src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.jbgui.GAlignFrame;
  85 import jalview.schemes.ColourSchemeI;
  86 import jalview.schemes.ColourSchemes;
  87 import jalview.schemes.ResidueColourScheme;
  88 import jalview.schemes.TCoffeeColourScheme;
  89 import jalview.util.MessageManager;
  90 import jalview.viewmodel.AlignmentViewport;
  91 import jalview.viewmodel.ViewportRanges;
  92 import jalview.ws.DBRefFetcher;
  93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  94 import jalview.ws.jws1.Discoverer;
  95 import jalview.ws.jws2.Jws2Discoverer;
  96 import jalview.ws.jws2.jabaws2.Jws2Instance;
  97 import jalview.ws.seqfetcher.DbSourceProxy;
  98
  99 import java.awt.BorderLayout;
 100 import java.awt.Component;
 101 import java.awt.Rectangle;
 102 import java.awt.Toolkit;
 103 import java.awt.datatransfer.Clipboard;
 104 import java.awt.datatransfer.DataFlavor;
 105 import java.awt.datatransfer.StringSelection;
 106 import java.awt.datatransfer.Transferable;
 107 import java.awt.dnd.DnDConstants;
 108 import java.awt.dnd.DropTargetDragEvent;
 109 import java.awt.dnd.DropTargetDropEvent;
 110 import java.awt.dnd.DropTargetEvent;
 111 import java.awt.dnd.DropTargetListener;
 112 import java.awt.event.ActionEvent;
 113 import java.awt.event.ActionListener;
 114 import java.awt.event.FocusAdapter;
 115 import java.awt.event.FocusEvent;
 116 import java.awt.event.ItemEvent;
 117 import java.awt.event.ItemListener;
 118 import java.awt.event.KeyAdapter;
 119 import java.awt.event.KeyEvent;
 120 import java.awt.event.MouseEvent;
 121 import java.awt.print.PageFormat;
 122 import java.awt.print.PrinterJob;
 123 import java.beans.PropertyChangeEvent;
 124 import java.io.File;
 125 import java.io.FileWriter;
 126 import java.io.PrintWriter;
 127 import java.net.URL;
 128 import java.util.ArrayList;
 129 import java.util.Arrays;
 130 import java.util.Deque;
 131 import java.util.Enumeration;
 132 import java.util.Hashtable;
 133 import java.util.List;
 134 import java.util.Vector;
 135
 136 import javax.swing.JCheckBoxMenuItem;
 137 import javax.swing.JEditorPane;
 138 import javax.swing.JInternalFrame;
 139 import javax.swing.JLayeredPane;
 140 import javax.swing.JMenu;
 141 import javax.swing.JMenuItem;
 142 import javax.swing.JScrollPane;
 143 import javax.swing.SwingUtilities;
 144
 145 /**
 146  * DOCUMENT ME!
 147  *
 148  * @author $author$
 149  * @version $Revision$
 150  */
 151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 152         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 153 {
 154
 155   public static final int DEFAULT_WIDTH = 700;
 156
 157   public static final int DEFAULT_HEIGHT = 500;
 158
 159   /*
 160    * The currently displayed panel (selected tabbed view if more than one)
 161    */
 162   public AlignmentPanel alignPanel;
 163
 164   AlignViewport viewport;
 165
 166   ViewportRanges vpRanges;
 167
 168   public AlignViewControllerI avc;
 169
 170   List<AlignmentPanel> alignPanels = new ArrayList<>();
 171
 172   /**
 173    * Last format used to load or save alignments in this window
 174    */
 175   FileFormatI currentFileFormat = null;
 176
 177   /**
 178    * Current filename for this alignment
 179    */
 180   String fileName = null;
 181
 182   /**
 183    * Creates a new AlignFrame object with specific width and height.
 184    *
 185    * @param al
 186    * @param width
 187    * @param height
 188    */
 189   public AlignFrame(AlignmentI al, int width, int height)
 190   {
 191     this(al, null, width, height);
 192   }
 193
 194   /**
 195    * Creates a new AlignFrame object with specific width, height and
 196    * sequenceSetId
 197    *
 198    * @param al
 199    * @param width
 200    * @param height
 201    * @param sequenceSetId
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height,
 204           String sequenceSetId)
 205   {
 206     this(al, null, width, height, sequenceSetId);
 207   }
 208
 209   /**
 210    * Creates a new AlignFrame object with specific width, height and
 211    * sequenceSetId
 212    *
 213    * @param al
 214    * @param width
 215    * @param height
 216    * @param sequenceSetId
 217    * @param viewId
 218    */
 219   public AlignFrame(AlignmentI al, int width, int height,
 220           String sequenceSetId, String viewId)
 221   {
 222     this(al, null, width, height, sequenceSetId, viewId);
 223   }
 224
 225   /**
 226    * new alignment window with hidden columns
 227    *
 228    * @param al
 229    *          AlignmentI
 230    * @param hiddenColumns
 231    *          ColumnSelection or null
 232    * @param width
 233    *          Width of alignment frame
 234    * @param height
 235    *          height of frame.
 236    */
 237   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 238           int width, int height)
 239   {
 240     this(al, hiddenColumns, width, height, null);
 241   }
 242
 243   /**
 244    * Create alignment frame for al with hiddenColumns, a specific width and
 245    * height, and specific sequenceId
 246    *
 247    * @param al
 248    * @param hiddenColumns
 249    * @param width
 250    * @param height
 251    * @param sequenceSetId
 252    *          (may be null)
 253    */
 254   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 255           int width, int height, String sequenceSetId)
 256   {
 257     this(al, hiddenColumns, width, height, sequenceSetId, null);
 258   }
 259
 260   /**
 261    * Create alignment frame for al with hiddenColumns, a specific width and
 262    * height, and specific sequenceId
 263    *
 264    * @param al
 265    * @param hiddenColumns
 266    * @param width
 267    * @param height
 268    * @param sequenceSetId
 269    *          (may be null)
 270    * @param viewId
 271    *          (may be null)
 272    */
 273   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 274           int width, int height, String sequenceSetId, String viewId)
 275   {
 276     setSize(width, height);
 277
 278     if (al.getDataset() == null)
 279     {
 280       al.setDataset(null);
 281     }
 282
 283     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 284
 285     alignPanel = new AlignmentPanel(this, viewport);
 286
 287     addAlignmentPanel(alignPanel, true);
 288     init();
 289   }
 290
 291   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 292           HiddenColumns hiddenColumns, int width, int height)
 293   {
 294     setSize(width, height);
 295
 296     if (al.getDataset() == null)
 297     {
 298       al.setDataset(null);
 299     }
 300
 301     viewport = new AlignViewport(al, hiddenColumns);
 302
 303     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 304     {
 305       viewport.hideSequence(hiddenSeqs);
 306     }
 307     alignPanel = new AlignmentPanel(this, viewport);
 308     addAlignmentPanel(alignPanel, true);
 309     init();
 310   }
 311
 312   /**
 313    * Make a new AlignFrame from existing alignmentPanels
 314    *
 315    * @param ap
 316    *          AlignmentPanel
 317    * @param av
 318    *          AlignViewport
 319    */
 320   public AlignFrame(AlignmentPanel ap)
 321   {
 322     viewport = ap.av;
 323     alignPanel = ap;
 324     addAlignmentPanel(ap, false);
 325     init();
 326   }
 327
 328   /**
 329    * initalise the alignframe from the underlying viewport data and the
 330    * configurations
 331    */
 332   void init()
 333   {
 334     if (!Jalview.isHeadlessMode())
 335     {
 336       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 337     }
 338
 339     vpRanges = viewport.getRanges();
 340     avc = new jalview.controller.AlignViewController(this, viewport,
 341             alignPanel);
 342     if (viewport.getAlignmentConservationAnnotation() == null)
 343     {
 344       // BLOSUM62Colour.setEnabled(false);
 345       conservationMenuItem.setEnabled(false);
 346       modifyConservation.setEnabled(false);
 347       // PIDColour.setEnabled(false);
 348       // abovePIDThreshold.setEnabled(false);
 349       // modifyPID.setEnabled(false);
 350     }
 351
 352     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 353             "No sort");
 354
 355     if (sortby.equals("Id"))
 356     {
 357       sortIDMenuItem_actionPerformed(null);
 358     }
 359     else if (sortby.equals("Pairwise Identity"))
 360     {
 361       sortPairwiseMenuItem_actionPerformed(null);
 362     }
 363
 364     this.alignPanel.av
 365             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 366
 367     setMenusFromViewport(viewport);
 368     buildSortByAnnotationScoresMenu();
 369     calculateTree.addActionListener(new ActionListener()
 370     {
 371
 372       @Override
 373       public void actionPerformed(ActionEvent e)
 374       {
 375         openTreePcaDialog();
 376       }
 377     });
 378     buildColourMenu();
 379
 380     if (Desktop.desktop != null)
 381     {
 382       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 383       addServiceListeners();
 384       setGUINucleotide();
 385     }
 386
 387     if (viewport.getWrapAlignment())
 388     {
 389       wrapMenuItem_actionPerformed(null);
 390     }
 391
 392     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 393     {
 394       this.overviewMenuItem_actionPerformed(null);
 395     }
 396
 397     addKeyListener();
 398
 399     final List<AlignmentPanel> selviews = new ArrayList<>();
 400     final List<AlignmentPanel> origview = new ArrayList<>();
 401     final String menuLabel = MessageManager
 402             .getString("label.copy_format_from");
 403     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 404             new ViewSetProvider()
 405             {
 406
 407               @Override
 408               public AlignmentPanel[] getAllAlignmentPanels()
 409               {
 410                 origview.clear();
 411                 origview.add(alignPanel);
 412                 // make an array of all alignment panels except for this one
 413                 List<AlignmentPanel> aps = new ArrayList<>(
 414                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 415                 aps.remove(AlignFrame.this.alignPanel);
 416                 return aps.toArray(new AlignmentPanel[aps.size()]);
 417               }
 418             }, selviews, new ItemListener()
 419             {
 420
 421               @Override
 422               public void itemStateChanged(ItemEvent e)
 423               {
 424                 if (origview.size() > 0)
 425                 {
 426                   final AlignmentPanel ap = origview.get(0);
 427
 428                   /*
 429                    * Copy the ViewStyle of the selected panel to 'this one'.
 430                    * Don't change value of 'scaleProteinAsCdna' unless copying
 431                    * from a SplitFrame.
 432                    */
 433                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 434                           .getViewStyle();
 435                   boolean fromSplitFrame = selviews.get(0)
 436                           .getAlignViewport().getCodingComplement() != null;
 437                   if (!fromSplitFrame)
 438                   {
 439                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 440                             .getViewStyle().isScaleProteinAsCdna());
 441                   }
 442                   ap.getAlignViewport().setViewStyle(vs);
 443
 444                   /*
 445                    * Also rescale ViewStyle of SplitFrame complement if there is
 446                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 447                    * the whole ViewStyle (allow cDNA protein to have different
 448                    * fonts)
 449                    */
 450                   AlignViewportI complement = ap.getAlignViewport()
 451                           .getCodingComplement();
 452                   if (complement != null && vs.isScaleProteinAsCdna())
 453                   {
 454                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 455                     ((SplitFrame) af.getSplitViewContainer())
 456                             .adjustLayout();
 457                     af.setMenusForViewport();
 458                   }
 459
 460                   ap.updateLayout();
 461                   ap.setSelected(true);
 462                   ap.alignFrame.setMenusForViewport();
 463
 464                 }
 465               }
 466             });
 467     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 468             .indexOf("devel") > -1
 469             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 470                     .indexOf("test") > -1)
 471     {
 472       formatMenu.add(vsel);
 473     }
 474     addFocusListener(new FocusAdapter()
 475     {
 476       @Override
 477       public void focusGained(FocusEvent e)
 478       {
 479         Jalview.setCurrentAlignFrame(AlignFrame.this);
 480       }
 481     });
 482
 483   }
 484
 485   /**
 486    * Change the filename and format for the alignment, and enable the 'reload'
 487    * button functionality.
 488    *
 489    * @param file
 490    *          valid filename
 491    * @param format
 492    *          format of file
 493    */
 494   public void setFileName(String file, FileFormatI format)
 495   {
 496     fileName = file;
 497     setFileFormat(format);
 498     reload.setEnabled(true);
 499   }
 500
 501   /**
 502    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 503    * events
 504    */
 505   void addKeyListener()
 506   {
 507     addKeyListener(new KeyAdapter()
 508     {
 509       @Override
 510       public void keyPressed(KeyEvent evt)
 511       {
 512         if (viewport.cursorMode
 513                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 514                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 515                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 516                 && Character.isDigit(evt.getKeyChar()))
 517         {
 518           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 519         }
 520
 521         switch (evt.getKeyCode())
 522         {
 523
 524         case 27: // escape key
 525           deselectAllSequenceMenuItem_actionPerformed(null);
 526
 527           break;
 528
 529         case KeyEvent.VK_DOWN:
 530           if (evt.isAltDown() || !viewport.cursorMode)
 531           {
 532             moveSelectedSequences(false);
 533           }
 534           if (viewport.cursorMode)
 535           {
 536             alignPanel.getSeqPanel().moveCursor(0, 1);
 537           }
 538           break;
 539
 540         case KeyEvent.VK_UP:
 541           if (evt.isAltDown() || !viewport.cursorMode)
 542           {
 543             moveSelectedSequences(true);
 544           }
 545           if (viewport.cursorMode)
 546           {
 547             alignPanel.getSeqPanel().moveCursor(0, -1);
 548           }
 549
 550           break;
 551
 552         case KeyEvent.VK_LEFT:
 553           if (evt.isAltDown() || !viewport.cursorMode)
 554           {
 555             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 556           }
 557           else
 558           {
 559             alignPanel.getSeqPanel().moveCursor(-1, 0);
 560           }
 561
 562           break;
 563
 564         case KeyEvent.VK_RIGHT:
 565           if (evt.isAltDown() || !viewport.cursorMode)
 566           {
 567             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 568           }
 569           else
 570           {
 571             alignPanel.getSeqPanel().moveCursor(1, 0);
 572           }
 573           break;
 574
 575         case KeyEvent.VK_SPACE:
 576           if (viewport.cursorMode)
 577           {
 578             alignPanel.getSeqPanel().insertGapAtCursor(
 579                     evt.isControlDown() || evt.isShiftDown()
 580                             || evt.isAltDown());
 581           }
 582           break;
 583
 584         // case KeyEvent.VK_A:
 585         // if (viewport.cursorMode)
 586         // {
 587         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 588         // //System.out.println("A");
 589         // }
 590         // break;
 591         /*
 592          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 593          * System.out.println("closing bracket"); } break;
 594          */
 595         case KeyEvent.VK_DELETE:
 596         case KeyEvent.VK_BACK_SPACE:
 597           if (!viewport.cursorMode)
 598           {
 599             cut_actionPerformed(null);
 600           }
 601           else
 602           {
 603             alignPanel.getSeqPanel().deleteGapAtCursor(
 604                     evt.isControlDown() || evt.isShiftDown()
 605                             || evt.isAltDown());
 606           }
 607
 608           break;
 609
 610         case KeyEvent.VK_S:
 611           if (viewport.cursorMode)
 612           {
 613             alignPanel.getSeqPanel().setCursorRow();
 614           }
 615           break;
 616         case KeyEvent.VK_C:
 617           if (viewport.cursorMode && !evt.isControlDown())
 618           {
 619             alignPanel.getSeqPanel().setCursorColumn();
 620           }
 621           break;
 622         case KeyEvent.VK_P:
 623           if (viewport.cursorMode)
 624           {
 625             alignPanel.getSeqPanel().setCursorPosition();
 626           }
 627           break;
 628
 629         case KeyEvent.VK_ENTER:
 630         case KeyEvent.VK_COMMA:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setCursorRowAndColumn();
 634           }
 635           break;
 636
 637         case KeyEvent.VK_Q:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 641           }
 642           break;
 643         case KeyEvent.VK_M:
 644           if (viewport.cursorMode)
 645           {
 646             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 647           }
 648           break;
 649
 650         case KeyEvent.VK_F2:
 651           viewport.cursorMode = !viewport.cursorMode;
 652           statusBar.setText(MessageManager.formatMessage(
 653                   "label.keyboard_editing_mode",
 654                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 655           if (viewport.cursorMode)
 656           {
 657             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 658                     .getStartRes();
 659             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 660                     .getStartSeq();
 661           }
 662           alignPanel.getSeqPanel().seqCanvas.repaint();
 663           break;
 664
 665         case KeyEvent.VK_F1:
 666           try
 667           {
 668             Help.showHelpWindow();
 669           } catch (Exception ex)
 670           {
 671             ex.printStackTrace();
 672           }
 673           break;
 674         case KeyEvent.VK_H:
 675         {
 676           boolean toggleSeqs = !evt.isControlDown();
 677           boolean toggleCols = !evt.isShiftDown();
 678           toggleHiddenRegions(toggleSeqs, toggleCols);
 679           break;
 680         }
 681         case KeyEvent.VK_B:
 682         {
 683           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 684           boolean modifyExisting = true; // always modify, don't clear
 685                                          // evt.isShiftDown();
 686           boolean invertHighlighted = evt.isAltDown();
 687           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 688                   toggleSel);
 689           break;
 690         }
 691         case KeyEvent.VK_PAGE_UP:
 692           if (viewport.getWrapAlignment())
 693           {
 694             vpRanges.scrollUp(true);
 695           }
 696           else
 697           {
 698             vpRanges.pageUp();
 699           }
 700           break;
 701         case KeyEvent.VK_PAGE_DOWN:
 702           if (viewport.getWrapAlignment())
 703           {
 704             vpRanges.scrollUp(false);
 705           }
 706           else
 707           {
 708             vpRanges.pageDown();
 709           }
 710           break;
 711         }
 712       }
 713
 714       @Override
 715       public void keyReleased(KeyEvent evt)
 716       {
 717         switch (evt.getKeyCode())
 718         {
 719         case KeyEvent.VK_LEFT:
 720           if (evt.isAltDown() || !viewport.cursorMode)
 721           {
 722             viewport.firePropertyChange("alignment", null, viewport
 723                     .getAlignment().getSequences());
 724           }
 725           break;
 726
 727         case KeyEvent.VK_RIGHT:
 728           if (evt.isAltDown() || !viewport.cursorMode)
 729           {
 730             viewport.firePropertyChange("alignment", null, viewport
 731                     .getAlignment().getSequences());
 732           }
 733           break;
 734         }
 735       }
 736     });
 737   }
 738
 739   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 740   {
 741     ap.alignFrame = this;
 742     avc = new jalview.controller.AlignViewController(this, viewport,
 743             alignPanel);
 744
 745     alignPanels.add(ap);
 746
 747     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 748
 749     int aSize = alignPanels.size();
 750
 751     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 752
 753     if (aSize == 1 && ap.av.viewName == null)
 754     {
 755       this.getContentPane().add(ap, BorderLayout.CENTER);
 756     }
 757     else
 758     {
 759       if (aSize == 2)
 760       {
 761         setInitialTabVisible();
 762       }
 763
 764       expandViews.setEnabled(true);
 765       gatherViews.setEnabled(true);
 766       tabbedPane.addTab(ap.av.viewName, ap);
 767
 768       ap.setVisible(false);
 769     }
 770
 771     if (newPanel)
 772     {
 773       if (ap.av.isPadGaps())
 774       {
 775         ap.av.getAlignment().padGaps();
 776       }
 777       ap.av.updateConservation(ap);
 778       ap.av.updateConsensus(ap);
 779       ap.av.updateStrucConsensus(ap);
 780     }
 781   }
 782
 783   public void setInitialTabVisible()
 784   {
 785     expandViews.setEnabled(true);
 786     gatherViews.setEnabled(true);
 787     tabbedPane.setVisible(true);
 788     AlignmentPanel first = alignPanels.get(0);
 789     tabbedPane.addTab(first.av.viewName, first);
 790     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 791   }
 792
 793   public AlignViewport getViewport()
 794   {
 795     return viewport;
 796   }
 797
 798   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 799   private void addServiceListeners()
 800   {
 801     final java.beans.PropertyChangeListener thisListener;
 802     Desktop.instance.addJalviewPropertyChangeListener("services",
 803             thisListener = new java.beans.PropertyChangeListener()
 804             {
 805               @Override
 806               public void propertyChange(PropertyChangeEvent evt)
 807               {
 808                 // // System.out.println("Discoverer property change.");
 809                 // if (evt.getPropertyName().equals("services"))
 810                 {
 811                   SwingUtilities.invokeLater(new Runnable()
 812                   {
 813
 814                     @Override
 815                     public void run()
 816                     {
 817                       System.err
 818                               .println("Rebuild WS Menu for service change");
 819                       BuildWebServiceMenu();
 820                     }
 821
 822                   });
 823                 }
 824               }
 825             });
 826     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 827     {
 828       @Override
 829       public void internalFrameClosed(
 830               javax.swing.event.InternalFrameEvent evt)
 831       {
 832         // System.out.println("deregistering discoverer listener");
 833         Desktop.instance.removeJalviewPropertyChangeListener("services",
 834                 thisListener);
 835         closeMenuItem_actionPerformed(true);
 836       };
 837     });
 838     // Finally, build the menu once to get current service state
 839     new Thread(new Runnable()
 840     {
 841       @Override
 842       public void run()
 843       {
 844         BuildWebServiceMenu();
 845       }
 846     }).start();
 847   }
 848
 849   /**
 850    * Configure menu items that vary according to whether the alignment is
 851    * nucleotide or protein
 852    */
 853   public void setGUINucleotide()
 854   {
 855     AlignmentI al = getViewport().getAlignment();
 856     boolean nucleotide = al.isNucleotide();
 857
 858     showTranslation.setVisible(nucleotide);
 859     showReverse.setVisible(nucleotide);
 860     showReverseComplement.setVisible(nucleotide);
 861     conservationMenuItem.setEnabled(!nucleotide);
 862     modifyConservation.setEnabled(!nucleotide
 863             && conservationMenuItem.isSelected());
 864     showGroupConservation.setEnabled(!nucleotide);
 865
 866     showComplementMenuItem.setText(nucleotide ? MessageManager
 867             .getString("label.protein") : MessageManager
 868             .getString("label.nucleotide"));
 869   }
 870
 871   /**
 872    * set up menus for the current viewport. This may be called after any
 873    * operation that affects the data in the current view (selection changed,
 874    * etc) to update the menus to reflect the new state.
