
3422    * Action on selecting or deselecting (Colour) Above PID Threshold
3423    */
3424   @Override
3425   public void abovePIDThreshold_actionPerformed(boolean selected)
3426   {
3427     modifyPID.setEnabled(selected);
3428     viewport.setAbovePIDThreshold(selected);
3429     if (!selected)
3430     {
3431       viewport.getResidueShading().setThreshold(0,
3432               viewport.isIgnoreGapsConsensus());
3433     }
3434
3435     changeColour(viewport.getGlobalColourScheme());
3436     if (selected)
3437     {
3438       modifyPID_actionPerformed();
3439     }
3440     else
3441     {
3442       SliderPanel.hidePIDSlider();
3443     }
3444   }
3445
3446   /**
3447    * DOCUMENT ME!
3448    *
3449    * @param e
3450    *          DOCUMENT ME!
3451    */
3452   @Override
3453   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3454   {
3455     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3457             .getAlignment().getSequenceAt(0));
3458     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3459             viewport.getAlignment()));
3460     alignPanel.paintAlignment(true);
3461   }
3462
3463   /**
3464    * DOCUMENT ME!
3465    *
3466    * @param e
3467    *          DOCUMENT ME!
3468    */
3469   @Override
3470   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3471   {
3472     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473     AlignmentSorter.sortByID(viewport.getAlignment());
3474     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3475             viewport.getAlignment()));
3476     alignPanel.paintAlignment(true);
3477   }
3478
3479   /**
3480    * DOCUMENT ME!
3481    *
3482    * @param e
3483    *          DOCUMENT ME!
3484    */
3485   @Override
3486   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3487   {
3488     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489     AlignmentSorter.sortByLength(viewport.getAlignment());
3490     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3491             viewport.getAlignment()));
3492     alignPanel.paintAlignment(true);
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param e
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3503   {
3504     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505     AlignmentSorter.sortByGroup(viewport.getAlignment());
3506     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3507             viewport.getAlignment()));
3508
3509     alignPanel.paintAlignment(true);
3510   }
3511
3512   /**
3513    * DOCUMENT ME!
3514    *
3515    * @param e
3516    *          DOCUMENT ME!
3517    */
3518   @Override
3519   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3520   {
3521     new RedundancyPanel(alignPanel, this);
3522   }
3523
3524   /**
3525    * DOCUMENT ME!
3526    *
3527    * @param e
3528    *          DOCUMENT ME!
3529    */
3530   @Override
3531   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3532   {
3533     if ((viewport.getSelectionGroup() == null)
3534             || (viewport.getSelectionGroup().getSize() < 2))
3535     {
3536       JvOptionPane.showInternalMessageDialog(this, MessageManager
3537               .getString("label.you_must_select_least_two_sequences"),
3538               MessageManager.getString("label.invalid_selection"),
3539               JvOptionPane.WARNING_MESSAGE);
3540     }
3541     else
3542     {
3543       JInternalFrame frame = new JInternalFrame();
3544       frame.setContentPane(new PairwiseAlignPanel(viewport));
3545       Desktop.addInternalFrame(frame,
3546               MessageManager.getString("action.pairwise_alignment"), 600,
3547               500);
3548     }
3549   }
3550
3551   @Override
3552   public void autoCalculate_actionPerformed(ActionEvent e)
3553   {
3554     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3555     if (viewport.autoCalculateConsensus)
3556     {
3557       viewport.firePropertyChange("alignment", null, viewport
3558               .getAlignment().getSequences());
3559     }
3560   }
3561
3562   @Override
3563   public void sortByTreeOption_actionPerformed(ActionEvent e)
3564   {
3565     viewport.sortByTree = sortByTree.isSelected();
3566   }
3567
3568   @Override
3569   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3570   {
3571     viewport.followSelection = listenToViewSelections.isSelected();
3572   }
3573
3574   /**
3575    * Constructs a tree panel and adds it to the desktop
3576    *
3577    * @param type
3578    *          tree type (NJ or AV)
3579    * @param modelName
3580    *          name of score model used to compute the tree
3581    * @param options
3582    *          parameters for the distance or similarity calculation
3583    */
3584   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3585   {
3586     String frameTitle = "";
3587     TreePanel tp;
3588
3589     boolean onSelection = false;
3590     if (viewport.getSelectionGroup() != null
3591             && viewport.getSelectionGroup().getSize() > 0)
3592     {
3593       SequenceGroup sg = viewport.getSelectionGroup();
3594
3595       /* Decide if the selection is a column region */
3596       for (SequenceI _s : sg.getSequences())
3597       {
3598         if (_s.getLength() < sg.getEndRes())
3599         {
3600           JvOptionPane
3601                   .showMessageDialog(
3602                           Desktop.desktop,
3603                           MessageManager
3604                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3605                           MessageManager
3606                                   .getString("label.sequences_selection_not_aligned"),
3607                           JvOptionPane.WARNING_MESSAGE);
3608
3609           return;
3610         }
3611       }
3612       onSelection = true;
3613     }
3614     else
3615     {
3616       if (viewport.getAlignment().getHeight() < 2)
3617       {
3618         return;
3619       }
3620     }
3621
3622     tp = new TreePanel(alignPanel, type, modelName, options);
3623     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3624
3625     frameTitle += " from ";
3626
3627     if (viewport.viewName != null)
3628     {
3629       frameTitle += viewport.viewName + " of ";
3630     }
3631
3632     frameTitle += this.title;
3633
3634     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3635   }
3636
3637   /**
3638    * DOCUMENT ME!
3639    *
3640    * @param title
3641    *          DOCUMENT ME!
3642    * @param order
3643    *          DOCUMENT ME!
3644    */
3645   public void addSortByOrderMenuItem(String title,
3646           final AlignmentOrder order)
3647   {
3648     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3649             "action.by_title_param", new Object[] { title }));
3650     sort.add(item);
3651     item.addActionListener(new java.awt.event.ActionListener()
3652     {
3653       @Override
3654       public void actionPerformed(ActionEvent e)
3655       {
3656         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3657
3658         // TODO: JBPNote - have to map order entries to curent SequenceI
3659         // pointers
3660         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3661
3662         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3663                 .getAlignment()));
3664
3665         alignPanel.paintAlignment(true);
3666       }
3667     });
3668   }
3669
3670   /**
3671    * Add a new sort by annotation score menu item
3672    *
3673    * @param sort
3674    *          the menu to add the option to
3675    * @param scoreLabel
3676    *          the label used to retrieve scores for each sequence on the
3677    *          alignment
3678    */
3679   public void addSortByAnnotScoreMenuItem(JMenu sort,
3680           final String scoreLabel)
3681   {
3682     final JMenuItem item = new JMenuItem(scoreLabel);
3683     sort.add(item);
3684     item.addActionListener(new java.awt.event.ActionListener()
3685     {
3686       @Override
3687       public void actionPerformed(ActionEvent e)
3688       {
3689         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3690         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3691                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3692         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3693                 viewport.getAlignment()));
3694         alignPanel.paintAlignment(true);
3695       }
3696     });
3697   }
3698
3699   /**
3700    * last hash for alignment's annotation array - used to minimise cost of
3701    * rebuild.
3702    */
3703   protected int _annotationScoreVectorHash;
3704
3705   /**
3706    * search the alignment and rebuild the sort by annotation score submenu the
3707    * last alignment annotation vector hash is stored to minimize cost of
3708    * rebuilding in subsequence calls.
