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.HiddenMarkovModel;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.hmmer.HMMAlignThread;
  67 import jalview.hmmer.HMMBuildThread;
  68 import jalview.io.AlignmentProperties;
  69 import jalview.io.AnnotationFile;
  70 import jalview.io.BioJsHTMLOutput;
  71 import jalview.io.DataSourceType;
  72 import jalview.io.FileFormat;
  73 import jalview.io.FileFormatI;
  74 import jalview.io.FileFormats;
  75 import jalview.io.FileLoader;
  76 import jalview.io.FileParse;
  77 import jalview.io.FormatAdapter;
  78 import jalview.io.HMMFile;
  79 import jalview.io.HtmlSvgOutput;
  80 import jalview.io.IdentifyFile;
  81 import jalview.io.JPredFile;
  82 import jalview.io.JalviewFileChooser;
  83 import jalview.io.JalviewFileView;
  84 import jalview.io.JnetAnnotationMaker;
  85 import jalview.io.NewickFile;
  86 import jalview.io.ScoreMatrixFile;
  87 import jalview.io.TCoffeeScoreFile;
  88 import jalview.jbgui.GAlignFrame;
  89 import jalview.schemes.ColourSchemeI;
  90 import jalview.schemes.ColourSchemes;
  91 import jalview.schemes.ResidueColourScheme;
  92 import jalview.schemes.TCoffeeColourScheme;
  93 import jalview.util.MessageManager;
  94 import jalview.viewmodel.AlignmentViewport;
  95 import jalview.viewmodel.ViewportRanges;
  96 import jalview.ws.DBRefFetcher;
  97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  98 import jalview.ws.jws1.Discoverer;
  99 import jalview.ws.jws2.Jws2Discoverer;
 100 import jalview.ws.jws2.jabaws2.Jws2Instance;
 101 import jalview.ws.seqfetcher.DbSourceProxy;
 102
 103 import java.awt.BorderLayout;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseEvent;
 125 import java.awt.print.PageFormat;
 126 import java.awt.print.PrinterJob;
 127 import java.beans.PropertyChangeEvent;
 128 import java.io.File;
 129 import java.io.FileWriter;
 130 import java.io.IOException;
 131 import java.io.PrintWriter;
 132 import java.net.URL;
 133 import java.util.ArrayList;
 134 import java.util.Arrays;
 135 import java.util.Deque;
 136 import java.util.Enumeration;
 137 import java.util.HashMap;
 138 import java.util.Hashtable;
 139 import java.util.List;
 140 import java.util.Map;
 141 import java.util.Vector;
 142
 143 import javax.swing.JCheckBoxMenuItem;
 144 import javax.swing.JEditorPane;
 145 import javax.swing.JInternalFrame;
 146 import javax.swing.JLayeredPane;
 147 import javax.swing.JMenu;
 148 import javax.swing.JMenuItem;
 149 import javax.swing.JOptionPane;
 150 import javax.swing.JScrollPane;
 151 import javax.swing.SwingUtilities;
 152
 153 /**
 154  * DOCUMENT ME!
 155  *
 156  * @author $author$
 157  * @version $Revision$
 158  */
 159 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 160         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 161 {
 162
 163   Map<String, Float> distribution = new HashMap<>(); // temporary
 164
 165   public static final int DEFAULT_WIDTH = 700;
 166
 167   public static final int DEFAULT_HEIGHT = 500;
 168
 169   boolean autoAlignNewSequences;
 170
 171   boolean recurring;
 172
 173   /*
 174    * The currently displayed panel (selected tabbed view if more than one)
 175    */
 176   public AlignmentPanel alignPanel;
 177
 178   AlignViewport viewport;
 179
 180   ViewportRanges vpRanges;
 181
 182   public AlignViewControllerI avc;
 183
 184   List<AlignmentPanel> alignPanels = new ArrayList<>();
 185
 186   /**
 187    * Last format used to load or save alignments in this window
 188    */
 189   FileFormatI currentFileFormat = null;
 190
 191   /**
 192    * Current filename for this alignment
 193    */
 194   String fileName = null;
 195
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width and height.
 199    *
 200    * @param al
 201    * @param width
 202    * @param height
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height)
 205   {
 206     this(al, null, width, height);
 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    */
 218   public AlignFrame(AlignmentI al, int width, int height,
 219           String sequenceSetId)
 220   {
 221     this(al, null, width, height, sequenceSetId);
 222   }
 223
 224   /**
 225    * Creates a new AlignFrame object with specific width, height and
 226    * sequenceSetId
 227    *
 228    * @param al
 229    * @param width
 230    * @param height
 231    * @param sequenceSetId
 232    * @param viewId
 233    */
 234   public AlignFrame(AlignmentI al, int width, int height,
 235           String sequenceSetId, String viewId)
 236   {
 237     this(al, null, width, height, sequenceSetId, viewId);
 238   }
 239
 240   /**
 241    * new alignment window with hidden columns
 242    *
 243    * @param al
 244    *          AlignmentI
 245    * @param hiddenColumns
 246    *          ColumnSelection or null
 247    * @param width
 248    *          Width of alignment frame
 249    * @param height
 250    *          height of frame.
 251    */
 252   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 253           int width, int height)
 254   {
 255     this(al, hiddenColumns, width, height, null);
 256   }
 257
 258   /**
 259    * Create alignment frame for al with hiddenColumns, a specific width and
 260    * height, and specific sequenceId
 261    *
 262    * @param al
 263    * @param hiddenColumns
 264    * @param width
 265    * @param height
 266    * @param sequenceSetId
 267    *          (may be null)
 268    */
 269   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 270           int width, int height, String sequenceSetId)
 271   {
 272     this(al, hiddenColumns, width, height, sequenceSetId, null);
 273   }
 274
 275   /**
 276    * Create alignment frame for al with hiddenColumns, a specific width and
 277    * height, and specific sequenceId
 278    *
 279    * @param al
 280    * @param hiddenColumns
 281    * @param width
 282    * @param height
 283    * @param sequenceSetId
 284    *          (may be null)
 285    * @param viewId
 286    *          (may be null)
 287    */
 288   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 289           int width, int height, String sequenceSetId, String viewId)
 290   {
 291     setSize(width, height);
 292
 293     if (al.getDataset() == null)
 294     {
 295       al.setDataset(null);
 296     }
 297
 298     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 299
 300     alignPanel = new AlignmentPanel(this, viewport);
 301
 302     addAlignmentPanel(alignPanel, true);
 303     init();
 304   }
 305
 306   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 307           HiddenColumns hiddenColumns, int width, int height)
 308   {
 309     setSize(width, height);
 310
 311     if (al.getDataset() == null)
 312     {
 313       al.setDataset(null);
 314     }
 315
 316     viewport = new AlignViewport(al, hiddenColumns);
 317
 318     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 319     {
 320       viewport.hideSequence(hiddenSeqs);
 321     }
 322     alignPanel = new AlignmentPanel(this, viewport);
 323     addAlignmentPanel(alignPanel, true);
 324     init();
 325   }
 326
 327   /**
 328    * Make a new AlignFrame from existing alignmentPanels
 329    *
 330    * @param ap
 331    *          AlignmentPanel
 332    * @param av
 333    *          AlignViewport
 334    */
 335   public AlignFrame(AlignmentPanel ap)
 336   {
 337     viewport = ap.av;
 338     alignPanel = ap;
 339     addAlignmentPanel(ap, false);
 340     init();
 341   }
 342
 343   public void setIsRecurring(boolean status)
 344   {
 345     recurring = status;
 346   }
 347
 348   /**
 349    * initalise the alignframe from the underlying viewport data and the
 350    * configurations
 351    */
 352   void init()
 353   {
 354     if (!Jalview.isHeadlessMode())
 355     {
 356       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 357     }
 358
 359     vpRanges = viewport.getRanges();
 360     avc = new jalview.controller.AlignViewController(this, viewport,
 361             alignPanel);
 362     if (viewport.getAlignmentConservationAnnotation() == null)
 363     {
 364       // BLOSUM62Colour.setEnabled(false);
 365       conservationMenuItem.setEnabled(false);
 366       modifyConservation.setEnabled(false);
 367       // PIDColour.setEnabled(false);
 368       // abovePIDThreshold.setEnabled(false);
 369       // modifyPID.setEnabled(false);
 370     }
 371
 372     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 373             "No sort");
 374
 375     if (sortby.equals("Id"))
 376     {
 377       sortIDMenuItem_actionPerformed(null);
 378     }
 379     else if (sortby.equals("Pairwise Identity"))
 380     {
 381       sortPairwiseMenuItem_actionPerformed(null);
 382     }
 383
 384     this.alignPanel.av
 385             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 386
 387     setMenusFromViewport(viewport);
 388     buildSortByAnnotationScoresMenu();
 389     calculateTree.addActionListener(new ActionListener()
 390     {
 391
 392       @Override
 393       public void actionPerformed(ActionEvent e)
 394       {
 395         openTreePcaDialog();
 396       }
 397     });
 398     buildColourMenu();
 399     buildHMMERMenu();
 400
 401     if (Desktop.desktop != null)
 402     {
 403       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 404       addServiceListeners();
 405       setGUINucleotide();
 406     }
 407
 408     if (viewport.getWrapAlignment())
 409     {
 410       wrapMenuItem_actionPerformed(null);
 411     }
 412
 413     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 414     {
 415       this.overviewMenuItem_actionPerformed(null);
 416     }
 417
 418     addKeyListener();
 419
 420     final List<AlignmentPanel> selviews = new ArrayList<>();
 421     final List<AlignmentPanel> origview = new ArrayList<>();
 422     final String menuLabel = MessageManager
 423             .getString("label.copy_format_from");
 424     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 425             new ViewSetProvider()
 426             {
 427
 428               @Override
 429               public AlignmentPanel[] getAllAlignmentPanels()
 430               {
 431                 origview.clear();
 432                 origview.add(alignPanel);
 433                 // make an array of all alignment panels except for this one
 434                 List<AlignmentPanel> aps = new ArrayList<>(
 435                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 436                 aps.remove(AlignFrame.this.alignPanel);
 437                 return aps.toArray(new AlignmentPanel[aps.size()]);
 438               }
 439             }, selviews, new ItemListener()
 440             {
 441
 442               @Override
 443               public void itemStateChanged(ItemEvent e)
 444               {
 445                 if (origview.size() > 0)
 446                 {
 447                   final AlignmentPanel ap = origview.get(0);
 448
 449                   /*
 450                    * Copy the ViewStyle of the selected panel to 'this one'.
 451                    * Don't change value of 'scaleProteinAsCdna' unless copying
 452                    * from a SplitFrame.
 453                    */
 454                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 455                           .getViewStyle();
 456                   boolean fromSplitFrame = selviews.get(0)
 457                           .getAlignViewport().getCodingComplement() != null;
 458                   if (!fromSplitFrame)
 459                   {
 460                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 461                             .getViewStyle().isScaleProteinAsCdna());
 462                   }
 463                   ap.getAlignViewport().setViewStyle(vs);
 464
 465                   /*
 466                    * Also rescale ViewStyle of SplitFrame complement if there is
 467                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 468                    * the whole ViewStyle (allow cDNA protein to have different
 469                    * fonts)
 470                    */
 471                   AlignViewportI complement = ap.getAlignViewport()
 472                           .getCodingComplement();
 473                   if (complement != null && vs.isScaleProteinAsCdna())
 474                   {
 475                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 476                     ((SplitFrame) af.getSplitViewContainer())
 477                             .adjustLayout();
 478                     af.setMenusForViewport();
 479                   }
 480
 481                   ap.updateLayout();
 482                   ap.setSelected(true);
 483                   ap.alignFrame.setMenusForViewport();
 484
 485                 }
 486               }
 487             });
 488     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 489             .indexOf("devel") > -1
 490             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 491                     .indexOf("test") > -1)
 492     {
 493       formatMenu.add(vsel);
 494     }
 495     addFocusListener(new FocusAdapter()
 496     {
 497       @Override
 498       public void focusGained(FocusEvent e)
 499       {
 500         Jalview.setCurrentAlignFrame(AlignFrame.this);
 501       }
 502     });
 503
 504   }
 505
 506   private void buildHMMERMenu()
 507   {
 508     hmmerMenu.removeAll();
 509
 510     hmmerMenu.add(changeHMMERLocation);
 511     hmmerMenu.addSeparator();
 512
 513     hmmerMenu.add(autoAlignSeqs);
 514     hmmerMenu.addSeparator();
 515
 516     hmmerMenu.add(hmmAlign);
 517     hmmerMenu.add(hmmBuild);
 518     hmmerMenu.add(hmmSearch);
 519
 520   }
 521
 522   /**
 523    * Change the filename and format for the alignment, and enable the 'reload'
 524    * button functionality.