 875    */
 876   @Override
 877   public void setMenusForViewport()
 878   {
 879     setMenusFromViewport(viewport);
 880   }
 881
 882   /**
 883    * Need to call this method when tabs are selected for multiple views, or when
 884    * loading from Jalview2XML.java
 885    *
 886    * @param av
 887    *          AlignViewport
 888    */
 889   void setMenusFromViewport(AlignViewport av)
 890   {
 891     padGapsMenuitem.setSelected(av.isPadGaps());
 892     colourTextMenuItem.setSelected(av.isShowColourText());
 893     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 894     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 895     conservationMenuItem.setSelected(av.getConservationSelected());
 896     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 897     seqLimits.setSelected(av.getShowJVSuffix());
 898     idRightAlign.setSelected(av.isRightAlignIds());
 899     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 900     renderGapsMenuItem.setSelected(av.isRenderGaps());
 901     wrapMenuItem.setSelected(av.getWrapAlignment());
 902     scaleAbove.setVisible(av.getWrapAlignment());
 903     scaleLeft.setVisible(av.getWrapAlignment());
 904     scaleRight.setVisible(av.getWrapAlignment());
 905     annotationPanelMenuItem.setState(av.isShowAnnotation());
 906     /*
 907      * Show/hide annotations only enabled if annotation panel is shown
 908      */
 909     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 910     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 911     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 912     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 913     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 914     viewTextMenuItem.setSelected(av.getShowText());
 915     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 916     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 917     showGroupConservation.setSelected(av.isShowGroupConservation());
 918     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 919     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 920     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 921
 922     ColourMenuHelper.setColourSelected(colourMenu,
 923             av.getGlobalColourScheme());
 924
 925     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 926     hiddenMarkers.setState(av.getShowHiddenMarkers());
 927     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 928     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 929     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 930     autoCalculate.setSelected(av.autoCalculateConsensus);
 931     sortByTree.setSelected(av.sortByTree);
 932     listenToViewSelections.setSelected(av.followSelection);
 933
 934     showProducts.setEnabled(canShowProducts());
 935     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 936
 937     updateEditMenuBar();
 938   }
 939
 940   /**
 941    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 942    *
 943    * @param b
 944    */
 945   public void setGroovyEnabled(boolean b)
 946   {
 947     runGroovy.setEnabled(b);
 948   }
 949
 950   private IProgressIndicator progressBar;
 951
 952   /*
 953    * (non-Javadoc)
 954    *
 955    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 956    */
 957   @Override
 958   public void setProgressBar(String message, long id)
 959   {
 960     progressBar.setProgressBar(message, id);
 961   }
 962
 963   @Override
 964   public void registerHandler(final long id,
 965           final IProgressIndicatorHandler handler)
 966   {
 967     progressBar.registerHandler(id, handler);
 968   }
 969
 970   /**
 971    *
 972    * @return true if any progress bars are still active
 973    */
 974   @Override
 975   public boolean operationInProgress()
 976   {
 977     return progressBar.operationInProgress();
 978   }
 979
 980   @Override
 981   public void setStatus(String text)
 982   {
 983     statusBar.setText(text);
 984   }
 985
 986   /*
 987    * Added so Castor Mapping file can obtain Jalview Version
 988    */
 989   public String getVersion()
 990   {
 991     return jalview.bin.Cache.getProperty("VERSION");
 992   }
 993
 994   public FeatureRenderer getFeatureRenderer()
 995   {
 996     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 997   }
 998
 999   @Override
1000   public void fetchSequence_actionPerformed(ActionEvent e)
1001   {
1002     new jalview.gui.SequenceFetcher(this);
1003   }
1004
1005   @Override
1006   public void addFromFile_actionPerformed(ActionEvent e)
1007   {
1008     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1009   }
1010
1011   @Override
1012   public void reload_actionPerformed(ActionEvent e)
1013   {
1014     if (fileName != null)
1015     {
1016       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1017       // originating file's format
1018       // TODO: work out how to recover feature settings for correct view(s) when
1019       // file is reloaded.
1020       if (FileFormat.Jalview.equals(currentFileFormat))
1021       {
1022         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1023         for (int i = 0; i < frames.length; i++)
1024         {
1025           if (frames[i] instanceof AlignFrame && frames[i] != this
1026                   && ((AlignFrame) frames[i]).fileName != null
1027                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1028           {
1029             try
1030             {
1031               frames[i].setSelected(true);
1032               Desktop.instance.closeAssociatedWindows();
1033             } catch (java.beans.PropertyVetoException ex)
1034             {
1035             }
1036           }
1037
1038         }
1039         Desktop.instance.closeAssociatedWindows();
1040
1041         FileLoader loader = new FileLoader();
1042         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1043                 : DataSourceType.FILE;
1044         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1045       }
1046       else
1047       {
1048         Rectangle bounds = this.getBounds();
1049
1050         FileLoader loader = new FileLoader();
1051         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1052                 : DataSourceType.FILE;
1053         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1054                 protocol, currentFileFormat);
1055
1056         newframe.setBounds(bounds);
1057         if (featureSettings != null && featureSettings.isShowing())
1058         {
1059           final Rectangle fspos = featureSettings.frame.getBounds();
1060           // TODO: need a 'show feature settings' function that takes bounds -
1061           // need to refactor Desktop.addFrame
1062           newframe.featureSettings_actionPerformed(null);
1063           final FeatureSettings nfs = newframe.featureSettings;
1064           SwingUtilities.invokeLater(new Runnable()
1065           {
1066             @Override
1067             public void run()
1068             {
1069               nfs.frame.setBounds(fspos);
1070             }
1071           });
1072           this.featureSettings.close();
1073           this.featureSettings = null;
1074         }
1075         this.closeMenuItem_actionPerformed(true);
1076       }
1077     }
1078   }
1079
1080   @Override
1081   public void addFromText_actionPerformed(ActionEvent e)
1082   {
1083     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1084             .getAlignPanel());
1085   }
1086
1087   @Override
1088   public void addFromURL_actionPerformed(ActionEvent e)
1089   {
1090     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1091   }
1092
1093   @Override
1094   public void save_actionPerformed(ActionEvent e)
1095   {
1096     if (fileName == null || (currentFileFormat == null)
1097             || fileName.startsWith("http"))
1098     {
1099       saveAs_actionPerformed(null);
1100     }
1101     else
1102     {
1103       saveAlignment(fileName, currentFileFormat);
1104     }
1105   }
1106
1107   /**
1108    * DOCUMENT ME!
1109    *
1110    * @param e
1111    *          DOCUMENT ME!
1112    */
1113   @Override
1114   public void saveAs_actionPerformed(ActionEvent e)
1115   {
1116     String format = currentFileFormat == null ? null : currentFileFormat
1117             .getName();
1118     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1119             Cache.getProperty("LAST_DIRECTORY"), format);
1120
1121     chooser.setFileView(new JalviewFileView());
1122     chooser.setDialogTitle(MessageManager
1123             .getString("label.save_alignment_to_file"));
1124     chooser.setToolTipText(MessageManager.getString("action.save"));
1125
1126     int value = chooser.showSaveDialog(this);
1127
1128     if (value == JalviewFileChooser.APPROVE_OPTION)
1129     {
1130       currentFileFormat = chooser.getSelectedFormat();
1131       while (currentFileFormat == null)
1132       {
1133         JvOptionPane
1134                 .showInternalMessageDialog(
1135                         Desktop.desktop,
1136                         MessageManager
1137                                 .getString("label.select_file_format_before_saving"),
1138                         MessageManager
1139                                 .getString("label.file_format_not_specified"),
1140                         JvOptionPane.WARNING_MESSAGE);
1141         currentFileFormat = chooser.getSelectedFormat();
1142         value = chooser.showSaveDialog(this);
1143         if (value != JalviewFileChooser.APPROVE_OPTION)
1144         {
1145           return;
1146         }
1147       }
1148
1149       fileName = chooser.getSelectedFile().getPath();
1150
1151       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1152
1153       Cache.setProperty("LAST_DIRECTORY", fileName);
1154       saveAlignment(fileName, currentFileFormat);
1155     }
1156   }
1157
1158   public boolean saveAlignment(String file, FileFormatI format)
1159   {
1160     boolean success = true;
1161
1162     if (FileFormat.Jalview.equals(format))
1163     {
1164       String shortName = title;
1165
1166       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1167       {
1168         shortName = shortName.substring(shortName
1169                 .lastIndexOf(java.io.File.separatorChar) + 1);
1170       }
1171
1172       success = new Jalview2XML().saveAlignment(this, file, shortName);
1173
1174       statusBar.setText(MessageManager.formatMessage(
1175               "label.successfully_saved_to_file_in_format", new Object[] {
1176                   fileName, format }));
1177
1178     }
1179     else
1180     {
1181       AlignmentExportData exportData = getAlignmentForExport(format,
1182               viewport, null);
1183       if (exportData.getSettings().isCancelled())
1184       {
1185         return false;
1186       }
1187       FormatAdapter f = new FormatAdapter(alignPanel,
1188               exportData.getSettings());
1189       String output = f.formatSequences(
1190               format,
1191               exportData.getAlignment(), // class cast exceptions will
1192               // occur in the distant future
1193               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1194               f.getCacheSuffixDefault(format), viewport.getAlignment()
1195                       .getHiddenColumns());
1196
1197       if (output == null)
1198       {
1199         success = false;
1200       }
1201       else
1202       {
1203         try
1204         {
1205           PrintWriter out = new PrintWriter(new FileWriter(file));
1206
1207           out.print(output);
1208           out.close();
1209           this.setTitle(file);
1210           statusBar.setText(MessageManager.formatMessage(
1211                   "label.successfully_saved_to_file_in_format",
1212                   new Object[] { fileName, format.getName() }));
1213         } catch (Exception ex)
1214         {
1215           success = false;
1216           ex.printStackTrace();
1217         }
1218       }
1219     }
1220
1221     if (!success)
1222     {
1223       JvOptionPane.showInternalMessageDialog(this, MessageManager
1224               .formatMessage("label.couldnt_save_file",
1225                       new Object[] { fileName }), MessageManager
1226               .getString("label.error_saving_file"),
1227               JvOptionPane.WARNING_MESSAGE);
1228     }
1229
1230     return success;
1231   }
1232
1233   private void warningMessage(String warning, String title)
1234   {
1235     if (new jalview.util.Platform().isHeadless())
1236     {
1237       System.err.println("Warning: " + title + "\nWarning: " + warning);
1238
1239     }
1240     else
1241     {
1242       JvOptionPane.showInternalMessageDialog(this, warning, title,
1243               JvOptionPane.WARNING_MESSAGE);
1244     }
1245     return;
1246   }
1247
1248   /**
1249    * DOCUMENT ME!
1250    *
1251    * @param e
1252    *          DOCUMENT ME!
1253    */
1254   @Override
1255   protected void outputText_actionPerformed(ActionEvent e)
1256   {
1257     FileFormatI fileFormat = FileFormats.getInstance().forName(
1258             e.getActionCommand());
1259     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1260             viewport, null);
1261     if (exportData.getSettings().isCancelled())
1262     {
1263       return;
1264     }
1265     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1266     cap.setForInput(null);
1267     try
1268     {
1269       FileFormatI format = fileFormat;
1270       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1271               .formatSequences(format, exportData.getAlignment(),
1272                       exportData.getOmitHidden(),
1273  exportData
1274                               .getStartEndPostions(), viewport
1275                               .getAlignment().getHiddenColumns()));
1276       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1277               "label.alignment_output_command",
1278               new Object[] { e.getActionCommand() }), 600, 500);
1279     } catch (OutOfMemoryError oom)
1280     {
1281       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1282       cap.dispose();
1283     }
1284
1285   }
1286
1287   public static AlignmentExportData getAlignmentForExport(
1288           FileFormatI format, AlignViewportI viewport,
1289           AlignExportSettingI exportSettings)
1290   {
1291     AlignmentI alignmentToExport = null;
1292     AlignExportSettingI settings = exportSettings;
1293     String[] omitHidden = null;
1294
1295     HiddenSequences hiddenSeqs = viewport.getAlignment()
1296             .getHiddenSequences();
1297
1298     alignmentToExport = viewport.getAlignment();
1299
1300     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1301     if (settings == null)
1302     {
1303       settings = new AlignExportSettings(hasHiddenSeqs,
1304               viewport.hasHiddenColumns(), format);
1305     }
1306     // settings.isExportAnnotations();
1307
1308     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1309     {
1310       omitHidden = viewport.getViewAsString(false,
1311               settings.isExportHiddenSequences());
1312     }
1313
1314     int[] alignmentStartEnd = new int[2];
1315     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1316     {
1317       alignmentToExport = hiddenSeqs.getFullAlignment();
1318     }
1319     else
1320     {
1321       alignmentToExport = viewport.getAlignment();
1322     }
1323     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1324             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1325     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1326             omitHidden, alignmentStartEnd, settings);
1327     return ed;
1328   }
1329
1330   /**
1331    * DOCUMENT ME!
1332    *
1333    * @param e
1334    *          DOCUMENT ME!
1335    */
1336   @Override
1337   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1338   {
1339     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1340     htmlSVG.exportHTML(null);
1341   }
1342
1343   @Override
1344   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1345   {
1346     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1347     bjs.exportHTML(null);
1348   }
1349
1350   public void createImageMap(File file, String image)
1351   {
1352     alignPanel.makePNGImageMap(file, image);
1353   }
1354
1355   /**
1356    * DOCUMENT ME!
1357    *
1358    * @param e
1359    *          DOCUMENT ME!
1360    */
1361   @Override
1362   public void createPNG(File f)
1363   {
1364     alignPanel.makePNG(f);
1365   }
1366
1367   /**
1368    * DOCUMENT ME!
1369    *
1370    * @param e
1371    *          DOCUMENT ME!
1372    */
1373   @Override
1374   public void createEPS(File f)
1375   {
1376     alignPanel.makeEPS(f);
1377   }
1378
1379   @Override
1380   public void createSVG(File f)
1381   {
1382     alignPanel.makeSVG(f);
1383   }
1384
1385   @Override
1386   public void pageSetup_actionPerformed(ActionEvent e)
1387   {
1388     PrinterJob printJob = PrinterJob.getPrinterJob();
1389     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1390   }
1391
1392   /**
1393    * DOCUMENT ME!
1394    *
1395    * @param e
1396    *          DOCUMENT ME!
1397    */
1398   @Override
1399   public void printMenuItem_actionPerformed(ActionEvent e)
1400   {
1401     // Putting in a thread avoids Swing painting problems
1402     PrintThread thread = new PrintThread(alignPanel);
1403     thread.start();
1404   }
1405
1406   @Override
1407   public void exportFeatures_actionPerformed(ActionEvent e)
1408   {
1409     new AnnotationExporter().exportFeatures(alignPanel);
1410   }
1411
1412   @Override
1413   public void exportAnnotations_actionPerformed(ActionEvent e)
1414   {
1415     new AnnotationExporter().exportAnnotations(alignPanel);
1416   }
1417
1418   @Override
1419   public void associatedData_actionPerformed(ActionEvent e)
1420   {
1421     // Pick the tree file
1422     JalviewFileChooser chooser = new JalviewFileChooser(
1423             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1424     chooser.setFileView(new JalviewFileView());
1425     chooser.setDialogTitle(MessageManager
1426             .getString("label.load_jalview_annotations"));
1427     chooser.setToolTipText(MessageManager
1428             .getString("label.load_jalview_annotations"));
1429
1430     int value = chooser.showOpenDialog(null);
1431
1432     if (value == JalviewFileChooser.APPROVE_OPTION)
1433     {
1434       String choice = chooser.getSelectedFile().getPath();
1435       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1436       loadJalviewDataFile(choice, null, null, null);
1437     }
1438
1439   }
1440
1441   /**
1442    * Close the current view or all views in the alignment frame. If the frame
1443    * only contains one view then the alignment will be removed from memory.