3709    *
3710    */
3711   @Override
3712   public void buildSortByAnnotationScoresMenu()
3713   {
3714     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3715     {
3716       return;
3717     }
3718
3719     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3720     {
3721       sortByAnnotScore.removeAll();
3722       // almost certainly a quicker way to do this - but we keep it simple
3723       Hashtable scoreSorts = new Hashtable();
3724       AlignmentAnnotation aann[];
3725       for (SequenceI sqa : viewport.getAlignment().getSequences())
3726       {
3727         aann = sqa.getAnnotation();
3728         for (int i = 0; aann != null && i < aann.length; i++)
3729         {
3730           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3731           {
3732             scoreSorts.put(aann[i].label, aann[i].label);
3733           }
3734         }
3735       }
3736       Enumeration labels = scoreSorts.keys();
3737       while (labels.hasMoreElements())
3738       {
3739         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3740                 (String) labels.nextElement());
3741       }
3742       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3743       scoreSorts.clear();
3744
3745       _annotationScoreVectorHash = viewport.getAlignment()
3746               .getAlignmentAnnotation().hashCode();
3747     }
3748   }
3749
3750   /**
3751    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3752    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3753    * call. Listeners are added to remove the menu item when the treePanel is
3754    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3755    * modified.
3756    */
3757   @Override
3758   public void buildTreeSortMenu()
3759   {
3760     sortByTreeMenu.removeAll();
3761
3762     List<Component> comps = PaintRefresher.components.get(viewport
3763             .getSequenceSetId());
3764     List<TreePanel> treePanels = new ArrayList<>();
3765     for (Component comp : comps)
3766     {
3767       if (comp instanceof TreePanel)
3768       {
3769         treePanels.add((TreePanel) comp);
3770       }
3771     }
3772
3773     if (treePanels.size() < 1)
3774     {
3775       sortByTreeMenu.setVisible(false);
3776       return;
3777     }
3778
3779     sortByTreeMenu.setVisible(true);
3780
3781     for (final TreePanel tp : treePanels)
3782     {
3783       final JMenuItem item = new JMenuItem(tp.getTitle());
3784       item.addActionListener(new java.awt.event.ActionListener()
3785       {
3786         @Override
3787         public void actionPerformed(ActionEvent e)
3788         {
3789           tp.sortByTree_actionPerformed();
3790           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3791
3792         }
3793       });
3794
3795       sortByTreeMenu.add(item);
3796     }
3797   }
3798
3799   public boolean sortBy(AlignmentOrder alorder, String undoname)
3800   {
3801     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3802     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3803     if (undoname != null)
3804     {
3805       addHistoryItem(new OrderCommand(undoname, oldOrder,
3806               viewport.getAlignment()));
3807     }
3808     alignPanel.paintAlignment(true);
3809     return true;
3810   }
3811
3812   /**
3813    * Work out whether the whole set of sequences or just the selected set will
3814    * be submitted for multiple alignment.
3815    *
3816    */
3817   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3818   {
3819     // Now, check we have enough sequences
3820     AlignmentView msa = null;
3821
3822     if ((viewport.getSelectionGroup() != null)
3823             && (viewport.getSelectionGroup().getSize() > 1))
3824     {
3825       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3826       // some common interface!
3827       /*
3828        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3829        * SequenceI[sz = seqs.getSize(false)];
3830        *
3831        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3832        * seqs.getSequenceAt(i); }
3833        */
3834       msa = viewport.getAlignmentView(true);
3835     }
3836     else if (viewport.getSelectionGroup() != null
3837             && viewport.getSelectionGroup().getSize() == 1)
3838     {
3839       int option = JvOptionPane.showConfirmDialog(this,
3840               MessageManager.getString("warn.oneseq_msainput_selection"),
3841               MessageManager.getString("label.invalid_selection"),
3842               JvOptionPane.OK_CANCEL_OPTION);
3843       if (option == JvOptionPane.OK_OPTION)
3844       {
3845         msa = viewport.getAlignmentView(false);
3846       }
3847     }
3848     else
3849     {
3850       msa = viewport.getAlignmentView(false);
3851     }
3852     return msa;
3853   }
3854
3855   /**
3856    * Decides what is submitted to a secondary structure prediction service: the
3857    * first sequence in the alignment, or in the current selection, or, if the
3858    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3859    * region or the whole alignment. (where the first sequence in the set is the
3860    * one that the prediction will be for).
3861    */
3862   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3863   {
3864     AlignmentView seqs = null;
3865
3866     if ((viewport.getSelectionGroup() != null)
3867             && (viewport.getSelectionGroup().getSize() > 0))
3868     {
3869       seqs = viewport.getAlignmentView(true);
3870     }
3871     else
3872     {
3873       seqs = viewport.getAlignmentView(false);
3874     }
3875     // limit sequences - JBPNote in future - could spawn multiple prediction
3876     // jobs
3877     // TODO: viewport.getAlignment().isAligned is a global state - the local
3878     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3879     if (!viewport.getAlignment().isAligned(false))
3880     {
3881       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3882       // TODO: if seqs.getSequences().length>1 then should really have warned
3883       // user!
3884
3885     }
3886     return seqs;
3887   }
3888
3889   /**
3890    * DOCUMENT ME!
3891    *
3892    * @param e
3893    *          DOCUMENT ME!
3894    */
3895   @Override
3896   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3897   {
3898     // Pick the tree file
3899     JalviewFileChooser chooser = new JalviewFileChooser(
3900             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3901     chooser.setFileView(new JalviewFileView());
3902     chooser.setDialogTitle(MessageManager
3903             .getString("label.select_newick_like_tree_file"));
3904     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3905
3906     int value = chooser.showOpenDialog(null);
3907
3908     if (value == JalviewFileChooser.APPROVE_OPTION)
3909     {
3910       String filePath = chooser.getSelectedFile().getPath();
3911       Cache.setProperty("LAST_DIRECTORY", filePath);
3912       NewickFile fin = null;
3913       try
3914       {
3915         fin = new NewickFile(filePath, DataSourceType.FILE);
3916         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3917       } catch (Exception ex)
3918       {
3919         JvOptionPane
3920                 .showMessageDialog(
3921                         Desktop.desktop,
3922                         ex.getMessage(),
3923                         MessageManager
3924                                 .getString("label.problem_reading_tree_file"),
3925                         JvOptionPane.WARNING_MESSAGE);
3926         ex.printStackTrace();
3927       }
3928       if (fin != null && fin.hasWarningMessage())
3929       {
3930         JvOptionPane.showMessageDialog(Desktop.desktop, fin
3931                 .getWarningMessage(), MessageManager
3932                 .getString("label.possible_problem_with_tree_file"),
3933                 JvOptionPane.WARNING_MESSAGE);
3934       }
3935     }
3936   }
3937
3938   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3939   {
3940     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3941   }
3942
3943   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3944           int h, int x, int y)
3945   {
3946     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3947   }
3948
3949   /**
3950    * Add a treeviewer for the tree extracted from a Newick file object to the
3951    * current alignment view
3952    *
3953    * @param nf
3954    *          the tree
3955    * @param title
3956    *          tree viewer title
3957    * @param input
3958    *          Associated alignment input data (or null)
3959    * @param w
3960    *          width
3961    * @param h
3962    *          height
3963    * @param x
3964    *          position
3965    * @param y
3966    *          position
3967    * @return TreePanel handle
3968    */
3969   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3970           AlignmentView input, int w, int h, int x, int y)
3971   {
3972     TreePanel tp = null;
3973
3974     try
3975     {
3976       nf.parse();
3977
3978       if (nf.getTree() != null)
3979       {
3980         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3981
3982         tp.setSize(w, h);
3983
3984         if (x > 0 && y > 0)
3985         {
3986           tp.setLocation(x, y);
3987         }
3988
3989         Desktop.addInternalFrame(tp, treeTitle, w, h);
3990       }
3991     } catch (Exception ex)
3992     {
3993       ex.printStackTrace();
3994     }
3995
3996     return tp;
3997   }
3998
3999   private boolean buildingMenu = false;
4000
4001   /**
4002    * Generates menu items and listener event actions for web service clients
4003    *
4004    */
4005   public void BuildWebServiceMenu()
4006   {
4007     while (buildingMenu)
4008     {
4009       try
4010       {
4011         System.err.println("Waiting for building menu to finish.");
4012         Thread.sleep(10);
4013       } catch (Exception e)
4014       {
4015       }
4016     }
4017     final AlignFrame me = this;
4018     buildingMenu = true;
4019     new Thread(new Runnable()
4020     {
4021       @Override
4022       public void run()
4023       {
4024         final List<JMenuItem> legacyItems = new ArrayList<>();
4025         try
4026         {
4027           // System.err.println("Building ws menu again "
4028           // + Thread.currentThread());
4029           // TODO: add support for context dependent disabling of services based
4030           // on
4031           // alignment and current selection
4032           // TODO: add additional serviceHandle parameter to specify abstract
4033           // handler
4034           // class independently of AbstractName
4035           // TODO: add in rediscovery GUI function to restart discoverer
4036           // TODO: group services by location as well as function and/or
4037           // introduce
4038           // object broker mechanism.