 525    *
 526    * @param file
 527    *          valid filename
 528    * @param format
 529    *          format of file
 530    */
 531   public void setFileName(String file, FileFormatI format)
 532   {
 533     fileName = file;
 534     setFileFormat(format);
 535     reload.setEnabled(true);
 536   }
 537
 538   /**
 539    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 540    * events
 541    */
 542   void addKeyListener()
 543   {
 544     addKeyListener(new KeyAdapter()
 545     {
 546       @Override
 547       public void keyPressed(KeyEvent evt)
 548       {
 549         if (viewport.cursorMode
 550                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 551                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 552                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 553                 && Character.isDigit(evt.getKeyChar()))
 554         {
 555           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 556         }
 557
 558         switch (evt.getKeyCode())
 559         {
 560
 561         case 27: // escape key
 562           deselectAllSequenceMenuItem_actionPerformed(null);
 563
 564           break;
 565
 566         case KeyEvent.VK_DOWN:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             moveSelectedSequences(false);
 570           }
 571           if (viewport.cursorMode)
 572           {
 573             alignPanel.getSeqPanel().moveCursor(0, 1);
 574           }
 575           break;
 576
 577         case KeyEvent.VK_UP:
 578           if (evt.isAltDown() || !viewport.cursorMode)
 579           {
 580             moveSelectedSequences(true);
 581           }
 582           if (viewport.cursorMode)
 583           {
 584             alignPanel.getSeqPanel().moveCursor(0, -1);
 585           }
 586
 587           break;
 588
 589         case KeyEvent.VK_LEFT:
 590           if (evt.isAltDown() || !viewport.cursorMode)
 591           {
 592             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 593           }
 594           else
 595           {
 596             alignPanel.getSeqPanel().moveCursor(-1, 0);
 597           }
 598
 599           break;
 600
 601         case KeyEvent.VK_RIGHT:
 602           if (evt.isAltDown() || !viewport.cursorMode)
 603           {
 604             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 605           }
 606           else
 607           {
 608             alignPanel.getSeqPanel().moveCursor(1, 0);
 609           }
 610           break;
 611
 612         case KeyEvent.VK_SPACE:
 613           if (viewport.cursorMode)
 614           {
 615             alignPanel.getSeqPanel().insertGapAtCursor(
 616                     evt.isControlDown() || evt.isShiftDown()
 617                             || evt.isAltDown());
 618           }
 619           break;
 620
 621         // case KeyEvent.VK_A:
 622         // if (viewport.cursorMode)
 623         // {
 624         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 625         // //System.out.println("A");
 626         // }
 627         // break;
 628         /*
 629          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 630          * System.out.println("closing bracket"); } break;
 631          */
 632         case KeyEvent.VK_DELETE:
 633         case KeyEvent.VK_BACK_SPACE:
 634           if (!viewport.cursorMode)
 635           {
 636             cut_actionPerformed(null);
 637           }
 638           else
 639           {
 640             alignPanel.getSeqPanel().deleteGapAtCursor(
 641                     evt.isControlDown() || evt.isShiftDown()
 642                             || evt.isAltDown());
 643           }
 644
 645           break;
 646
 647         case KeyEvent.VK_S:
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().setCursorRow();
 651           }
 652           break;
 653         case KeyEvent.VK_C:
 654           if (viewport.cursorMode && !evt.isControlDown())
 655           {
 656             alignPanel.getSeqPanel().setCursorColumn();
 657           }
 658           break;
 659         case KeyEvent.VK_P:
 660           if (viewport.cursorMode)
 661           {
 662             alignPanel.getSeqPanel().setCursorPosition();
 663           }
 664           break;
 665
 666         case KeyEvent.VK_ENTER:
 667         case KeyEvent.VK_COMMA:
 668           if (viewport.cursorMode)
 669           {
 670             alignPanel.getSeqPanel().setCursorRowAndColumn();
 671           }
 672           break;
 673
 674         case KeyEvent.VK_Q:
 675           if (viewport.cursorMode)
 676           {
 677             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 678           }
 679           break;
 680         case KeyEvent.VK_M:
 681           if (viewport.cursorMode)
 682           {
 683             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 684           }
 685           break;
 686
 687         case KeyEvent.VK_F2:
 688           viewport.cursorMode = !viewport.cursorMode;
 689           statusBar.setText(MessageManager.formatMessage(
 690                   "label.keyboard_editing_mode",
 691                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 692           if (viewport.cursorMode)
 693           {
 694             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 695                     .getStartRes();
 696             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 697                     .getStartSeq();
 698           }
 699           alignPanel.getSeqPanel().seqCanvas.repaint();
 700           break;
 701
 702         case KeyEvent.VK_F1:
 703           try
 704           {
 705             Help.showHelpWindow();
 706           } catch (Exception ex)
 707           {
 708             ex.printStackTrace();
 709           }
 710           break;
 711         case KeyEvent.VK_H:
 712         {
 713           boolean toggleSeqs = !evt.isControlDown();
 714           boolean toggleCols = !evt.isShiftDown();
 715           toggleHiddenRegions(toggleSeqs, toggleCols);
 716           break;
 717         }
 718         case KeyEvent.VK_B:
 719         {
 720           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 721           boolean modifyExisting = true; // always modify, don't clear
 722                                          // evt.isShiftDown();
 723           boolean invertHighlighted = evt.isAltDown();
 724           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 725                   toggleSel);
 726           break;
 727         }
 728         case KeyEvent.VK_PAGE_UP:
 729           if (viewport.getWrapAlignment())
 730           {
 731             vpRanges.scrollUp(true);
 732           }
 733           else
 734           {
 735             vpRanges.pageUp();
 736           }
 737           break;
 738         case KeyEvent.VK_PAGE_DOWN:
 739           if (viewport.getWrapAlignment())
 740           {
 741             vpRanges.scrollUp(false);
 742           }
 743           else
 744           {
 745             vpRanges.pageDown();
 746           }
 747           break;
 748         }
 749       }
 750
 751       @Override
 752       public void keyReleased(KeyEvent evt)
 753       {
 754         switch (evt.getKeyCode())
 755         {
 756         case KeyEvent.VK_LEFT:
 757           if (evt.isAltDown() || !viewport.cursorMode)
 758           {
 759             viewport.firePropertyChange("alignment", null, viewport
 760                     .getAlignment().getSequences());
 761           }
 762           break;
 763
 764         case KeyEvent.VK_RIGHT:
 765           if (evt.isAltDown() || !viewport.cursorMode)
 766           {
 767             viewport.firePropertyChange("alignment", null, viewport
 768                     .getAlignment().getSequences());
 769           }
 770           break;
 771         }
 772       }
 773     });
 774   }
 775
 776   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 777   {
 778     ap.alignFrame = this;
 779     avc = new jalview.controller.AlignViewController(this, viewport,
 780             alignPanel);
 781
 782     alignPanels.add(ap);
 783
 784     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 785
 786     int aSize = alignPanels.size();
 787
 788     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 789
 790     if (aSize == 1 && ap.av.viewName == null)
 791     {
 792       this.getContentPane().add(ap, BorderLayout.CENTER);
 793     }
 794     else
 795     {
 796       if (aSize == 2)
 797       {
 798         setInitialTabVisible();
 799       }
 800
 801       expandViews.setEnabled(true);
 802       gatherViews.setEnabled(true);
 803       tabbedPane.addTab(ap.av.viewName, ap);
 804
 805       ap.setVisible(false);
 806     }
 807
 808     if (newPanel)
 809     {
 810       if (ap.av.isPadGaps())
 811       {
 812         ap.av.getAlignment().padGaps();
 813       }
 814       ap.av.updateConservation(ap);
 815       ap.av.updateConsensus(ap);
 816       ap.av.updateStrucConsensus(ap);
 817       ap.av.updateInformation(ap);
 818     }
 819   }
 820
 821   public void setInitialTabVisible()
 822   {
 823     expandViews.setEnabled(true);
 824     gatherViews.setEnabled(true);
 825     tabbedPane.setVisible(true);
 826     AlignmentPanel first = alignPanels.get(0);
 827     tabbedPane.addTab(first.av.viewName, first);
 828     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 829   }
 830
 831   public AlignViewport getViewport()
 832   {
 833     return viewport;
 834   }
 835
 836   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 837   private void addServiceListeners()
 838   {
 839     final java.beans.PropertyChangeListener thisListener;
 840     Desktop.instance.addJalviewPropertyChangeListener("services",
 841             thisListener = new java.beans.PropertyChangeListener()
 842             {
 843               @Override
 844               public void propertyChange(PropertyChangeEvent evt)
 845               {
 846                 // // System.out.println("Discoverer property change.");
 847                 // if (evt.getPropertyName().equals("services"))
 848                 {
 849                   SwingUtilities.invokeLater(new Runnable()
 850                   {
 851
 852                     @Override
 853                     public void run()
 854                     {
 855                       System.err
 856                               .println("Rebuild WS Menu for service change");
 857                       BuildWebServiceMenu();
 858                     }
 859
 860                   });
 861                 }
 862               }
 863             });
 864     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 865     {
 866       @Override
 867       public void internalFrameClosed(
 868               javax.swing.event.InternalFrameEvent evt)
 869       {
 870         // System.out.println("deregistering discoverer listener");
 871         Desktop.instance.removeJalviewPropertyChangeListener("services",
 872                 thisListener);
 873         closeMenuItem_actionPerformed(true);
 874       };
 875     });
 876     // Finally, build the menu once to get current service state
 877     new Thread(new Runnable()
 878     {
 879       @Override
 880       public void run()
 881       {
 882         BuildWebServiceMenu();
 883       }
 884     }).start();
 885   }
 886
 887   /**
 888    * Configure menu items that vary according to whether the alignment is
 889    * nucleotide or protein
 890    */
 891   public void setGUINucleotide()
 892   {
 893     AlignmentI al = getViewport().getAlignment();
 894     boolean nucleotide = al.isNucleotide();
 895
 896     showTranslation.setVisible(nucleotide);
 897     showReverse.setVisible(nucleotide);
 898     showReverseComplement.setVisible(nucleotide);
 899     conservationMenuItem.setEnabled(!nucleotide);
 900     modifyConservation.setEnabled(!nucleotide
 901             && conservationMenuItem.isSelected());
 902     showGroupConservation.setEnabled(!nucleotide);
 903
 904     showComplementMenuItem.setText(nucleotide ? MessageManager
 905             .getString("label.protein") : MessageManager
 906             .getString("label.nucleotide"));
 907   }
 908
 909   /**
 910    * set up menus for the current viewport. This may be called after any
 911    * operation that affects the data in the current view (selection changed,
 912    * etc) to update the menus to reflect the new state.
 913    */
 914   @Override
 915   public void setMenusForViewport()
 916   {
 917     setMenusFromViewport(viewport);
 918   }
 919
 920   /**
 921    * Need to call this method when tabs are selected for multiple views, or when
 922    * loading from Jalview2XML.java
 923    *
 924    * @param av
 925    *          AlignViewport
 926    */
 927   void setMenusFromViewport(AlignViewport av)
 928   {
 929     padGapsMenuitem.setSelected(av.isPadGaps());
 930     colourTextMenuItem.setSelected(av.isShowColourText());
 931     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 932     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 933     conservationMenuItem.setSelected(av.getConservationSelected());
 934     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 935     seqLimits.setSelected(av.getShowJVSuffix());
 936     idRightAlign.setSelected(av.isRightAlignIds());
 937     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 938     renderGapsMenuItem.setSelected(av.isRenderGaps());
 939     wrapMenuItem.setSelected(av.getWrapAlignment());
 940     scaleAbove.setVisible(av.getWrapAlignment());
 941     scaleLeft.setVisible(av.getWrapAlignment());
 942     scaleRight.setVisible(av.getWrapAlignment());
 943     annotationPanelMenuItem.setState(av.isShowAnnotation());
 944     /*
 945      * Show/hide annotations only enabled if annotation panel is shown
 946      */
 947     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 948     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 949     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 950     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 951     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 952     viewTextMenuItem.setSelected(av.getShowText());
 953     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 954     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 955     showGroupConservation.setSelected(av.isShowGroupConservation());
 956     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 957     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 958     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 959     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 960     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 961     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 962
 963     ColourMenuHelper.setColourSelected(colourMenu,
 964             av.getGlobalColourScheme());
 965
 966     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 967     hiddenMarkers.setState(av.getShowHiddenMarkers());
 968     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 969     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 970     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 971     autoCalculate.setSelected(av.autoCalculateConsensus);
 972     sortByTree.setSelected(av.sortByTree);
 973     listenToViewSelections.setSelected(av.followSelection);
 974
 975     showProducts.setEnabled(canShowProducts());
 976     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 977
 978     updateEditMenuBar();
 979   }
 980
 981   /**
 982    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 983    *
 984    * @param b
 985    */
 986   public void setGroovyEnabled(boolean b)
 987   {
 988     runGroovy.setEnabled(b);
 989   }
 990
 991   private IProgressIndicator progressBar;
 992
 993   /*
 994    * (non-Javadoc)
 995    *
 996    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 997    */
 998   @Override
 999   public void setProgressBar(String message, long id)
1000   {
1001     progressBar.setProgressBar(message, id);
1002   }
1003
1004   @Override
1005   public void registerHandler(final long id,
1006           final IProgressIndicatorHandler handler)
1007   {
1008     progressBar.registerHandler(id, handler);
1009   }
1010
1011   /**
1012    *
1013    * @return true if any progress bars are still active
1014    */
1015   @Override
1016   public boolean operationInProgress()
1017   {
1018     return progressBar.operationInProgress();
1019   }
1020
1021   @Override
1022   public void setStatus(String text)
1023   {
1024     statusBar.setText(text);
1025   }
1026
1027   /*
1028    * Added so Castor Mapping file can obtain Jalview Version
1029    */
1030   public String getVersion()
1031   {
1032     return jalview.bin.Cache.getProperty("VERSION");
1033   }
1034
1035   public FeatureRenderer getFeatureRenderer()
1036   {
1037     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1038   }
1039
1040   @Override
1041   public void fetchSequence_actionPerformed(ActionEvent e)
1042   {
1043     new jalview.gui.SequenceFetcher(this);
1044   }
1045
1046   @Override
1047   public void addFromFile_actionPerformed(ActionEvent e)
1048   {
1049     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1050   }
1051
1052   @Override
1053   public void hmmBuild_actionPerformed(ActionEvent e)
1054           throws IOException, InterruptedException
1055   {
1056     new Thread(new HMMBuildThread(this)).start();
1057     alignPanel.repaint();
1058
1059   }
1060
1061   @Override
1062   public void hmmAlign_actionPerformed(ActionEvent e)
1063           throws IOException, InterruptedException
1064   {
1065     new Thread(new HMMAlignThread(this, true)).start();
1066     alignPanel.repaint();
1067   }
1068
1069   @Override
1070   public void changeHMMERLocation_actionPerformed(ActionEvent e)
1071   {
1072     String location = JOptionPane.showInputDialog(
1073             MessageManager.getString("label.enter_location"));
1074     Cache.setProperty(Preferences.HMMER_PATH, location);
1075   }
1076
1077   @Override
1078   public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1079   {
1080     autoAlignNewSequences = autoAlignSeqs;
1081     alignPanel.repaint();
1082   }
1083
1084   @Override
1085   public void hmmSearch_actionPerformed(ActionEvent e)
1086   {
1087     alignPanel.repaint();
1088   }
1089
1090   @Override
1091   public void reload_actionPerformed(ActionEvent e)
1092   {
1093     if (fileName != null)
1094     {
1095       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1096       // originating file's format
1097       // TODO: work out how to recover feature settings for correct view(s) when
1098       // file is reloaded.
1099       if (FileFormat.Jalview.equals(currentFileFormat))
1100       {
1101         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1102         for (int i = 0; i < frames.length; i++)
1103         {
1104           if (frames[i] instanceof AlignFrame && frames[i] != this
1105                   && ((AlignFrame) frames[i]).fileName != null
1106                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1107           {
1108             try
1109             {
1110               frames[i].setSelected(true);
1111               Desktop.instance.closeAssociatedWindows();
1112             } catch (java.beans.PropertyVetoException ex)
1113             {
1114             }
1115           }
1116
1117         }
1118         Desktop.instance.closeAssociatedWindows();
1119
1120         FileLoader loader = new FileLoader();
1121         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1122                 : DataSourceType.FILE;
1123         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1124       }
1125       else
1126       {
1127         Rectangle bounds = this.getBounds();
1128
1129         FileLoader loader = new FileLoader();
1130         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1131                 : DataSourceType.FILE;
1132         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1133                 protocol, currentFileFormat);
1134
1135         newframe.setBounds(bounds);
1136         if (featureSettings != null && featureSettings.isShowing())
1137         {
1138           final Rectangle fspos = featureSettings.frame.getBounds();
1139           // TODO: need a 'show feature settings' function that takes bounds -
1140           // need to refactor Desktop.addFrame
1141           newframe.featureSettings_actionPerformed(null);
1142           final FeatureSettings nfs = newframe.featureSettings;
1143           SwingUtilities.invokeLater(new Runnable()
1144           {
1145             @Override
1146             public void run()
1147             {
1148               nfs.frame.setBounds(fspos);
1149             }
1150           });
1151           this.featureSettings.close();
1152           this.featureSettings = null;
1153         }
1154         this.closeMenuItem_actionPerformed(true);
1155       }
1156     }
1157   }
1158
1159   @Override
1160   public void addFromText_actionPerformed(ActionEvent e)
1161   {
1162     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1163             .getAlignPanel());
1164   }
1165
1166   @Override
1167   public void addFromURL_actionPerformed(ActionEvent e)
1168   {
1169     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1170   }
1171
1172   @Override
1173   public void save_actionPerformed(ActionEvent e)
1174   {
1175     if (fileName == null || (currentFileFormat == null)
1176             || fileName.startsWith("http"))
1177     {
1178       saveAs_actionPerformed(null);
1179     }
1180     else
1181     {
1182       saveAlignment(fileName, currentFileFormat);
1183     }
1184   }
1185
1186   /**
1187    * DOCUMENT ME!
1188    *
1189    * @param e
1190    *          DOCUMENT ME!
1191    */
1192   @Override
1193   public void saveAs_actionPerformed(ActionEvent e)
1194   {
1195     String format = currentFileFormat == null ? null : currentFileFormat
1196             .getName();
1197     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1198             Cache.getProperty("LAST_DIRECTORY"), format);
1199
1200     chooser.setFileView(new JalviewFileView());
1201     chooser.setDialogTitle(MessageManager
1202             .getString("label.save_alignment_to_file"));
1203     chooser.setToolTipText(MessageManager.getString("action.save"));
1204
1205     int value = chooser.showSaveDialog(this);
1206
1207     if (value == JalviewFileChooser.APPROVE_OPTION)
1208     {
1209       currentFileFormat = chooser.getSelectedFormat();
1210       while (currentFileFormat == null)
1211       {
1212         JvOptionPane
1213                 .showInternalMessageDialog(
1214                         Desktop.desktop,
1215                         MessageManager
1216                                 .getString("label.select_file_format_before_saving"),
1217                         MessageManager
1218                                 .getString("label.file_format_not_specified"),
1219                         JvOptionPane.WARNING_MESSAGE);
1220         currentFileFormat = chooser.getSelectedFormat();
1221         value = chooser.showSaveDialog(this);
1222         if (value != JalviewFileChooser.APPROVE_OPTION)
1223         {
1224           return;
1225         }
1226       }
1227
1228       fileName = chooser.getSelectedFile().getPath();
1229
1230       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1231
1232       Cache.setProperty("LAST_DIRECTORY", fileName);
1233       saveAlignment(fileName, currentFileFormat);
1234     }
1235   }
1236
1237   public boolean saveAlignment(String file, FileFormatI format)
1238   {
1239     boolean success = true;
1240
1241     if (FileFormat.Jalview.equals(format))
1242     {
1243       String shortName = title;
1244
1245       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1246       {
1247         shortName = shortName.substring(shortName
1248                 .lastIndexOf(java.io.File.separatorChar) + 1);
1249       }
1250
1251       success = new Jalview2XML().saveAlignment(this, file, shortName);
1252
1253       statusBar.setText(MessageManager.formatMessage(
1254               "label.successfully_saved_to_file_in_format", new Object[] {
1255                   fileName, format }));
1256
1257     }
1258     else
1259     {
1260       AlignmentExportData exportData = getAlignmentForExport(format,
1261               viewport, null);
1262       if (exportData.getSettings().isCancelled())
1263       {
1264         return false;
1265       }
1266       FormatAdapter f = new FormatAdapter(alignPanel,
1267               exportData.getSettings());
1268       String output = f.formatSequences(
1269               format,
1270               exportData.getAlignment(), // class cast exceptions will
1271               // occur in the distant future
1272               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1273               f.getCacheSuffixDefault(format), viewport.getAlignment()
1274                       .getHiddenColumns());
1275
1276       if (output == null)
1277       {
1278         success = false;
1279       }
1280       else
1281       {
1282         try
1283         {
1284           PrintWriter out = new PrintWriter(new FileWriter(file));
1285
1286           out.print(output);
1287           out.close();
1288           this.setTitle(file);
1289           statusBar.setText(MessageManager.formatMessage(
1290                   "label.successfully_saved_to_file_in_format",
1291                   new Object[] { fileName, format.getName() }));
1292         } catch (Exception ex)
1293         {
1294           success = false;
1295           ex.printStackTrace();
1296         }
1297       }
1298     }
1299
1300     if (!success)
1301     {
1302       JvOptionPane.showInternalMessageDialog(this, MessageManager
1303               .formatMessage("label.couldnt_save_file",
1304                       new Object[] { fileName }), MessageManager
1305               .getString("label.error_saving_file"),
1306               JvOptionPane.WARNING_MESSAGE);
1307     }
1308
1309     return success;
1310   }
1311
1312   private void warningMessage(String warning, String title)
1313   {
1314     if (new jalview.util.Platform().isHeadless())
1315     {
1316       System.err.println("Warning: " + title + "\nWarning: " + warning);
1317
1318     }
1319     else
1320     {
1321       JvOptionPane.showInternalMessageDialog(this, warning, title,
1322               JvOptionPane.WARNING_MESSAGE);
1323     }
1324     return;
1325   }
1326
1327   /**
1328    * DOCUMENT ME!