1444    *
1445    * @param closeAllTabs
1446    */
1447   @Override
1448   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1449   {
1450     if (alignPanels != null && alignPanels.size() < 2)
1451     {
1452       closeAllTabs = true;
1453     }
1454
1455     try
1456     {
1457       if (alignPanels != null)
1458       {
1459         if (closeAllTabs)
1460         {
1461           if (this.isClosed())
1462           {
1463             // really close all the windows - otherwise wait till
1464             // setClosed(true) is called
1465             for (int i = 0; i < alignPanels.size(); i++)
1466             {
1467               AlignmentPanel ap = alignPanels.get(i);
1468               ap.closePanel();
1469             }
1470           }
1471         }
1472         else
1473         {
1474           closeView(alignPanel);
1475         }
1476       }
1477
1478       if (closeAllTabs)
1479       {
1480         /*
1481          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1482          * be called recursively, with the frame now in 'closed' state
1483          */
1484         this.setClosed(true);
1485       }
1486     } catch (Exception ex)
1487     {
1488       ex.printStackTrace();
1489     }
1490   }
1491
1492   /**
1493    * Close the specified panel and close up tabs appropriately.
1494    *
1495    * @param panelToClose
1496    */
1497   public void closeView(AlignmentPanel panelToClose)
1498   {
1499     int index = tabbedPane.getSelectedIndex();
1500     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1501     alignPanels.remove(panelToClose);
1502     panelToClose.closePanel();
1503     panelToClose = null;
1504
1505     tabbedPane.removeTabAt(closedindex);
1506     tabbedPane.validate();
1507
1508     if (index > closedindex || index == tabbedPane.getTabCount())
1509     {
1510       // modify currently selected tab index if necessary.
1511       index--;
1512     }
1513
1514     this.tabSelectionChanged(index);
1515   }
1516
1517   /**
1518    * DOCUMENT ME!
1519    */
1520   void updateEditMenuBar()
1521   {
1522
1523     if (viewport.getHistoryList().size() > 0)
1524     {
1525       undoMenuItem.setEnabled(true);
1526       CommandI command = viewport.getHistoryList().peek();
1527       undoMenuItem.setText(MessageManager.formatMessage(
1528               "label.undo_command",
1529               new Object[] { command.getDescription() }));
1530     }
1531     else
1532     {
1533       undoMenuItem.setEnabled(false);
1534       undoMenuItem.setText(MessageManager.getString("action.undo"));
1535     }
1536
1537     if (viewport.getRedoList().size() > 0)
1538     {
1539       redoMenuItem.setEnabled(true);
1540
1541       CommandI command = viewport.getRedoList().peek();
1542       redoMenuItem.setText(MessageManager.formatMessage(
1543               "label.redo_command",
1544               new Object[] { command.getDescription() }));
1545     }
1546     else
1547     {
1548       redoMenuItem.setEnabled(false);
1549       redoMenuItem.setText(MessageManager.getString("action.redo"));
1550     }
1551   }
1552
1553   @Override
1554   public void addHistoryItem(CommandI command)
1555   {
1556     if (command.getSize() > 0)
1557     {
1558       viewport.addToHistoryList(command);
1559       viewport.clearRedoList();
1560       updateEditMenuBar();
1561       viewport.updateHiddenColumns();
1562       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1563       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1564       // viewport.getColumnSelection()
1565       // .getHiddenColumns().size() > 0);
1566     }
1567   }
1568
1569   /**
1570    *
1571    * @return alignment objects for all views
1572    */
1573   AlignmentI[] getViewAlignments()
1574   {
1575     if (alignPanels != null)
1576     {
1577       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1578       int i = 0;
1579       for (AlignmentPanel ap : alignPanels)
1580       {
1581         als[i++] = ap.av.getAlignment();
1582       }
1583       return als;
1584     }
1585     if (viewport != null)
1586     {
1587       return new AlignmentI[] { viewport.getAlignment() };
1588     }
1589     return null;
1590   }
1591
1592   /**
1593    * DOCUMENT ME!
1594    *
1595    * @param e
1596    *          DOCUMENT ME!
1597    */
1598   @Override
1599   protected void undoMenuItem_actionPerformed(ActionEvent e)
1600   {
1601     if (viewport.getHistoryList().isEmpty())
1602     {
1603       return;
1604     }
1605     CommandI command = viewport.getHistoryList().pop();
1606     viewport.addToRedoList(command);
1607     command.undoCommand(getViewAlignments());
1608
1609     AlignmentViewport originalSource = getOriginatingSource(command);
1610     updateEditMenuBar();
1611
1612     if (originalSource != null)
1613     {
1614       if (originalSource != viewport)
1615       {
1616         Cache.log
1617                 .warn("Implementation worry: mismatch of viewport origin for undo");
1618       }
1619       originalSource.updateHiddenColumns();
1620       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1621       // null
1622       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1623       // viewport.getColumnSelection()
1624       // .getHiddenColumns().size() > 0);
1625       originalSource.firePropertyChange("alignment", null, originalSource
1626               .getAlignment().getSequences());
1627     }
1628   }
1629
1630   /**
1631    * DOCUMENT ME!
1632    *
1633    * @param e
1634    *          DOCUMENT ME!
1635    */
1636   @Override
1637   protected void redoMenuItem_actionPerformed(ActionEvent e)
1638   {
1639     if (viewport.getRedoList().size() < 1)
1640     {
1641       return;
1642     }
1643
1644     CommandI command = viewport.getRedoList().pop();
1645     viewport.addToHistoryList(command);
1646     command.doCommand(getViewAlignments());
1647
1648     AlignmentViewport originalSource = getOriginatingSource(command);
1649     updateEditMenuBar();
1650
1651     if (originalSource != null)
1652     {
1653
1654       if (originalSource != viewport)
1655       {
1656         Cache.log
1657                 .warn("Implementation worry: mismatch of viewport origin for redo");
1658       }
1659       originalSource.updateHiddenColumns();
1660       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1661       // null
1662       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1663       // viewport.getColumnSelection()
1664       // .getHiddenColumns().size() > 0);
1665       originalSource.firePropertyChange("alignment", null, originalSource
1666               .getAlignment().getSequences());
1667     }
1668   }
1669
1670   AlignmentViewport getOriginatingSource(CommandI command)
1671   {
1672     AlignmentViewport originalSource = null;
1673     // For sequence removal and addition, we need to fire
1674     // the property change event FROM the viewport where the
1675     // original alignment was altered
1676     AlignmentI al = null;
1677     if (command instanceof EditCommand)
1678     {
1679       EditCommand editCommand = (EditCommand) command;
1680       al = editCommand.getAlignment();
1681       List<Component> comps = PaintRefresher.components.get(viewport
1682               .getSequenceSetId());
1683
1684       for (Component comp : comps)
1685       {
1686         if (comp instanceof AlignmentPanel)
1687         {
1688           if (al == ((AlignmentPanel) comp).av.getAlignment())
1689           {
1690             originalSource = ((AlignmentPanel) comp).av;
1691             break;
1692           }
1693         }
1694       }
1695     }
1696
1697     if (originalSource == null)
1698     {
1699       // The original view is closed, we must validate
1700       // the current view against the closed view first
1701       if (al != null)
1702       {
1703         PaintRefresher.validateSequences(al, viewport.getAlignment());
1704       }
1705
1706       originalSource = viewport;
1707     }
1708
1709     return originalSource;
1710   }
1711
1712   /**
1713    * DOCUMENT ME!
1714    *
1715    * @param up
1716    *          DOCUMENT ME!
1717    */
1718   public void moveSelectedSequences(boolean up)
1719   {
1720     SequenceGroup sg = viewport.getSelectionGroup();
1721
1722     if (sg == null)
1723     {
1724       return;
1725     }
1726     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1727             viewport.getHiddenRepSequences(), up);
1728     alignPanel.paintAlignment(true);
1729   }
1730
1731   synchronized void slideSequences(boolean right, int size)
1732   {
1733     List<SequenceI> sg = new ArrayList<>();
1734     if (viewport.cursorMode)
1735     {
1736       sg.add(viewport.getAlignment().getSequenceAt(
1737               alignPanel.getSeqPanel().seqCanvas.cursorY));
1738     }
1739     else if (viewport.getSelectionGroup() != null
1740             && viewport.getSelectionGroup().getSize() != viewport
1741                     .getAlignment().getHeight())
1742     {
1743       sg = viewport.getSelectionGroup().getSequences(
1744               viewport.getHiddenRepSequences());
1745     }
1746
1747     if (sg.size() < 1)
1748     {
1749       return;
1750     }
1751
1752     List<SequenceI> invertGroup = new ArrayList<>();
1753
1754     for (SequenceI seq : viewport.getAlignment().getSequences())
1755     {
1756       if (!sg.contains(seq))
1757       {
1758         invertGroup.add(seq);
1759       }
1760     }
1761
1762     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1763
1764     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1765     for (int i = 0; i < invertGroup.size(); i++)
1766     {
1767       seqs2[i] = invertGroup.get(i);
1768     }
1769
1770     SlideSequencesCommand ssc;
1771     if (right)
1772     {
1773       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1774               size, viewport.getGapCharacter());
1775     }
1776     else
1777     {
1778       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1779               size, viewport.getGapCharacter());
1780     }
1781
1782     int groupAdjustment = 0;
1783     if (ssc.getGapsInsertedBegin() && right)
1784     {
1785       if (viewport.cursorMode)
1786       {
1787         alignPanel.getSeqPanel().moveCursor(size, 0);
1788       }
1789       else
1790       {
1791         groupAdjustment = size;
1792       }
1793     }
1794     else if (!ssc.getGapsInsertedBegin() && !right)
1795     {
1796       if (viewport.cursorMode)
1797       {
1798         alignPanel.getSeqPanel().moveCursor(-size, 0);
1799       }
1800       else
1801       {
1802         groupAdjustment = -size;
1803       }
1804     }
1805
1806     if (groupAdjustment != 0)
1807     {
1808       viewport.getSelectionGroup().setStartRes(
1809               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1810       viewport.getSelectionGroup().setEndRes(
1811               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1812     }
1813
1814     /*
1815      * just extend the last slide command if compatible; but not if in
1816      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1817      */
1818     boolean appendHistoryItem = false;
1819     Deque<CommandI> historyList = viewport.getHistoryList();
1820     boolean inSplitFrame = getSplitViewContainer() != null;
1821     if (!inSplitFrame && historyList != null && historyList.size() > 0
1822             && historyList.peek() instanceof SlideSequencesCommand)
1823     {
1824       appendHistoryItem = ssc
1825               .appendSlideCommand((SlideSequencesCommand) historyList
1826                       .peek());
1827     }
1828
1829     if (!appendHistoryItem)
1830     {
1831       addHistoryItem(ssc);
1832     }
1833
1834     repaint();
1835   }
1836
1837   /**
1838    * DOCUMENT ME!
1839    *
1840    * @param e
1841    *          DOCUMENT ME!
1842    */
1843   @Override
1844   protected void copy_actionPerformed(ActionEvent e)
1845   {
1846     System.gc();
1847     if (viewport.getSelectionGroup() == null)
1848     {
1849       return;
1850     }
1851     // TODO: preserve the ordering of displayed alignment annotation in any
1852     // internal paste (particularly sequence associated annotation)
1853     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1854     String[] omitHidden = null;
1855
1856     if (viewport.hasHiddenColumns())
1857     {
1858       omitHidden = viewport.getViewAsString(true);
1859     }
1860
1861     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1862             seqs, omitHidden, null);
1863
1864     StringSelection ss = new StringSelection(output);
1865
1866     try
1867     {
1868       jalview.gui.Desktop.internalCopy = true;
1869       // Its really worth setting the clipboard contents
1870       // to empty before setting the large StringSelection!!
1871       Toolkit.getDefaultToolkit().getSystemClipboard()
1872               .setContents(new StringSelection(""), null);
1873
1874       Toolkit.getDefaultToolkit().getSystemClipboard()
1875               .setContents(ss, Desktop.instance);
1876     } catch (OutOfMemoryError er)
1877     {
1878       new OOMWarning("copying region", er);
1879       return;
1880     }
1881
1882     ArrayList<int[]> hiddenColumns = null;
1883     if (viewport.hasHiddenColumns())
1884     {
1885       hiddenColumns = new ArrayList<>();
1886       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1887       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1888       for (int[] region : viewport.getAlignment().getHiddenColumns())
1889       {
1890         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1891         {
1892           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1893               region[1] - hiddenOffset });
1894         }
1895       }
1896     }
1897
1898     Desktop.jalviewClipboard = new Object[] { seqs,
1899         viewport.getAlignment().getDataset(), hiddenColumns };
1900     statusBar.setText(MessageManager.formatMessage(
1901             "label.copied_sequences_to_clipboard", new Object[] { Integer
1902                     .valueOf(seqs.length).toString() }));
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void pasteNew_actionPerformed(ActionEvent e)
1913   {
1914     paste(true);
1915   }
1916
1917   /**
1918    * DOCUMENT ME!
1919    *
1920    * @param e
1921    *          DOCUMENT ME!
1922    */
1923   @Override
1924   protected void pasteThis_actionPerformed(ActionEvent e)
1925   {
1926     paste(false);
1927   }
1928
1929   /**
1930    * Paste contents of Jalview clipboard
1931    *
1932    * @param newAlignment
1933    *          true to paste to a new alignment, otherwise add to this.
1934    */
1935   void paste(boolean newAlignment)
1936   {
1937     boolean externalPaste = true;
1938     try
1939     {
1940       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1941       Transferable contents = c.getContents(this);
1942
1943       if (contents == null)
1944       {
1945         return;
1946       }
1947
1948       String str;
1949       FileFormatI format;
1950       try
1951       {
1952         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1953         if (str.length() < 1)
1954         {
1955           return;
1956         }
1957
1958         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1959
1960       } catch (OutOfMemoryError er)
1961       {
1962         new OOMWarning("Out of memory pasting sequences!!", er);
1963         return;
1964       }
1965
1966       SequenceI[] sequences;
1967       boolean annotationAdded = false;
1968       AlignmentI alignment = null;
1969
1970       if (Desktop.jalviewClipboard != null)
1971       {
1972         // The clipboard was filled from within Jalview, we must use the
1973         // sequences
1974         // And dataset from the copied alignment
1975         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1976         // be doubly sure that we create *new* sequence objects.
1977         sequences = new SequenceI[newseq.length];
1978         for (int i = 0; i < newseq.length; i++)
1979         {
1980           sequences[i] = new Sequence(newseq[i]);
1981         }
1982         alignment = new Alignment(sequences);
1983         externalPaste = false;
1984       }
1985       else
1986       {
1987         // parse the clipboard as an alignment.
1988         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1989                 format);
1990         sequences = alignment.getSequencesArray();
1991       }
1992
1993       int alwidth = 0;
1994       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1995       int fgroup = -1;
1996
1997       if (newAlignment)
1998       {
1999
2000         if (Desktop.jalviewClipboard != null)
2001         {
2002           // dataset is inherited
2003           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2004         }
2005         else
2006         {
2007           // new dataset is constructed
2008           alignment.setDataset(null);
2009         }
2010         alwidth = alignment.getWidth() + 1;
2011       }
2012       else
2013       {
2014         AlignmentI pastedal = alignment; // preserve pasted alignment object
2015         // Add pasted sequences and dataset into existing alignment.
2016         alignment = viewport.getAlignment();
2017         alwidth = alignment.getWidth() + 1;
2018         // decide if we need to import sequences from an existing dataset
2019         boolean importDs = Desktop.jalviewClipboard != null
2020                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2021         // importDs==true instructs us to copy over new dataset sequences from
2022         // an existing alignment
2023         Vector newDs = (importDs) ? new Vector() : null; // used to create
2024         // minimum dataset set
2025
2026         for (int i = 0; i < sequences.length; i++)
2027         {
2028           if (importDs)
2029           {
2030             newDs.addElement(null);
2031           }
2032           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2033           // paste
2034           if (importDs && ds != null)
2035           {
2036             if (!newDs.contains(ds))
2037             {
2038               newDs.setElementAt(ds, i);
2039               ds = new Sequence(ds);
2040               // update with new dataset sequence
2041               sequences[i].setDatasetSequence(ds);
2042             }
2043             else
2044             {
2045               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2046             }
2047           }
2048           else
2049           {
2050             // copy and derive new dataset sequence
2051             sequences[i] = sequences[i].deriveSequence();
2052             alignment.getDataset().addSequence(
2053                     sequences[i].getDatasetSequence());
2054             // TODO: avoid creation of duplicate dataset sequences with a
2055             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2056           }
2057           alignment.addSequence(sequences[i]); // merges dataset
2058         }
2059         if (newDs != null)
2060         {
2061           newDs.clear(); // tidy up
2062         }
2063         if (alignment.getAlignmentAnnotation() != null)
2064         {
2065           for (AlignmentAnnotation alan : alignment
2066                   .getAlignmentAnnotation())
2067           {
2068             if (alan.graphGroup > fgroup)
2069             {
2070               fgroup = alan.graphGroup;
2071             }
2072           }
2073         }
2074         if (pastedal.getAlignmentAnnotation() != null)
2075         {
2076           // Add any annotation attached to alignment.
2077           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2078           for (int i = 0; i < alann.length; i++)
2079           {
2080             annotationAdded = true;
2081             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2082             {
2083               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2084               if (newann.graphGroup > -1)
2085               {
2086                 if (newGraphGroups.size() <= newann.graphGroup
2087                         || newGraphGroups.get(newann.graphGroup) == null)
2088                 {
2089                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2090                   {
2091                     newGraphGroups.add(q, null);
2092                   }
2093                   newGraphGroups.set(newann.graphGroup, new Integer(
2094                           ++fgroup));
2095                 }
2096                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2097                         .intValue();
2098               }
2099
2100               newann.padAnnotation(alwidth);
2101               alignment.addAnnotation(newann);
2102             }
2103           }
2104         }
2105       }
2106       if (!newAlignment)
2107       {
2108         // /////
2109         // ADD HISTORY ITEM
2110         //
2111         addHistoryItem(new EditCommand(
2112                 MessageManager.getString("label.add_sequences"),
2113                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2114       }
2115       // Add any annotations attached to sequences
2116       for (int i = 0; i < sequences.length; i++)
2117       {
2118         if (sequences[i].getAnnotation() != null)
2119         {
2120           AlignmentAnnotation newann;
2121           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2122           {
2123             annotationAdded = true;
2124             newann = sequences[i].getAnnotation()[a];
2125             newann.adjustForAlignment();
2126             newann.padAnnotation(alwidth);
2127             if (newann.graphGroup > -1)
2128             {
2129               if (newann.graphGroup > -1)
2130               {
2131                 if (newGraphGroups.size() <= newann.graphGroup
2132                         || newGraphGroups.get(newann.graphGroup) == null)
2133                 {
2134                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2135                   {
2136                     newGraphGroups.add(q, null);
2137                   }
2138                   newGraphGroups.set(newann.graphGroup, new Integer(
2139                           ++fgroup));
2140                 }
2141                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2142                         .intValue();
2143               }
2144             }
2145             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2146             // was
2147             // duplicated
2148             // earlier
2149             alignment
2150                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2151           }
2152         }
2153       }
2154       if (!newAlignment)
2155       {
2156
2157         // propagate alignment changed.