4039           final Vector<JMenu> wsmenu = new Vector<>();
4040           final IProgressIndicator af = me;
4041
4042           /*
4043            * do not i18n these strings - they are hard-coded in class
4044            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4045            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4046            */
4047           final JMenu msawsmenu = new JMenu("Alignment");
4048           final JMenu secstrmenu = new JMenu(
4049                   "Secondary Structure Prediction");
4050           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4051           final JMenu analymenu = new JMenu("Analysis");
4052           final JMenu dismenu = new JMenu("Protein Disorder");
4053           // JAL-940 - only show secondary structure prediction services from
4054           // the legacy server
4055           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4056               // &&
4057           Discoverer.services != null && (Discoverer.services.size() > 0))
4058           {
4059             // TODO: refactor to allow list of AbstractName/Handler bindings to
4060             // be
4061             // stored or retrieved from elsewhere
4062             // No MSAWS used any more:
4063             // Vector msaws = null; // (Vector)
4064             // Discoverer.services.get("MsaWS");
4065             Vector secstrpr = (Vector) Discoverer.services
4066                     .get("SecStrPred");
4067             if (secstrpr != null)
4068             {
4069               // Add any secondary structure prediction services
4070               for (int i = 0, j = secstrpr.size(); i < j; i++)
4071               {
4072                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4073                         .get(i);
4074                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4075                         .getServiceClient(sh);
4076                 int p = secstrmenu.getItemCount();
4077                 impl.attachWSMenuEntry(secstrmenu, me);
4078                 int q = secstrmenu.getItemCount();
4079                 for (int litm = p; litm < q; litm++)
4080                 {
4081                   legacyItems.add(secstrmenu.getItem(litm));
4082                 }
4083               }
4084             }
4085           }
4086
4087           // Add all submenus in the order they should appear on the web
4088           // services menu
4089           wsmenu.add(msawsmenu);
4090           wsmenu.add(secstrmenu);
4091           wsmenu.add(dismenu);
4092           wsmenu.add(analymenu);
4093           // No search services yet
4094           // wsmenu.add(seqsrchmenu);
4095
4096           javax.swing.SwingUtilities.invokeLater(new Runnable()
4097           {
4098             @Override
4099             public void run()
4100             {
4101               try
4102               {
4103                 webService.removeAll();
4104                 // first, add discovered services onto the webservices menu
4105                 if (wsmenu.size() > 0)
4106                 {
4107                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4108                   {
4109                     webService.add(wsmenu.get(i));
4110                   }
4111                 }
4112                 else
4113                 {
4114                   webService.add(me.webServiceNoServices);
4115                 }
4116                 // TODO: move into separate menu builder class.
4117                 boolean new_sspred = false;
4118                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4119                 {
4120                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4121                   if (jws2servs != null)
4122                   {
4123                     if (jws2servs.hasServices())
4124                     {
4125                       jws2servs.attachWSMenuEntry(webService, me);
4126                       for (Jws2Instance sv : jws2servs.getServices())
4127                       {
4128                         if (sv.description.toLowerCase().contains("jpred"))
4129                         {
4130                           for (JMenuItem jmi : legacyItems)
4131                           {
4132                             jmi.setVisible(false);
4133                           }
4134                         }
4135                       }
4136
4137                     }
4138                     if (jws2servs.isRunning())
4139                     {
4140                       JMenuItem tm = new JMenuItem(
4141                               "Still discovering JABA Services");
4142                       tm.setEnabled(false);
4143                       webService.add(tm);
4144                     }
4145                   }
4146                 }
4147                 build_urlServiceMenu(me.webService);
4148                 build_fetchdbmenu(webService);
4149                 for (JMenu item : wsmenu)
4150                 {
4151                   if (item.getItemCount() == 0)
4152                   {
4153                     item.setEnabled(false);
4154                   }
4155                   else
4156                   {
4157                     item.setEnabled(true);
4158                   }
4159                 }
4160               } catch (Exception e)
4161               {
4162                 Cache.log
4163                         .debug("Exception during web service menu building process.",
4164                                 e);
4165               }
4166             }
4167           });
4168         } catch (Exception e)
4169         {
4170         }
4171         buildingMenu = false;
4172       }
4173     }).start();
4174
4175   }
4176
4177   /**
4178    * construct any groupURL type service menu entries.
4179    *
4180    * @param webService
4181    */
4182   private void build_urlServiceMenu(JMenu webService)
4183   {
4184     // TODO: remove this code when 2.7 is released
4185     // DEBUG - alignmentView
4186     /*
4187      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4188      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4189      *
4190      * @Override public void actionPerformed(ActionEvent e) {
4191      * jalview.datamodel.AlignmentView
4192      * .testSelectionViews(af.viewport.getAlignment(),
4193      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4194      *
4195      * }); webService.add(testAlView);
4196      */
4197     // TODO: refactor to RestClient discoverer and merge menu entries for
4198     // rest-style services with other types of analysis/calculation service
4199     // SHmmr test client - still being implemented.
4200     // DEBUG - alignmentView
4201
4202     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4203             .getRestClients())
4204     {
4205       client.attachWSMenuEntry(
4206               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4207               this);
4208     }
4209   }
4210
4211   /**
4212    * Searches the alignment sequences for xRefs and builds the Show
4213    * Cross-References menu (formerly called Show Products), with database
4214    * sources for which cross-references are found (protein sources for a
4215    * nucleotide alignment and vice versa)
4216    *
4217    * @return true if Show Cross-references menu should be enabled
4218    */
4219   public boolean canShowProducts()
4220   {
4221     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4222     AlignmentI dataset = viewport.getAlignment().getDataset();
4223
4224     showProducts.removeAll();
4225     final boolean dna = viewport.getAlignment().isNucleotide();
4226
4227     if (seqs == null || seqs.length == 0)
4228     {
4229       // nothing to see here.
4230       return false;
4231     }
4232
4233     boolean showp = false;
4234     try
4235     {
4236       List<String> ptypes = new CrossRef(seqs, dataset)
4237               .findXrefSourcesForSequences(dna);
4238
4239       for (final String source : ptypes)
4240       {
4241         showp = true;
4242         final AlignFrame af = this;
4243         JMenuItem xtype = new JMenuItem(source);
4244         xtype.addActionListener(new ActionListener()
4245         {
4246           @Override
4247           public void actionPerformed(ActionEvent e)
4248           {
4249             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4250           }
4251         });
4252         showProducts.add(xtype);
4253       }
4254       showProducts.setVisible(showp);
4255       showProducts.setEnabled(showp);
4256     } catch (Exception e)
4257     {
4258       Cache.log
4259               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4260                       e);
4261       return false;
4262     }
4263     return showp;
4264   }
4265
4266   /**
4267    * Finds and displays cross-references for the selected sequences (protein
4268    * products for nucleotide sequences, dna coding sequences for peptides).