1329    *
1330    * @param e
1331    *          DOCUMENT ME!
1332    */
1333   @Override
1334   protected void outputText_actionPerformed(ActionEvent e)
1335   {
1336     FileFormatI fileFormat = FileFormats.getInstance().forName(
1337             e.getActionCommand());
1338     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1339             viewport, null);
1340     if (exportData.getSettings().isCancelled())
1341     {
1342       return;
1343     }
1344     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1345     cap.setForInput(null);
1346     try
1347     {
1348       FileFormatI format = fileFormat;
1349       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1350               .formatSequences(format, exportData.getAlignment(),
1351                       exportData.getOmitHidden(),
1352  exportData
1353                               .getStartEndPostions(), viewport
1354                               .getAlignment().getHiddenColumns()));
1355       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1356               "label.alignment_output_command",
1357               new Object[] { e.getActionCommand() }), 600, 500);
1358     } catch (OutOfMemoryError oom)
1359     {
1360       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1361       cap.dispose();
1362     }
1363
1364   }
1365
1366   public static AlignmentExportData getAlignmentForExport(
1367           FileFormatI format, AlignViewportI viewport,
1368           AlignExportSettingI exportSettings)
1369   {
1370     AlignmentI alignmentToExport = null;
1371     AlignExportSettingI settings = exportSettings;
1372     String[] omitHidden = null;
1373
1374     HiddenSequences hiddenSeqs = viewport.getAlignment()
1375             .getHiddenSequences();
1376
1377     alignmentToExport = viewport.getAlignment();
1378
1379     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1380     if (settings == null)
1381     {
1382       settings = new AlignExportSettings(hasHiddenSeqs,
1383               viewport.hasHiddenColumns(), format);
1384     }
1385     // settings.isExportAnnotations();
1386
1387     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1388     {
1389       omitHidden = viewport.getViewAsString(false,
1390               settings.isExportHiddenSequences());
1391     }
1392
1393     int[] alignmentStartEnd = new int[2];
1394     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1395     {
1396       alignmentToExport = hiddenSeqs.getFullAlignment();
1397     }
1398     else
1399     {
1400       alignmentToExport = viewport.getAlignment();
1401     }
1402     alignmentStartEnd = alignmentToExport
1403             .getVisibleStartAndEndIndex(viewport.getAlignment()
1404                     .getHiddenColumns()
1405                     .getHiddenRegions());
1406     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1407             omitHidden, alignmentStartEnd, settings);
1408     return ed;
1409   }
1410
1411   /**
1412    * DOCUMENT ME!
1413    *
1414    * @param e
1415    *          DOCUMENT ME!
1416    */
1417   @Override
1418   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1419   {
1420     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1421     htmlSVG.exportHTML(null);
1422   }
1423
1424   @Override
1425   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1426   {
1427     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1428     bjs.exportHTML(null);
1429   }
1430
1431   public void createImageMap(File file, String image)
1432   {
1433     alignPanel.makePNGImageMap(file, image);
1434   }
1435
1436   /**
1437    * DOCUMENT ME!
1438    *
1439    * @param e
1440    *          DOCUMENT ME!
1441    */
1442   @Override
1443   public void createPNG(File f)
1444   {
1445     alignPanel.makePNG(f);
1446   }
1447
1448   /**
1449    * DOCUMENT ME!
1450    *
1451    * @param e
1452    *          DOCUMENT ME!
1453    */
1454   @Override
1455   public void createEPS(File f)
1456   {
1457     alignPanel.makeEPS(f);
1458   }
1459
1460   @Override
1461   public void createSVG(File f)
1462   {
1463     alignPanel.makeSVG(f);
1464   }
1465
1466   @Override
1467   public void pageSetup_actionPerformed(ActionEvent e)
1468   {
1469     PrinterJob printJob = PrinterJob.getPrinterJob();
1470     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1471   }
1472
1473   /**
1474    * DOCUMENT ME!
1475    *
1476    * @param e
1477    *          DOCUMENT ME!
1478    */
1479   @Override
1480   public void printMenuItem_actionPerformed(ActionEvent e)
1481   {
1482     // Putting in a thread avoids Swing painting problems
1483     PrintThread thread = new PrintThread(alignPanel);
1484     thread.start();
1485   }
1486
1487   @Override
1488   public void exportFeatures_actionPerformed(ActionEvent e)
1489   {
1490     new AnnotationExporter().exportFeatures(alignPanel);
1491   }
1492
1493   @Override
1494   public void exportAnnotations_actionPerformed(ActionEvent e)
1495   {
1496     new AnnotationExporter().exportAnnotations(alignPanel);
1497   }
1498
1499   @Override
1500   public void associatedData_actionPerformed(ActionEvent e)
1501           throws IOException, InterruptedException
1502   {
1503     // Pick the tree file
1504     JalviewFileChooser chooser = new JalviewFileChooser(
1505             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1506     chooser.setFileView(new JalviewFileView());
1507     chooser.setDialogTitle(MessageManager
1508             .getString("label.load_jalview_annotations"));
1509     chooser.setToolTipText(MessageManager
1510             .getString("label.load_jalview_annotations"));
1511
1512     int value = chooser.showOpenDialog(null);
1513
1514     if (value == JalviewFileChooser.APPROVE_OPTION)
1515     {
1516       String choice = chooser.getSelectedFile().getPath();
1517       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1518       loadJalviewDataFile(choice, null, null, null);
1519     }
1520
1521   }
1522
1523   /**
1524    * Close the current view or all views in the alignment frame. If the frame
1525    * only contains one view then the alignment will be removed from memory.
1526    *
1527    * @param closeAllTabs
1528    */
1529   @Override
1530   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1531   {
1532     if (alignPanels != null && alignPanels.size() < 2)
1533     {
1534       closeAllTabs = true;
1535     }
1536
1537     try
1538     {
1539       if (alignPanels != null)
1540       {
1541         if (closeAllTabs)
1542         {
1543           if (this.isClosed())
1544           {
1545             // really close all the windows - otherwise wait till
1546             // setClosed(true) is called
1547             for (int i = 0; i < alignPanels.size(); i++)
1548             {
1549               AlignmentPanel ap = alignPanels.get(i);
1550               ap.closePanel();
1551             }
1552           }
1553         }
1554         else
1555         {
1556           closeView(alignPanel);
1557         }
1558       }
1559
1560       if (closeAllTabs)
1561       {
1562         /*
1563          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1564          * be called recursively, with the frame now in 'closed' state
1565          */
1566         this.setClosed(true);
1567       }
1568     } catch (Exception ex)
1569     {
1570       ex.printStackTrace();
1571     }
1572   }
1573
1574   /**
1575    * Close the specified panel and close up tabs appropriately.
1576    *
1577    * @param panelToClose
1578    */
1579   public void closeView(AlignmentPanel panelToClose)
1580   {
1581     int index = tabbedPane.getSelectedIndex();
1582     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1583     alignPanels.remove(panelToClose);
1584     panelToClose.closePanel();
1585     panelToClose = null;
1586
1587     tabbedPane.removeTabAt(closedindex);
1588     tabbedPane.validate();
1589
1590     if (index > closedindex || index == tabbedPane.getTabCount())
1591     {
1592       // modify currently selected tab index if necessary.
1593       index--;
1594     }
1595
1596     this.tabSelectionChanged(index);
1597   }
1598
1599   /**
1600    * DOCUMENT ME!
1601    */
1602   void updateEditMenuBar()
1603   {
1604
1605     if (viewport.getHistoryList().size() > 0)
1606     {
1607       undoMenuItem.setEnabled(true);
1608       CommandI command = viewport.getHistoryList().peek();
1609       undoMenuItem.setText(MessageManager.formatMessage(
1610               "label.undo_command",
1611               new Object[] { command.getDescription() }));
1612     }
1613     else
1614     {
1615       undoMenuItem.setEnabled(false);
1616       undoMenuItem.setText(MessageManager.getString("action.undo"));
1617     }
1618
1619     if (viewport.getRedoList().size() > 0)
1620     {
1621       redoMenuItem.setEnabled(true);
1622
1623       CommandI command = viewport.getRedoList().peek();
1624       redoMenuItem.setText(MessageManager.formatMessage(
1625               "label.redo_command",
1626               new Object[] { command.getDescription() }));
1627     }
1628     else
1629     {
1630       redoMenuItem.setEnabled(false);
1631       redoMenuItem.setText(MessageManager.getString("action.redo"));
1632     }
1633   }
1634
1635   @Override
1636   public void addHistoryItem(CommandI command)
1637   {
1638     if (command.getSize() > 0)
1639     {
1640       viewport.addToHistoryList(command);
1641       viewport.clearRedoList();
1642       updateEditMenuBar();
1643       viewport.updateHiddenColumns();
1644       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1645       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1646       // viewport.getColumnSelection()
1647       // .getHiddenColumns().size() > 0);
1648     }
1649   }
1650
1651   /**
1652    *
1653    * @return alignment objects for all views
1654    */
1655   AlignmentI[] getViewAlignments()
1656   {
1657     if (alignPanels != null)
1658     {
1659       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1660       int i = 0;
1661       for (AlignmentPanel ap : alignPanels)
1662       {
1663         als[i++] = ap.av.getAlignment();
1664       }
1665       return als;
1666     }
1667     if (viewport != null)
1668     {
1669       return new AlignmentI[] { viewport.getAlignment() };
1670     }
1671     return null;
1672   }
1673
1674   /**
1675    * DOCUMENT ME!
1676    *
1677    * @param e
1678    *          DOCUMENT ME!
1679    */
1680   @Override
1681   protected void undoMenuItem_actionPerformed(ActionEvent e)
1682   {
1683     if (viewport.getHistoryList().isEmpty())
1684     {
1685       return;
1686     }
1687     CommandI command = viewport.getHistoryList().pop();
1688     viewport.addToRedoList(command);
1689     command.undoCommand(getViewAlignments());
1690
1691     AlignmentViewport originalSource = getOriginatingSource(command);
1692     updateEditMenuBar();
1693
1694     if (originalSource != null)
1695     {
1696       if (originalSource != viewport)
1697       {
1698         Cache.log
1699                 .warn("Implementation worry: mismatch of viewport origin for undo");
1700       }
1701       originalSource.updateHiddenColumns();
1702       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1703       // null
1704       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1705       // viewport.getColumnSelection()
1706       // .getHiddenColumns().size() > 0);
1707       originalSource.firePropertyChange("alignment", null, originalSource
1708               .getAlignment().getSequences());
1709     }
1710   }
1711
1712   /**
1713    * DOCUMENT ME!
1714    *
1715    * @param e
1716    *          DOCUMENT ME!
1717    */
1718   @Override
1719   protected void redoMenuItem_actionPerformed(ActionEvent e)
1720   {
1721     if (viewport.getRedoList().size() < 1)
1722     {
1723       return;
1724     }
1725
1726     CommandI command = viewport.getRedoList().pop();
1727     viewport.addToHistoryList(command);
1728     command.doCommand(getViewAlignments());
1729
1730     AlignmentViewport originalSource = getOriginatingSource(command);
1731     updateEditMenuBar();
1732
1733     if (originalSource != null)
1734     {
1735
1736       if (originalSource != viewport)
1737       {
1738         Cache.log
1739                 .warn("Implementation worry: mismatch of viewport origin for redo");
1740       }
1741       originalSource.updateHiddenColumns();
1742       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1743       // null
1744       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1745       // viewport.getColumnSelection()
1746       // .getHiddenColumns().size() > 0);
1747       originalSource.firePropertyChange("alignment", null, originalSource
1748               .getAlignment().getSequences());
1749     }
1750   }
1751
1752   AlignmentViewport getOriginatingSource(CommandI command)
1753   {
1754     AlignmentViewport originalSource = null;
1755     // For sequence removal and addition, we need to fire
1756     // the property change event FROM the viewport where the
1757     // original alignment was altered
1758     AlignmentI al = null;
1759     if (command instanceof EditCommand)
1760     {
1761       EditCommand editCommand = (EditCommand) command;
1762       al = editCommand.getAlignment();
1763       List<Component> comps = PaintRefresher.components.get(viewport
1764               .getSequenceSetId());
1765
1766       for (Component comp : comps)
1767       {
1768         if (comp instanceof AlignmentPanel)
1769         {
1770           if (al == ((AlignmentPanel) comp).av.getAlignment())
1771           {
1772             originalSource = ((AlignmentPanel) comp).av;
1773             break;
1774           }
1775         }
1776       }
1777     }
1778
1779     if (originalSource == null)
1780     {
1781       // The original view is closed, we must validate
1782       // the current view against the closed view first
1783       if (al != null)
1784       {
1785         PaintRefresher.validateSequences(al, viewport.getAlignment());
1786       }
1787
1788       originalSource = viewport;
1789     }
1790
1791     return originalSource;
1792   }
1793
1794   /**
1795    * DOCUMENT ME!
1796    *
1797    * @param up
1798    *          DOCUMENT ME!
1799    */
1800   public void moveSelectedSequences(boolean up)
1801   {
1802     SequenceGroup sg = viewport.getSelectionGroup();
1803
1804     if (sg == null)
1805     {
1806       return;
1807     }
1808     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1809             viewport.getHiddenRepSequences(), up);
1810     alignPanel.paintAlignment(true);
1811   }
1812
1813   synchronized void slideSequences(boolean right, int size)
1814   {
1815     List<SequenceI> sg = new ArrayList<>();
1816     if (viewport.cursorMode)
1817     {
1818       sg.add(viewport.getAlignment().getSequenceAt(
1819               alignPanel.getSeqPanel().seqCanvas.cursorY));
1820     }
1821     else if (viewport.getSelectionGroup() != null
1822             && viewport.getSelectionGroup().getSize() != viewport
1823                     .getAlignment().getHeight())
1824     {
1825       sg = viewport.getSelectionGroup().getSequences(
1826               viewport.getHiddenRepSequences());
1827     }
1828
1829     if (sg.size() < 1)
1830     {
1831       return;
1832     }
1833
1834     List<SequenceI> invertGroup = new ArrayList<>();
1835
1836     for (SequenceI seq : viewport.getAlignment().getSequences())
1837     {
1838       if (!sg.contains(seq))
1839       {
1840         invertGroup.add(seq);
1841       }
1842     }
1843
1844     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1845
1846     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1847     for (int i = 0; i < invertGroup.size(); i++)
1848     {
1849       seqs2[i] = invertGroup.get(i);
1850     }
1851
1852     SlideSequencesCommand ssc;
1853     if (right)
1854     {
1855       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1856               size, viewport.getGapCharacter());
1857     }
1858     else
1859     {
1860       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1861               size, viewport.getGapCharacter());
1862     }
1863
1864     int groupAdjustment = 0;
1865     if (ssc.getGapsInsertedBegin() && right)
1866     {
1867       if (viewport.cursorMode)
1868       {
1869         alignPanel.getSeqPanel().moveCursor(size, 0);
1870       }
1871       else
1872       {
1873         groupAdjustment = size;
1874       }
1875     }
1876     else if (!ssc.getGapsInsertedBegin() && !right)
1877     {
1878       if (viewport.cursorMode)
1879       {
1880         alignPanel.getSeqPanel().moveCursor(-size, 0);
1881       }
1882       else
1883       {
1884         groupAdjustment = -size;
1885       }
1886     }
1887
1888     if (groupAdjustment != 0)
1889     {
1890       viewport.getSelectionGroup().setStartRes(
1891               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1892       viewport.getSelectionGroup().setEndRes(
1893               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1894     }
1895
1896     /*
1897      * just extend the last slide command if compatible; but not if in
1898      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1899      */
1900     boolean appendHistoryItem = false;
1901     Deque<CommandI> historyList = viewport.getHistoryList();
1902     boolean inSplitFrame = getSplitViewContainer() != null;
1903     if (!inSplitFrame && historyList != null && historyList.size() > 0
1904             && historyList.peek() instanceof SlideSequencesCommand)
1905     {
1906       appendHistoryItem = ssc
1907               .appendSlideCommand((SlideSequencesCommand) historyList
1908                       .peek());
1909     }
1910
1911     if (!appendHistoryItem)
1912     {
1913       addHistoryItem(ssc);
1914     }
1915
1916     repaint();
1917   }
1918
1919   /**
1920    * DOCUMENT ME!
1921    *
1922    * @param e
1923    *          DOCUMENT ME!
1924    */
1925   @Override
1926   protected void copy_actionPerformed(ActionEvent e)
1927   {
1928     System.gc();
1929     if (viewport.getSelectionGroup() == null)
1930     {
1931       return;
1932     }
1933     // TODO: preserve the ordering of displayed alignment annotation in any
1934     // internal paste (particularly sequence associated annotation)
1935     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1936     String[] omitHidden = null;
1937
1938     if (viewport.hasHiddenColumns())
1939     {
1940       omitHidden = viewport.getViewAsString(true);
1941     }
1942
1943     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1944             seqs, omitHidden, null);
1945
1946     StringSelection ss = new StringSelection(output);
1947
1948     try
1949     {
1950       jalview.gui.Desktop.internalCopy = true;
1951       // Its really worth setting the clipboard contents
1952       // to empty before setting the large StringSelection!!