2158         vpRanges.setEndSeq(alignment.getHeight());
2159         if (annotationAdded)
2160         {
2161           // Duplicate sequence annotation in all views.
2162           AlignmentI[] alview = this.getViewAlignments();
2163           for (int i = 0; i < sequences.length; i++)
2164           {
2165             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2166             if (sann == null)
2167             {
2168               continue;
2169             }
2170             for (int avnum = 0; avnum < alview.length; avnum++)
2171             {
2172               if (alview[avnum] != alignment)
2173               {
2174                 // duplicate in a view other than the one with input focus
2175                 int avwidth = alview[avnum].getWidth() + 1;
2176                 // this relies on sann being preserved after we
2177                 // modify the sequence's annotation array for each duplication
2178                 for (int a = 0; a < sann.length; a++)
2179                 {
2180                   AlignmentAnnotation newann = new AlignmentAnnotation(
2181                           sann[a]);
2182                   sequences[i].addAlignmentAnnotation(newann);
2183                   newann.padAnnotation(avwidth);
2184                   alview[avnum].addAnnotation(newann); // annotation was
2185                   // duplicated earlier
2186                   // TODO JAL-1145 graphGroups are not updated for sequence
2187                   // annotation added to several views. This may cause
2188                   // strangeness
2189                   alview[avnum].setAnnotationIndex(newann, a);
2190                 }
2191               }
2192             }
2193           }
2194           buildSortByAnnotationScoresMenu();
2195         }
2196         viewport.firePropertyChange("alignment", null,
2197                 alignment.getSequences());
2198         if (alignPanels != null)
2199         {
2200           for (AlignmentPanel ap : alignPanels)
2201           {
2202             ap.validateAnnotationDimensions(false);
2203           }
2204         }
2205         else
2206         {
2207           alignPanel.validateAnnotationDimensions(false);
2208         }
2209
2210       }
2211       else
2212       {
2213         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2214                 DEFAULT_HEIGHT);
2215         String newtitle = new String("Copied sequences");
2216
2217         if (Desktop.jalviewClipboard != null
2218                 && Desktop.jalviewClipboard[2] != null)
2219         {
2220           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2221           for (int[] region : hc)
2222           {
2223             af.viewport.hideColumns(region[0], region[1]);
2224           }
2225         }
2226
2227         // >>>This is a fix for the moment, until a better solution is
2228         // found!!<<<
2229         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2230                 .transferSettings(
2231                         alignPanel.getSeqPanel().seqCanvas
2232                                 .getFeatureRenderer());
2233
2234         // TODO: maintain provenance of an alignment, rather than just make the
2235         // title a concatenation of operations.
2236         if (!externalPaste)
2237         {
2238           if (title.startsWith("Copied sequences"))
2239           {
2240             newtitle = title;
2241           }
2242           else
2243           {
2244             newtitle = newtitle.concat("- from " + title);
2245           }
2246         }
2247         else
2248         {
2249           newtitle = new String("Pasted sequences");
2250         }
2251
2252         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2253                 DEFAULT_HEIGHT);
2254
2255       }
2256
2257     } catch (Exception ex)
2258     {
2259       ex.printStackTrace();
2260       System.out.println("Exception whilst pasting: " + ex);
2261       // could be anything being pasted in here
2262     }
2263
2264   }
2265
2266   @Override
2267   protected void expand_newalign(ActionEvent e)
2268   {
2269     try
2270     {
2271       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2272               .getAlignment(), -1);
2273       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2274               DEFAULT_HEIGHT);
2275       String newtitle = new String("Flanking alignment");
2276
2277       if (Desktop.jalviewClipboard != null
2278               && Desktop.jalviewClipboard[2] != null)
2279       {
2280         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2281         for (int region[] : hc)
2282         {
2283           af.viewport.hideColumns(region[0], region[1]);
2284         }
2285       }
2286
2287       // >>>This is a fix for the moment, until a better solution is
2288       // found!!<<<
2289       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2290               .transferSettings(
2291                       alignPanel.getSeqPanel().seqCanvas
2292                               .getFeatureRenderer());
2293
2294       // TODO: maintain provenance of an alignment, rather than just make the
2295       // title a concatenation of operations.
2296       {
2297         if (title.startsWith("Copied sequences"))
2298         {
2299           newtitle = title;
2300         }
2301         else
2302         {
2303           newtitle = newtitle.concat("- from " + title);
2304         }
2305       }
2306
2307       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2308
2309     } catch (Exception ex)
2310     {
2311       ex.printStackTrace();
2312       System.out.println("Exception whilst pasting: " + ex);
2313       // could be anything being pasted in here
2314     } catch (OutOfMemoryError oom)
2315     {
2316       new OOMWarning("Viewing flanking region of alignment", oom);
2317     }
2318   }
2319
2320   /**
2321    * DOCUMENT ME!
2322    *
2323    * @param e
2324    *          DOCUMENT ME!
2325    */
2326   @Override
2327   protected void cut_actionPerformed(ActionEvent e)
2328   {
2329     copy_actionPerformed(null);
2330     delete_actionPerformed(null);
2331   }
2332
2333   /**
2334    * DOCUMENT ME!
2335    *
2336    * @param e
2337    *          DOCUMENT ME!
2338    */
2339   @Override
2340   protected void delete_actionPerformed(ActionEvent evt)
2341   {
2342
2343     SequenceGroup sg = viewport.getSelectionGroup();
2344     if (sg == null)
2345     {
2346       return;
2347     }
2348
2349     /*
2350      * If the cut affects all sequences, warn, remove highlighted columns
2351      */
2352     if (sg.getSize() == viewport.getAlignment().getHeight())
2353     {
2354       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2355               .getAlignment().getWidth()) ? true : false;
2356       if (isEntireAlignWidth)
2357       {
2358         int confirm = JvOptionPane.showConfirmDialog(this,
2359                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2360                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2361                 JvOptionPane.OK_CANCEL_OPTION);
2362
2363         if (confirm == JvOptionPane.CANCEL_OPTION
2364                 || confirm == JvOptionPane.CLOSED_OPTION)
2365         {
2366           return;
2367         }
2368       }
2369       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2370               sg.getEndRes() + 1);
2371     }
2372     SequenceI[] cut = sg.getSequences()
2373             .toArray(new SequenceI[sg.getSize()]);
2374
2375     addHistoryItem(new EditCommand(
2376             MessageManager.getString("label.cut_sequences"), Action.CUT,
2377             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2378             viewport.getAlignment()));
2379
2380     viewport.setSelectionGroup(null);
2381     viewport.sendSelection();
2382     viewport.getAlignment().deleteGroup(sg);
2383
2384     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2385             .getSequences());
2386     if (viewport.getAlignment().getHeight() < 1)
2387     {
2388       try
2389       {
2390         this.setClosed(true);
2391       } catch (Exception ex)
2392       {
2393       }
2394     }
2395   }
2396
2397   /**
2398    * DOCUMENT ME!
2399    *
2400    * @param e
2401    *          DOCUMENT ME!
2402    */
2403   @Override
2404   protected void deleteGroups_actionPerformed(ActionEvent e)
2405   {
2406     if (avc.deleteGroups())
2407     {
2408       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2409       alignPanel.updateAnnotation();
2410       alignPanel.paintAlignment(true);
2411     }
2412   }
2413
2414   /**
2415    * DOCUMENT ME!
2416    *
2417    * @param e
2418    *          DOCUMENT ME!
2419    */
2420   @Override
2421   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2422   {
2423     SequenceGroup sg = new SequenceGroup();
2424
2425     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2426     {
2427       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2428     }
2429
2430     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2431     viewport.setSelectionGroup(sg);
2432     viewport.sendSelection();
2433     // JAL-2034 - should delegate to
2434     // alignPanel to decide if overview needs
2435     // updating.
2436     alignPanel.paintAlignment(false);
2437     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2438   }
2439
2440   /**
2441    * DOCUMENT ME!
2442    *
2443    * @param e
2444    *          DOCUMENT ME!
2445    */
2446   @Override
2447   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2448   {
2449     if (viewport.cursorMode)
2450     {
2451       alignPanel.getSeqPanel().keyboardNo1 = null;
2452       alignPanel.getSeqPanel().keyboardNo2 = null;
2453     }
2454     viewport.setSelectionGroup(null);
2455     viewport.getColumnSelection().clear();
2456     viewport.setSelectionGroup(null);
2457     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2458     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2459     // JAL-2034 - should delegate to
2460     // alignPanel to decide if overview needs
2461     // updating.
2462     alignPanel.paintAlignment(false);
2463     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2464     viewport.sendSelection();
2465   }
2466
2467   /**
2468    * DOCUMENT ME!
2469    *
2470    * @param e
2471    *          DOCUMENT ME!
2472    */
2473   @Override
2474   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2475   {
2476     SequenceGroup sg = viewport.getSelectionGroup();
2477
2478     if (sg == null)
2479     {
2480       selectAllSequenceMenuItem_actionPerformed(null);
2481
2482       return;
2483     }
2484
2485     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2486     {
2487       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2488     }
2489     // JAL-2034 - should delegate to
2490     // alignPanel to decide if overview needs
2491     // updating.
2492
2493     alignPanel.paintAlignment(true);
2494     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2495     viewport.sendSelection();
2496   }
2497
2498   @Override
2499   public void invertColSel_actionPerformed(ActionEvent e)
2500   {
2501     viewport.invertColumnSelection();
2502     alignPanel.paintAlignment(true);
2503     viewport.sendSelection();
2504   }
2505
2506   /**
2507    * DOCUMENT ME!
2508    *
2509    * @param e
2510    *          DOCUMENT ME!
2511    */
2512   @Override
2513   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2514   {
2515     trimAlignment(true);
2516   }
2517
2518   /**
2519    * DOCUMENT ME!
2520    *
2521    * @param e
2522    *          DOCUMENT ME!
2523    */
2524   @Override
2525   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2526   {
2527     trimAlignment(false);
2528   }
2529
2530   void trimAlignment(boolean trimLeft)
2531   {
2532     ColumnSelection colSel = viewport.getColumnSelection();
2533     int column;
2534
2535     if (!colSel.isEmpty())
2536     {
2537       if (trimLeft)
2538       {
2539         column = colSel.getMin();
2540       }
2541       else
2542       {
2543         column = colSel.getMax();
2544       }
2545
2546       SequenceI[] seqs;
2547       if (viewport.getSelectionGroup() != null)
2548       {
2549         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2550                 viewport.getHiddenRepSequences());
2551       }
2552       else
2553       {
2554         seqs = viewport.getAlignment().getSequencesArray();
2555       }
2556
2557       TrimRegionCommand trimRegion;
2558       if (trimLeft)
2559       {
2560         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2561                 column, viewport.getAlignment());
2562         vpRanges.setStartRes(0);
2563       }
2564       else
2565       {
2566         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2567                 column, viewport.getAlignment());
2568       }
2569
2570       statusBar.setText(MessageManager.formatMessage(
2571               "label.removed_columns",
2572               new String[] { Integer.valueOf(trimRegion.getSize())
2573                       .toString() }));
2574
2575       addHistoryItem(trimRegion);
2576
2577       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2578       {
2579         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2580                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2581         {
2582           viewport.getAlignment().deleteGroup(sg);
2583         }
2584       }
2585
2586       viewport.firePropertyChange("alignment", null, viewport
2587               .getAlignment().getSequences());
2588     }
2589   }
2590
2591   /**
2592    * DOCUMENT ME!
2593    *
2594    * @param e
2595    *          DOCUMENT ME!
2596    */
2597   @Override
2598   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2599   {
2600     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2601
2602     SequenceI[] seqs;
2603     if (viewport.getSelectionGroup() != null)
2604     {
2605       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2606               viewport.getHiddenRepSequences());
2607       start = viewport.getSelectionGroup().getStartRes();
2608       end = viewport.getSelectionGroup().getEndRes();
2609     }
2610     else
2611     {
2612       seqs = viewport.getAlignment().getSequencesArray();
2613     }
2614
2615     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2616             "Remove Gapped Columns", seqs, start, end,
2617             viewport.getAlignment());
2618
2619     addHistoryItem(removeGapCols);
2620
2621     statusBar.setText(MessageManager.formatMessage(
2622             "label.removed_empty_columns",
2623             new Object[] { Integer.valueOf(removeGapCols.getSize())
2624                     .toString() }));
2625
2626     // This is to maintain viewport position on first residue
2627     // of first sequence
2628     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2629     int startRes = seq.findPosition(vpRanges.getStartRes());
2630     // ShiftList shifts;
2631     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2632     // edit.alColumnChanges=shifts.getInverse();
2633     // if (viewport.hasHiddenColumns)
2634     // viewport.getColumnSelection().compensateForEdits(shifts);
2635     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2636     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2637             .getSequences());
2638
2639   }
2640
2641   /**
2642    * DOCUMENT ME!
2643    *
2644    * @param e
2645    *          DOCUMENT ME!
2646    */
2647   @Override
2648   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2649   {
2650     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2651
2652     SequenceI[] seqs;
2653     if (viewport.getSelectionGroup() != null)
2654     {
2655       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2656               viewport.getHiddenRepSequences());
2657       start = viewport.getSelectionGroup().getStartRes();
2658       end = viewport.getSelectionGroup().getEndRes();
2659     }
2660     else
2661     {
2662       seqs = viewport.getAlignment().getSequencesArray();
2663     }
2664
2665     // This is to maintain viewport position on first residue
2666     // of first sequence
2667     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2668     int startRes = seq.findPosition(vpRanges.getStartRes());
2669
2670     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2671             viewport.getAlignment()));
2672
2673     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2674
2675     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2676             .getSequences());
2677
2678   }
2679
2680   /**
2681    * DOCUMENT ME!
2682    *
2683    * @param e
2684    *          DOCUMENT ME!
2685    */
2686   @Override
2687   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2688   {
2689     viewport.setPadGaps(padGapsMenuitem.isSelected());
2690     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2691             .getSequences());
2692   }
2693
2694   /**
2695    * DOCUMENT ME!
2696    *
2697    * @param e
2698    *          DOCUMENT ME!
2699    */
2700   @Override
2701   public void findMenuItem_actionPerformed(ActionEvent e)
2702   {
2703     new Finder();
2704   }
2705
2706   /**
2707    * Create a new view of the current alignment.
2708    */
2709   @Override
2710   public void newView_actionPerformed(ActionEvent e)
2711   {
2712     newView(null, true);
2713   }
2714
2715   /**
2716    * Creates and shows a new view of the current alignment.
2717    *
2718    * @param viewTitle
2719    *          title of newly created view; if null, one will be generated
2720    * @param copyAnnotation
2721    *          if true then duplicate all annnotation, groups and settings
2722    * @return new alignment panel, already displayed.
2723    */
2724   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2725   {
2726     /*
2727      * Create a new AlignmentPanel (with its own, new Viewport)
2728      */
2729     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2730             true);
2731     if (!copyAnnotation)
2732     {
2733       /*
2734        * remove all groups and annotation except for the automatic stuff
2735        */
2736       newap.av.getAlignment().deleteAllGroups();
2737       newap.av.getAlignment().deleteAllAnnotations(false);
2738     }
2739
2740     newap.av.setGatherViewsHere(false);
2741
2742     if (viewport.viewName == null)
2743     {
2744       viewport.viewName = MessageManager
2745               .getString("label.view_name_original");
2746     }
2747
2748     /*
2749      * Views share the same edits undo and redo stacks
2750      */
2751     newap.av.setHistoryList(viewport.getHistoryList());
2752     newap.av.setRedoList(viewport.getRedoList());
2753
2754     /*
2755      * Views share the same mappings; need to deregister any new mappings
2756      * created by copyAlignPanel, and register the new reference to the shared
2757      * mappings
2758      */
2759     newap.av.replaceMappings(viewport.getAlignment());
2760
2761     /*
2762      * start up cDNA consensus (if applicable) now mappings are in place
2763      */
2764     if (newap.av.initComplementConsensus())
2765     {
2766       newap.refresh(true); // adjust layout of annotations
2767     }
2768
2769     newap.av.viewName = getNewViewName(viewTitle);
2770
2771     addAlignmentPanel(newap, true);
2772     newap.alignmentChanged();
2773
2774     if (alignPanels.size() == 2)
2775     {
2776       viewport.setGatherViewsHere(true);
2777     }
2778     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2779     return newap;
2780   }
2781
2782   /**
2783    * Make a new name for the view, ensuring it is unique within the current
2784    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2785    * these now use viewId. Unique view names are still desirable for usability.)
2786    *
2787    * @param viewTitle
2788    * @return
2789    */
2790   protected String getNewViewName(String viewTitle)
2791   {
2792     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2793     boolean addFirstIndex = false;
2794     if (viewTitle == null || viewTitle.trim().length() == 0)
2795     {
2796       viewTitle = MessageManager.getString("action.view");
2797       addFirstIndex = true;
2798     }
2799     else
2800     {
2801       index = 1;// we count from 1 if given a specific name
2802     }
2803     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2804
2805     List<Component> comps = PaintRefresher.components.get(viewport
2806             .getSequenceSetId());
2807
2808     List<String> existingNames = getExistingViewNames(comps);
2809
2810     while (existingNames.contains(newViewName))
2811     {
2812       newViewName = viewTitle + " " + (++index);
2813     }
2814     return newViewName;
2815   }
2816
2817   /**
2818    * Returns a list of distinct view names found in the given list of
2819    * components. View names are held on the viewport of an AlignmentPanel.
2820    *
2821    * @param comps
2822    * @return
2823    */
2824   protected List<String> getExistingViewNames(List<Component> comps)
2825   {
2826     List<String> existingNames = new ArrayList<>();
2827     for (Component comp : comps)
2828     {
2829       if (comp instanceof AlignmentPanel)
2830       {
2831         AlignmentPanel ap = (AlignmentPanel) comp;
2832         if (!existingNames.contains(ap.av.viewName))
2833         {
2834           existingNames.add(ap.av.viewName);
2835         }
2836       }
2837     }
2838     return existingNames;
2839   }
2840
2841   /**
2842    * Explode tabbed views into separate windows.
2843    */
2844   @Override
2845   public void expandViews_actionPerformed(ActionEvent e)
2846   {
2847     Desktop.explodeViews(this);
2848   }
2849
2850   /**
2851    * Gather views in separate windows back into a tabbed presentation.
2852    */
2853   @Override
2854   public void gatherViews_actionPerformed(ActionEvent e)
2855   {
2856     Desktop.instance.gatherViews(this);
2857   }
2858
2859   /**
2860    * DOCUMENT ME!
2861    *
2862    * @param e
2863    *          DOCUMENT ME!
2864    */
2865   @Override
2866   public void font_actionPerformed(ActionEvent e)
2867   {
2868     new FontChooser(alignPanel);
2869   }
2870
2871   /**
2872    * DOCUMENT ME!
2873    *
2874    * @param e
2875    *          DOCUMENT ME!