4269    *
4270    * @param sel
4271    *          the sequences to show cross-references for
4272    * @param dna
4273    *          true if from a nucleotide alignment (so showing proteins)
4274    * @param source
4275    *          the database to show cross-references for
4276    */
4277   protected void showProductsFor(final SequenceI[] sel,
4278           final boolean _odna, final String source)
4279   {
4280     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4281             .start();
4282   }
4283
4284   /**
4285    * Construct and display a new frame containing the translation of this
4286    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4287    */
4288   @Override
4289   public void showTranslation_actionPerformed(ActionEvent e)
4290   {
4291     AlignmentI al = null;
4292     try
4293     {
4294       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4295
4296       al = dna.translateCdna();
4297     } catch (Exception ex)
4298     {
4299       jalview.bin.Cache.log.error(
4300               "Exception during translation. Please report this !", ex);
4301       final String msg = MessageManager
4302               .getString("label.error_when_translating_sequences_submit_bug_report");
4303       final String errorTitle = MessageManager
4304               .getString("label.implementation_error")
4305               + MessageManager.getString("label.translation_failed");
4306       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4307               JvOptionPane.ERROR_MESSAGE);
4308       return;
4309     }
4310     if (al == null || al.getHeight() == 0)
4311     {
4312       final String msg = MessageManager
4313               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4314       final String errorTitle = MessageManager
4315               .getString("label.translation_failed");
4316       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4317               JvOptionPane.WARNING_MESSAGE);
4318     }
4319     else
4320     {
4321       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4322       af.setFileFormat(this.currentFileFormat);
4323       final String newTitle = MessageManager.formatMessage(
4324               "label.translation_of_params",
4325               new Object[] { this.getTitle() });
4326       af.setTitle(newTitle);
4327       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4328       {
4329         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4330         viewport.openSplitFrame(af, new Alignment(seqs));
4331       }
4332       else
4333       {
4334         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4335                 DEFAULT_HEIGHT);
4336       }
4337     }
4338   }
4339
4340   /**
4341    * Set the file format
4342    *
4343    * @param format
4344    */
4345   public void setFileFormat(FileFormatI format)
4346   {
4347     this.currentFileFormat = format;
4348   }
4349
4350   /**
4351    * Try to load a features file onto the alignment.
4352    *
4353    * @param file
4354    *          contents or path to retrieve file
4355    * @param sourceType
4356    *          access mode of file (see jalview.io.AlignFile)
4357    * @return true if features file was parsed correctly.
4358    */
4359   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4360   {
4361     return avc.parseFeaturesFile(file, sourceType,
4362             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4363
4364   }
4365
4366   @Override
4367   public void refreshFeatureUI(boolean enableIfNecessary)
4368   {
4369     // note - currently this is only still here rather than in the controller
4370     // because of the featureSettings hard reference that is yet to be
4371     // abstracted
4372     if (enableIfNecessary)
4373     {
4374       viewport.setShowSequenceFeatures(true);
4375       showSeqFeatures.setSelected(true);
4376     }
4377
4378   }
4379
4380   @Override
4381   public void dragEnter(DropTargetDragEvent evt)
4382   {
4383   }
4384
4385   @Override
4386   public void dragExit(DropTargetEvent evt)
4387   {
4388   }
4389
4390   @Override
4391   public void dragOver(DropTargetDragEvent evt)
4392   {
4393   }
4394
4395   @Override
4396   public void dropActionChanged(DropTargetDragEvent evt)
4397   {
4398   }
4399
4400   @Override
4401   public void drop(DropTargetDropEvent evt)
4402   {
4403     // JAL-1552 - acceptDrop required before getTransferable call for
4404     // Java's Transferable for native dnd
4405     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4406     Transferable t = evt.getTransferable();
4407     List<String> files = new ArrayList<>();
4408     List<DataSourceType> protocols = new ArrayList<>();
4409
4410     try
4411     {
4412       Desktop.transferFromDropTarget(files, protocols, evt, t);
4413     } catch (Exception e)
4414     {
4415       e.printStackTrace();
4416     }
4417     if (files != null)
4418     {
4419       try
4420       {
4421         // check to see if any of these files have names matching sequences in
4422         // the alignment
4423         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4424                 .getAlignment().getSequencesArray());
4425         /**
4426          * Object[] { String,SequenceI}
4427          */
4428         ArrayList<Object[]> filesmatched = new ArrayList<>();
4429         ArrayList<String> filesnotmatched = new ArrayList<>();
4430         for (int i = 0; i < files.size(); i++)
4431         {
4432           String file = files.get(i).toString();
4433           String pdbfn = "";
4434           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4435           if (protocol == DataSourceType.FILE)
4436           {
4437             File fl = new File(file);
4438             pdbfn = fl.getName();
4439           }
4440           else if (protocol == DataSourceType.URL)
4441           {
4442             URL url = new URL(file);
4443             pdbfn = url.getFile();
4444           }
4445           if (pdbfn.length() > 0)
4446           {
4447             // attempt to find a match in the alignment
4448             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4449             int l = 0, c = pdbfn.indexOf(".");
4450             while (mtch == null && c != -1)
4451             {
4452               do
4453               {
4454                 l = c;
4455               } while ((c = pdbfn.indexOf(".", l)) > l);
4456               if (l > -1)
4457               {
4458                 pdbfn = pdbfn.substring(0, l);
4459               }
4460               mtch = idm.findAllIdMatches(pdbfn);
4461             }
4462             if (mtch != null)
4463             {
4464               FileFormatI type = null;
4465               try
4466               {
4467                 type = new IdentifyFile().identify(file, protocol);
4468               } catch (Exception ex)
4469               {
4470                 type = null;
4471               }
4472               if (type != null && type.isStructureFile())
4473               {
4474                 filesmatched.add(new Object[] { file, protocol, mtch });
4475                 continue;
4476               }
4477             }
4478             // File wasn't named like one of the sequences or wasn't a PDB file.
4479             filesnotmatched.add(file);
4480           }
4481         }
4482         int assocfiles = 0;
4483         if (filesmatched.size() > 0)
4484         {
4485           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4486                   || JvOptionPane
4487                           .showConfirmDialog(
4488                                   this,
4489                                   MessageManager
4490                                           .formatMessage(
4491                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4492                                                   new Object[] { Integer
4493                                                           .valueOf(
4494                                                                   filesmatched
4495                                                                           .size())
4496                                                           .toString() }),
4497                                   MessageManager
4498                                           .getString("label.automatically_associate_structure_files_by_name"),
4499                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4500
4501           {
4502             for (Object[] fm : filesmatched)
4503             {
4504               // try and associate
4505               // TODO: may want to set a standard ID naming formalism for
4506               // associating PDB files which have no IDs.
4507               for (SequenceI toassoc : (SequenceI[]) fm[2])
4508               {
4509                 PDBEntry pe = new AssociatePdbFileWithSeq()
4510                         .associatePdbWithSeq((String) fm[0],
4511                                 (DataSourceType) fm[1], toassoc, false,
4512                                 Desktop.instance);
4513                 if (pe != null)
4514                 {
4515                   System.err.println("Associated file : "
4516                           + ((String) fm[0]) + " with "
4517                           + toassoc.getDisplayId(true));
4518                   assocfiles++;
4519                 }
4520               }
4521               alignPanel.paintAlignment(true);
4522             }
4523           }
4524         }
4525         if (filesnotmatched.size() > 0)
4526         {
4527           if (assocfiles > 0
4528                   && (Cache.getDefault(
4529                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4530                           .showConfirmDialog(
4531                                   this,
4532                                   "<html>"
4533                                           + MessageManager
4534                                                   .formatMessage(
4535                                                           "label.ignore_unmatched_dropped_files_info",
4536                                                           new Object[] { Integer
4537                                                                   .valueOf(
4538                                                                           filesnotmatched
4539                                                                                   .size())
4540                                                                   .toString() })
4541                                           + "</html>",
4542                                   MessageManager
4543                                           .getString("label.ignore_unmatched_dropped_files"),
4544                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4545           {
4546             return;
4547           }
4548           for (String fn : filesnotmatched)
4549           {
4550             loadJalviewDataFile(fn, null, null, null);
4551           }
4552
4553         }
4554       } catch (Exception ex)
4555       {
4556         ex.printStackTrace();
4557       }
4558     }
4559   }
4560
4561   /**
4562    * Attempt to load a "dropped" file or URL string, by testing in turn for
4563    * <ul>
4564    * <li>an Annotation file</li>
4565    * <li>a JNet file</li>
4566    * <li>a features file</li>
4567    * <li>else try to interpret as an alignment file</li>
4568    * </ul>
4569    *
4570    * @param file
4571    *          either a filename or a URL string.