1953       Toolkit.getDefaultToolkit().getSystemClipboard()
1954               .setContents(new StringSelection(""), null);
1955
1956       Toolkit.getDefaultToolkit().getSystemClipboard()
1957               .setContents(ss, Desktop.instance);
1958     } catch (OutOfMemoryError er)
1959     {
1960       new OOMWarning("copying region", er);
1961       return;
1962     }
1963
1964     ArrayList<int[]> hiddenColumns = null;
1965     if (viewport.hasHiddenColumns())
1966     {
1967       hiddenColumns = new ArrayList<>();
1968       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1969               .getSelectionGroup().getEndRes();
1970       for (int[] region : viewport.getAlignment().getHiddenColumns()
1971               .getHiddenRegions())
1972       {
1973         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1974         {
1975           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1976               region[1] - hiddenOffset });
1977         }
1978       }
1979     }
1980
1981     Desktop.jalviewClipboard = new Object[] { seqs,
1982         viewport.getAlignment().getDataset(), hiddenColumns };
1983     statusBar.setText(MessageManager.formatMessage(
1984             "label.copied_sequences_to_clipboard", new Object[] { Integer
1985                     .valueOf(seqs.length).toString() }));
1986   }
1987
1988   /**
1989    * DOCUMENT ME!
1990    *
1991    * @param e
1992    *          DOCUMENT ME!
1993    * @throws InterruptedException
1994    * @throws IOException
1995    */
1996   @Override
1997   protected void pasteNew_actionPerformed(ActionEvent e)
1998           throws IOException, InterruptedException
1999   {
2000     paste(true);
2001   }
2002
2003   /**
2004    * DOCUMENT ME!
2005    *
2006    * @param e
2007    *          DOCUMENT ME!
2008    * @throws InterruptedException
2009    * @throws IOException
2010    */
2011   @Override
2012   protected void pasteThis_actionPerformed(ActionEvent e)
2013           throws IOException, InterruptedException
2014   {
2015     paste(false);
2016   }
2017
2018   /**
2019    * Paste contents of Jalview clipboard
2020    *
2021    * @param newAlignment
2022    *          true to paste to a new alignment, otherwise add to this.
2023    * @throws InterruptedException
2024    * @throws IOException
2025    */
2026   void paste(boolean newAlignment) throws IOException, InterruptedException
2027   {
2028     boolean externalPaste = true;
2029     try
2030     {
2031       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2032       Transferable contents = c.getContents(this);
2033
2034       if (contents == null)
2035       {
2036         return;
2037       }
2038
2039       String str;
2040       FileFormatI format;
2041       try
2042       {
2043         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2044         if (str.length() < 1)
2045         {
2046           return;
2047         }
2048
2049         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2050
2051       } catch (OutOfMemoryError er)
2052       {
2053         new OOMWarning("Out of memory pasting sequences!!", er);
2054         return;
2055       }
2056
2057       SequenceI[] sequences;
2058       boolean annotationAdded = false;
2059       AlignmentI alignment = null;
2060
2061       if (Desktop.jalviewClipboard != null)
2062       {
2063         // The clipboard was filled from within Jalview, we must use the
2064         // sequences
2065         // And dataset from the copied alignment
2066         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2067         // be doubly sure that we create *new* sequence objects.
2068         sequences = new SequenceI[newseq.length];
2069         for (int i = 0; i < newseq.length; i++)
2070         {
2071           sequences[i] = new Sequence(newseq[i]);
2072         }
2073         alignment = new Alignment(sequences);
2074         externalPaste = false;
2075       }
2076       else
2077       {
2078         // parse the clipboard as an alignment.
2079         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2080                 format);
2081         sequences = alignment.getSequencesArray();
2082       }
2083
2084       int alwidth = 0;
2085       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2086       int fgroup = -1;
2087
2088       if (newAlignment)
2089       {
2090
2091         if (Desktop.jalviewClipboard != null)
2092         {
2093           // dataset is inherited
2094           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2095         }
2096         else
2097         {
2098           // new dataset is constructed
2099           alignment.setDataset(null);
2100         }
2101         alwidth = alignment.getWidth() + 1;
2102       }
2103       else
2104       {
2105         AlignmentI pastedal = alignment; // preserve pasted alignment object
2106         // Add pasted sequences and dataset into existing alignment.
2107         alignment = viewport.getAlignment();
2108         alwidth = alignment.getWidth() + 1;
2109         // decide if we need to import sequences from an existing dataset
2110         boolean importDs = Desktop.jalviewClipboard != null
2111                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2112         // importDs==true instructs us to copy over new dataset sequences from
2113         // an existing alignment
2114         Vector newDs = (importDs) ? new Vector() : null; // used to create
2115         // minimum dataset set
2116
2117         for (int i = 0; i < sequences.length; i++)
2118         {
2119           if (importDs)
2120           {
2121             newDs.addElement(null);
2122           }
2123           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2124           // paste
2125           if (importDs && ds != null)
2126           {
2127             if (!newDs.contains(ds))
2128             {
2129               newDs.setElementAt(ds, i);
2130               ds = new Sequence(ds);
2131               // update with new dataset sequence
2132               sequences[i].setDatasetSequence(ds);
2133             }
2134             else
2135             {
2136               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2137             }
2138           }
2139           else
2140           {
2141             // copy and derive new dataset sequence
2142             sequences[i] = sequences[i].deriveSequence();
2143             alignment.getDataset().addSequence(
2144                     sequences[i].getDatasetSequence());
2145             // TODO: avoid creation of duplicate dataset sequences with a
2146             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2147           }
2148           alignment.addSequence(sequences[i]); // merges dataset
2149         }
2150         if (newDs != null)
2151         {
2152           newDs.clear(); // tidy up
2153         }
2154         if (alignment.getAlignmentAnnotation() != null)
2155         {
2156           for (AlignmentAnnotation alan : alignment
2157                   .getAlignmentAnnotation())
2158           {
2159             if (alan.graphGroup > fgroup)
2160             {
2161               fgroup = alan.graphGroup;
2162             }
2163           }
2164         }
2165         if (pastedal.getAlignmentAnnotation() != null)
2166         {
2167           // Add any annotation attached to alignment.
2168           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2169           for (int i = 0; i < alann.length; i++)
2170           {
2171             annotationAdded = true;
2172             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2173             {
2174               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2175               if (newann.graphGroup > -1)
2176               {
2177                 if (newGraphGroups.size() <= newann.graphGroup
2178                         || newGraphGroups.get(newann.graphGroup) == null)
2179                 {
2180                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2181                   {
2182                     newGraphGroups.add(q, null);
2183                   }
2184                   newGraphGroups.set(newann.graphGroup, new Integer(
2185                           ++fgroup));
2186                 }
2187                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2188                         .intValue();
2189               }
2190
2191               newann.padAnnotation(alwidth);
2192               alignment.addAnnotation(newann);
2193             }
2194           }
2195         }
2196       }
2197       if (!newAlignment)
2198       {
2199         // /////
2200         // ADD HISTORY ITEM
2201         //
2202         addHistoryItem(new EditCommand(
2203                 MessageManager.getString("label.add_sequences"),
2204                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2205       }
2206       // Add any annotations attached to sequences
2207       for (int i = 0; i < sequences.length; i++)
2208       {
2209         if (sequences[i].getAnnotation() != null)
2210         {
2211           AlignmentAnnotation newann;
2212           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2213           {
2214             annotationAdded = true;
2215             newann = sequences[i].getAnnotation()[a];
2216             newann.adjustForAlignment();
2217             newann.padAnnotation(alwidth);
2218             if (newann.graphGroup > -1)
2219             {
2220               if (newann.graphGroup > -1)
2221               {
2222                 if (newGraphGroups.size() <= newann.graphGroup
2223                         || newGraphGroups.get(newann.graphGroup) == null)
2224                 {
2225                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2226                   {
2227                     newGraphGroups.add(q, null);
2228                   }
2229                   newGraphGroups.set(newann.graphGroup, new Integer(
2230                           ++fgroup));
2231                 }
2232                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2233                         .intValue();
2234               }
2235             }
2236             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2237             // was
2238             // duplicated
2239             // earlier
2240             alignment
2241                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2242           }
2243         }
2244       }
2245       if (!newAlignment)
2246       {
2247
2248         // propagate alignment changed.
2249         vpRanges.setEndSeq(alignment.getHeight());
2250         if (annotationAdded)
2251         {
2252           // Duplicate sequence annotation in all views.
2253           AlignmentI[] alview = this.getViewAlignments();
2254           for (int i = 0; i < sequences.length; i++)
2255           {
2256             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2257             if (sann == null)
2258             {
2259               continue;
2260             }
2261             for (int avnum = 0; avnum < alview.length; avnum++)
2262             {
2263               if (alview[avnum] != alignment)
2264               {
2265                 // duplicate in a view other than the one with input focus
2266                 int avwidth = alview[avnum].getWidth() + 1;
2267                 // this relies on sann being preserved after we
2268                 // modify the sequence's annotation array for each duplication
2269                 for (int a = 0; a < sann.length; a++)
2270                 {
2271                   AlignmentAnnotation newann = new AlignmentAnnotation(
2272                           sann[a]);
2273                   sequences[i].addAlignmentAnnotation(newann);
2274                   newann.padAnnotation(avwidth);
2275                   alview[avnum].addAnnotation(newann); // annotation was
2276                   // duplicated earlier
2277                   // TODO JAL-1145 graphGroups are not updated for sequence
2278                   // annotation added to several views. This may cause
2279                   // strangeness
2280                   alview[avnum].setAnnotationIndex(newann, a);
2281                 }
2282               }
2283             }
2284           }
2285           buildSortByAnnotationScoresMenu();
2286         }
2287         viewport.firePropertyChange("alignment", null,
2288                 alignment.getSequences());
2289         if (alignPanels != null)
2290         {
2291           for (AlignmentPanel ap : alignPanels)
2292           {
2293             ap.validateAnnotationDimensions(false);
2294           }
2295         }
2296         else
2297         {
2298           alignPanel.validateAnnotationDimensions(false);
2299         }
2300
2301       }
2302       else
2303       {
2304         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2305                 DEFAULT_HEIGHT);
2306         String newtitle = new String("Copied sequences");
2307
2308         if (Desktop.jalviewClipboard != null
2309                 && Desktop.jalviewClipboard[2] != null)
2310         {
2311           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2312           for (int[] region : hc)
2313           {
2314             af.viewport.hideColumns(region[0], region[1]);
2315           }
2316         }
2317
2318         // >>>This is a fix for the moment, until a better solution is
2319         // found!!<<<
2320         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2321                 .transferSettings(
2322                         alignPanel.getSeqPanel().seqCanvas
2323                                 .getFeatureRenderer());
2324
2325         // TODO: maintain provenance of an alignment, rather than just make the
2326         // title a concatenation of operations.
2327         if (!externalPaste)
2328         {
2329           if (title.startsWith("Copied sequences"))
2330           {
2331             newtitle = title;
2332           }
2333           else
2334           {
2335             newtitle = newtitle.concat("- from " + title);
2336           }
2337         }
2338         else
2339         {
2340           newtitle = new String("Pasted sequences");
2341         }
2342
2343         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2344                 DEFAULT_HEIGHT);
2345
2346       }
2347
2348     } catch (Exception ex)
2349     {
2350       ex.printStackTrace();
2351       System.out.println("Exception whilst pasting: " + ex);
2352       // could be anything being pasted in here
2353     }
2354   }
2355
2356   @Override
2357   protected void expand_newalign(ActionEvent e)
2358   {
2359     try
2360     {
2361       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2362               .getAlignment(), -1);
2363       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2364               DEFAULT_HEIGHT);
2365       String newtitle = new String("Flanking alignment");
2366
2367       if (Desktop.jalviewClipboard != null
2368               && Desktop.jalviewClipboard[2] != null)
2369       {
2370         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2371         for (int region[] : hc)
2372         {
2373           af.viewport.hideColumns(region[0], region[1]);
2374         }
2375       }
2376
2377       // >>>This is a fix for the moment, until a better solution is
2378       // found!!<<<
2379       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2380               .transferSettings(
2381                       alignPanel.getSeqPanel().seqCanvas
2382                               .getFeatureRenderer());
2383
2384       // TODO: maintain provenance of an alignment, rather than just make the
2385       // title a concatenation of operations.
2386       {
2387         if (title.startsWith("Copied sequences"))
2388         {
2389           newtitle = title;
2390         }
2391         else
2392         {
2393           newtitle = newtitle.concat("- from " + title);
2394         }
2395       }
2396
2397       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2398
2399     } catch (Exception ex)
2400     {
2401       ex.printStackTrace();
2402       System.out.println("Exception whilst pasting: " + ex);
2403       // could be anything being pasted in here
2404     } catch (OutOfMemoryError oom)
2405     {
2406       new OOMWarning("Viewing flanking region of alignment", oom);
2407     }
2408   }
2409
2410   /**
2411    * DOCUMENT ME!
2412    *
2413    * @param e
2414    *          DOCUMENT ME!
2415    */
2416   @Override
2417   protected void cut_actionPerformed(ActionEvent e)
2418   {
2419     copy_actionPerformed(null);
2420     delete_actionPerformed(null);
2421   }
2422
2423   /**
2424    * DOCUMENT ME!
2425    *
2426    * @param e
2427    *          DOCUMENT ME!
2428    */
2429   @Override
2430   protected void delete_actionPerformed(ActionEvent evt)
2431   {
2432
2433     SequenceGroup sg = viewport.getSelectionGroup();
2434     if (sg == null)
2435     {
2436       return;
2437     }
2438
2439     /*
2440      * If the cut affects all sequences, warn, remove highlighted columns
2441      */
2442     if (sg.getSize() == viewport.getAlignment().getHeight())
2443     {
2444       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2445               .getAlignment().getWidth()) ? true : false;
2446       if (isEntireAlignWidth)
2447       {
2448         int confirm = JvOptionPane.showConfirmDialog(this,
2449                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2450                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2451                 JvOptionPane.OK_CANCEL_OPTION);
2452
2453         if (confirm == JvOptionPane.CANCEL_OPTION
2454                 || confirm == JvOptionPane.CLOSED_OPTION)
2455         {
2456           return;
2457         }
2458       }
2459       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2460               sg.getEndRes() + 1);
2461     }
2462     SequenceI[] cut = sg.getSequences()
2463             .toArray(new SequenceI[sg.getSize()]);
2464
2465     addHistoryItem(new EditCommand(
2466             MessageManager.getString("label.cut_sequences"), Action.CUT,
2467             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2468             viewport.getAlignment()));
2469
2470     viewport.setSelectionGroup(null);
2471     viewport.sendSelection();
2472     viewport.getAlignment().deleteGroup(sg);
2473
2474     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2475             .getSequences());
2476     if (viewport.getAlignment().getHeight() < 1)
2477     {
2478       try
2479       {
2480         this.setClosed(true);
2481       } catch (Exception ex)
2482       {
2483       }
2484     }
2485   }
2486
2487   /**
2488    * DOCUMENT ME!
2489    *
2490    * @param e
2491    *          DOCUMENT ME!
2492    */
2493   @Override
2494   protected void deleteGroups_actionPerformed(ActionEvent e)
2495   {
2496     if (avc.deleteGroups())
2497     {
2498       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2499       alignPanel.updateAnnotation();
2500       alignPanel.paintAlignment(true);
2501     }
2502   }
2503
2504   /**
2505    * DOCUMENT ME!
2506    *
2507    * @param e
2508    *          DOCUMENT ME!
2509    */
2510   @Override
2511   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2512   {
2513     SequenceGroup sg = new SequenceGroup();
2514
2515     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2516     {
2517       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2518     }
2519
2520     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2521     viewport.setSelectionGroup(sg);
2522     viewport.sendSelection();
2523     // JAL-2034 - should delegate to
2524     // alignPanel to decide if overview needs
2525     // updating.
2526     alignPanel.paintAlignment(false);
2527     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2528   }
2529
2530   /**
2531    * DOCUMENT ME!
2532    *
2533    * @param e
2534    *          DOCUMENT ME!
2535    */
2536   @Override
2537   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2538   {
2539     if (viewport.cursorMode)
2540     {
2541       alignPanel.getSeqPanel().keyboardNo1 = null;
2542       alignPanel.getSeqPanel().keyboardNo2 = null;
2543     }
2544     viewport.setSelectionGroup(null);
2545     viewport.getColumnSelection().clear();
2546     viewport.setSelectionGroup(null);
2547     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2548     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2549     // JAL-2034 - should delegate to
2550     // alignPanel to decide if overview needs
2551     // updating.
2552     alignPanel.paintAlignment(false);
2553     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2554     viewport.sendSelection();
2555   }
2556
2557   /**
2558    * DOCUMENT ME!
2559    *
2560    * @param e
2561    *          DOCUMENT ME!
2562    */
2563   @Override
2564   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2565   {
2566     SequenceGroup sg = viewport.getSelectionGroup();
2567
2568     if (sg == null)
2569     {
2570       selectAllSequenceMenuItem_actionPerformed(null);
2571
2572       return;
2573     }
2574
2575     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2576     {
2577       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2578     }
2579     // JAL-2034 - should delegate to
2580     // alignPanel to decide if overview needs
2581     // updating.
2582
2583     alignPanel.paintAlignment(true);
2584     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2585     viewport.sendSelection();
2586   }
2587
2588   @Override
2589   public void invertColSel_actionPerformed(ActionEvent e)
2590   {
2591     viewport.invertColumnSelection();
2592     alignPanel.paintAlignment(true);
2593     viewport.sendSelection();
2594   }
2595
2596   /**
2597    * DOCUMENT ME!
2598    *
2599    * @param e
2600    *          DOCUMENT ME!
2601    */
2602   @Override
2603   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2604   {
2605     trimAlignment(true);
2606   }
2607
2608   /**
2609    * DOCUMENT ME!
2610    *
2611    * @param e
2612    *          DOCUMENT ME!