2876    */
2877   @Override
2878   protected void seqLimit_actionPerformed(ActionEvent e)
2879   {
2880     viewport.setShowJVSuffix(seqLimits.isSelected());
2881
2882     alignPanel.getIdPanel().getIdCanvas()
2883             .setPreferredSize(alignPanel.calculateIdWidth());
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   @Override
2888   public void idRightAlign_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setRightAlignIds(idRightAlign.isSelected());
2891     alignPanel.paintAlignment(true);
2892   }
2893
2894   @Override
2895   public void centreColumnLabels_actionPerformed(ActionEvent e)
2896   {
2897     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2898     alignPanel.paintAlignment(true);
2899   }
2900
2901   /*
2902    * (non-Javadoc)
2903    *
2904    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2905    */
2906   @Override
2907   protected void followHighlight_actionPerformed()
2908   {
2909     /*
2910      * Set the 'follow' flag on the Viewport (and scroll to position if now
2911      * true).
2912      */
2913     final boolean state = this.followHighlightMenuItem.getState();
2914     viewport.setFollowHighlight(state);
2915     if (state)
2916     {
2917       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2918     }
2919   }
2920
2921   /**
2922    * DOCUMENT ME!
2923    *
2924    * @param e
2925    *          DOCUMENT ME!
2926    */
2927   @Override
2928   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2929   {
2930     viewport.setColourText(colourTextMenuItem.isSelected());
2931     alignPanel.paintAlignment(true);
2932   }
2933
2934   /**
2935    * DOCUMENT ME!
2936    *
2937    * @param e
2938    *          DOCUMENT ME!
2939    */
2940   @Override
2941   public void wrapMenuItem_actionPerformed(ActionEvent e)
2942   {
2943     scaleAbove.setVisible(wrapMenuItem.isSelected());
2944     scaleLeft.setVisible(wrapMenuItem.isSelected());
2945     scaleRight.setVisible(wrapMenuItem.isSelected());
2946     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2947     alignPanel.updateLayout();
2948   }
2949
2950   @Override
2951   public void showAllSeqs_actionPerformed(ActionEvent e)
2952   {
2953     viewport.showAllHiddenSeqs();
2954   }
2955
2956   @Override
2957   public void showAllColumns_actionPerformed(ActionEvent e)
2958   {
2959     viewport.showAllHiddenColumns();
2960     repaint();
2961     viewport.sendSelection();
2962   }
2963
2964   @Override
2965   public void hideSelSequences_actionPerformed(ActionEvent e)
2966   {
2967     viewport.hideAllSelectedSeqs();
2968     // alignPanel.paintAlignment(true);
2969   }
2970
2971   /**
2972    * called by key handler and the hide all/show all menu items
2973    *
2974    * @param toggleSeqs
2975    * @param toggleCols
2976    */
2977   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2978   {
2979
2980     boolean hide = false;
2981     SequenceGroup sg = viewport.getSelectionGroup();
2982     if (!toggleSeqs && !toggleCols)
2983     {
2984       // Hide everything by the current selection - this is a hack - we do the
2985       // invert and then hide
2986       // first check that there will be visible columns after the invert.
2987       if (viewport.hasSelectedColumns()
2988               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2989                       .getEndRes()))
2990       {
2991         // now invert the sequence set, if required - empty selection implies
2992         // that no hiding is required.
2993         if (sg != null)
2994         {
2995           invertSequenceMenuItem_actionPerformed(null);
2996           sg = viewport.getSelectionGroup();
2997           toggleSeqs = true;
2998
2999         }
3000         viewport.expandColSelection(sg, true);
3001         // finally invert the column selection and get the new sequence
3002         // selection.
3003         invertColSel_actionPerformed(null);
3004         toggleCols = true;
3005       }
3006     }
3007
3008     if (toggleSeqs)
3009     {
3010       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3011       {
3012         hideSelSequences_actionPerformed(null);
3013         hide = true;
3014       }
3015       else if (!(toggleCols && viewport.hasSelectedColumns()))
3016       {
3017         showAllSeqs_actionPerformed(null);
3018       }
3019     }
3020
3021     if (toggleCols)
3022     {
3023       if (viewport.hasSelectedColumns())
3024       {
3025         hideSelColumns_actionPerformed(null);
3026         if (!toggleSeqs)
3027         {
3028           viewport.setSelectionGroup(sg);
3029         }
3030       }
3031       else if (!hide)
3032       {
3033         showAllColumns_actionPerformed(null);
3034       }
3035     }
3036   }
3037
3038   /*
3039    * (non-Javadoc)
3040    *
3041    * @see
3042    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3043    * event.ActionEvent)
3044    */
3045   @Override
3046   public void hideAllButSelection_actionPerformed(ActionEvent e)
3047   {
3048     toggleHiddenRegions(false, false);
3049     viewport.sendSelection();
3050   }
3051
3052   /*
3053    * (non-Javadoc)
3054    *
3055    * @see
3056    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3057    * .ActionEvent)
3058    */
3059   @Override
3060   public void hideAllSelection_actionPerformed(ActionEvent e)
3061   {
3062     SequenceGroup sg = viewport.getSelectionGroup();
3063     viewport.expandColSelection(sg, false);
3064     viewport.hideAllSelectedSeqs();
3065     viewport.hideSelectedColumns();
3066     alignPanel.paintAlignment(true);
3067     viewport.sendSelection();
3068   }
3069
3070   /*
3071    * (non-Javadoc)
3072    *
3073    * @see
3074    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3075    * ActionEvent)
3076    */
3077   @Override
3078   public void showAllhidden_actionPerformed(ActionEvent e)
3079   {
3080     viewport.showAllHiddenColumns();
3081     viewport.showAllHiddenSeqs();
3082     alignPanel.paintAlignment(true);
3083     viewport.sendSelection();
3084   }
3085
3086   @Override
3087   public void hideSelColumns_actionPerformed(ActionEvent e)
3088   {
3089     viewport.hideSelectedColumns();
3090     alignPanel.paintAlignment(true);
3091     viewport.sendSelection();
3092   }
3093
3094   @Override
3095   public void hiddenMarkers_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3098     repaint();
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   protected void scaleAbove_actionPerformed(ActionEvent e)
3109   {
3110     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3111     alignPanel.paintAlignment(true);
3112   }
3113
3114   /**
3115    * DOCUMENT ME!
3116    *
3117    * @param e
3118    *          DOCUMENT ME!
3119    */
3120   @Override
3121   protected void scaleLeft_actionPerformed(ActionEvent e)
3122   {
3123     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3124     alignPanel.paintAlignment(true);
3125   }
3126
3127   /**
3128    * DOCUMENT ME!
3129    *
3130    * @param e
3131    *          DOCUMENT ME!
3132    */
3133   @Override
3134   protected void scaleRight_actionPerformed(ActionEvent e)
3135   {
3136     viewport.setScaleRightWrapped(scaleRight.isSelected());
3137     alignPanel.paintAlignment(true);
3138   }
3139
3140   /**
3141    * DOCUMENT ME!
3142    *
3143    * @param e
3144    *          DOCUMENT ME!
3145    */
3146   @Override
3147   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3148   {
3149     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3150     alignPanel.paintAlignment(true);
3151   }
3152
3153   /**
3154    * DOCUMENT ME!
3155    *
3156    * @param e
3157    *          DOCUMENT ME!
3158    */
3159   @Override
3160   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3161   {
3162     viewport.setShowText(viewTextMenuItem.isSelected());
3163     alignPanel.paintAlignment(true);
3164   }
3165
3166   /**
3167    * DOCUMENT ME!
3168    *
3169    * @param e
3170    *          DOCUMENT ME!
3171    */
3172   @Override
3173   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3174   {
3175     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3176     alignPanel.paintAlignment(true);
3177   }
3178
3179   public FeatureSettings featureSettings;
3180
3181   @Override
3182   public FeatureSettingsControllerI getFeatureSettingsUI()
3183   {
3184     return featureSettings;
3185   }
3186
3187   @Override
3188   public void featureSettings_actionPerformed(ActionEvent e)
3189   {
3190     if (featureSettings != null)
3191     {
3192       featureSettings.close();
3193       featureSettings = null;
3194     }
3195     if (!showSeqFeatures.isSelected())
3196     {
3197       // make sure features are actually displayed
3198       showSeqFeatures.setSelected(true);
3199       showSeqFeatures_actionPerformed(null);
3200     }
3201     featureSettings = new FeatureSettings(this);
3202   }
3203
3204   /**
3205    * Set or clear 'Show Sequence Features'
3206    *
3207    * @param evt
3208    *          DOCUMENT ME!
3209    */
3210   @Override
3211   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3212   {
3213     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3214     alignPanel.paintAlignment(true);
3215     if (alignPanel.getOverviewPanel() != null)
3216     {
3217       alignPanel.getOverviewPanel().updateOverviewImage();
3218     }
3219   }
3220
3221   /**
3222    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3223    * the annotations panel as a whole.
3224    *
3225    * The options to show/hide all annotations should be enabled when the panel
3226    * is shown, and disabled when the panel is hidden.
3227    *
3228    * @param e
3229    */
3230   @Override
3231   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3232   {
3233     final boolean setVisible = annotationPanelMenuItem.isSelected();
3234     viewport.setShowAnnotation(setVisible);
3235     this.showAllSeqAnnotations.setEnabled(setVisible);
3236     this.hideAllSeqAnnotations.setEnabled(setVisible);
3237     this.showAllAlAnnotations.setEnabled(setVisible);
3238     this.hideAllAlAnnotations.setEnabled(setVisible);
3239     alignPanel.updateLayout();
3240   }
3241
3242   @Override
3243   public void alignmentProperties()
3244   {
3245     JEditorPane editPane = new JEditorPane("text/html", "");
3246     editPane.setEditable(false);
3247     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3248             .formatAsHtml();
3249     editPane.setText(MessageManager.formatMessage("label.html_content",
3250             new Object[] { contents.toString() }));
3251     JInternalFrame frame = new JInternalFrame();
3252     frame.getContentPane().add(new JScrollPane(editPane));
3253
3254     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3255             "label.alignment_properties", new Object[] { getTitle() }),
3256             500, 400);
3257   }
3258
3259   /**
3260    * DOCUMENT ME!
3261    *
3262    * @param e
3263    *          DOCUMENT ME!
3264    */
3265   @Override
3266   public void overviewMenuItem_actionPerformed(ActionEvent e)
3267   {
3268     if (alignPanel.overviewPanel != null)
3269     {
3270       return;
3271     }
3272
3273     JInternalFrame frame = new JInternalFrame();
3274     OverviewPanel overview = new OverviewPanel(alignPanel);
3275     frame.setContentPane(overview);
3276     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3277             "label.overview_params", new Object[] { this.getTitle() }),
3278             true, frame.getWidth(), frame.getHeight(), true, true);
3279     frame.pack();
3280     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3281     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3282     {
3283       @Override
3284       public void internalFrameClosed(
3285               javax.swing.event.InternalFrameEvent evt)
3286       {
3287         alignPanel.setOverviewPanel(null);
3288       };
3289     });
3290
3291     alignPanel.setOverviewPanel(overview);
3292   }
3293
3294   @Override
3295   public void textColour_actionPerformed()
3296   {
3297     new TextColourChooser().chooseColour(alignPanel, null);
3298   }
3299
3300   /*
3301    * public void covariationColour_actionPerformed() {
3302    * changeColour(new
3303    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3304    * ()[0])); }
3305    */
3306   @Override
3307   public void annotationColour_actionPerformed()
3308   {
3309     new AnnotationColourChooser(viewport, alignPanel);
3310   }
3311
3312   @Override
3313   public void annotationColumn_actionPerformed(ActionEvent e)
3314   {
3315     new AnnotationColumnChooser(viewport, alignPanel);
3316   }
3317
3318   /**
3319    * Action on the user checking or unchecking the option to apply the selected
3320    * colour scheme to all groups. If unchecked, groups may have their own
3321    * independent colour schemes.
3322    *
3323    * @param selected
3324    */
3325   @Override
3326   public void applyToAllGroups_actionPerformed(boolean selected)
3327   {
3328     viewport.setColourAppliesToAllGroups(selected);
3329   }
3330
3331   /**
3332    * Action on user selecting a colour from the colour menu
3333    *
3334    * @param name
3335    *          the name (not the menu item label!) of the colour scheme
3336    */
3337   @Override
3338   public void changeColour_actionPerformed(String name)
3339   {
3340     /*
3341      * 'User Defined' opens a panel to configure or load a
3342      * user-defined colour scheme
3343      */
3344     if (ResidueColourScheme.USER_DEFINED.equals(name))
3345     {
3346       new UserDefinedColours(alignPanel);
3347       return;
3348     }
3349
3350     /*
3351      * otherwise set the chosen colour scheme (or null for 'None')
3352      */
3353     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3354             viewport.getAlignment(), viewport.getHiddenRepSequences());
3355     changeColour(cs);
3356   }
3357
3358   /**
3359    * Actions on setting or changing the alignment colour scheme
3360    *
3361    * @param cs
3362    */
3363   @Override
3364   public void changeColour(ColourSchemeI cs)
3365   {
3366     // TODO: pull up to controller method
3367     ColourMenuHelper.setColourSelected(colourMenu, cs);
3368
3369     viewport.setGlobalColourScheme(cs);
3370
3371     alignPanel.paintAlignment(true);
3372   }
3373
3374   /**
3375    * Show the PID threshold slider panel
3376    */
3377   @Override
3378   protected void modifyPID_actionPerformed()
3379   {
3380     SliderPanel.setPIDSliderSource(alignPanel,
3381             viewport.getResidueShading(), alignPanel.getViewName());
3382     SliderPanel.showPIDSlider();
3383   }
3384
3385   /**
3386    * Show the Conservation slider panel
3387    */
3388   @Override
3389   protected void modifyConservation_actionPerformed()
3390   {
3391     SliderPanel.setConservationSlider(alignPanel,
3392             viewport.getResidueShading(), alignPanel.getViewName());
3393     SliderPanel.showConservationSlider();
3394   }
3395
3396   /**
3397    * Action on selecting or deselecting (Colour) By Conservation
3398    */
3399   @Override
3400   public void conservationMenuItem_actionPerformed(boolean selected)
3401   {
3402     modifyConservation.setEnabled(selected);
3403     viewport.setConservationSelected(selected);
3404     viewport.getResidueShading().setConservationApplied(selected);
3405
3406     changeColour(viewport.getGlobalColourScheme());
3407     if (selected)
3408     {
3409       modifyConservation_actionPerformed();
3410     }
3411     else
3412     {
3413       SliderPanel.hideConservationSlider();
3414     }
3415   }
3416
3417   /**
3418    * Action on selecting or deselecting (Colour) Above PID Threshold
3419    */
3420   @Override
3421   public void abovePIDThreshold_actionPerformed(boolean selected)
3422   {
3423     modifyPID.setEnabled(selected);
3424     viewport.setAbovePIDThreshold(selected);
3425     if (!selected)
3426     {
3427       viewport.getResidueShading().setThreshold(0,
3428               viewport.isIgnoreGapsConsensus());
3429     }
3430
3431     changeColour(viewport.getGlobalColourScheme());
3432     if (selected)
3433     {
3434       modifyPID_actionPerformed();
3435     }
3436     else
3437     {
3438       SliderPanel.hidePIDSlider();
3439     }
3440   }
3441
3442   /**
3443    * DOCUMENT ME!
3444    *
3445    * @param e
3446    *          DOCUMENT ME!
3447    */
3448   @Override
3449   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3450   {
3451     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3452     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3453             .getAlignment().getSequenceAt(0));
3454     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3455             viewport.getAlignment()));
3456     alignPanel.paintAlignment(true);
3457   }
3458
3459   /**
3460    * DOCUMENT ME!
3461    *
3462    * @param e
3463    *          DOCUMENT ME!
3464    */
3465   @Override
3466   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3467   {
3468     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3469     AlignmentSorter.sortByID(viewport.getAlignment());
3470     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3471             viewport.getAlignment()));
3472     alignPanel.paintAlignment(true);
3473   }
3474
3475   /**
3476    * DOCUMENT ME!
3477    *
3478    * @param e
3479    *          DOCUMENT ME!
3480    */
3481   @Override
3482   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3483   {
3484     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3485     AlignmentSorter.sortByLength(viewport.getAlignment());
3486     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3487             viewport.getAlignment()));
3488     alignPanel.paintAlignment(true);
3489   }
3490
3491   /**
3492    * DOCUMENT ME!
3493    *
3494    * @param e
3495    *          DOCUMENT ME!
3496    */
3497   @Override
3498   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3499   {
3500     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3501     AlignmentSorter.sortByGroup(viewport.getAlignment());
3502     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3503             viewport.getAlignment()));
3504
3505     alignPanel.paintAlignment(true);
3506   }
3507
3508   /**
3509    * DOCUMENT ME!
3510    *
3511    * @param e
3512    *          DOCUMENT ME!
3513    */
3514   @Override
3515   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3516   {
3517     new RedundancyPanel(alignPanel, this);
3518   }
3519
3520   /**
3521    * DOCUMENT ME!
3522    *
3523    * @param e
3524    *          DOCUMENT ME!
3525    */
3526   @Override
3527   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3528   {
3529     if ((viewport.getSelectionGroup() == null)
3530             || (viewport.getSelectionGroup().getSize() < 2))
3531     {
3532       JvOptionPane.showInternalMessageDialog(this, MessageManager
3533               .getString("label.you_must_select_least_two_sequences"),
3534               MessageManager.getString("label.invalid_selection"),
3535               JvOptionPane.WARNING_MESSAGE);
3536     }
3537     else
3538     {
3539       JInternalFrame frame = new JInternalFrame();
3540       frame.setContentPane(new PairwiseAlignPanel(viewport));
3541       Desktop.addInternalFrame(frame,
3542               MessageManager.getString("action.pairwise_alignment"), 600,
3543               500);
3544     }
3545   }
3546
3547   @Override
3548   public void autoCalculate_actionPerformed(ActionEvent e)
3549   {
3550     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3551     if (viewport.autoCalculateConsensus)
3552     {
3553       viewport.firePropertyChange("alignment", null, viewport
3554               .getAlignment().getSequences());
3555     }
3556   }
3557
3558   @Override
3559   public void sortByTreeOption_actionPerformed(ActionEvent e)
3560   {
3561     viewport.sortByTree = sortByTree.isSelected();
3562   }
3563
3564   @Override
3565   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3566   {
3567     viewport.followSelection = listenToViewSelections.isSelected();
3568   }
3569
3570   /**
3571    * Constructs a tree panel and adds it to the desktop
3572    *
3573    * @param type
3574    *          tree type (NJ or AV)
3575    * @param modelName
3576    *          name of score model used to compute the tree
3577    * @param options
3578    *          parameters for the distance or similarity calculation
3579    */
3580   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3581   {
3582     String frameTitle = "";
3583     TreePanel tp;
3584
3585     boolean onSelection = false;
3586     if (viewport.getSelectionGroup() != null
3587             && viewport.getSelectionGroup().getSize() > 0)
3588     {
3589       SequenceGroup sg = viewport.getSelectionGroup();
3590
3591       /* Decide if the selection is a column region */
3592       for (SequenceI _s : sg.getSequences())
3593       {
3594         if (_s.getLength() < sg.getEndRes())
3595         {
3596           JvOptionPane
3597                   .showMessageDialog(
3598                           Desktop.desktop,
3599                           MessageManager
3600                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3601                           MessageManager
3602                                   .getString("label.sequences_selection_not_aligned"),
3603                           JvOptionPane.WARNING_MESSAGE);
3604
3605           return;
3606         }
3607       }
3608       onSelection = true;
3609     }
3610     else
3611     {
3612       if (viewport.getAlignment().getHeight() < 2)
3613       {
3614         return;
3615       }
3616     }
3617
3618     tp = new TreePanel(alignPanel, type, modelName, options);
3619     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3620
3621     frameTitle += " from ";
3622
3623     if (viewport.viewName != null)
3624     {
3625       frameTitle += viewport.viewName + " of ";
3626     }
3627
3628     frameTitle += this.title;
3629
3630     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3631   }
3632
3633   /**
3634    * DOCUMENT ME!