4572    */
4573   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4574           FileFormatI format, SequenceI assocSeq)
4575   {
4576     try
4577     {
4578       if (sourceType == null)
4579       {
4580         sourceType = FormatAdapter.checkProtocol(file);
4581       }
4582       // if the file isn't identified, or not positively identified as some
4583       // other filetype (PFAM is default unidentified alignment file type) then
4584       // try to parse as annotation.
4585       boolean isAnnotation = (format == null || FileFormat.Pfam
4586               .equals(format)) ? new AnnotationFile()
4587               .annotateAlignmentView(viewport, file, sourceType) : false;
4588
4589       if (!isAnnotation)
4590       {
4591         // first see if its a T-COFFEE score file
4592         TCoffeeScoreFile tcf = null;
4593         try
4594         {
4595           tcf = new TCoffeeScoreFile(file, sourceType);
4596           if (tcf.isValid())
4597           {
4598             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4599             {
4600               buildColourMenu();
4601               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4602               isAnnotation = true;
4603               statusBar
4604                       .setText(MessageManager
4605                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4606             }
4607             else
4608             {
4609               // some problem - if no warning its probable that the ID matching
4610               // process didn't work
4611               JvOptionPane
4612                       .showMessageDialog(
4613                               Desktop.desktop,
4614                               tcf.getWarningMessage() == null ? MessageManager
4615                                       .getString("label.check_file_matches_sequence_ids_alignment")
4616                                       : tcf.getWarningMessage(),
4617                               MessageManager
4618                                       .getString("label.problem_reading_tcoffee_score_file"),
4619                               JvOptionPane.WARNING_MESSAGE);
4620             }
4621           }
4622           else
4623           {
4624             tcf = null;
4625           }
4626         } catch (Exception x)
4627         {
4628           Cache.log
4629                   .debug("Exception when processing data source as T-COFFEE score file",
4630                           x);
4631           tcf = null;
4632         }
4633         if (tcf == null)
4634         {
4635           // try to see if its a JNet 'concise' style annotation file *before*
4636           // we
4637           // try to parse it as a features file
4638           if (format == null)
4639           {
4640             format = new IdentifyFile().identify(file, sourceType);
4641           }
4642           if (FileFormat.ScoreMatrix == format)
4643           {
4644             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4645                     sourceType));
4646             sm.parse();
4647             // todo: i18n this message
4648             statusBar
4649                     .setText(MessageManager.formatMessage(
4650                             "label.successfully_loaded_matrix",
4651                             sm.getMatrixName()));
4652           }
4653           else if (FileFormat.HMMER3.equals(format))
4654           {
4655             HMMFile hmm = new HMMFile(new FileParse(file, sourceType));
4656             hmm.parse();
4657             System.out.println("successful");
4658           }
4659           else if (FileFormat.Jnet.equals(format))
4660           {
4661             JPredFile predictions = new JPredFile(file, sourceType);
4662             new JnetAnnotationMaker();
4663             JnetAnnotationMaker.add_annotation(predictions,
4664                     viewport.getAlignment(), 0, false);
4665             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4666             viewport.getAlignment().setSeqrep(repseq);
4667             HiddenColumns cs = new HiddenColumns();
4668             cs.hideInsertionsFor(repseq);
4669             viewport.getAlignment().setHiddenColumns(cs);
4670             isAnnotation = true;
4671           }
4672           // else if (IdentifyFile.FeaturesFile.equals(format))
4673           else if (FileFormat.Features.equals(format))
4674           {
4675             if (parseFeaturesFile(file, sourceType))
4676             {
4677               alignPanel.paintAlignment(true);
4678             }
4679           }
4680           else
4681           {
4682             new FileLoader().LoadFile(viewport, file, sourceType, format);
4683           }
4684         }
4685       }
4686       if (isAnnotation)
4687       {
4688
4689         alignPanel.adjustAnnotationHeight();
4690         viewport.updateSequenceIdColours();
4691         buildSortByAnnotationScoresMenu();
4692         alignPanel.paintAlignment(true);
4693       }
4694     } catch (Exception ex)
4695     {
4696       ex.printStackTrace();
4697     } catch (OutOfMemoryError oom)
4698     {
4699       try
4700       {
4701         System.gc();
4702       } catch (Exception x)
4703       {
4704       }
4705       new OOMWarning(
4706               "loading data "
4707                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4708                               : "using " + sourceType + " from " + file)
4709                               : ".")
4710                       + (format != null ? "(parsing as '" + format
4711                               + "' file)" : ""), oom, Desktop.desktop);
4712     }
4713   }
4714
4715   /**
4716    * Method invoked by the ChangeListener on the tabbed pane, in other words
4717    * when a different tabbed pane is selected by the user or programmatically.
4718    */
4719   @Override
4720   public void tabSelectionChanged(int index)
4721   {
4722     if (index > -1)
4723     {
4724       alignPanel = alignPanels.get(index);
4725       viewport = alignPanel.av;
4726       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4727       setMenusFromViewport(viewport);
4728     }
4729
4730     /*
4731      * 'focus' any colour slider that is open to the selected viewport
4732      */
4733     if (viewport.getConservationSelected())
4734     {
4735       SliderPanel.setConservationSlider(alignPanel,
4736               viewport.getResidueShading(), alignPanel.getViewName());
4737     }
4738     else
4739     {
4740       SliderPanel.hideConservationSlider();
4741     }
4742     if (viewport.getAbovePIDThreshold())
4743     {
4744       SliderPanel.setPIDSliderSource(alignPanel,
4745               viewport.getResidueShading(), alignPanel.getViewName());
4746     }
4747     else
4748     {
4749       SliderPanel.hidePIDSlider();
4750     }
4751
4752     /*
4753      * If there is a frame linked to this one in a SplitPane, switch it to the
4754      * same view tab index. No infinite recursion of calls should happen, since
4755      * tabSelectionChanged() should not get invoked on setting the selected
4756      * index to an unchanged value. Guard against setting an invalid index
4757      * before the new view peer tab has been created.
4758      */
4759     final AlignViewportI peer = viewport.getCodingComplement();
4760     if (peer != null)
4761     {
4762       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4763       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4764       {
4765         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4766       }
4767     }
4768   }
4769
4770   /**
4771    * On right mouse click on view tab, prompt for and set new view name.
4772    */
4773   @Override
4774   public void tabbedPane_mousePressed(MouseEvent e)
4775   {
4776     if (e.isPopupTrigger())
4777     {
4778       String msg = MessageManager.getString("label.enter_view_name");
4779       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4780               JvOptionPane.QUESTION_MESSAGE);
4781
4782       if (reply != null)
4783       {
4784         viewport.viewName = reply;
4785         // TODO warn if reply is in getExistingViewNames()?
4786         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4787       }
4788     }
4789   }
4790
4791   public AlignViewport getCurrentView()
4792   {
4793     return viewport;
4794   }
4795
4796   /**
4797    * Open the dialog for regex description parsing.