2613    */
2614   @Override
2615   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2616   {
2617     trimAlignment(false);
2618   }
2619
2620   void trimAlignment(boolean trimLeft)
2621   {
2622     ColumnSelection colSel = viewport.getColumnSelection();
2623     int column;
2624
2625     if (!colSel.isEmpty())
2626     {
2627       if (trimLeft)
2628       {
2629         column = colSel.getMin();
2630       }
2631       else
2632       {
2633         column = colSel.getMax();
2634       }
2635
2636       SequenceI[] seqs;
2637       if (viewport.getSelectionGroup() != null)
2638       {
2639         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2640                 viewport.getHiddenRepSequences());
2641       }
2642       else
2643       {
2644         seqs = viewport.getAlignment().getSequencesArray();
2645       }
2646
2647       TrimRegionCommand trimRegion;
2648       if (trimLeft)
2649       {
2650         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2651                 column, viewport.getAlignment());
2652         vpRanges.setStartRes(0);
2653       }
2654       else
2655       {
2656         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2657                 column, viewport.getAlignment());
2658       }
2659
2660       statusBar.setText(MessageManager.formatMessage(
2661               "label.removed_columns",
2662               new String[] { Integer.valueOf(trimRegion.getSize())
2663                       .toString() }));
2664
2665       addHistoryItem(trimRegion);
2666
2667       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2668       {
2669         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2670                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2671         {
2672           viewport.getAlignment().deleteGroup(sg);
2673         }
2674       }
2675
2676       viewport.firePropertyChange("alignment", null, viewport
2677               .getAlignment().getSequences());
2678     }
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2689   {
2690     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2691
2692     SequenceI[] seqs;
2693     if (viewport.getSelectionGroup() != null)
2694     {
2695       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2696               viewport.getHiddenRepSequences());
2697       start = viewport.getSelectionGroup().getStartRes();
2698       end = viewport.getSelectionGroup().getEndRes();
2699     }
2700     else
2701     {
2702       seqs = viewport.getAlignment().getSequencesArray();
2703     }
2704
2705     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2706             "Remove Gapped Columns", seqs, start, end,
2707             viewport.getAlignment());
2708
2709     addHistoryItem(removeGapCols);
2710
2711     statusBar.setText(MessageManager.formatMessage(
2712             "label.removed_empty_columns",
2713             new Object[] { Integer.valueOf(removeGapCols.getSize())
2714                     .toString() }));
2715
2716     // This is to maintain viewport position on first residue
2717     // of first sequence
2718     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2719     int startRes = seq.findPosition(vpRanges.getStartRes());
2720     // ShiftList shifts;
2721     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2722     // edit.alColumnChanges=shifts.getInverse();
2723     // if (viewport.hasHiddenColumns)
2724     // viewport.getColumnSelection().compensateForEdits(shifts);
2725     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2726     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2727             .getSequences());
2728
2729   }
2730
2731   /**
2732    * DOCUMENT ME!
2733    *
2734    * @param e
2735    *          DOCUMENT ME!
2736    */
2737   @Override
2738   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2739   {
2740     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2741
2742     SequenceI[] seqs;
2743     if (viewport.getSelectionGroup() != null)
2744     {
2745       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2746               viewport.getHiddenRepSequences());
2747       start = viewport.getSelectionGroup().getStartRes();
2748       end = viewport.getSelectionGroup().getEndRes();
2749     }
2750     else
2751     {
2752       seqs = viewport.getAlignment().getSequencesArray();
2753     }
2754
2755     // This is to maintain viewport position on first residue
2756     // of first sequence
2757     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2758     int startRes = seq.findPosition(vpRanges.getStartRes());
2759
2760     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2761             viewport.getAlignment()));
2762
2763     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2764
2765     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2766             .getSequences());
2767
2768   }
2769
2770   /**
2771    * DOCUMENT ME!
2772    *
2773    * @param e
2774    *          DOCUMENT ME!
2775    */
2776   @Override
2777   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2778   {
2779     viewport.setPadGaps(padGapsMenuitem.isSelected());
2780     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2781             .getSequences());
2782   }
2783
2784   /**
2785    * DOCUMENT ME!
2786    *
2787    * @param e
2788    *          DOCUMENT ME!
2789    */
2790   @Override
2791   public void findMenuItem_actionPerformed(ActionEvent e)
2792   {
2793     new Finder();
2794   }
2795
2796   /**
2797    * Create a new view of the current alignment.
2798    */
2799   @Override
2800   public void newView_actionPerformed(ActionEvent e)
2801   {
2802     newView(null, true);
2803   }
2804
2805   /**
2806    * Creates and shows a new view of the current alignment.
2807    *
2808    * @param viewTitle
2809    *          title of newly created view; if null, one will be generated
2810    * @param copyAnnotation
2811    *          if true then duplicate all annnotation, groups and settings
2812    * @return new alignment panel, already displayed.
2813    */
2814   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2815   {
2816     /*
2817      * Create a new AlignmentPanel (with its own, new Viewport)
2818      */
2819     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2820             true);
2821     if (!copyAnnotation)
2822     {
2823       /*
2824        * remove all groups and annotation except for the automatic stuff
2825        */
2826       newap.av.getAlignment().deleteAllGroups();
2827       newap.av.getAlignment().deleteAllAnnotations(false);
2828     }
2829
2830     newap.av.setGatherViewsHere(false);
2831
2832     if (viewport.viewName == null)
2833     {
2834       viewport.viewName = MessageManager
2835               .getString("label.view_name_original");
2836     }
2837
2838     /*
2839      * Views share the same edits undo and redo stacks
2840      */
2841     newap.av.setHistoryList(viewport.getHistoryList());
2842     newap.av.setRedoList(viewport.getRedoList());
2843
2844     /*
2845      * Views share the same mappings; need to deregister any new mappings
2846      * created by copyAlignPanel, and register the new reference to the shared
2847      * mappings
2848      */
2849     newap.av.replaceMappings(viewport.getAlignment());
2850
2851     /*
2852      * start up cDNA consensus (if applicable) now mappings are in place
2853      */
2854     if (newap.av.initComplementConsensus())
2855     {
2856       newap.refresh(true); // adjust layout of annotations
2857     }
2858
2859     newap.av.viewName = getNewViewName(viewTitle);
2860
2861     addAlignmentPanel(newap, true);
2862     newap.alignmentChanged();
2863
2864     if (alignPanels.size() == 2)
2865     {
2866       viewport.setGatherViewsHere(true);
2867     }
2868     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2869     return newap;
2870   }
2871
2872   /**
2873    * Make a new name for the view, ensuring it is unique within the current
2874    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2875    * these now use viewId. Unique view names are still desirable for usability.)
2876    *
2877    * @param viewTitle
2878    * @return
2879    */
2880   protected String getNewViewName(String viewTitle)
2881   {
2882     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2883     boolean addFirstIndex = false;
2884     if (viewTitle == null || viewTitle.trim().length() == 0)
2885     {
2886       viewTitle = MessageManager.getString("action.view");
2887       addFirstIndex = true;
2888     }
2889     else
2890     {
2891       index = 1;// we count from 1 if given a specific name
2892     }
2893     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2894
2895     List<Component> comps = PaintRefresher.components.get(viewport
2896             .getSequenceSetId());
2897
2898     List<String> existingNames = getExistingViewNames(comps);
2899
2900     while (existingNames.contains(newViewName))
2901     {
2902       newViewName = viewTitle + " " + (++index);
2903     }
2904     return newViewName;
2905   }
2906
2907   /**
2908    * Returns a list of distinct view names found in the given list of
2909    * components. View names are held on the viewport of an AlignmentPanel.
2910    *
2911    * @param comps
2912    * @return
2913    */
2914   protected List<String> getExistingViewNames(List<Component> comps)
2915   {
2916     List<String> existingNames = new ArrayList<>();
2917     for (Component comp : comps)
2918     {
2919       if (comp instanceof AlignmentPanel)
2920       {
2921         AlignmentPanel ap = (AlignmentPanel) comp;
2922         if (!existingNames.contains(ap.av.viewName))
2923         {
2924           existingNames.add(ap.av.viewName);
2925         }
2926       }
2927     }
2928     return existingNames;
2929   }
2930
2931   /**
2932    * Explode tabbed views into separate windows.
2933    */
2934   @Override
2935   public void expandViews_actionPerformed(ActionEvent e)
2936   {
2937     Desktop.explodeViews(this);
2938   }
2939
2940   /**
2941    * Gather views in separate windows back into a tabbed presentation.
2942    */
2943   @Override
2944   public void gatherViews_actionPerformed(ActionEvent e)
2945   {
2946     Desktop.instance.gatherViews(this);
2947   }
2948
2949   /**
2950    * DOCUMENT ME!
2951    *
2952    * @param e
2953    *          DOCUMENT ME!
2954    */
2955   @Override
2956   public void font_actionPerformed(ActionEvent e)
2957   {
2958     new FontChooser(alignPanel);
2959   }
2960
2961   /**
2962    * DOCUMENT ME!
2963    *
2964    * @param e
2965    *          DOCUMENT ME!
2966    */
2967   @Override
2968   protected void seqLimit_actionPerformed(ActionEvent e)
2969   {
2970     viewport.setShowJVSuffix(seqLimits.isSelected());
2971
2972     alignPanel.getIdPanel().getIdCanvas()
2973             .setPreferredSize(alignPanel.calculateIdWidth());
2974     alignPanel.paintAlignment(true);
2975   }
2976
2977   @Override
2978   public void idRightAlign_actionPerformed(ActionEvent e)
2979   {
2980     viewport.setRightAlignIds(idRightAlign.isSelected());
2981     alignPanel.paintAlignment(true);
2982   }
2983
2984   @Override
2985   public void centreColumnLabels_actionPerformed(ActionEvent e)
2986   {
2987     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2988     alignPanel.paintAlignment(true);
2989   }
2990
2991   /*
2992    * (non-Javadoc)
2993    *
2994    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2995    */
2996   @Override
2997   protected void followHighlight_actionPerformed()
2998   {
2999     /*
3000      * Set the 'follow' flag on the Viewport (and scroll to position if now
3001      * true).
3002      */
3003     final boolean state = this.followHighlightMenuItem.getState();
3004     viewport.setFollowHighlight(state);
3005     if (state)
3006     {
3007       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3008     }
3009   }
3010
3011   /**
3012    * DOCUMENT ME!
3013    *
3014    * @param e
3015    *          DOCUMENT ME!
3016    */
3017   @Override
3018   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3019   {
3020     viewport.setColourText(colourTextMenuItem.isSelected());
3021     alignPanel.paintAlignment(true);
3022   }
3023
3024   /**
3025    * DOCUMENT ME!
3026    *
3027    * @param e
3028    *          DOCUMENT ME!
3029    */
3030   @Override
3031   public void wrapMenuItem_actionPerformed(ActionEvent e)
3032   {
3033     scaleAbove.setVisible(wrapMenuItem.isSelected());
3034     scaleLeft.setVisible(wrapMenuItem.isSelected());
3035     scaleRight.setVisible(wrapMenuItem.isSelected());
3036     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3037     alignPanel.updateLayout();
3038   }
3039
3040   @Override
3041   public void showAllSeqs_actionPerformed(ActionEvent e)
3042   {
3043     viewport.showAllHiddenSeqs();
3044   }
3045
3046   @Override
3047   public void showAllColumns_actionPerformed(ActionEvent e)
3048   {
3049     viewport.showAllHiddenColumns();
3050     repaint();
3051     viewport.sendSelection();
3052   }
3053
3054   @Override
3055   public void hideSelSequences_actionPerformed(ActionEvent e)
3056   {
3057     viewport.hideAllSelectedSeqs();
3058     // alignPanel.paintAlignment(true);
3059   }
3060
3061   /**
3062    * called by key handler and the hide all/show all menu items
3063    *
3064    * @param toggleSeqs
3065    * @param toggleCols
3066    */
3067   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3068   {
3069
3070     boolean hide = false;
3071     SequenceGroup sg = viewport.getSelectionGroup();
3072     if (!toggleSeqs && !toggleCols)
3073     {
3074       // Hide everything by the current selection - this is a hack - we do the
3075       // invert and then hide
3076       // first check that there will be visible columns after the invert.
3077       if (viewport.hasSelectedColumns()
3078               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3079                       .getEndRes()))
3080       {
3081         // now invert the sequence set, if required - empty selection implies
3082         // that no hiding is required.
3083         if (sg != null)
3084         {
3085           invertSequenceMenuItem_actionPerformed(null);
3086           sg = viewport.getSelectionGroup();
3087           toggleSeqs = true;
3088
3089         }
3090         viewport.expandColSelection(sg, true);
3091         // finally invert the column selection and get the new sequence
3092         // selection.
3093         invertColSel_actionPerformed(null);
3094         toggleCols = true;
3095       }
3096     }
3097
3098     if (toggleSeqs)
3099     {
3100       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3101       {
3102         hideSelSequences_actionPerformed(null);
3103         hide = true;
3104       }
3105       else if (!(toggleCols && viewport.hasSelectedColumns()))
3106       {
3107         showAllSeqs_actionPerformed(null);
3108       }
3109     }
3110
3111     if (toggleCols)
3112     {
3113       if (viewport.hasSelectedColumns())
3114       {
3115         hideSelColumns_actionPerformed(null);
3116         if (!toggleSeqs)
3117         {
3118           viewport.setSelectionGroup(sg);
3119         }
3120       }
3121       else if (!hide)
3122       {
3123         showAllColumns_actionPerformed(null);
3124       }
3125     }
3126   }
3127
3128   /*
3129    * (non-Javadoc)
3130    *
3131    * @see
3132    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3133    * event.ActionEvent)
3134    */
3135   @Override
3136   public void hideAllButSelection_actionPerformed(ActionEvent e)
3137   {
3138     toggleHiddenRegions(false, false);
3139     viewport.sendSelection();
3140   }
3141
3142   /*
3143    * (non-Javadoc)
3144    *
3145    * @see
3146    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3147    * .ActionEvent)
3148    */
3149   @Override
3150   public void hideAllSelection_actionPerformed(ActionEvent e)
3151   {
3152     SequenceGroup sg = viewport.getSelectionGroup();
3153     viewport.expandColSelection(sg, false);
3154     viewport.hideAllSelectedSeqs();
3155     viewport.hideSelectedColumns();
3156     alignPanel.paintAlignment(true);
3157     viewport.sendSelection();
3158   }
3159
3160   /*
3161    * (non-Javadoc)
3162    *
3163    * @see
3164    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3165    * ActionEvent)
3166    */
3167   @Override
3168   public void showAllhidden_actionPerformed(ActionEvent e)
3169   {
3170     viewport.showAllHiddenColumns();
3171     viewport.showAllHiddenSeqs();
3172     alignPanel.paintAlignment(true);
3173     viewport.sendSelection();
3174   }
3175
3176   @Override
3177   public void hideSelColumns_actionPerformed(ActionEvent e)
3178   {
3179     viewport.hideSelectedColumns();
3180     alignPanel.paintAlignment(true);
3181     viewport.sendSelection();
3182   }
3183
3184   @Override
3185   public void hiddenMarkers_actionPerformed(ActionEvent e)
3186   {
3187     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3188     repaint();
3189   }
3190
3191   /**
3192    * DOCUMENT ME!
3193    *
3194    * @param e
3195    *          DOCUMENT ME!
3196    */
3197   @Override
3198   protected void scaleAbove_actionPerformed(ActionEvent e)
3199   {
3200     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3201     alignPanel.paintAlignment(true);
3202   }
3203
3204   /**
3205    * DOCUMENT ME!
3206    *
3207    * @param e
3208    *          DOCUMENT ME!
3209    */
3210   @Override
3211   protected void scaleLeft_actionPerformed(ActionEvent e)
3212   {
3213     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3214     alignPanel.paintAlignment(true);
3215   }
3216
3217   /**
3218    * DOCUMENT ME!
3219    *
3220    * @param e
3221    *          DOCUMENT ME!
3222    */
3223   @Override
3224   protected void scaleRight_actionPerformed(ActionEvent e)
3225   {
3226     viewport.setScaleRightWrapped(scaleRight.isSelected());
3227     alignPanel.paintAlignment(true);
3228   }
3229
3230   /**
3231    * DOCUMENT ME!
3232    *
3233    * @param e
3234    *          DOCUMENT ME!
3235    */
3236   @Override
3237   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3238   {
3239     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3240     alignPanel.paintAlignment(true);
3241   }
3242
3243   /**
3244    * DOCUMENT ME!
3245    *
3246    * @param e
3247    *          DOCUMENT ME!
3248    */
3249   @Override
3250   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3251   {
3252     viewport.setShowText(viewTextMenuItem.isSelected());
3253     alignPanel.paintAlignment(true);
3254   }
3255
3256   /**
3257    * DOCUMENT ME!
3258    *
3259    * @param e
3260    *          DOCUMENT ME!
3261    */
3262   @Override
3263   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3264   {
3265     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3266     alignPanel.paintAlignment(true);
3267   }
3268
3269   public FeatureSettings featureSettings;
3270
3271   @Override
3272   public FeatureSettingsControllerI getFeatureSettingsUI()
3273   {
3274     return featureSettings;
3275   }
3276
3277   @Override
3278   public void featureSettings_actionPerformed(ActionEvent e)
3279   {
3280     if (featureSettings != null)
3281     {
3282       featureSettings.close();
3283       featureSettings = null;
3284     }
3285     if (!showSeqFeatures.isSelected())
3286     {
3287       // make sure features are actually displayed
3288       showSeqFeatures.setSelected(true);
3289       showSeqFeatures_actionPerformed(null);
3290     }
3291     featureSettings = new FeatureSettings(this);
3292   }
3293
3294   /**
3295    * Set or clear 'Show Sequence Features'
3296    *
3297    * @param evt
3298    *          DOCUMENT ME!
