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