3635    *
3636    * @param title
3637    *          DOCUMENT ME!
3638    * @param order
3639    *          DOCUMENT ME!
3640    */
3641   public void addSortByOrderMenuItem(String title,
3642           final AlignmentOrder order)
3643   {
3644     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3645             "action.by_title_param", new Object[] { title }));
3646     sort.add(item);
3647     item.addActionListener(new java.awt.event.ActionListener()
3648     {
3649       @Override
3650       public void actionPerformed(ActionEvent e)
3651       {
3652         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3653
3654         // TODO: JBPNote - have to map order entries to curent SequenceI
3655         // pointers
3656         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3657
3658         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3659                 .getAlignment()));
3660
3661         alignPanel.paintAlignment(true);
3662       }
3663     });
3664   }
3665
3666   /**
3667    * Add a new sort by annotation score menu item
3668    *
3669    * @param sort
3670    *          the menu to add the option to
3671    * @param scoreLabel
3672    *          the label used to retrieve scores for each sequence on the
3673    *          alignment
3674    */
3675   public void addSortByAnnotScoreMenuItem(JMenu sort,
3676           final String scoreLabel)
3677   {
3678     final JMenuItem item = new JMenuItem(scoreLabel);
3679     sort.add(item);
3680     item.addActionListener(new java.awt.event.ActionListener()
3681     {
3682       @Override
3683       public void actionPerformed(ActionEvent e)
3684       {
3685         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3686         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3687                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3688         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3689                 viewport.getAlignment()));
3690         alignPanel.paintAlignment(true);
3691       }
3692     });
3693   }
3694
3695   /**
3696    * last hash for alignment's annotation array - used to minimise cost of
3697    * rebuild.
3698    */
3699   protected int _annotationScoreVectorHash;
3700
3701   /**
3702    * search the alignment and rebuild the sort by annotation score submenu the
3703    * last alignment annotation vector hash is stored to minimize cost of
3704    * rebuilding in subsequence calls.
3705    *
3706    */
3707   @Override
3708   public void buildSortByAnnotationScoresMenu()
3709   {
3710     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3711     {
3712       return;
3713     }
3714
3715     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3716     {
3717       sortByAnnotScore.removeAll();
3718       // almost certainly a quicker way to do this - but we keep it simple
3719       Hashtable scoreSorts = new Hashtable();
3720       AlignmentAnnotation aann[];
3721       for (SequenceI sqa : viewport.getAlignment().getSequences())
3722       {
3723         aann = sqa.getAnnotation();
3724         for (int i = 0; aann != null && i < aann.length; i++)
3725         {
3726           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3727           {
3728             scoreSorts.put(aann[i].label, aann[i].label);
3729           }
3730         }
3731       }
3732       Enumeration labels = scoreSorts.keys();
3733       while (labels.hasMoreElements())
3734       {
3735         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3736                 (String) labels.nextElement());
3737       }
3738       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3739       scoreSorts.clear();
3740
3741       _annotationScoreVectorHash = viewport.getAlignment()
3742               .getAlignmentAnnotation().hashCode();
3743     }
3744   }
3745
3746   /**
3747    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3748    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3749    * call. Listeners are added to remove the menu item when the treePanel is
3750    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3751    * modified.
3752    */
3753   @Override
3754   public void buildTreeSortMenu()
3755   {
3756     sortByTreeMenu.removeAll();
3757
3758     List<Component> comps = PaintRefresher.components.get(viewport
3759             .getSequenceSetId());
3760     List<TreePanel> treePanels = new ArrayList<>();
3761     for (Component comp : comps)
3762     {
3763       if (comp instanceof TreePanel)
3764       {
3765         treePanels.add((TreePanel) comp);
3766       }
3767     }
3768
3769     if (treePanels.size() < 1)
3770     {
3771       sortByTreeMenu.setVisible(false);
3772       return;
3773     }
3774
3775     sortByTreeMenu.setVisible(true);
3776
3777     for (final TreePanel tp : treePanels)
3778     {
3779       final JMenuItem item = new JMenuItem(tp.getTitle());
3780       item.addActionListener(new java.awt.event.ActionListener()
3781       {
3782         @Override
3783         public void actionPerformed(ActionEvent e)
3784         {
3785           tp.sortByTree_actionPerformed();
3786           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3787
3788         }
3789       });
3790
3791       sortByTreeMenu.add(item);
3792     }
3793   }
3794
3795   public boolean sortBy(AlignmentOrder alorder, String undoname)
3796   {
3797     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3798     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3799     if (undoname != null)
3800     {
3801       addHistoryItem(new OrderCommand(undoname, oldOrder,
3802               viewport.getAlignment()));
3803     }
3804     alignPanel.paintAlignment(true);
3805     return true;
3806   }
3807
3808   /**
3809    * Work out whether the whole set of sequences or just the selected set will
3810    * be submitted for multiple alignment.
3811    *
3812    */
3813   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3814   {
3815     // Now, check we have enough sequences
3816     AlignmentView msa = null;
3817
3818     if ((viewport.getSelectionGroup() != null)
3819             && (viewport.getSelectionGroup().getSize() > 1))
3820     {
3821       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3822       // some common interface!
3823       /*
3824        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3825        * SequenceI[sz = seqs.getSize(false)];
3826        *
3827        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3828        * seqs.getSequenceAt(i); }
3829        */
3830       msa = viewport.getAlignmentView(true);
3831     }
3832     else if (viewport.getSelectionGroup() != null
3833             && viewport.getSelectionGroup().getSize() == 1)
3834     {
3835       int option = JvOptionPane.showConfirmDialog(this,
3836               MessageManager.getString("warn.oneseq_msainput_selection"),
3837               MessageManager.getString("label.invalid_selection"),
3838               JvOptionPane.OK_CANCEL_OPTION);
3839       if (option == JvOptionPane.OK_OPTION)
3840       {
3841         msa = viewport.getAlignmentView(false);
3842       }
3843     }
3844     else
3845     {
3846       msa = viewport.getAlignmentView(false);
3847     }
3848     return msa;
3849   }
3850
3851   /**
3852    * Decides what is submitted to a secondary structure prediction service: the
3853    * first sequence in the alignment, or in the current selection, or, if the
3854    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3855    * region or the whole alignment. (where the first sequence in the set is the
3856    * one that the prediction will be for).
3857    */
3858   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3859   {
3860     AlignmentView seqs = null;
3861
3862     if ((viewport.getSelectionGroup() != null)
3863             && (viewport.getSelectionGroup().getSize() > 0))
3864     {
3865       seqs = viewport.getAlignmentView(true);
3866     }
3867     else
3868     {
3869       seqs = viewport.getAlignmentView(false);
3870     }
3871     // limit sequences - JBPNote in future - could spawn multiple prediction
3872     // jobs
3873     // TODO: viewport.getAlignment().isAligned is a global state - the local
3874     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3875     if (!viewport.getAlignment().isAligned(false))
3876     {
3877       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3878       // TODO: if seqs.getSequences().length>1 then should really have warned
3879       // user!
3880
3881     }
3882     return seqs;
3883   }
3884
3885   /**
3886    * DOCUMENT ME!
3887    *
3888    * @param e
3889    *          DOCUMENT ME!
3890    */
3891   @Override
3892   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3893   {
3894     // Pick the tree file
3895     JalviewFileChooser chooser = new JalviewFileChooser(
3896             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3897     chooser.setFileView(new JalviewFileView());
3898     chooser.setDialogTitle(MessageManager
3899             .getString("label.select_newick_like_tree_file"));
3900     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3901
3902     int value = chooser.showOpenDialog(null);
3903
3904     if (value == JalviewFileChooser.APPROVE_OPTION)
3905     {
3906       String filePath = chooser.getSelectedFile().getPath();
3907       Cache.setProperty("LAST_DIRECTORY", filePath);
3908       NewickFile fin = null;
3909       try
3910       {
3911         fin = new NewickFile(filePath, DataSourceType.FILE);
3912         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3913       } catch (Exception ex)
3914       {
3915         JvOptionPane
3916                 .showMessageDialog(
3917                         Desktop.desktop,
3918                         ex.getMessage(),
3919                         MessageManager
3920                                 .getString("label.problem_reading_tree_file"),
3921                         JvOptionPane.WARNING_MESSAGE);
3922         ex.printStackTrace();
3923       }
3924       if (fin != null && fin.hasWarningMessage())
3925       {
3926         JvOptionPane.showMessageDialog(Desktop.desktop, fin
3927                 .getWarningMessage(), MessageManager
3928                 .getString("label.possible_problem_with_tree_file"),
3929                 JvOptionPane.WARNING_MESSAGE);
3930       }
3931     }
3932   }
3933
3934   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3935   {
3936     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3937   }
3938
3939   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3940           int h, int x, int y)
3941   {
3942     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3943   }
3944
3945   /**
3946    * Add a treeviewer for the tree extracted from a Newick file object to the
3947    * current alignment view
3948    *
3949    * @param nf
3950    *          the tree
3951    * @param title
3952    *          tree viewer title
3953    * @param input
3954    *          Associated alignment input data (or null)
3955    * @param w
3956    *          width
3957    * @param h
3958    *          height
3959    * @param x
3960    *          position
3961    * @param y
3962    *          position
3963    * @return TreePanel handle
3964    */
3965   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3966           AlignmentView input, int w, int h, int x, int y)
3967   {
3968     TreePanel tp = null;
3969
3970     try
3971     {
3972       nf.parse();
3973
3974       if (nf.getTree() != null)
3975       {
3976         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3977
3978         tp.setSize(w, h);
3979
3980         if (x > 0 && y > 0)
3981         {
3982           tp.setLocation(x, y);
3983         }
3984
3985         Desktop.addInternalFrame(tp, treeTitle, w, h);
3986       }
3987     } catch (Exception ex)
3988     {
3989       ex.printStackTrace();
3990     }
3991
3992     return tp;
3993   }
3994
3995   private boolean buildingMenu = false;
3996
3997   /**
3998    * Generates menu items and listener event actions for web service clients
3999    *
4000    */
4001   public void BuildWebServiceMenu()
4002   {
4003     while (buildingMenu)
4004     {
4005       try
4006       {
4007         System.err.println("Waiting for building menu to finish.");
4008         Thread.sleep(10);
4009       } catch (Exception e)
4010       {
4011       }
4012     }
4013     final AlignFrame me = this;
4014     buildingMenu = true;
4015     new Thread(new Runnable()
4016     {
4017       @Override
4018       public void run()
4019       {
4020         final List<JMenuItem> legacyItems = new ArrayList<>();
4021         try
4022         {
4023           // System.err.println("Building ws menu again "
4024           // + Thread.currentThread());
4025           // TODO: add support for context dependent disabling of services based
4026           // on
4027           // alignment and current selection
4028           // TODO: add additional serviceHandle parameter to specify abstract
4029           // handler
4030           // class independently of AbstractName
4031           // TODO: add in rediscovery GUI function to restart discoverer
4032           // TODO: group services by location as well as function and/or
4033           // introduce
4034           // object broker mechanism.
4035           final Vector<JMenu> wsmenu = new Vector<>();
4036           final IProgressIndicator af = me;
4037
4038           /*
4039            * do not i18n these strings - they are hard-coded in class
4040            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4041            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4042            */
4043           final JMenu msawsmenu = new JMenu("Alignment");
4044           final JMenu secstrmenu = new JMenu(
4045                   "Secondary Structure Prediction");
4046           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4047           final JMenu analymenu = new JMenu("Analysis");
4048           final JMenu dismenu = new JMenu("Protein Disorder");
4049           // JAL-940 - only show secondary structure prediction services from
4050           // the legacy server
4051           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4052               // &&
4053           Discoverer.services != null && (Discoverer.services.size() > 0))
4054           {
4055             // TODO: refactor to allow list of AbstractName/Handler bindings to
4056             // be
4057             // stored or retrieved from elsewhere
4058             // No MSAWS used any more:
4059             // Vector msaws = null; // (Vector)
4060             // Discoverer.services.get("MsaWS");
4061             Vector secstrpr = (Vector) Discoverer.services
4062                     .get("SecStrPred");
4063             if (secstrpr != null)
4064             {
4065               // Add any secondary structure prediction services
4066               for (int i = 0, j = secstrpr.size(); i < j; i++)
4067               {
4068                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4069                         .get(i);
4070                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4071                         .getServiceClient(sh);
4072                 int p = secstrmenu.getItemCount();
4073                 impl.attachWSMenuEntry(secstrmenu, me);
4074                 int q = secstrmenu.getItemCount();
4075                 for (int litm = p; litm < q; litm++)
4076                 {
4077                   legacyItems.add(secstrmenu.getItem(litm));
4078                 }
4079               }
4080             }
4081           }
4082
4083           // Add all submenus in the order they should appear on the web
4084           // services menu
4085           wsmenu.add(msawsmenu);
4086           wsmenu.add(secstrmenu);
4087           wsmenu.add(dismenu);
4088           wsmenu.add(analymenu);
4089           // No search services yet
4090           // wsmenu.add(seqsrchmenu);
4091
4092           javax.swing.SwingUtilities.invokeLater(new Runnable()
4093           {
4094             @Override
4095             public void run()
4096             {
4097               try
4098               {
4099                 webService.removeAll();
4100                 // first, add discovered services onto the webservices menu
4101                 if (wsmenu.size() > 0)
4102                 {
4103                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4104                   {
4105                     webService.add(wsmenu.get(i));
4106                   }
4107                 }
4108                 else
4109                 {
4110                   webService.add(me.webServiceNoServices);
4111                 }
4112                 // TODO: move into separate menu builder class.
4113                 boolean new_sspred = false;
4114                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4115                 {
4116                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4117                   if (jws2servs != null)
4118                   {
4119                     if (jws2servs.hasServices())
4120                     {
4121                       jws2servs.attachWSMenuEntry(webService, me);
4122                       for (Jws2Instance sv : jws2servs.getServices())
4123                       {
4124                         if (sv.description.toLowerCase().contains("jpred"))
4125                         {
4126                           for (JMenuItem jmi : legacyItems)
4127                           {
4128                             jmi.setVisible(false);
4129                           }
4130                         }
4131                       }
4132
4133                     }
4134                     if (jws2servs.isRunning())
4135                     {
4136                       JMenuItem tm = new JMenuItem(
4137                               "Still discovering JABA Services");
4138                       tm.setEnabled(false);
4139                       webService.add(tm);
4140                     }
4141                   }
4142                 }
4143                 build_urlServiceMenu(me.webService);
4144                 build_fetchdbmenu(webService);
4145                 for (JMenu item : wsmenu)
4146                 {
4147                   if (item.getItemCount() == 0)
4148                   {
4149                     item.setEnabled(false);
4150                   }
4151                   else
4152                   {
4153                     item.setEnabled(true);
4154                   }
4155                 }
4156               } catch (Exception e)
4157               {
4158                 Cache.log
4159                         .debug("Exception during web service menu building process.",
4160                                 e);
4161               }
4162             }
4163           });
4164         } catch (Exception e)
4165         {
4166         }
4167         buildingMenu = false;
4168       }
4169     }).start();
4170
4171   }
4172
4173   /**
4174    * construct any groupURL type service menu entries.
4175    *
4176    * @param webService
4177    */
4178   private void build_urlServiceMenu(JMenu webService)
4179   {
4180     // TODO: remove this code when 2.7 is released
4181     // DEBUG - alignmentView
4182     /*
4183      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4184      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4185      *
4186      * @Override public void actionPerformed(ActionEvent e) {
4187      * jalview.datamodel.AlignmentView
4188      * .testSelectionViews(af.viewport.getAlignment(),
4189      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4190      *
4191      * }); webService.add(testAlView);
4192      */
4193     // TODO: refactor to RestClient discoverer and merge menu entries for
4194     // rest-style services with other types of analysis/calculation service
4195     // SHmmr test client - still being implemented.
4196     // DEBUG - alignmentView
4197
4198     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4199             .getRestClients())
4200     {
4201       client.attachWSMenuEntry(
4202               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4203               this);
4204     }
4205   }
4206
4207   /**
4208    * Searches the alignment sequences for xRefs and builds the Show
4209    * Cross-References menu (formerly called Show Products), with database
4210    * sources for which cross-references are found (protein sources for a
4211    * nucleotide alignment and vice versa)
4212    *
4213    * @return true if Show Cross-references menu should be enabled
4214    */
4215   public boolean canShowProducts()
4216   {
4217     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4218     AlignmentI dataset = viewport.getAlignment().getDataset();
4219
4220     showProducts.removeAll();
4221     final boolean dna = viewport.getAlignment().isNucleotide();
4222
4223     if (seqs == null || seqs.length == 0)
4224     {
4225       // nothing to see here.
4226       return false;
4227     }
4228
4229     boolean showp = false;
4230     try
4231     {
4232       List<String> ptypes = new CrossRef(seqs, dataset)
4233               .findXrefSourcesForSequences(dna);
4234
4235       for (final String source : ptypes)
4236       {
4237         showp = true;
4238         final AlignFrame af = this;
4239         JMenuItem xtype = new JMenuItem(source);
4240         xtype.addActionListener(new ActionListener()
4241         {
4242           @Override
4243           public void actionPerformed(ActionEvent e)
4244           {
4245             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4246           }
4247         });
4248         showProducts.add(xtype);
4249       }
4250       showProducts.setVisible(showp);
4251       showProducts.setEnabled(showp);
4252     } catch (Exception e)
4253     {
4254       Cache.log
4255               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4256                       e);
4257       return false;
4258     }
4259     return showp;
4260   }
4261
4262   /**
4263    * Finds and displays cross-references for the selected sequences (protein
4264    * products for nucleotide sequences, dna coding sequences for peptides).