3299    */
3300   @Override
3301   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3302   {
3303     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3304     alignPanel.paintAlignment(true);
3305     if (alignPanel.getOverviewPanel() != null)
3306     {
3307       alignPanel.getOverviewPanel().updateOverviewImage();
3308     }
3309   }
3310
3311   /**
3312    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3313    * the annotations panel as a whole.
3314    *
3315    * The options to show/hide all annotations should be enabled when the panel
3316    * is shown, and disabled when the panel is hidden.
3317    *
3318    * @param e
3319    */
3320   @Override
3321   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3322   {
3323     final boolean setVisible = annotationPanelMenuItem.isSelected();
3324     viewport.setShowAnnotation(setVisible);
3325     this.showAllSeqAnnotations.setEnabled(setVisible);
3326     this.hideAllSeqAnnotations.setEnabled(setVisible);
3327     this.showAllAlAnnotations.setEnabled(setVisible);
3328     this.hideAllAlAnnotations.setEnabled(setVisible);
3329     alignPanel.updateLayout();
3330   }
3331
3332   @Override
3333   public void alignmentProperties()
3334   {
3335     JEditorPane editPane = new JEditorPane("text/html", "");
3336     editPane.setEditable(false);
3337     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3338             .formatAsHtml();
3339     editPane.setText(MessageManager.formatMessage("label.html_content",
3340             new Object[] { contents.toString() }));
3341     JInternalFrame frame = new JInternalFrame();
3342     frame.getContentPane().add(new JScrollPane(editPane));
3343
3344     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3345             "label.alignment_properties", new Object[] { getTitle() }),
3346             500, 400);
3347   }
3348
3349   /**
3350    * DOCUMENT ME!
3351    *
3352    * @param e
3353    *          DOCUMENT ME!
3354    */
3355   @Override
3356   public void overviewMenuItem_actionPerformed(ActionEvent e)
3357   {
3358     if (alignPanel.overviewPanel != null)
3359     {
3360       return;
3361     }
3362
3363     JInternalFrame frame = new JInternalFrame();
3364     OverviewPanel overview = new OverviewPanel(alignPanel);
3365     frame.setContentPane(overview);
3366     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3367             "label.overview_params", new Object[] { this.getTitle() }),
3368             true, frame.getWidth(), frame.getHeight(), true, true);
3369     frame.pack();
3370     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3371     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3372     {
3373       @Override
3374       public void internalFrameClosed(
3375               javax.swing.event.InternalFrameEvent evt)
3376       {
3377         alignPanel.setOverviewPanel(null);
3378       };
3379     });
3380
3381     alignPanel.setOverviewPanel(overview);
3382   }
3383
3384   @Override
3385   public void textColour_actionPerformed()
3386   {
3387     new TextColourChooser().chooseColour(alignPanel, null);
3388   }
3389
3390   /*
3391    * public void covariationColour_actionPerformed() {
3392    * changeColour(new
3393    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3394    * ()[0])); }
3395    */
3396   @Override
3397   public void annotationColour_actionPerformed()
3398   {
3399     new AnnotationColourChooser(viewport, alignPanel);
3400   }
3401
3402   @Override
3403   public void annotationColumn_actionPerformed(ActionEvent e)
3404   {
3405     new AnnotationColumnChooser(viewport, alignPanel);
3406   }
3407
3408   /**
3409    * Action on the user checking or unchecking the option to apply the selected
3410    * colour scheme to all groups. If unchecked, groups may have their own
3411    * independent colour schemes.
3412    *
3413    * @param selected
3414    */
3415   @Override
3416   public void applyToAllGroups_actionPerformed(boolean selected)
3417   {
3418     viewport.setColourAppliesToAllGroups(selected);
3419   }
3420
3421   /**
3422    * Action on user selecting a colour from the colour menu
3423    *
3424    * @param name
3425    *          the name (not the menu item label!) of the colour scheme
3426    */
3427   @Override
3428   public void changeColour_actionPerformed(String name)
3429   {
3430     /*
3431      * 'User Defined' opens a panel to configure or load a
3432      * user-defined colour scheme
3433      */
3434     if (ResidueColourScheme.USER_DEFINED.equals(name))
3435     {
3436       new UserDefinedColours(alignPanel);
3437       return;
3438     }
3439
3440     /*
3441      * otherwise set the chosen colour scheme (or null for 'None')
3442      */
3443     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3444             viewport.getAlignment(), viewport.getHiddenRepSequences());
3445     changeColour(cs);
3446   }
3447
3448   /**
3449    * Actions on setting or changing the alignment colour scheme
3450    *
3451    * @param cs
3452    */
3453   @Override
3454   public void changeColour(ColourSchemeI cs)
3455   {
3456     // TODO: pull up to controller method
3457     ColourMenuHelper.setColourSelected(colourMenu, cs);
3458
3459     viewport.setGlobalColourScheme(cs);
3460
3461     alignPanel.paintAlignment(true);
3462   }
3463
3464   /**
3465    * Show the PID threshold slider panel
3466    */
3467   @Override
3468   protected void modifyPID_actionPerformed()
3469   {
3470     SliderPanel.setPIDSliderSource(alignPanel,
3471             viewport.getResidueShading(), alignPanel.getViewName());
3472     SliderPanel.showPIDSlider();
3473   }
3474
3475   /**
3476    * Show the Conservation slider panel
3477    */
3478   @Override
3479   protected void modifyConservation_actionPerformed()
3480   {
3481     SliderPanel.setConservationSlider(alignPanel,
3482             viewport.getResidueShading(), alignPanel.getViewName());
3483     SliderPanel.showConservationSlider();
3484   }
3485
3486   /**
3487    * Action on selecting or deselecting (Colour) By Conservation
3488    */
3489   @Override
3490   public void conservationMenuItem_actionPerformed(boolean selected)
3491   {
3492     modifyConservation.setEnabled(selected);
3493     viewport.setConservationSelected(selected);
3494     viewport.getResidueShading().setConservationApplied(selected);
3495
3496     changeColour(viewport.getGlobalColourScheme());
3497     if (selected)
3498     {
3499       modifyConservation_actionPerformed();
3500     }
3501     else
3502     {
3503       SliderPanel.hideConservationSlider();
3504     }
3505   }
3506
3507   /**
3508    * Action on selecting or deselecting (Colour) Above PID Threshold
3509    */
3510   @Override
3511   public void abovePIDThreshold_actionPerformed(boolean selected)
3512   {
3513     modifyPID.setEnabled(selected);
3514     viewport.setAbovePIDThreshold(selected);
3515     if (!selected)
3516     {
3517       viewport.getResidueShading().setThreshold(0,
3518               viewport.isIgnoreGapsConsensus());
3519     }
3520
3521     changeColour(viewport.getGlobalColourScheme());
3522     if (selected)
3523     {
3524       modifyPID_actionPerformed();
3525     }
3526     else
3527     {
3528       SliderPanel.hidePIDSlider();
3529     }
3530   }
3531
3532   /**
3533    * DOCUMENT ME!
3534    *
3535    * @param e
3536    *          DOCUMENT ME!
3537    */
3538   @Override
3539   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3540   {
3541     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3542     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3543             .getAlignment().getSequenceAt(0));
3544     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3545             viewport.getAlignment()));
3546     alignPanel.paintAlignment(true);
3547   }
3548
3549   /**
3550    * DOCUMENT ME!
3551    *
3552    * @param e
3553    *          DOCUMENT ME!
3554    */
3555   @Override
3556   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3557   {
3558     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3559     AlignmentSorter.sortByID(viewport.getAlignment());
3560     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3561             viewport.getAlignment()));
3562     alignPanel.paintAlignment(true);
3563   }
3564
3565   /**
3566    * DOCUMENT ME!
3567    *
3568    * @param e
3569    *          DOCUMENT ME!
3570    */
3571   @Override
3572   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3573   {
3574     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3575     AlignmentSorter.sortByLength(viewport.getAlignment());
3576     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3577             viewport.getAlignment()));
3578     alignPanel.paintAlignment(true);
3579   }
3580
3581   /**
3582    * DOCUMENT ME!
3583    *
3584    * @param e
3585    *          DOCUMENT ME!
3586    */
3587   @Override
3588   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3589   {
3590     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3591     AlignmentSorter.sortByGroup(viewport.getAlignment());
3592     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3593             viewport.getAlignment()));
3594
3595     alignPanel.paintAlignment(true);
3596   }
3597
3598   /**
3599    * DOCUMENT ME!
3600    *
3601    * @param e
3602    *          DOCUMENT ME!
3603    */
3604   @Override
3605   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3606   {
3607     new RedundancyPanel(alignPanel, this);
3608   }
3609
3610   /**
3611    * DOCUMENT ME!
3612    *
3613    * @param e
3614    *          DOCUMENT ME!
3615    */
3616   @Override
3617   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3618   {
3619     if ((viewport.getSelectionGroup() == null)
3620             || (viewport.getSelectionGroup().getSize() < 2))
3621     {
3622       JvOptionPane.showInternalMessageDialog(this, MessageManager
3623               .getString("label.you_must_select_least_two_sequences"),
3624               MessageManager.getString("label.invalid_selection"),
3625               JvOptionPane.WARNING_MESSAGE);
3626     }
3627     else
3628     {
3629       JInternalFrame frame = new JInternalFrame();
3630       frame.setContentPane(new PairwiseAlignPanel(viewport));
3631       Desktop.addInternalFrame(frame,
3632               MessageManager.getString("action.pairwise_alignment"), 600,
3633               500);
3634     }
3635   }
3636
3637   @Override
3638   public void autoCalculate_actionPerformed(ActionEvent e)
3639   {
3640     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3641     if (viewport.autoCalculateConsensus)
3642     {
3643       viewport.firePropertyChange("alignment", null, viewport
3644               .getAlignment().getSequences());
3645     }
3646   }
3647
3648   @Override
3649   public void sortByTreeOption_actionPerformed(ActionEvent e)
3650   {
3651     viewport.sortByTree = sortByTree.isSelected();
3652   }
3653
3654   @Override
3655   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3656   {
3657     viewport.followSelection = listenToViewSelections.isSelected();
3658   }
3659
3660   /**
3661    * Constructs a tree panel and adds it to the desktop
3662    *
3663    * @param type
3664    *          tree type (NJ or AV)
3665    * @param modelName
3666    *          name of score model used to compute the tree
3667    * @param options
3668    *          parameters for the distance or similarity calculation
3669    */
3670   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3671   {
3672     String frameTitle = "";
3673     TreePanel tp;
3674
3675     boolean onSelection = false;
3676     if (viewport.getSelectionGroup() != null
3677             && viewport.getSelectionGroup().getSize() > 0)
3678     {
3679       SequenceGroup sg = viewport.getSelectionGroup();
3680
3681       /* Decide if the selection is a column region */
3682       for (SequenceI _s : sg.getSequences())
3683       {
3684         if (_s.getLength() < sg.getEndRes())
3685         {
3686           JvOptionPane
3687                   .showMessageDialog(
3688                           Desktop.desktop,
3689                           MessageManager
3690                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3691                           MessageManager
3692                                   .getString("label.sequences_selection_not_aligned"),
3693                           JvOptionPane.WARNING_MESSAGE);
3694
3695           return;
3696         }
3697       }
3698       onSelection = true;
3699     }
3700     else
3701     {
3702       if (viewport.getAlignment().getHeight() < 2)
3703       {
3704         return;
3705       }
3706     }
3707
3708     tp = new TreePanel(alignPanel, type, modelName, options);
3709     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3710
3711     frameTitle += " from ";
3712
3713     if (viewport.viewName != null)
3714     {
3715       frameTitle += viewport.viewName + " of ";
3716     }
3717
3718     frameTitle += this.title;
3719
3720     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3721   }
3722
3723   /**
3724    * DOCUMENT ME!
3725    *
3726    * @param title
3727    *          DOCUMENT ME!
3728    * @param order
3729    *          DOCUMENT ME!
3730    */
3731   public void addSortByOrderMenuItem(String title,
3732           final AlignmentOrder order)
3733   {
3734     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3735             "action.by_title_param", new Object[] { title }));
3736     sort.add(item);
3737     item.addActionListener(new java.awt.event.ActionListener()
3738     {
3739       @Override
3740       public void actionPerformed(ActionEvent e)
3741       {
3742         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3743
3744         // TODO: JBPNote - have to map order entries to curent SequenceI
3745         // pointers
3746         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3747
3748         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3749                 .getAlignment()));
3750
3751         alignPanel.paintAlignment(true);
3752       }
3753     });
3754   }
3755
3756   /**
3757    * Add a new sort by annotation score menu item
3758    *
3759    * @param sort
3760    *          the menu to add the option to
3761    * @param scoreLabel
3762    *          the label used to retrieve scores for each sequence on the
3763    *          alignment
3764    */
3765   public void addSortByAnnotScoreMenuItem(JMenu sort,
3766           final String scoreLabel)
3767   {
3768     final JMenuItem item = new JMenuItem(scoreLabel);
3769     sort.add(item);
3770     item.addActionListener(new java.awt.event.ActionListener()
3771     {
3772       @Override
3773       public void actionPerformed(ActionEvent e)
3774       {
3775         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3776         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3777                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3778         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3779                 viewport.getAlignment()));
3780         alignPanel.paintAlignment(true);
3781       }
3782     });
3783   }
3784
3785   /**
3786    * last hash for alignment's annotation array - used to minimise cost of
3787    * rebuild.
3788    */
3789   protected int _annotationScoreVectorHash;
3790
3791   /**
3792    * search the alignment and rebuild the sort by annotation score submenu the
3793    * last alignment annotation vector hash is stored to minimize cost of
3794    * rebuilding in subsequence calls.
3795    *
3796    */
3797   @Override
3798   public void buildSortByAnnotationScoresMenu()
3799   {
3800     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3801     {
3802       return;
3803     }
3804
3805     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3806     {
3807       sortByAnnotScore.removeAll();
3808       // almost certainly a quicker way to do this - but we keep it simple
3809       Hashtable scoreSorts = new Hashtable();
3810       AlignmentAnnotation aann[];
3811       for (SequenceI sqa : viewport.getAlignment().getSequences())
3812       {
3813         aann = sqa.getAnnotation();
3814         for (int i = 0; aann != null && i < aann.length; i++)
3815         {
3816           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3817           {
3818             scoreSorts.put(aann[i].label, aann[i].label);
3819           }
3820         }
3821       }
3822       Enumeration labels = scoreSorts.keys();
3823       while (labels.hasMoreElements())
3824       {
3825         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3826                 (String) labels.nextElement());
3827       }
3828       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3829       scoreSorts.clear();
3830
3831       _annotationScoreVectorHash = viewport.getAlignment()
3832               .getAlignmentAnnotation().hashCode();
3833     }
3834   }
3835
3836   /**
3837    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3838    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3839    * call. Listeners are added to remove the menu item when the treePanel is
3840    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3841    * modified.
3842    */
3843   @Override
3844   public void buildTreeSortMenu()
3845   {
3846     sortByTreeMenu.removeAll();
3847
3848     List<Component> comps = PaintRefresher.components.get(viewport
3849             .getSequenceSetId());
3850     List<TreePanel> treePanels = new ArrayList<>();
3851     for (Component comp : comps)
3852     {
3853       if (comp instanceof TreePanel)
3854       {
3855         treePanels.add((TreePanel) comp);
3856       }
3857     }
3858
3859     if (treePanels.size() < 1)
3860     {
3861       sortByTreeMenu.setVisible(false);
3862       return;
3863     }
3864
3865     sortByTreeMenu.setVisible(true);
3866
3867     for (final TreePanel tp : treePanels)
3868     {
3869       final JMenuItem item = new JMenuItem(tp.getTitle());
3870       item.addActionListener(new java.awt.event.ActionListener()
3871       {
3872         @Override
3873         public void actionPerformed(ActionEvent e)
3874         {
3875           tp.sortByTree_actionPerformed();
3876           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3877
3878         }
3879       });
3880
3881       sortByTreeMenu.add(item);
3882     }
3883   }
3884
3885   public boolean sortBy(AlignmentOrder alorder, String undoname)
3886   {
3887     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3888     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3889     if (undoname != null)
3890     {
3891       addHistoryItem(new OrderCommand(undoname, oldOrder,
3892               viewport.getAlignment()));
3893     }
3894     alignPanel.paintAlignment(true);
3895     return true;
3896   }
3897
3898   /**
3899    * Work out whether the whole set of sequences or just the selected set will
3900    * be submitted for multiple alignment.
3901    *
3902    */
3903   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3904   {
3905     // Now, check we have enough sequences
3906     AlignmentView msa = null;
3907
3908     if ((viewport.getSelectionGroup() != null)
3909             && (viewport.getSelectionGroup().getSize() > 1))
3910     {
3911       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3912       // some common interface!