4798    */
4799   @Override
4800   protected void extractScores_actionPerformed(ActionEvent e)
4801   {
4802     ParseProperties pp = new jalview.analysis.ParseProperties(
4803             viewport.getAlignment());
4804     // TODO: verify regex and introduce GUI dialog for version 2.5
4805     // if (pp.getScoresFromDescription("col", "score column ",
4806     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4807     // true)>0)
4808     if (pp.getScoresFromDescription("description column",
4809             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4810     {
4811       buildSortByAnnotationScoresMenu();
4812     }
4813   }
4814
4815   /*
4816    * (non-Javadoc)
4817    *
4818    * @see
4819    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4820    * )
4821    */
4822   @Override
4823   protected void showDbRefs_actionPerformed(ActionEvent e)
4824   {
4825     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4826   }
4827
4828   /*
4829    * (non-Javadoc)
4830    *
4831    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4832    * ActionEvent)
4833    */
4834   @Override
4835   protected void showNpFeats_actionPerformed(ActionEvent e)
4836   {
4837     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4838   }
4839
4840   /**
4841    * find the viewport amongst the tabs in this alignment frame and close that
4842    * tab
4843    *
4844    * @param av
4845    */
4846   public boolean closeView(AlignViewportI av)
4847   {
4848     if (viewport == av)
4849     {
4850       this.closeMenuItem_actionPerformed(false);
4851       return true;
4852     }
4853     Component[] comp = tabbedPane.getComponents();
4854     for (int i = 0; comp != null && i < comp.length; i++)
4855     {
4856       if (comp[i] instanceof AlignmentPanel)
4857       {
4858         if (((AlignmentPanel) comp[i]).av == av)
4859         {
4860           // close the view.
4861           closeView((AlignmentPanel) comp[i]);
4862           return true;
4863         }
4864       }
4865     }
4866     return false;
4867   }
4868
4869   protected void build_fetchdbmenu(JMenu webService)
4870   {
4871     // Temporary hack - DBRef Fetcher always top level ws entry.
4872     // TODO We probably want to store a sequence database checklist in
4873     // preferences and have checkboxes.. rather than individual sources selected
4874     // here
4875     final JMenu rfetch = new JMenu(
4876             MessageManager.getString("action.fetch_db_references"));
4877     rfetch.setToolTipText(MessageManager
4878             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4879     webService.add(rfetch);
4880
4881     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4882             MessageManager.getString("option.trim_retrieved_seqs"));
4883     trimrs.setToolTipText(MessageManager
4884             .getString("label.trim_retrieved_sequences"));
4885     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4886     trimrs.addActionListener(new ActionListener()
4887     {
4888       @Override
4889       public void actionPerformed(ActionEvent e)
4890       {
4891         trimrs.setSelected(trimrs.isSelected());
4892         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4893                 Boolean.valueOf(trimrs.isSelected()).toString());
4894       };
4895     });
4896     rfetch.add(trimrs);
4897     JMenuItem fetchr = new JMenuItem(
4898             MessageManager.getString("label.standard_databases"));
4899     fetchr.setToolTipText(MessageManager
4900             .getString("label.fetch_embl_uniprot"));
4901     fetchr.addActionListener(new ActionListener()
4902     {
4903
4904       @Override
4905       public void actionPerformed(ActionEvent e)
4906       {
4907         new Thread(new Runnable()
4908         {
4909           @Override
4910           public void run()
4911           {
4912             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4913                     .getAlignment().isNucleotide();
4914             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4915                     .getSequenceSelection(), alignPanel.alignFrame, null,
4916                     alignPanel.alignFrame.featureSettings, isNucleotide);
4917             dbRefFetcher.addListener(new FetchFinishedListenerI()
4918             {
4919               @Override
4920               public void finished()
4921               {
4922                 AlignFrame.this.setMenusForViewport();
4923               }
4924             });
4925             dbRefFetcher.fetchDBRefs(false);
4926           }
4927         }).start();
4928
4929       }
4930
4931     });
4932     rfetch.add(fetchr);
4933     final AlignFrame me = this;
4934     new Thread(new Runnable()
4935     {
4936       @Override
4937       public void run()
4938       {
4939         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4940                 .getSequenceFetcherSingleton(me);
4941         javax.swing.SwingUtilities.invokeLater(new Runnable()
4942         {
4943           @Override
4944           public void run()
4945           {
4946             String[] dbclasses = sf.getOrderedSupportedSources();
4947             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4948             // jalview.util.QuickSort.sort(otherdb, otherdb);
4949             List<DbSourceProxy> otherdb;
4950             JMenu dfetch = new JMenu();
4951             JMenu ifetch = new JMenu();
4952             JMenuItem fetchr = null;
4953             int comp = 0, icomp = 0, mcomp = 15;
4954             String mname = null;
4955             int dbi = 0;
4956             for (String dbclass : dbclasses)
4957             {
4958               otherdb = sf.getSourceProxy(dbclass);
4959               // add a single entry for this class, or submenu allowing 'fetch
4960               // all' or pick one
4961               if (otherdb == null || otherdb.size() < 1)
4962               {
4963                 continue;
4964               }
4965               // List<DbSourceProxy> dbs=otherdb;
4966               // otherdb=new ArrayList<DbSourceProxy>();
4967               // for (DbSourceProxy db:dbs)
4968               // {
4969               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4970               // }
4971               if (mname == null)
4972               {
4973                 mname = "From " + dbclass;
4974               }
4975               if (otherdb.size() == 1)
4976               {
4977                 final DbSourceProxy[] dassource = otherdb
4978                         .toArray(new DbSourceProxy[0]);
4979                 DbSourceProxy src = otherdb.get(0);
4980                 fetchr = new JMenuItem(src.getDbSource());
4981                 fetchr.addActionListener(new ActionListener()
4982                 {
4983
4984                   @Override
4985                   public void actionPerformed(ActionEvent e)
4986                   {
4987                     new Thread(new Runnable()
4988                     {
4989
4990                       @Override
4991                       public void run()
4992                       {
4993                         boolean isNucleotide = alignPanel.alignFrame
4994                                 .getViewport().getAlignment()
4995                                 .isNucleotide();
4996                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4997                                 alignPanel.av.getSequenceSelection(),
4998                                 alignPanel.alignFrame, dassource,
4999                                 alignPanel.alignFrame.featureSettings,
5000                                 isNucleotide);
5001                         dbRefFetcher
5002                                 .addListener(new FetchFinishedListenerI()
5003                                 {
5004                                   @Override
5005                                   public void finished()
5006                                   {
5007                                     AlignFrame.this.setMenusForViewport();
5008                                   }
5009                                 });
5010                         dbRefFetcher.fetchDBRefs(false);
5011                       }
5012                     }).start();
5013                   }
5014
5015                 });
5016                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5017                         MessageManager.formatMessage(
5018                                 "label.fetch_retrieve_from",
5019                                 new Object[] { src.getDbName() })));
5020                 dfetch.add(fetchr);
5021                 comp++;
5022               }
5023               else
5024               {
5025                 final DbSourceProxy[] dassource = otherdb
5026                         .toArray(new DbSourceProxy[0]);
5027                 // fetch all entry
5028                 DbSourceProxy src = otherdb.get(0);
5029                 fetchr = new JMenuItem(MessageManager.formatMessage(
5030                         "label.fetch_all_param",
5031                         new Object[] { src.getDbSource() }));
5032                 fetchr.addActionListener(new ActionListener()
5033                 {
5034                   @Override
5035                   public void actionPerformed(ActionEvent e)
5036                   {
5037                     new Thread(new Runnable()
5038                     {
5039
5040                       @Override
5041                       public void run()
5042                       {
5043                         boolean isNucleotide = alignPanel.alignFrame
5044                                 .getViewport().getAlignment()
5045                                 .isNucleotide();
5046                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5047                                 alignPanel.av.getSequenceSelection(),
5048                                 alignPanel.alignFrame, dassource,
5049                                 alignPanel.alignFrame.featureSettings,
5050                                 isNucleotide);
5051                         dbRefFetcher
5052                                 .addListener(new FetchFinishedListenerI()
5053                                 {
5054                                   @Override
5055                                   public void finished()
5056                                   {