4265    *
4266    * @param sel
4267    *          the sequences to show cross-references for
4268    * @param dna
4269    *          true if from a nucleotide alignment (so showing proteins)
4270    * @param source
4271    *          the database to show cross-references for
4272    */
4273   protected void showProductsFor(final SequenceI[] sel,
4274           final boolean _odna, final String source)
4275   {
4276     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4277             .start();
4278   }
4279
4280   /**
4281    * Construct and display a new frame containing the translation of this
4282    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4283    */
4284   @Override
4285   public void showTranslation_actionPerformed(ActionEvent e)
4286   {
4287     AlignmentI al = null;
4288     try
4289     {
4290       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4291
4292       al = dna.translateCdna();
4293     } catch (Exception ex)
4294     {
4295       jalview.bin.Cache.log.error(
4296               "Exception during translation. Please report this !", ex);
4297       final String msg = MessageManager
4298               .getString("label.error_when_translating_sequences_submit_bug_report");
4299       final String errorTitle = MessageManager
4300               .getString("label.implementation_error")
4301               + MessageManager.getString("label.translation_failed");
4302       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4303               JvOptionPane.ERROR_MESSAGE);
4304       return;
4305     }
4306     if (al == null || al.getHeight() == 0)
4307     {
4308       final String msg = MessageManager
4309               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4310       final String errorTitle = MessageManager
4311               .getString("label.translation_failed");
4312       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4313               JvOptionPane.WARNING_MESSAGE);
4314     }
4315     else
4316     {
4317       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4318       af.setFileFormat(this.currentFileFormat);
4319       final String newTitle = MessageManager.formatMessage(
4320               "label.translation_of_params",
4321               new Object[] { this.getTitle() });
4322       af.setTitle(newTitle);
4323       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4324       {
4325         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4326         viewport.openSplitFrame(af, new Alignment(seqs));
4327       }
4328       else
4329       {
4330         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4331                 DEFAULT_HEIGHT);
4332       }
4333     }
4334   }
4335
4336   /**
4337    * Set the file format
4338    *
4339    * @param format
4340    */
4341   public void setFileFormat(FileFormatI format)
4342   {
4343     this.currentFileFormat = format;
4344   }
4345
4346   /**
4347    * Try to load a features file onto the alignment.
4348    *
4349    * @param file
4350    *          contents or path to retrieve file
4351    * @param sourceType
4352    *          access mode of file (see jalview.io.AlignFile)
4353    * @return true if features file was parsed correctly.
4354    */
4355   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4356   {
4357     return avc.parseFeaturesFile(file, sourceType,
4358             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4359
4360   }
4361
4362   @Override
4363   public void refreshFeatureUI(boolean enableIfNecessary)
4364   {
4365     // note - currently this is only still here rather than in the controller
4366     // because of the featureSettings hard reference that is yet to be
4367     // abstracted
4368     if (enableIfNecessary)
4369     {
4370       viewport.setShowSequenceFeatures(true);
4371       showSeqFeatures.setSelected(true);
4372     }
4373
4374   }
4375
4376   @Override
4377   public void dragEnter(DropTargetDragEvent evt)
4378   {
4379   }
4380
4381   @Override
4382   public void dragExit(DropTargetEvent evt)
4383   {
4384   }
4385
4386   @Override
4387   public void dragOver(DropTargetDragEvent evt)
4388   {
4389   }
4390
4391   @Override
4392   public void dropActionChanged(DropTargetDragEvent evt)
4393   {
4394   }
4395
4396   @Override
4397   public void drop(DropTargetDropEvent evt)
4398   {
4399     // JAL-1552 - acceptDrop required before getTransferable call for
4400     // Java's Transferable for native dnd
4401     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4402     Transferable t = evt.getTransferable();
4403     List<String> files = new ArrayList<>();
4404     List<DataSourceType> protocols = new ArrayList<>();
4405
4406     try
4407     {
4408       Desktop.transferFromDropTarget(files, protocols, evt, t);
4409     } catch (Exception e)
4410     {
4411       e.printStackTrace();
4412     }
4413     if (files != null)
4414     {
4415       try
4416       {
4417         // check to see if any of these files have names matching sequences in
4418         // the alignment
4419         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4420                 .getAlignment().getSequencesArray());
4421         /**
4422          * Object[] { String,SequenceI}
4423          */
4424         ArrayList<Object[]> filesmatched = new ArrayList<>();
4425         ArrayList<String> filesnotmatched = new ArrayList<>();
4426         for (int i = 0; i < files.size(); i++)
4427         {
4428           String file = files.get(i).toString();
4429           String pdbfn = "";
4430           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4431           if (protocol == DataSourceType.FILE)
4432           {
4433             File fl = new File(file);
4434             pdbfn = fl.getName();
4435           }
4436           else if (protocol == DataSourceType.URL)
4437           {
4438             URL url = new URL(file);
4439             pdbfn = url.getFile();
4440           }
4441           if (pdbfn.length() > 0)
4442           {
4443             // attempt to find a match in the alignment
4444             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4445             int l = 0, c = pdbfn.indexOf(".");
4446             while (mtch == null && c != -1)
4447             {
4448               do
4449               {
4450                 l = c;
4451               } while ((c = pdbfn.indexOf(".", l)) > l);
4452               if (l > -1)
4453               {
4454                 pdbfn = pdbfn.substring(0, l);
4455               }
4456               mtch = idm.findAllIdMatches(pdbfn);
4457             }
4458             if (mtch != null)
4459             {
4460               FileFormatI type = null;
4461               try
4462               {
4463                 type = new IdentifyFile().identify(file, protocol);
4464               } catch (Exception ex)
4465               {
4466                 type = null;
4467               }
4468               if (type != null && type.isStructureFile())
4469               {
4470                 filesmatched.add(new Object[] { file, protocol, mtch });
4471                 continue;
4472               }
4473             }
4474             // File wasn't named like one of the sequences or wasn't a PDB file.
4475             filesnotmatched.add(file);
4476           }
4477         }
4478         int assocfiles = 0;
4479         if (filesmatched.size() > 0)
4480         {
4481           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4482                   || JvOptionPane
4483                           .showConfirmDialog(
4484                                   this,
4485                                   MessageManager
4486                                           .formatMessage(
4487                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4488                                                   new Object[] { Integer
4489                                                           .valueOf(
4490                                                                   filesmatched
4491                                                                           .size())
4492                                                           .toString() }),
4493                                   MessageManager
4494                                           .getString("label.automatically_associate_structure_files_by_name"),
4495                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4496
4497           {
4498             for (Object[] fm : filesmatched)
4499             {
4500               // try and associate
4501               // TODO: may want to set a standard ID naming formalism for
4502               // associating PDB files which have no IDs.
4503               for (SequenceI toassoc : (SequenceI[]) fm[2])
4504               {
4505                 PDBEntry pe = new AssociatePdbFileWithSeq()
4506                         .associatePdbWithSeq((String) fm[0],
4507                                 (DataSourceType) fm[1], toassoc, false,
4508                                 Desktop.instance);
4509                 if (pe != null)
4510                 {
4511                   System.err.println("Associated file : "
4512                           + ((String) fm[0]) + " with "
4513                           + toassoc.getDisplayId(true));
4514                   assocfiles++;
4515                 }
4516               }
4517               alignPanel.paintAlignment(true);
4518             }
4519           }
4520         }
4521         if (filesnotmatched.size() > 0)
4522         {
4523           if (assocfiles > 0
4524                   && (Cache.getDefault(
4525                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4526                           .showConfirmDialog(
4527                                   this,
4528                                   "<html>"
4529                                           + MessageManager
4530                                                   .formatMessage(
4531                                                           "label.ignore_unmatched_dropped_files_info",
4532                                                           new Object[] { Integer
4533                                                                   .valueOf(
4534                                                                           filesnotmatched
4535                                                                                   .size())
4536                                                                   .toString() })
4537                                           + "</html>",
4538                                   MessageManager
4539                                           .getString("label.ignore_unmatched_dropped_files"),
4540                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4541           {
4542             return;
4543           }
4544           for (String fn : filesnotmatched)
4545           {
4546             loadJalviewDataFile(fn, null, null, null);
4547           }
4548
4549         }
4550       } catch (Exception ex)
4551       {
4552         ex.printStackTrace();
4553       }
4554     }
4555   }
4556
4557   /**
4558    * Attempt to load a "dropped" file or URL string, by testing in turn for
4559    * <ul>
4560    * <li>an Annotation file</li>
4561    * <li>a JNet file</li>
4562    * <li>a features file</li>
4563    * <li>else try to interpret as an alignment file</li>
4564    * </ul>
4565    *
4566    * @param file
4567    *          either a filename or a URL string.
4568    */
4569   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4570           FileFormatI format, SequenceI assocSeq)
4571   {
4572     try
4573     {
4574       if (sourceType == null)
4575       {
4576         sourceType = FormatAdapter.checkProtocol(file);
4577       }
4578       // if the file isn't identified, or not positively identified as some
4579       // other filetype (PFAM is default unidentified alignment file type) then
4580       // try to parse as annotation.
4581       boolean isAnnotation = (format == null || FileFormat.Pfam
4582               .equals(format)) ? new AnnotationFile()
4583               .annotateAlignmentView(viewport, file, sourceType) : false;
4584
4585       if (!isAnnotation)
4586       {
4587         // first see if its a T-COFFEE score file
4588         TCoffeeScoreFile tcf = null;
4589         try
4590         {
4591           tcf = new TCoffeeScoreFile(file, sourceType);
4592           if (tcf.isValid())
4593           {
4594             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4595             {
4596               buildColourMenu();
4597               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4598               isAnnotation = true;
4599               statusBar
4600                       .setText(MessageManager
4601                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4602             }
4603             else
4604             {
4605               // some problem - if no warning its probable that the ID matching
4606               // process didn't work
4607               JvOptionPane
4608                       .showMessageDialog(
4609                               Desktop.desktop,
4610                               tcf.getWarningMessage() == null ? MessageManager
4611                                       .getString("label.check_file_matches_sequence_ids_alignment")
4612                                       : tcf.getWarningMessage(),
4613                               MessageManager
4614                                       .getString("label.problem_reading_tcoffee_score_file"),
4615                               JvOptionPane.WARNING_MESSAGE);
4616             }
4617           }
4618           else
4619           {
4620             tcf = null;
4621           }
4622         } catch (Exception x)
4623         {
4624           Cache.log
4625                   .debug("Exception when processing data source as T-COFFEE score file",
4626                           x);
4627           tcf = null;
4628         }
4629         if (tcf == null)
4630         {
4631           // try to see if its a JNet 'concise' style annotation file *before*
4632           // we
4633           // try to parse it as a features file
4634           if (format == null)
4635           {
4636             format = new IdentifyFile().identify(file, sourceType);
4637           }
4638           if (FileFormat.ScoreMatrix == format)
4639           {
4640             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4641                     sourceType));
4642             sm.parse();
4643             // todo: i18n this message
4644             statusBar
4645                     .setText(MessageManager.formatMessage(
4646                             "label.successfully_loaded_matrix",
4647                             sm.getMatrixName()));
4648           }
4649           else if (FileFormat.Jnet.equals(format))
4650           {
4651             JPredFile predictions = new JPredFile(file, sourceType);
4652             new JnetAnnotationMaker();
4653             JnetAnnotationMaker.add_annotation(predictions,
4654                     viewport.getAlignment(), 0, false);
4655             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4656             viewport.getAlignment().setSeqrep(repseq);
4657             HiddenColumns cs = new HiddenColumns();
4658             cs.hideInsertionsFor(repseq);
4659             viewport.getAlignment().setHiddenColumns(cs);
4660             isAnnotation = true;
4661           }
4662           // else if (IdentifyFile.FeaturesFile.equals(format))
4663           else if (FileFormat.Features.equals(format))
4664           {
4665             if (parseFeaturesFile(file, sourceType))
4666             {
4667               alignPanel.paintAlignment(true);
4668             }
4669           }
4670           else
4671           {
4672             new FileLoader().LoadFile(viewport, file, sourceType, format);
4673           }
4674         }
4675       }
4676       if (isAnnotation)
4677       {
4678
4679         alignPanel.adjustAnnotationHeight();
4680         viewport.updateSequenceIdColours();
4681         buildSortByAnnotationScoresMenu();
4682         alignPanel.paintAlignment(true);
4683       }
4684     } catch (Exception ex)
4685     {
4686       ex.printStackTrace();
4687     } catch (OutOfMemoryError oom)
4688     {
4689       try
4690       {
4691         System.gc();
4692       } catch (Exception x)
4693       {
4694       }
4695       new OOMWarning(
4696               "loading data "
4697                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4698                               : "using " + sourceType + " from " + file)
4699                               : ".")
4700                       + (format != null ? "(parsing as '" + format
4701                               + "' file)" : ""), oom, Desktop.desktop);
4702     }
4703   }
4704
4705   /**
4706    * Method invoked by the ChangeListener on the tabbed pane, in other words
4707    * when a different tabbed pane is selected by the user or programmatically.
4708    */
4709   @Override
4710   public void tabSelectionChanged(int index)
4711   {
4712     if (index > -1)
4713     {
4714       alignPanel = alignPanels.get(index);
4715       viewport = alignPanel.av;
4716       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4717       setMenusFromViewport(viewport);
4718     }
4719
4720     /*
4721      * 'focus' any colour slider that is open to the selected viewport
4722      */
4723     if (viewport.getConservationSelected())
4724     {
4725       SliderPanel.setConservationSlider(alignPanel,
4726               viewport.getResidueShading(), alignPanel.getViewName());
4727     }
4728     else
4729     {
4730       SliderPanel.hideConservationSlider();
4731     }
4732     if (viewport.getAbovePIDThreshold())
4733     {
4734       SliderPanel.setPIDSliderSource(alignPanel,
4735               viewport.getResidueShading(), alignPanel.getViewName());
4736     }
4737     else
4738     {
4739       SliderPanel.hidePIDSlider();
4740     }
4741
4742     /*
4743      * If there is a frame linked to this one in a SplitPane, switch it to the
4744      * same view tab index. No infinite recursion of calls should happen, since
4745      * tabSelectionChanged() should not get invoked on setting the selected
4746      * index to an unchanged value. Guard against setting an invalid index
4747      * before the new view peer tab has been created.
4748      */
4749     final AlignViewportI peer = viewport.getCodingComplement();
4750     if (peer != null)
4751     {
4752       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4753       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4754       {
4755         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4756       }
4757     }
4758   }
4759
4760   /**
4761    * On right mouse click on view tab, prompt for and set new view name.
4762    */
4763   @Override
4764   public void tabbedPane_mousePressed(MouseEvent e)
4765   {
4766     if (e.isPopupTrigger())
4767     {
4768       String msg = MessageManager.getString("label.enter_view_name");
4769       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4770               JvOptionPane.QUESTION_MESSAGE);
4771
4772       if (reply != null)
4773       {
4774         viewport.viewName = reply;
4775         // TODO warn if reply is in getExistingViewNames()?
4776         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4777       }
4778     }
4779   }
4780
4781   public AlignViewport getCurrentView()
4782   {
4783     return viewport;
4784   }
4785
4786   /**
4787    * Open the dialog for regex description parsing.
4788    */
4789   @Override
4790   protected void extractScores_actionPerformed(ActionEvent e)
4791   {
4792     ParseProperties pp = new jalview.analysis.ParseProperties(
4793             viewport.getAlignment());
4794     // TODO: verify regex and introduce GUI dialog for version 2.5
4795     // if (pp.getScoresFromDescription("col", "score column ",
4796     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4797     // true)>0)
4798     if (pp.getScoresFromDescription("description column",
4799             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4800     {
4801       buildSortByAnnotationScoresMenu();
4802     }
4803   }
4804
4805   /*
4806    * (non-Javadoc)
4807    *
4808    * @see
4809    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4810    * )
4811    */
4812   @Override
4813   protected void showDbRefs_actionPerformed(ActionEvent e)
4814   {
4815     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4816   }
4817
4818   /*
4819    * (non-Javadoc)
4820    *
4821    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4822    * ActionEvent)
4823    */
4824   @Override
4825   protected void showNpFeats_actionPerformed(ActionEvent e)
4826   {
4827     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4828   }
4829
4830   /**
4831    * find the viewport amongst the tabs in this alignment frame and close that
4832    * tab
4833    *
4834    * @param av
4835    */
4836   public boolean closeView(AlignViewportI av)
4837   {
4838     if (viewport == av)
4839     {
4840       this.closeMenuItem_actionPerformed(false);
4841       return true;
4842     }
4843     Component[] comp = tabbedPane.getComponents();
4844     for (int i = 0; comp != null && i < comp.length; i++)
4845     {
4846       if (comp[i] instanceof AlignmentPanel)
4847       {
4848         if (((AlignmentPanel) comp[i]).av == av)
4849         {
4850           // close the view.
4851           closeView((AlignmentPanel) comp[i]);
4852           return true;
4853         }
4854       }
4855     }
4856     return false;
4857   }
4858
4859   protected void build_fetchdbmenu(JMenu webService)
4860   {
4861     // Temporary hack - DBRef Fetcher always top level ws entry.