3913       /*
3914        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3915        * SequenceI[sz = seqs.getSize(false)];
3916        *
3917        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3918        * seqs.getSequenceAt(i); }
3919        */
3920       msa = viewport.getAlignmentView(true);
3921     }
3922     else if (viewport.getSelectionGroup() != null
3923             && viewport.getSelectionGroup().getSize() == 1)
3924     {
3925       int option = JvOptionPane.showConfirmDialog(this,
3926               MessageManager.getString("warn.oneseq_msainput_selection"),
3927               MessageManager.getString("label.invalid_selection"),
3928               JvOptionPane.OK_CANCEL_OPTION);
3929       if (option == JvOptionPane.OK_OPTION)
3930       {
3931         msa = viewport.getAlignmentView(false);
3932       }
3933     }
3934     else
3935     {
3936       msa = viewport.getAlignmentView(false);
3937     }
3938     return msa;
3939   }
3940
3941   /**
3942    * Decides what is submitted to a secondary structure prediction service: the
3943    * first sequence in the alignment, or in the current selection, or, if the
3944    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3945    * region or the whole alignment. (where the first sequence in the set is the
3946    * one that the prediction will be for).
3947    */
3948   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3949   {
3950     AlignmentView seqs = null;
3951
3952     if ((viewport.getSelectionGroup() != null)
3953             && (viewport.getSelectionGroup().getSize() > 0))
3954     {
3955       seqs = viewport.getAlignmentView(true);
3956     }
3957     else
3958     {
3959       seqs = viewport.getAlignmentView(false);
3960     }
3961     // limit sequences - JBPNote in future - could spawn multiple prediction
3962     // jobs
3963     // TODO: viewport.getAlignment().isAligned is a global state - the local
3964     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3965     if (!viewport.getAlignment().isAligned(false))
3966     {
3967       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3968       // TODO: if seqs.getSequences().length>1 then should really have warned
3969       // user!
3970
3971     }
3972     return seqs;
3973   }
3974
3975   /**
3976    * DOCUMENT ME!
3977    *
3978    * @param e
3979    *          DOCUMENT ME!
3980    */
3981   @Override
3982   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3983   {
3984     // Pick the tree file
3985     JalviewFileChooser chooser = new JalviewFileChooser(
3986             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3987     chooser.setFileView(new JalviewFileView());
3988     chooser.setDialogTitle(MessageManager
3989             .getString("label.select_newick_like_tree_file"));
3990     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3991
3992     int value = chooser.showOpenDialog(null);
3993
3994     if (value == JalviewFileChooser.APPROVE_OPTION)
3995     {
3996       String filePath = chooser.getSelectedFile().getPath();
3997       Cache.setProperty("LAST_DIRECTORY", filePath);
3998       NewickFile fin = null;
3999       try
4000       {
4001         fin = new NewickFile(filePath, DataSourceType.FILE);
4002         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4003       } catch (Exception ex)
4004       {
4005         JvOptionPane
4006                 .showMessageDialog(
4007                         Desktop.desktop,
4008                         ex.getMessage(),
4009                         MessageManager
4010                                 .getString("label.problem_reading_tree_file"),
4011                         JvOptionPane.WARNING_MESSAGE);
4012         ex.printStackTrace();
4013       }
4014       if (fin != null && fin.hasWarningMessage())
4015       {
4016         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4017                 .getWarningMessage(), MessageManager
4018                 .getString("label.possible_problem_with_tree_file"),
4019                 JvOptionPane.WARNING_MESSAGE);
4020       }
4021     }
4022   }
4023
4024   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4025   {
4026     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4027   }
4028
4029   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4030           int h, int x, int y)
4031   {
4032     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4033   }
4034
4035   /**
4036    * Add a treeviewer for the tree extracted from a Newick file object to the
4037    * current alignment view
4038    *
4039    * @param nf
4040    *          the tree
4041    * @param title
4042    *          tree viewer title
4043    * @param input
4044    *          Associated alignment input data (or null)
4045    * @param w
4046    *          width
4047    * @param h
4048    *          height
4049    * @param x
4050    *          position
4051    * @param y
4052    *          position
4053    * @return TreePanel handle
4054    */
4055   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4056           AlignmentView input, int w, int h, int x, int y)
4057   {
4058     TreePanel tp = null;
4059
4060     try
4061     {
4062       nf.parse();
4063
4064       if (nf.getTree() != null)
4065       {
4066         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4067
4068         tp.setSize(w, h);
4069
4070         if (x > 0 && y > 0)
4071         {
4072           tp.setLocation(x, y);
4073         }
4074
4075         Desktop.addInternalFrame(tp, treeTitle, w, h);
4076       }
4077     } catch (Exception ex)
4078     {
4079       ex.printStackTrace();
4080     }
4081
4082     return tp;
4083   }
4084
4085   private boolean buildingMenu = false;
4086
4087   /**
4088    * Generates menu items and listener event actions for web service clients
4089    *
4090    */
4091   public void BuildWebServiceMenu()
4092   {
4093     while (buildingMenu)
4094     {
4095       try
4096       {
4097         System.err.println("Waiting for building menu to finish.");
4098         Thread.sleep(10);
4099       } catch (Exception e)
4100       {
4101       }
4102     }
4103     final AlignFrame me = this;
4104     buildingMenu = true;
4105     new Thread(new Runnable()
4106     {
4107       @Override
4108       public void run()
4109       {
4110         final List<JMenuItem> legacyItems = new ArrayList<>();
4111         try
4112         {
4113           // System.err.println("Building ws menu again "
4114           // + Thread.currentThread());
4115           // TODO: add support for context dependent disabling of services based
4116           // on
4117           // alignment and current selection
4118           // TODO: add additional serviceHandle parameter to specify abstract
4119           // handler
4120           // class independently of AbstractName
4121           // TODO: add in rediscovery GUI function to restart discoverer
4122           // TODO: group services by location as well as function and/or
4123           // introduce
4124           // object broker mechanism.
4125           final Vector<JMenu> wsmenu = new Vector<>();
4126           final IProgressIndicator af = me;
4127
4128           /*
4129            * do not i18n these strings - they are hard-coded in class
4130            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4131            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4132            */
4133           final JMenu msawsmenu = new JMenu("Alignment");
4134           final JMenu secstrmenu = new JMenu(
4135                   "Secondary Structure Prediction");
4136           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4137           final JMenu analymenu = new JMenu("Analysis");
4138           final JMenu dismenu = new JMenu("Protein Disorder");
4139           // JAL-940 - only show secondary structure prediction services from
4140           // the legacy server
4141           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4142               // &&
4143           Discoverer.services != null && (Discoverer.services.size() > 0))
4144           {
4145             // TODO: refactor to allow list of AbstractName/Handler bindings to
4146             // be
4147             // stored or retrieved from elsewhere
4148             // No MSAWS used any more:
4149             // Vector msaws = null; // (Vector)
4150             // Discoverer.services.get("MsaWS");
4151             Vector secstrpr = (Vector) Discoverer.services
4152                     .get("SecStrPred");
4153             if (secstrpr != null)
4154             {
4155               // Add any secondary structure prediction services
4156               for (int i = 0, j = secstrpr.size(); i < j; i++)
4157               {
4158                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4159                         .get(i);
4160                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4161                         .getServiceClient(sh);
4162                 int p = secstrmenu.getItemCount();
4163                 impl.attachWSMenuEntry(secstrmenu, me);
4164                 int q = secstrmenu.getItemCount();
4165                 for (int litm = p; litm < q; litm++)
4166                 {
4167                   legacyItems.add(secstrmenu.getItem(litm));
4168                 }
4169               }
4170             }
4171           }
4172
4173           // Add all submenus in the order they should appear on the web
4174           // services menu
4175           wsmenu.add(msawsmenu);
4176           wsmenu.add(secstrmenu);
4177           wsmenu.add(dismenu);
4178           wsmenu.add(analymenu);
4179           // No search services yet
4180           // wsmenu.add(seqsrchmenu);
4181
4182           javax.swing.SwingUtilities.invokeLater(new Runnable()
4183           {
4184             @Override
4185             public void run()
4186             {
4187               try
4188               {
4189                 webService.removeAll();
4190                 // first, add discovered services onto the webservices menu
4191                 if (wsmenu.size() > 0)
4192                 {
4193                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4194                   {
4195                     webService.add(wsmenu.get(i));
4196                   }
4197                 }
4198                 else
4199                 {
4200                   webService.add(me.webServiceNoServices);
4201                 }
4202                 // TODO: move into separate menu builder class.
4203                 boolean new_sspred = false;
4204                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4205                 {
4206                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4207                   if (jws2servs != null)
4208                   {
4209                     if (jws2servs.hasServices())
4210                     {
4211                       jws2servs.attachWSMenuEntry(webService, me);
4212                       for (Jws2Instance sv : jws2servs.getServices())
4213                       {
4214                         if (sv.description.toLowerCase().contains("jpred"))
4215                         {
4216                           for (JMenuItem jmi : legacyItems)
4217                           {
4218                             jmi.setVisible(false);
4219                           }
4220                         }
4221                       }
4222
4223                     }
4224                     if (jws2servs.isRunning())
4225                     {
4226                       JMenuItem tm = new JMenuItem(
4227                               "Still discovering JABA Services");
4228                       tm.setEnabled(false);
4229                       webService.add(tm);
4230                     }
4231                   }
4232                 }
4233                 build_urlServiceMenu(me.webService);
4234                 build_fetchdbmenu(webService);
4235                 for (JMenu item : wsmenu)
4236                 {
4237                   if (item.getItemCount() == 0)
4238                   {
4239                     item.setEnabled(false);
4240                   }
4241                   else
4242                   {
4243                     item.setEnabled(true);
4244                   }
4245                 }
4246               } catch (Exception e)
4247               {
4248                 Cache.log
4249                         .debug("Exception during web service menu building process.",
4250                                 e);
4251               }
4252             }
4253           });
4254         } catch (Exception e)
4255         {
4256         }
4257         buildingMenu = false;
4258       }
4259     }).start();
4260
4261   }
4262
4263   /**
4264    * construct any groupURL type service menu entries.
4265    *
4266    * @param webService
4267    */
4268   private void build_urlServiceMenu(JMenu webService)
4269   {
4270     // TODO: remove this code when 2.7 is released
4271     // DEBUG - alignmentView
4272     /*
4273      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4274      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4275      *
4276      * @Override public void actionPerformed(ActionEvent e) {
4277      * jalview.datamodel.AlignmentView
4278      * .testSelectionViews(af.viewport.getAlignment(),
4279      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4280      *
4281      * }); webService.add(testAlView);
4282      */
4283     // TODO: refactor to RestClient discoverer and merge menu entries for
4284     // rest-style services with other types of analysis/calculation service
4285     // SHmmr test client - still being implemented.
4286     // DEBUG - alignmentView
4287
4288     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4289             .getRestClients())
4290     {
4291       client.attachWSMenuEntry(
4292               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4293               this);
4294     }
4295   }
4296
4297   /**
4298    * Searches the alignment sequences for xRefs and builds the Show
4299    * Cross-References menu (formerly called Show Products), with database
4300    * sources for which cross-references are found (protein sources for a
4301    * nucleotide alignment and vice versa)
4302    *
4303    * @return true if Show Cross-references menu should be enabled
4304    */
4305   public boolean canShowProducts()
4306   {
4307     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4308     AlignmentI dataset = viewport.getAlignment().getDataset();
4309
4310     showProducts.removeAll();
4311     final boolean dna = viewport.getAlignment().isNucleotide();
4312
4313     if (seqs == null || seqs.length == 0)
4314     {
4315       // nothing to see here.
4316       return false;
4317     }
4318
4319     boolean showp = false;
4320     try
4321     {
4322       List<String> ptypes = new CrossRef(seqs, dataset)
4323               .findXrefSourcesForSequences(dna);
4324
4325       for (final String source : ptypes)
4326       {
4327         showp = true;
4328         final AlignFrame af = this;
4329         JMenuItem xtype = new JMenuItem(source);
4330         xtype.addActionListener(new ActionListener()
4331         {
4332           @Override
4333           public void actionPerformed(ActionEvent e)
4334           {
4335             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4336           }
4337         });
4338         showProducts.add(xtype);
4339       }
4340       showProducts.setVisible(showp);
4341       showProducts.setEnabled(showp);
4342     } catch (Exception e)
4343     {
4344       Cache.log
4345               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4346                       e);
4347       return false;
4348     }
4349     return showp;
4350   }
4351
4352   /**
4353    * Finds and displays cross-references for the selected sequences (protein
4354    * products for nucleotide sequences, dna coding sequences for peptides).
4355    *
4356    * @param sel
4357    *          the sequences to show cross-references for
4358    * @param dna
4359    *          true if from a nucleotide alignment (so showing proteins)
4360    * @param source
4361    *          the database to show cross-references for
4362    */
4363   protected void showProductsFor(final SequenceI[] sel,
4364           final boolean _odna, final String source)
4365   {
4366     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4367             .start();
4368   }
4369
4370   /**
4371    * Construct and display a new frame containing the translation of this
4372    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4373    */
4374   @Override
4375   public void showTranslation_actionPerformed(ActionEvent e)
4376   {
4377     AlignmentI al = null;
4378     try
4379     {
4380       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4381
4382       al = dna.translateCdna();
4383     } catch (Exception ex)
4384     {
4385       jalview.bin.Cache.log.error(
4386               "Exception during translation. Please report this !", ex);
4387       final String msg = MessageManager
4388               .getString("label.error_when_translating_sequences_submit_bug_report");
4389       final String errorTitle = MessageManager
4390               .getString("label.implementation_error")
4391               + MessageManager.getString("label.translation_failed");
4392       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4393               JvOptionPane.ERROR_MESSAGE);
4394       return;
4395     }
4396     if (al == null || al.getHeight() == 0)
4397     {
4398       final String msg = MessageManager
4399               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4400       final String errorTitle = MessageManager
4401               .getString("label.translation_failed");
4402       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4403               JvOptionPane.WARNING_MESSAGE);
4404     }
4405     else
4406     {
4407       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4408       af.setFileFormat(this.currentFileFormat);
4409       final String newTitle = MessageManager.formatMessage(
4410               "label.translation_of_params",
4411               new Object[] { this.getTitle() });
4412       af.setTitle(newTitle);
4413       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4414       {
4415         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4416         viewport.openSplitFrame(af, new Alignment(seqs));
4417       }
4418       else
4419       {
4420         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4421                 DEFAULT_HEIGHT);
4422       }
4423     }
4424   }
4425
4426   /**
4427    * Set the file format
4428    *
4429    * @param format
4430    */
4431   public void setFileFormat(FileFormatI format)
4432   {
4433     this.currentFileFormat = format;
4434   }
4435
4436   /**
4437    * Try to load a features file onto the alignment.
4438    *
4439    * @param file
4440    *          contents or path to retrieve file
4441    * @param sourceType
4442    *          access mode of file (see jalview.io.AlignFile)
4443    * @return true if features file was parsed correctly.
4444    */
4445   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4446   {
4447     return avc.parseFeaturesFile(file, sourceType,
4448             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4449
4450   }
4451
4452   @Override
4453   public void refreshFeatureUI(boolean enableIfNecessary)
4454   {
4455     // note - currently this is only still here rather than in the controller
4456     // because of the featureSettings hard reference that is yet to be
4457     // abstracted
4458     if (enableIfNecessary)
4459     {
4460       viewport.setShowSequenceFeatures(true);
4461       showSeqFeatures.setSelected(true);
4462     }
4463
4464   }
4465
4466   @Override
4467   public void dragEnter(DropTargetDragEvent evt)
4468   {
4469   }
4470
4471   @Override
4472   public void dragExit(DropTargetEvent evt)
4473   {
4474   }
4475
4476   @Override
4477   public void dragOver(DropTargetDragEvent evt)
4478   {
4479   }
4480
4481   @Override
4482   public void dropActionChanged(DropTargetDragEvent evt)
4483   {
4484   }
4485
4486   @Override
4487   public void drop(DropTargetDropEvent evt)
4488   {
4489     // JAL-1552 - acceptDrop required before getTransferable call for
4490     // Java's Transferable for native dnd
4491     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4492     Transferable t = evt.getTransferable();
4493     List<String> files = new ArrayList<>();
4494     List<DataSourceType> protocols = new ArrayList<>();
4495
4496     try
4497     {
4498       Desktop.transferFromDropTarget(files, protocols, evt, t);
4499     } catch (Exception e)
4500     {
4501       e.printStackTrace();
4502     }
4503     if (files != null)
4504     {
4505       try
4506       {
4507         // check to see if any of these files have names matching sequences in
4508         // the alignment
4509         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4510                 .getAlignment().getSequencesArray());
4511         /**
4512          * Object[] { String,SequenceI}
4513          */
4514         ArrayList<Object[]> filesmatched = new ArrayList<>();
4515         ArrayList<String> filesnotmatched = new ArrayList<>();
4516         for (int i = 0; i < files.size(); i++)
4517         {
4518           String file = files.get(i).toString();
4519           String pdbfn = "";
4520           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4521           if (protocol == DataSourceType.FILE)
4522           {
4523             File fl = new File(file);
4524             pdbfn = fl.getName();
4525           }
4526           else if (protocol == DataSourceType.URL)
4527           {
4528             URL url = new URL(file);
4529             pdbfn = url.getFile();
4530           }
4531           if (pdbfn.length() > 0)
4532           {
4533             // attempt to find a match in the alignment
4534             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4535             int l = 0, c = pdbfn.indexOf(".");
4536             while (mtch == null && c != -1)
4537             {
4538               do
4539               {
4540                 l = c;
4541               } while ((c = pdbfn.indexOf(".", l)) > l);
4542               if (l > -1)
4543               {
4544                 pdbfn = pdbfn.substring(0, l);
4545               }
4546               mtch = idm.findAllIdMatches(pdbfn);
4547             }
4548             if (mtch != null)
4549             {
4550               FileFormatI type = null;
4551               try
4552               {
4553                 type = new IdentifyFile().identify(file, protocol);
4554               } catch (Exception ex)
4555               {
4556                 type = null;
4557               }
4558               if (type != null && type.isStructureFile())
4559               {
4560                 filesmatched.add(new Object[] { file, protocol, mtch });
4561                 continue;
4562               }
4563             }
4564             // File wasn't named like one of the sequences or wasn't a PDB file.