5057                                     AlignFrame.this.setMenusForViewport();
5058                                   }
5059                                 });
5060                         dbRefFetcher.fetchDBRefs(false);
5061                       }
5062                     }).start();
5063                   }
5064                 });
5065
5066                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5067                         MessageManager.formatMessage(
5068                                 "label.fetch_retrieve_from_all_sources",
5069                                 new Object[] {
5070                                     Integer.valueOf(otherdb.size())
5071                                             .toString(), src.getDbSource(),
5072                                     src.getDbName() })));
5073                 dfetch.add(fetchr);
5074                 comp++;
5075                 // and then build the rest of the individual menus
5076                 ifetch = new JMenu(MessageManager.formatMessage(
5077                         "label.source_from_db_source",
5078                         new Object[] { src.getDbSource() }));
5079                 icomp = 0;
5080                 String imname = null;
5081                 int i = 0;
5082                 for (DbSourceProxy sproxy : otherdb)
5083                 {
5084                   String dbname = sproxy.getDbName();
5085                   String sname = dbname.length() > 5 ? dbname.substring(0,
5086                           5) + "..." : dbname;
5087                   String msname = dbname.length() > 10 ? dbname.substring(
5088                           0, 10) + "..." : dbname;
5089                   if (imname == null)
5090                   {
5091                     imname = MessageManager.formatMessage(
5092                             "label.from_msname", new Object[] { sname });
5093                   }
5094                   fetchr = new JMenuItem(msname);
5095                   final DbSourceProxy[] dassrc = { sproxy };
5096                   fetchr.addActionListener(new ActionListener()
5097                   {
5098
5099                     @Override
5100                     public void actionPerformed(ActionEvent e)
5101                     {
5102                       new Thread(new Runnable()
5103                       {
5104
5105                         @Override
5106                         public void run()
5107                         {
5108                           boolean isNucleotide = alignPanel.alignFrame
5109                                   .getViewport().getAlignment()
5110                                   .isNucleotide();
5111                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5112                                   alignPanel.av.getSequenceSelection(),
5113                                   alignPanel.alignFrame, dassrc,
5114                                   alignPanel.alignFrame.featureSettings,
5115                                   isNucleotide);
5116                           dbRefFetcher
5117                                   .addListener(new FetchFinishedListenerI()
5118                                   {
5119                                     @Override
5120                                     public void finished()
5121                                     {
5122                                       AlignFrame.this.setMenusForViewport();
5123                                     }
5124                                   });
5125                           dbRefFetcher.fetchDBRefs(false);
5126                         }
5127                       }).start();
5128                     }
5129
5130                   });
5131                   fetchr.setToolTipText("<html>"
5132                           + MessageManager.formatMessage(
5133                                   "label.fetch_retrieve_from", new Object[]
5134                                   { dbname }));
5135                   ifetch.add(fetchr);
5136                   ++i;
5137                   if (++icomp >= mcomp || i == (otherdb.size()))
5138                   {
5139                     ifetch.setText(MessageManager.formatMessage(
5140                             "label.source_to_target", imname, sname));
5141                     dfetch.add(ifetch);
5142                     ifetch = new JMenu();
5143                     imname = null;
5144                     icomp = 0;
5145                     comp++;
5146                   }
5147                 }
5148               }
5149               ++dbi;
5150               if (comp >= mcomp || dbi >= (dbclasses.length))
5151               {
5152                 dfetch.setText(MessageManager.formatMessage(
5153                         "label.source_to_target", mname, dbclass));
5154                 rfetch.add(dfetch);
5155                 dfetch = new JMenu();
5156                 mname = null;
5157                 comp = 0;
5158               }
5159             }
5160           }
5161         });
5162       }
5163     }).start();
5164
5165   }
5166
5167   /**
5168    * Left justify the whole alignment.
5169    */
5170   @Override
5171   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5172   {
5173     AlignmentI al = viewport.getAlignment();
5174     al.justify(false);
5175     viewport.firePropertyChange("alignment", null, al);
5176   }
5177
5178   /**
5179    * Right justify the whole alignment.
5180    */
5181   @Override
5182   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5183   {
5184     AlignmentI al = viewport.getAlignment();
5185     al.justify(true);
5186     viewport.firePropertyChange("alignment", null, al);
5187   }
5188
5189   @Override
5190   public void setShowSeqFeatures(boolean b)
5191   {
5192     showSeqFeatures.setSelected(b);
5193     viewport.setShowSequenceFeatures(b);
5194   }
5195
5196   /*
5197    * (non-Javadoc)
5198    *
5199    * @see
5200    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5201    * awt.event.ActionEvent)
5202    */
5203   @Override
5204   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5205   {
5206     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5207     alignPanel.paintAlignment(true);
5208   }
5209
5210   /*
5211    * (non-Javadoc)
5212    *
5213    * @see
5214    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5215    * .ActionEvent)
5216    */
5217   @Override
5218   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5219   {
5220     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5221     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5222
5223   }
5224
5225   /*
5226    * (non-Javadoc)
5227    *
5228    * @see
5229    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5230    * .event.ActionEvent)
5231    */
5232   @Override
5233   protected void showGroupConservation_actionPerformed(ActionEvent e)
5234   {
5235     viewport.setShowGroupConservation(showGroupConservation.getState());
5236     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5237   }
5238
5239   /*
5240    * (non-Javadoc)
5241    *
5242    * @see
5243    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5244    * .event.ActionEvent)
5245    */
5246   @Override
5247   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5248   {
5249     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5250     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5251   }
5252
5253   /*
5254    * (non-Javadoc)
5255    *
5256    * @see
5257    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5258    * .event.ActionEvent)
5259    */
5260   @Override
5261   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5262   {
5263     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5264     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5265   }
5266
5267   @Override
5268   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5269   {
5270     showSequenceLogo.setState(true);
5271     viewport.setShowSequenceLogo(true);
5272     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5273     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5274   }
5275
5276   @Override
5277   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5278   {
5279     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5280   }
5281
5282   /*
5283    * (non-Javadoc)
5284    *
5285    * @see
5286    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5287    * .event.ActionEvent)
5288    */
5289   @Override
5290   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5291   {
5292     if (avc.makeGroupsFromSelection())
5293     {
5294       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5295       alignPanel.updateAnnotation();
5296       alignPanel.paintAlignment(true);
5297     }
5298   }
5299
5300   public void clearAlignmentSeqRep()
5301   {
5302     // TODO refactor alignmentseqrep to controller
5303     if (viewport.getAlignment().hasSeqrep())
5304     {
5305       viewport.getAlignment().setSeqrep(null);
5306       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5307       alignPanel.updateAnnotation();
5308       alignPanel.paintAlignment(true);
5309     }
5310   }
5311
5312   @Override
5313   protected void createGroup_actionPerformed(ActionEvent e)
5314   {
5315     if (avc.createGroup())
5316     {
5317       alignPanel.alignmentChanged();
5318     }
5319   }
5320
5321   @Override
5322   protected void unGroup_actionPerformed(ActionEvent e)
5323   {
5324     if (avc.unGroup())
5325     {
5326       alignPanel.alignmentChanged();
5327     }
5328   }
5329
5330   /**
5331    * make the given alignmentPanel the currently selected tab
5332    *
5333    * @param alignmentPanel
5334    */
5335   public void setDisplayedView(AlignmentPanel alignmentPanel)
5336   {
5337     if (!viewport.getSequenceSetId().equals(
5338             alignmentPanel.av.getSequenceSetId()))
5339     {
5340       throw new Error(
5341               MessageManager
5342                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5343     }
5344     if (tabbedPane != null
5345             && tabbedPane.getTabCount() > 0
5346             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5347                     .getSelectedIndex())
5348     {
5349       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5350     }
5351   }
5352
5353   /**
5354    * Action on selection of menu options to Show or Hide annotations.