4862     // TODO We probably want to store a sequence database checklist in
4863     // preferences and have checkboxes.. rather than individual sources selected
4864     // here
4865     final JMenu rfetch = new JMenu(
4866             MessageManager.getString("action.fetch_db_references"));
4867     rfetch.setToolTipText(MessageManager
4868             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4869     webService.add(rfetch);
4870
4871     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4872             MessageManager.getString("option.trim_retrieved_seqs"));
4873     trimrs.setToolTipText(MessageManager
4874             .getString("label.trim_retrieved_sequences"));
4875     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4876     trimrs.addActionListener(new ActionListener()
4877     {
4878       @Override
4879       public void actionPerformed(ActionEvent e)
4880       {
4881         trimrs.setSelected(trimrs.isSelected());
4882         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4883                 Boolean.valueOf(trimrs.isSelected()).toString());
4884       };
4885     });
4886     rfetch.add(trimrs);
4887     JMenuItem fetchr = new JMenuItem(
4888             MessageManager.getString("label.standard_databases"));
4889     fetchr.setToolTipText(MessageManager
4890             .getString("label.fetch_embl_uniprot"));
4891     fetchr.addActionListener(new ActionListener()
4892     {
4893
4894       @Override
4895       public void actionPerformed(ActionEvent e)
4896       {
4897         new Thread(new Runnable()
4898         {
4899           @Override
4900           public void run()
4901           {
4902             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4903                     .getAlignment().isNucleotide();
4904             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4905                     .getSequenceSelection(), alignPanel.alignFrame, null,
4906                     alignPanel.alignFrame.featureSettings, isNucleotide);
4907             dbRefFetcher.addListener(new FetchFinishedListenerI()
4908             {
4909               @Override
4910               public void finished()
4911               {
4912                 AlignFrame.this.setMenusForViewport();
4913               }
4914             });
4915             dbRefFetcher.fetchDBRefs(false);
4916           }
4917         }).start();
4918
4919       }
4920
4921     });
4922     rfetch.add(fetchr);
4923     final AlignFrame me = this;
4924     new Thread(new Runnable()
4925     {
4926       @Override
4927       public void run()
4928       {
4929         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4930                 .getSequenceFetcherSingleton(me);
4931         javax.swing.SwingUtilities.invokeLater(new Runnable()
4932         {
4933           @Override
4934           public void run()
4935           {
4936             String[] dbclasses = sf.getOrderedSupportedSources();
4937             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4938             // jalview.util.QuickSort.sort(otherdb, otherdb);
4939             List<DbSourceProxy> otherdb;
4940             JMenu dfetch = new JMenu();
4941             JMenu ifetch = new JMenu();
4942             JMenuItem fetchr = null;
4943             int comp = 0, icomp = 0, mcomp = 15;
4944             String mname = null;
4945             int dbi = 0;
4946             for (String dbclass : dbclasses)
4947             {
4948               otherdb = sf.getSourceProxy(dbclass);
4949               // add a single entry for this class, or submenu allowing 'fetch
4950               // all' or pick one
4951               if (otherdb == null || otherdb.size() < 1)
4952               {
4953                 continue;
4954               }
4955               // List<DbSourceProxy> dbs=otherdb;
4956               // otherdb=new ArrayList<DbSourceProxy>();
4957               // for (DbSourceProxy db:dbs)
4958               // {
4959               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4960               // }
4961               if (mname == null)
4962               {
4963                 mname = "From " + dbclass;
4964               }
4965               if (otherdb.size() == 1)
4966               {
4967                 final DbSourceProxy[] dassource = otherdb
4968                         .toArray(new DbSourceProxy[0]);
4969                 DbSourceProxy src = otherdb.get(0);
4970                 fetchr = new JMenuItem(src.getDbSource());
4971                 fetchr.addActionListener(new ActionListener()
4972                 {
4973
4974                   @Override
4975                   public void actionPerformed(ActionEvent e)
4976                   {
4977                     new Thread(new Runnable()
4978                     {
4979
4980                       @Override
4981                       public void run()
4982                       {
4983                         boolean isNucleotide = alignPanel.alignFrame
4984                                 .getViewport().getAlignment()
4985                                 .isNucleotide();
4986                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4987                                 alignPanel.av.getSequenceSelection(),
4988                                 alignPanel.alignFrame, dassource,
4989                                 alignPanel.alignFrame.featureSettings,
4990                                 isNucleotide);
4991                         dbRefFetcher
4992                                 .addListener(new FetchFinishedListenerI()
4993                                 {
4994                                   @Override
4995                                   public void finished()
4996                                   {
4997                                     AlignFrame.this.setMenusForViewport();
4998                                   }
4999                                 });
5000                         dbRefFetcher.fetchDBRefs(false);
5001                       }
5002                     }).start();
5003                   }
5004
5005                 });
5006                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5007                         MessageManager.formatMessage(
5008                                 "label.fetch_retrieve_from",
5009                                 new Object[] { src.getDbName() })));
5010                 dfetch.add(fetchr);
5011                 comp++;
5012               }
5013               else
5014               {
5015                 final DbSourceProxy[] dassource = otherdb
5016                         .toArray(new DbSourceProxy[0]);
5017                 // fetch all entry
5018                 DbSourceProxy src = otherdb.get(0);
5019                 fetchr = new JMenuItem(MessageManager.formatMessage(
5020                         "label.fetch_all_param",
5021                         new Object[] { src.getDbSource() }));
5022                 fetchr.addActionListener(new ActionListener()
5023                 {
5024                   @Override
5025                   public void actionPerformed(ActionEvent e)
5026                   {
5027                     new Thread(new Runnable()
5028                     {
5029
5030                       @Override
5031                       public void run()
5032                       {
5033                         boolean isNucleotide = alignPanel.alignFrame
5034                                 .getViewport().getAlignment()
5035                                 .isNucleotide();
5036                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5037                                 alignPanel.av.getSequenceSelection(),
5038                                 alignPanel.alignFrame, dassource,
5039                                 alignPanel.alignFrame.featureSettings,
5040                                 isNucleotide);
5041                         dbRefFetcher
5042                                 .addListener(new FetchFinishedListenerI()
5043                                 {
5044                                   @Override
5045                                   public void finished()
5046                                   {
5047                                     AlignFrame.this.setMenusForViewport();
5048                                   }
5049                                 });
5050                         dbRefFetcher.fetchDBRefs(false);
5051                       }
5052                     }).start();
5053                   }
5054                 });
5055
5056                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5057                         MessageManager.formatMessage(
5058                                 "label.fetch_retrieve_from_all_sources",
5059                                 new Object[] {
5060                                     Integer.valueOf(otherdb.size())
5061                                             .toString(), src.getDbSource(),
5062                                     src.getDbName() })));
5063                 dfetch.add(fetchr);
5064                 comp++;
5065                 // and then build the rest of the individual menus
5066                 ifetch = new JMenu(MessageManager.formatMessage(
5067                         "label.source_from_db_source",
5068                         new Object[] { src.getDbSource() }));
5069                 icomp = 0;
5070                 String imname = null;
5071                 int i = 0;
5072                 for (DbSourceProxy sproxy : otherdb)
5073                 {
5074                   String dbname = sproxy.getDbName();
5075                   String sname = dbname.length() > 5 ? dbname.substring(0,
5076                           5) + "..." : dbname;
5077                   String msname = dbname.length() > 10 ? dbname.substring(
5078                           0, 10) + "..." : dbname;
5079                   if (imname == null)
5080                   {
5081                     imname = MessageManager.formatMessage(
5082                             "label.from_msname", new Object[] { sname });
5083                   }
5084                   fetchr = new JMenuItem(msname);
5085                   final DbSourceProxy[] dassrc = { sproxy };
5086                   fetchr.addActionListener(new ActionListener()
5087                   {
5088
5089                     @Override
5090                     public void actionPerformed(ActionEvent e)
5091                     {
5092                       new Thread(new Runnable()
5093                       {
5094
5095                         @Override
5096                         public void run()
5097                         {
5098                           boolean isNucleotide = alignPanel.alignFrame
5099                                   .getViewport().getAlignment()
5100                                   .isNucleotide();
5101                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5102                                   alignPanel.av.getSequenceSelection(),
5103                                   alignPanel.alignFrame, dassrc,
5104                                   alignPanel.alignFrame.featureSettings,
5105                                   isNucleotide);
5106                           dbRefFetcher
5107                                   .addListener(new FetchFinishedListenerI()
5108                                   {
5109                                     @Override
5110                                     public void finished()
5111                                     {
5112                                       AlignFrame.this.setMenusForViewport();
5113                                     }
5114                                   });
5115                           dbRefFetcher.fetchDBRefs(false);
5116                         }
5117                       }).start();
5118                     }
5119
5120                   });
5121                   fetchr.setToolTipText("<html>"
5122                           + MessageManager.formatMessage(
5123                                   "label.fetch_retrieve_from", new Object[]
5124                                   { dbname }));
5125                   ifetch.add(fetchr);
5126                   ++i;
5127                   if (++icomp >= mcomp || i == (otherdb.size()))
5128                   {
5129                     ifetch.setText(MessageManager.formatMessage(
5130                             "label.source_to_target", imname, sname));
5131                     dfetch.add(ifetch);
5132                     ifetch = new JMenu();
5133                     imname = null;
5134                     icomp = 0;
5135                     comp++;
5136                   }
5137                 }
5138               }
5139               ++dbi;
5140               if (comp >= mcomp || dbi >= (dbclasses.length))
5141               {
5142                 dfetch.setText(MessageManager.formatMessage(
5143                         "label.source_to_target", mname, dbclass));
5144                 rfetch.add(dfetch);
5145                 dfetch = new JMenu();
5146                 mname = null;
5147                 comp = 0;
5148               }
5149             }
5150           }
5151         });
5152       }
5153     }).start();
5154
5155   }
5156
5157   /**
5158    * Left justify the whole alignment.
5159    */
5160   @Override
5161   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5162   {
5163     AlignmentI al = viewport.getAlignment();
5164     al.justify(false);
5165     viewport.firePropertyChange("alignment", null, al);
5166   }
5167
5168   /**
5169    * Right justify the whole alignment.
5170    */
5171   @Override
5172   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5173   {
5174     AlignmentI al = viewport.getAlignment();
5175     al.justify(true);
5176     viewport.firePropertyChange("alignment", null, al);
5177   }
5178
5179   @Override
5180   public void setShowSeqFeatures(boolean b)
5181   {
5182     showSeqFeatures.setSelected(b);
5183     viewport.setShowSequenceFeatures(b);
5184   }
5185
5186   /*
5187    * (non-Javadoc)
5188    *
5189    * @see
5190    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5191    * awt.event.ActionEvent)
5192    */
5193   @Override
5194   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5195   {
5196     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5197     alignPanel.paintAlignment(true);
5198   }
5199
5200   /*
5201    * (non-Javadoc)
5202    *
5203    * @see
5204    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5205    * .ActionEvent)
5206    */
5207   @Override
5208   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5209   {
5210     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5211     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5212
5213   }
5214
5215   /*
5216    * (non-Javadoc)
5217    *
5218    * @see
5219    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5220    * .event.ActionEvent)
5221    */
5222   @Override
5223   protected void showGroupConservation_actionPerformed(ActionEvent e)
5224   {
5225     viewport.setShowGroupConservation(showGroupConservation.getState());
5226     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5227   }
5228
5229   /*
5230    * (non-Javadoc)
5231    *
5232    * @see
5233    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5234    * .event.ActionEvent)
5235    */
5236   @Override
5237   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5238   {
5239     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5240     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5241   }
5242
5243   /*
5244    * (non-Javadoc)
5245    *
5246    * @see
5247    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5248    * .event.ActionEvent)
5249    */
5250   @Override
5251   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5252   {
5253     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5254     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5255   }
5256
5257   @Override
5258   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5259   {
5260     showSequenceLogo.setState(true);
5261     viewport.setShowSequenceLogo(true);
5262     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5263     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5264   }
5265
5266   @Override
5267   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5268   {
5269     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5270   }
5271
5272   /*
5273    * (non-Javadoc)
5274    *
5275    * @see
5276    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5277    * .event.ActionEvent)
5278    */
5279   @Override
5280   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5281   {
5282     if (avc.makeGroupsFromSelection())
5283     {
5284       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5285       alignPanel.updateAnnotation();
5286       alignPanel.paintAlignment(true);
5287     }
5288   }
5289
5290   public void clearAlignmentSeqRep()
5291   {
5292     // TODO refactor alignmentseqrep to controller
5293     if (viewport.getAlignment().hasSeqrep())
5294     {
5295       viewport.getAlignment().setSeqrep(null);
5296       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5297       alignPanel.updateAnnotation();
5298       alignPanel.paintAlignment(true);
5299     }
5300   }
5301
5302   @Override
5303   protected void createGroup_actionPerformed(ActionEvent e)
5304   {
5305     if (avc.createGroup())
5306     {
5307       alignPanel.alignmentChanged();
5308     }
5309   }
5310
5311   @Override
5312   protected void unGroup_actionPerformed(ActionEvent e)
5313   {
5314     if (avc.unGroup())
5315     {
5316       alignPanel.alignmentChanged();
5317     }
5318   }
5319
5320   /**
5321    * make the given alignmentPanel the currently selected tab
5322    *
5323    * @param alignmentPanel
5324    */
5325   public void setDisplayedView(AlignmentPanel alignmentPanel)
5326   {
5327     if (!viewport.getSequenceSetId().equals(
5328             alignmentPanel.av.getSequenceSetId()))
5329     {
5330       throw new Error(
5331               MessageManager
5332                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5333     }
5334     if (tabbedPane != null
5335             && tabbedPane.getTabCount() > 0
5336             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5337                     .getSelectedIndex())
5338     {
5339       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5340     }
5341   }
5342
5343   /**
5344    * Action on selection of menu options to Show or Hide annotations.
5345    *
5346    * @param visible
5347    * @param forSequences
5348    *          update sequence-related annotations
5349    * @param forAlignment
5350    *          update non-sequence-related annotations
5351    */
5352   @Override
5353   protected void setAnnotationsVisibility(boolean visible,
5354           boolean forSequences, boolean forAlignment)
5355   {
5356     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5357             .getAlignmentAnnotation();
5358     if (anns == null)
5359     {
5360       return;
5361     }
5362     for (AlignmentAnnotation aa : anns)
5363     {
5364       /*
5365        * don't display non-positional annotations on an alignment
5366        */
5367       if (aa.annotations == null)
5368       {
5369         continue;
5370       }
5371       boolean apply = (aa.sequenceRef == null && forAlignment)
5372               || (aa.sequenceRef != null && forSequences);
5373       if (apply)
5374       {
5375         aa.visible = visible;
5376       }
5377     }
5378     alignPanel.validateAnnotationDimensions(true);
5379     alignPanel.alignmentChanged();
5380   }
5381
5382   /**
5383    * Store selected annotation sort order for the view and repaint.
5384    */
5385   @Override
5386   protected void sortAnnotations_actionPerformed()
5387   {
5388     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5389     this.alignPanel.av
5390             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5391     alignPanel.paintAlignment(true);
5392   }
5393
5394   /**
5395    *
5396    * @return alignment panels in this alignment frame
5397    */
5398   public List<? extends AlignmentViewPanel> getAlignPanels()
5399   {
5400     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5401   }
5402
5403   /**
5404    * Open a new alignment window, with the cDNA associated with this (protein)
5405    * alignment, aligned as is the protein.
5406    */
5407   protected void viewAsCdna_actionPerformed()
5408   {
5409     // TODO no longer a menu action - refactor as required
5410     final AlignmentI alignment = getViewport().getAlignment();
5411     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5412     if (mappings == null)
5413     {
5414       return;
5415     }
5416     List<SequenceI> cdnaSeqs = new ArrayList<>();
5417     for (SequenceI aaSeq : alignment.getSequences())
5418     {
5419       for (AlignedCodonFrame acf : mappings)
5420       {
5421         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5422         if (dnaSeq != null)
5423         {
5424           /*
5425            * There is a cDNA mapping for this protein sequence - add to new
5426            * alignment. It will share the same dataset sequence as other mapped
5427            * cDNA (no new mappings need to be created).
5428            */
5429           final Sequence newSeq = new Sequence(dnaSeq);
5430           newSeq.setDatasetSequence(dnaSeq);
5431           cdnaSeqs.add(newSeq);
5432         }
5433       }
5434     }
5435     if (cdnaSeqs.size() == 0)
5436     {
5437       // show a warning dialog no mapped cDNA
5438       return;
5439     }
5440     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5441             .size()]));
5442     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5443             AlignFrame.DEFAULT_HEIGHT);
5444     cdna.alignAs(alignment);
5445     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5446             + this.title;
5447     Desktop.addInternalFrame(alignFrame, newtitle,
5448             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5449   }
5450
5451   /**
5452    * Set visibility of dna/protein complement view (available when shown in a
5453    * split frame).
5454    *
5455    * @param show
5456    */
5457   @Override
5458   protected void showComplement_actionPerformed(boolean show)
5459   {
5460     SplitContainerI sf = getSplitViewContainer();
5461     if (sf != null)
5462     {
5463       sf.setComplementVisible(this, show);
5464     }
5465   }
5466
5467   /**
5468    * Generate the reverse (optionally complemented) of the selected sequences,
5469    * and add them to the alignment
5470    */
5471   @Override
5472   protected void showReverse_actionPerformed(boolean complement)
5473   {
5474     AlignmentI al = null;
5475     try
5476     {
5477       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5478       al = dna.reverseCdna(complement);
5479       viewport.addAlignment(al, "");
5480       addHistoryItem(new EditCommand(
5481               MessageManager.getString("label.add_sequences"),
5482               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5483               viewport.getAlignment()));
5484     } catch (Exception ex)
5485     {
5486       System.err.println(ex.getMessage());
5487       return;
5488     }
5489   }
5490
5491   /**
5492    * Try to run a script in the Groovy console, having first ensured that this
5493    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5494    * be targeted at this alignment.
5495    */
5496   @Override
5497   protected void runGroovy_actionPerformed()
5498   {
5499     Jalview.setCurrentAlignFrame(this);
5500     groovy.ui.Console console = Desktop.getGroovyConsole();
5501     if (console != null)
5502     {
5503       try
5504       {
5505         console.runScript();
5506       } catch (Exception ex)
5507       {
5508         System.err.println((ex.toString()));
5509         JvOptionPane
5510                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5511                         .getString("label.couldnt_run_groovy_script"),
5512                         MessageManager
5513                                 .getString("label.groovy_support_failed"),
5514                         JvOptionPane.ERROR_MESSAGE);
5515       }
5516     }
5517     else
5518     {
5519       System.err.println("Can't run Groovy script as console not found");
5520     }
5521   }
5522
5523   /**
5524    * Hides columns containing (or not containing) a specified feature, provided
5525    * that would not leave all columns hidden
5526    *
5527    * @param featureType
5528    * @param columnsContaining
5529    * @return
5530    */
5531   public boolean hideFeatureColumns(String featureType,
5532           boolean columnsContaining)
5533   {
5534     boolean notForHiding = avc.markColumnsContainingFeatures(
5535             columnsContaining, false, false, featureType);
5536     if (notForHiding)
5537     {
5538       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5539               false, featureType))
5540       {
5541         getViewport().hideSelectedColumns();
5542         return true;
5543       }
5544     }
5545     return false;
5546   }
5547
5548   @Override
5549   protected void selectHighlightedColumns_actionPerformed(
5550           ActionEvent actionEvent)
5551   {
5552     // include key modifier check in case user selects from menu
5553     avc.markHighlightedColumns(
5554             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5555             true,
5556             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5557   }
5558
5559   /**
5560    * Rebuilds the Colour menu, including any user-defined colours which have
5561    * been loaded either on startup or during the session
5562    */
5563   public void buildColourMenu()
5564   {
5565     colourMenu.removeAll();
5566
5567     colourMenu.add(applyToAllGroups);
5568     colourMenu.add(textColour);
5569     colourMenu.addSeparator();
5570
5571     ColourMenuHelper.addMenuItems(colourMenu, this,
5572             viewport.getAlignment(), false);
5573
5574     colourMenu.addSeparator();
5575     colourMenu.add(conservationMenuItem);
5576     colourMenu.add(modifyConservation);
5577     colourMenu.add(abovePIDThreshold);
5578     colourMenu.add(modifyPID);
5579     colourMenu.add(annotationColour);
5580
5581     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5582     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5583   }
5584
5585   /**
5586    * Open a dialog (if not already open) that allows the user to select and
5587    * calculate PCA or Tree analysis
5588    */
5589   protected void openTreePcaDialog()
5590   {
5591     if (alignPanel.getCalculationDialog() == null)
5592     {
5593       new CalculationChooser(AlignFrame.this);
5594     }
5595   }
5596 }
5597
5598 class PrintThread extends Thread
5599 {
5600   AlignmentPanel ap;
5601
5602   public PrintThread(AlignmentPanel ap)
5603   {
5604     this.ap = ap;
5605   }
5606
5607   static PageFormat pf;
5608
5609   @Override
5610   public void run()
5611   {
5612     PrinterJob printJob = PrinterJob.getPrinterJob();
5613
5614     if (pf != null)
5615     {
5616       printJob.setPrintable(ap, pf);
5617     }
5618     else
5619     {
5620       printJob.setPrintable(ap);
5621     }
5622
5623     if (printJob.printDialog())
5624     {
5625       try
5626       {
5627         printJob.print();
5628       } catch (Exception PrintException)
5629       {
5630         PrintException.printStackTrace();
5631       }
5632     }
5633   }
5634 }