5355    *
5356    * @param visible
5357    * @param forSequences
5358    *          update sequence-related annotations
5359    * @param forAlignment
5360    *          update non-sequence-related annotations
5361    */
5362   @Override
5363   protected void setAnnotationsVisibility(boolean visible,
5364           boolean forSequences, boolean forAlignment)
5365   {
5366     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5367             .getAlignmentAnnotation();
5368     if (anns == null)
5369     {
5370       return;
5371     }
5372     for (AlignmentAnnotation aa : anns)
5373     {
5374       /*
5375        * don't display non-positional annotations on an alignment
5376        */
5377       if (aa.annotations == null)
5378       {
5379         continue;
5380       }
5381       boolean apply = (aa.sequenceRef == null && forAlignment)
5382               || (aa.sequenceRef != null && forSequences);
5383       if (apply)
5384       {
5385         aa.visible = visible;
5386       }
5387     }
5388     alignPanel.validateAnnotationDimensions(true);
5389     alignPanel.alignmentChanged();
5390   }
5391
5392   /**
5393    * Store selected annotation sort order for the view and repaint.
5394    */
5395   @Override
5396   protected void sortAnnotations_actionPerformed()
5397   {
5398     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5399     this.alignPanel.av
5400             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5401     alignPanel.paintAlignment(true);
5402   }
5403
5404   /**
5405    *
5406    * @return alignment panels in this alignment frame
5407    */
5408   public List<? extends AlignmentViewPanel> getAlignPanels()
5409   {
5410     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5411   }
5412
5413   /**
5414    * Open a new alignment window, with the cDNA associated with this (protein)
5415    * alignment, aligned as is the protein.
5416    */
5417   protected void viewAsCdna_actionPerformed()
5418   {
5419     // TODO no longer a menu action - refactor as required
5420     final AlignmentI alignment = getViewport().getAlignment();
5421     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5422     if (mappings == null)
5423     {
5424       return;
5425     }
5426     List<SequenceI> cdnaSeqs = new ArrayList<>();
5427     for (SequenceI aaSeq : alignment.getSequences())
5428     {
5429       for (AlignedCodonFrame acf : mappings)
5430       {
5431         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5432         if (dnaSeq != null)
5433         {
5434           /*
5435            * There is a cDNA mapping for this protein sequence - add to new
5436            * alignment. It will share the same dataset sequence as other mapped
5437            * cDNA (no new mappings need to be created).
5438            */
5439           final Sequence newSeq = new Sequence(dnaSeq);
5440           newSeq.setDatasetSequence(dnaSeq);
5441           cdnaSeqs.add(newSeq);
5442         }
5443       }
5444     }
5445     if (cdnaSeqs.size() == 0)
5446     {
5447       // show a warning dialog no mapped cDNA
5448       return;
5449     }
5450     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5451             .size()]));
5452     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5453             AlignFrame.DEFAULT_HEIGHT);
5454     cdna.alignAs(alignment);
5455     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5456             + this.title;
5457     Desktop.addInternalFrame(alignFrame, newtitle,
5458             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5459   }
5460
5461   /**
5462    * Set visibility of dna/protein complement view (available when shown in a
5463    * split frame).
5464    *
5465    * @param show
5466    */
5467   @Override
5468   protected void showComplement_actionPerformed(boolean show)
5469   {
5470     SplitContainerI sf = getSplitViewContainer();
5471     if (sf != null)
5472     {
5473       sf.setComplementVisible(this, show);
5474     }
5475   }
5476
5477   /**
5478    * Generate the reverse (optionally complemented) of the selected sequences,
5479    * and add them to the alignment
5480    */
5481   @Override
5482   protected void showReverse_actionPerformed(boolean complement)
5483   {
5484     AlignmentI al = null;
5485     try
5486     {
5487       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5488       al = dna.reverseCdna(complement);
5489       viewport.addAlignment(al, "");
5490       addHistoryItem(new EditCommand(
5491               MessageManager.getString("label.add_sequences"),
5492               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5493               viewport.getAlignment()));
5494     } catch (Exception ex)
5495     {
5496       System.err.println(ex.getMessage());
5497       return;
5498     }
5499   }
5500
5501   /**
5502    * Try to run a script in the Groovy console, having first ensured that this
5503    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5504    * be targeted at this alignment.
5505    */
5506   @Override
5507   protected void runGroovy_actionPerformed()
5508   {
5509     Jalview.setCurrentAlignFrame(this);
5510     groovy.ui.Console console = Desktop.getGroovyConsole();
5511     if (console != null)
5512     {
5513       try
5514       {
5515         console.runScript();
5516       } catch (Exception ex)
5517       {
5518         System.err.println((ex.toString()));
5519         JvOptionPane
5520                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5521                         .getString("label.couldnt_run_groovy_script"),
5522                         MessageManager
5523                                 .getString("label.groovy_support_failed"),
5524                         JvOptionPane.ERROR_MESSAGE);
5525       }
5526     }
5527     else
5528     {
5529       System.err.println("Can't run Groovy script as console not found");
5530     }
5531   }
5532
5533   /**
5534    * Hides columns containing (or not containing) a specified feature, provided
5535    * that would not leave all columns hidden
5536    *
5537    * @param featureType
5538    * @param columnsContaining
5539    * @return
5540    */
5541   public boolean hideFeatureColumns(String featureType,
5542           boolean columnsContaining)
5543   {
5544     boolean notForHiding = avc.markColumnsContainingFeatures(
5545             columnsContaining, false, false, featureType);
5546     if (notForHiding)
5547     {
5548       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5549               false, featureType))
5550       {
5551         getViewport().hideSelectedColumns();
5552         return true;
5553       }
5554     }
5555     return false;
5556   }
5557
5558   @Override
5559   protected void selectHighlightedColumns_actionPerformed(
5560           ActionEvent actionEvent)
5561   {
5562     // include key modifier check in case user selects from menu
5563     avc.markHighlightedColumns(
5564             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5565             true,
5566             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5567   }
5568
5569   /**
5570    * Rebuilds the Colour menu, including any user-defined colours which have
5571    * been loaded either on startup or during the session
5572    */
5573   public void buildColourMenu()
5574   {
5575     colourMenu.removeAll();
5576
5577     colourMenu.add(applyToAllGroups);
5578     colourMenu.add(textColour);
5579     colourMenu.addSeparator();
5580
5581     ColourMenuHelper.addMenuItems(colourMenu, this,
5582             viewport.getAlignment(), false);
5583
5584     colourMenu.addSeparator();
5585     colourMenu.add(conservationMenuItem);
5586     colourMenu.add(modifyConservation);
5587     colourMenu.add(abovePIDThreshold);
5588     colourMenu.add(modifyPID);
5589     colourMenu.add(annotationColour);
5590
5591     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5592     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5593   }
5594
5595   /**
5596    * Open a dialog (if not already open) that allows the user to select and
5597    * calculate PCA or Tree analysis
5598    */
5599   protected void openTreePcaDialog()
5600   {
5601     if (alignPanel.getCalculationDialog() == null)
5602     {
5603       new CalculationChooser(AlignFrame.this);
5604     }
5605   }
5606 }
5607
5608 class PrintThread extends Thread
5609 {
5610   AlignmentPanel ap;
5611
5612   public PrintThread(AlignmentPanel ap)
5613   {
5614     this.ap = ap;
5615   }
5616
5617   static PageFormat pf;
5618
5619   @Override
5620   public void run()
5621   {
5622     PrinterJob printJob = PrinterJob.getPrinterJob();
5623
5624     if (pf != null)
5625     {
5626       printJob.setPrintable(ap, pf);
5627     }
5628     else
5629     {
5630       printJob.setPrintable(ap);
5631     }
5632
5633     if (printJob.printDialog())
5634     {
5635       try
5636       {
5637         printJob.print();
5638       } catch (Exception PrintException)
5639       {
5640         PrintException.printStackTrace();
5641       }
5642     }
5643   }
5644 }