4565             filesnotmatched.add(file);
4566           }
4567         }
4568         int assocfiles = 0;
4569         if (filesmatched.size() > 0)
4570         {
4571           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4572                   || JvOptionPane
4573                           .showConfirmDialog(
4574                                   this,
4575                                   MessageManager
4576                                           .formatMessage(
4577                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4578                                                   new Object[] { Integer
4579                                                           .valueOf(
4580                                                                   filesmatched
4581                                                                           .size())
4582                                                           .toString() }),
4583                                   MessageManager
4584                                           .getString("label.automatically_associate_structure_files_by_name"),
4585                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4586
4587           {
4588             for (Object[] fm : filesmatched)
4589             {
4590               // try and associate
4591               // TODO: may want to set a standard ID naming formalism for
4592               // associating PDB files which have no IDs.
4593               for (SequenceI toassoc : (SequenceI[]) fm[2])
4594               {
4595                 PDBEntry pe = new AssociatePdbFileWithSeq()
4596                         .associatePdbWithSeq((String) fm[0],
4597                                 (DataSourceType) fm[1], toassoc, false,
4598                                 Desktop.instance);
4599                 if (pe != null)
4600                 {
4601                   System.err.println("Associated file : "
4602                           + ((String) fm[0]) + " with "
4603                           + toassoc.getDisplayId(true));
4604                   assocfiles++;
4605                 }
4606               }
4607               alignPanel.paintAlignment(true);
4608             }
4609           }
4610         }
4611         if (filesnotmatched.size() > 0)
4612         {
4613           if (assocfiles > 0
4614                   && (Cache.getDefault(
4615                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4616                           .showConfirmDialog(
4617                                   this,
4618                                   "<html>"
4619                                           + MessageManager
4620                                                   .formatMessage(
4621                                                           "label.ignore_unmatched_dropped_files_info",
4622                                                           new Object[] { Integer
4623                                                                   .valueOf(
4624                                                                           filesnotmatched
4625                                                                                   .size())
4626                                                                   .toString() })
4627                                           + "</html>",
4628                                   MessageManager
4629                                           .getString("label.ignore_unmatched_dropped_files"),
4630                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4631           {
4632             return;
4633           }
4634           for (String fn : filesnotmatched)
4635           {
4636             loadJalviewDataFile(fn, null, null, null);
4637           }
4638
4639         }
4640       } catch (Exception ex)
4641       {
4642         ex.printStackTrace();
4643       }
4644     }
4645   }
4646
4647   /**
4648    * Attempt to load a "dropped" file or URL string, by testing in turn for
4649    * <ul>
4650    * <li>an Annotation file</li>
4651    * <li>a JNet file</li>
4652    * <li>a features file</li>
4653    * <li>else try to interpret as an alignment file</li>
4654    * </ul>
4655    *
4656    * @param file
4657    *          either a filename or a URL string.
4658    * @throws InterruptedException
4659    * @throws IOException
4660    */
4661   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4662           FileFormatI format, SequenceI assocSeq)
4663   {
4664     try
4665     {
4666       if (sourceType == null)
4667       {
4668         sourceType = FormatAdapter.checkProtocol(file);
4669       }
4670       // if the file isn't identified, or not positively identified as some
4671       // other filetype (PFAM is default unidentified alignment file type) then
4672       // try to parse as annotation.
4673       boolean isAnnotation = (format == null || FileFormat.Pfam
4674               .equals(format)) ? new AnnotationFile()
4675               .annotateAlignmentView(viewport, file, sourceType) : false;
4676
4677       if (!isAnnotation)
4678       {
4679         // first see if its a T-COFFEE score file
4680         TCoffeeScoreFile tcf = null;
4681         try
4682         {
4683           tcf = new TCoffeeScoreFile(file, sourceType);
4684           if (tcf.isValid())
4685           {
4686             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4687             {
4688               buildColourMenu();
4689               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4690               isAnnotation = true;
4691               statusBar
4692                       .setText(MessageManager
4693                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4694             }
4695             else
4696             {
4697               // some problem - if no warning its probable that the ID matching
4698               // process didn't work
4699               JvOptionPane
4700                       .showMessageDialog(
4701                               Desktop.desktop,
4702                               tcf.getWarningMessage() == null ? MessageManager
4703                                       .getString("label.check_file_matches_sequence_ids_alignment")
4704                                       : tcf.getWarningMessage(),
4705                               MessageManager
4706                                       .getString("label.problem_reading_tcoffee_score_file"),
4707                               JvOptionPane.WARNING_MESSAGE);
4708             }
4709           }
4710           else
4711           {
4712             tcf = null;
4713           }
4714         } catch (Exception x)
4715         {
4716           Cache.log
4717                   .debug("Exception when processing data source as T-COFFEE score file",
4718                           x);
4719           tcf = null;
4720         }
4721         if (tcf == null)
4722         {
4723           // try to see if its a JNet 'concise' style annotation file *before*
4724           // we
4725           // try to parse it as a features file
4726           if (format == null)
4727           {
4728             format = new IdentifyFile().identify(file, sourceType);
4729           }
4730           if (FileFormat.ScoreMatrix == format)
4731           {
4732             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4733                     sourceType));
4734             sm.parse();
4735             // todo: i18n this message
4736             statusBar
4737                     .setText(MessageManager.formatMessage(
4738                             "label.successfully_loaded_matrix",
4739                             sm.getMatrixName()));
4740           }
4741           else if (FileFormat.HMMER3.equals(format))
4742           {
4743             HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType));
4744             HiddenMarkovModel hmm = hmmFile.getHMM();
4745             SequenceI hmmSeq = hmm.initHMMSequence(this, 0);
4746             getViewport().initInformation(hmmSeq);
4747             getViewport().updateInformation(alignPanel);
4748             getViewport().alignmentChanged(alignPanel);
4749             isAnnotation = true;
4750
4751           }
4752           else if (FileFormat.Jnet.equals(format))
4753           {
4754             JPredFile predictions = new JPredFile(file, sourceType);
4755             new JnetAnnotationMaker();
4756             JnetAnnotationMaker.add_annotation(predictions,
4757                     viewport.getAlignment(), 0, false);
4758             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4759             viewport.getAlignment().setSeqrep(repseq);
4760             HiddenColumns cs = new HiddenColumns();
4761             cs.hideInsertionsFor(repseq);
4762             viewport.getAlignment().setHiddenColumns(cs);
4763             isAnnotation = true;
4764           }
4765           // else if (IdentifyFile.FeaturesFile.equals(format))
4766           else if (FileFormat.Features.equals(format))
4767           {
4768             if (parseFeaturesFile(file, sourceType))
4769             {
4770               alignPanel.paintAlignment(true);
4771             }
4772           }
4773           else
4774           {
4775             new FileLoader().LoadFile(viewport, file, sourceType, format);
4776             if (autoAlignNewSequences && !recurring)
4777             {
4778               new Thread(new HMMAlignThread(this, false)).start();
4779             }
4780           }
4781         }
4782       }
4783       if (isAnnotation)
4784       {
4785         alignPanel.adjustAnnotationHeight();
4786         viewport.updateSequenceIdColours();
4787         buildSortByAnnotationScoresMenu();
4788         alignPanel.paintAlignment(true);
4789       }
4790     } catch (Exception ex)
4791     {
4792       ex.printStackTrace();
4793     } catch (OutOfMemoryError oom)
4794     {
4795       try
4796       {
4797         System.gc();
4798       } catch (Exception x)
4799       {
4800       }
4801       new OOMWarning(
4802               "loading data "
4803                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4804                               : "using " + sourceType + " from " + file)
4805                               : ".")
4806                       + (format != null ? "(parsing as '" + format
4807                               + "' file)" : ""), oom, Desktop.desktop);
4808     }
4809   }
4810
4811   /**
4812    * Method invoked by the ChangeListener on the tabbed pane, in other words
4813    * when a different tabbed pane is selected by the user or programmatically.
4814    */
4815   @Override
4816   public void tabSelectionChanged(int index)
4817   {
4818     if (index > -1)
4819     {
4820       alignPanel = alignPanels.get(index);
4821       viewport = alignPanel.av;
4822       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4823       setMenusFromViewport(viewport);
4824     }
4825
4826     /*
4827      * 'focus' any colour slider that is open to the selected viewport
4828      */
4829     if (viewport.getConservationSelected())
4830     {
4831       SliderPanel.setConservationSlider(alignPanel,
4832               viewport.getResidueShading(), alignPanel.getViewName());
4833     }
4834     else
4835     {
4836       SliderPanel.hideConservationSlider();
4837     }
4838     if (viewport.getAbovePIDThreshold())
4839     {
4840       SliderPanel.setPIDSliderSource(alignPanel,
4841               viewport.getResidueShading(), alignPanel.getViewName());
4842     }
4843     else
4844     {
4845       SliderPanel.hidePIDSlider();
4846     }
4847
4848     /*
4849      * If there is a frame linked to this one in a SplitPane, switch it to the
4850      * same view tab index. No infinite recursion of calls should happen, since
4851      * tabSelectionChanged() should not get invoked on setting the selected
4852      * index to an unchanged value. Guard against setting an invalid index
4853      * before the new view peer tab has been created.
4854      */
4855     final AlignViewportI peer = viewport.getCodingComplement();
4856     if (peer != null)
4857     {
4858       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4859       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4860       {
4861         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4862       }
4863     }
4864   }
4865
4866   /**
4867    * On right mouse click on view tab, prompt for and set new view name.
4868    */
4869   @Override
4870   public void tabbedPane_mousePressed(MouseEvent e)
4871   {
4872     if (e.isPopupTrigger())
4873     {
4874       String msg = MessageManager.getString("label.enter_view_name");
4875       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4876               JvOptionPane.QUESTION_MESSAGE);
4877
4878       if (reply != null)
4879       {
4880         viewport.viewName = reply;
4881         // TODO warn if reply is in getExistingViewNames()?
4882         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4883       }
4884     }
4885   }
4886
4887   public AlignViewport getCurrentView()
4888   {
4889     return viewport;
4890   }
4891
4892   /**
4893    * Open the dialog for regex description parsing.
4894    */
4895   @Override
4896   protected void extractScores_actionPerformed(ActionEvent e)
4897   {
4898     ParseProperties pp = new jalview.analysis.ParseProperties(
4899             viewport.getAlignment());
4900     // TODO: verify regex and introduce GUI dialog for version 2.5
4901     // if (pp.getScoresFromDescription("col", "score column ",
4902     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4903     // true)>0)
4904     if (pp.getScoresFromDescription("description column",
4905             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4906     {
4907       buildSortByAnnotationScoresMenu();
4908     }
4909   }
4910
4911   /*
4912    * (non-Javadoc)
4913    *
4914    * @see
4915    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4916    * )
4917    */
4918   @Override
4919   protected void showDbRefs_actionPerformed(ActionEvent e)
4920   {
4921     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4922   }
4923
4924   /*
4925    * (non-Javadoc)
4926    *
4927    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4928    * ActionEvent)
4929    */
4930   @Override
4931   protected void showNpFeats_actionPerformed(ActionEvent e)
4932   {
4933     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4934   }
4935
4936   /**
4937    * find the viewport amongst the tabs in this alignment frame and close that
4938    * tab
4939    *
4940    * @param av
4941    */
4942   public boolean closeView(AlignViewportI av)
4943   {
4944     if (viewport == av)
4945     {
4946       this.closeMenuItem_actionPerformed(false);
4947       return true;
4948     }
4949     Component[] comp = tabbedPane.getComponents();
4950     for (int i = 0; comp != null && i < comp.length; i++)
4951     {
4952       if (comp[i] instanceof AlignmentPanel)
4953       {
4954         if (((AlignmentPanel) comp[i]).av == av)
4955         {
4956           // close the view.
4957           closeView((AlignmentPanel) comp[i]);
4958           return true;
4959         }
4960       }
4961     }
4962     return false;
4963   }
4964
4965   protected void build_fetchdbmenu(JMenu webService)
4966   {
4967     // Temporary hack - DBRef Fetcher always top level ws entry.
4968     // TODO We probably want to store a sequence database checklist in
4969     // preferences and have checkboxes.. rather than individual sources selected
4970     // here
4971     final JMenu rfetch = new JMenu(
4972             MessageManager.getString("action.fetch_db_references"));
4973     rfetch.setToolTipText(MessageManager
4974             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4975     webService.add(rfetch);
4976
4977     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4978             MessageManager.getString("option.trim_retrieved_seqs"));
4979     trimrs.setToolTipText(MessageManager
4980             .getString("label.trim_retrieved_sequences"));
4981     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4982     trimrs.addActionListener(new ActionListener()
4983     {
4984       @Override
4985       public void actionPerformed(ActionEvent e)
4986       {
4987         trimrs.setSelected(trimrs.isSelected());
4988         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4989                 Boolean.valueOf(trimrs.isSelected()).toString());
4990       };
4991     });
4992     rfetch.add(trimrs);
4993     JMenuItem fetchr = new JMenuItem(
4994             MessageManager.getString("label.standard_databases"));
4995     fetchr.setToolTipText(MessageManager
4996             .getString("label.fetch_embl_uniprot"));
4997     fetchr.addActionListener(new ActionListener()
4998     {
4999
5000       @Override
5001       public void actionPerformed(ActionEvent e)
5002       {
5003         new Thread(new Runnable()
5004         {
5005           @Override
5006           public void run()
5007           {
5008             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5009                     .getAlignment().isNucleotide();
5010             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5011                     .getSequenceSelection(), alignPanel.alignFrame, null,
5012                     alignPanel.alignFrame.featureSettings, isNucleotide);
5013             dbRefFetcher.addListener(new FetchFinishedListenerI()
5014             {
5015               @Override
5016               public void finished()
5017               {
5018                 AlignFrame.this.setMenusForViewport();
5019               }
5020             });
5021             dbRefFetcher.fetchDBRefs(false);
5022           }
5023         }).start();
5024
5025       }
5026
5027     });
5028     rfetch.add(fetchr);
5029     final AlignFrame me = this;
5030     new Thread(new Runnable()
5031     {
5032       @Override
5033       public void run()
5034       {
5035         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5036                 .getSequenceFetcherSingleton(me);
5037         javax.swing.SwingUtilities.invokeLater(new Runnable()
5038         {
5039           @Override
5040           public void run()
5041           {
5042             String[] dbclasses = sf.getOrderedSupportedSources();
5043             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5044             // jalview.util.QuickSort.sort(otherdb, otherdb);
5045             List<DbSourceProxy> otherdb;
5046             JMenu dfetch = new JMenu();
5047             JMenu ifetch = new JMenu();
5048             JMenuItem fetchr = null;
5049             int comp = 0, icomp = 0, mcomp = 15;
5050             String mname = null;
5051             int dbi = 0;
5052             for (String dbclass : dbclasses)
5053             {
5054               otherdb = sf.getSourceProxy(dbclass);
5055               // add a single entry for this class, or submenu allowing 'fetch
5056               // all' or pick one
5057               if (otherdb == null || otherdb.size() < 1)
5058               {
5059                 continue;
5060               }
5061               // List<DbSourceProxy> dbs=otherdb;
5062               // otherdb=new ArrayList<DbSourceProxy>();
5063               // for (DbSourceProxy db:dbs)
5064               // {
5065               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5066               // }
5067               if (mname == null)
5068               {
5069                 mname = "From " + dbclass;
5070               }
5071               if (otherdb.size() == 1)
5072               {
5073                 final DbSourceProxy[] dassource = otherdb
5074                         .toArray(new DbSourceProxy[0]);
5075                 DbSourceProxy src = otherdb.get(0);
5076                 fetchr = new JMenuItem(src.getDbSource());
5077                 fetchr.addActionListener(new ActionListener()
5078                 {
5079
5080                   @Override
5081                   public void actionPerformed(ActionEvent e)
5082                   {
5083                     new Thread(new Runnable()
5084                     {
5085
5086                       @Override
5087                       public void run()
5088                       {
5089                         boolean isNucleotide = alignPanel.alignFrame
5090                                 .getViewport().getAlignment()
5091                                 .isNucleotide();
5092                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5093                                 alignPanel.av.getSequenceSelection(),
5094                                 alignPanel.alignFrame, dassource,
5095                                 alignPanel.alignFrame.featureSettings,
5096                                 isNucleotide);
5097                         dbRefFetcher
5098                                 .addListener(new FetchFinishedListenerI()
5099                                 {
5100                                   @Override
5101                                   public void finished()
5102                                   {
5103                                     AlignFrame.this.setMenusForViewport();
5104                                   }
5105                                 });
5106                         dbRefFetcher.fetchDBRefs(false);
5107                       }
5108                     }).start();
5109                   }
5110
5111                 });
5112                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5113                         MessageManager.formatMessage(
5114                                 "label.fetch_retrieve_from",
5115                                 new Object[] { src.getDbName() })));
5116                 dfetch.add(fetchr);
5117                 comp++;
5118               }
5119               else
5120               {
5121                 final DbSourceProxy[] dassource = otherdb
5122                         .toArray(new DbSourceProxy[0]);
5123                 // fetch all entry
5124                 DbSourceProxy src = otherdb.get(0);
5125                 fetchr = new JMenuItem(MessageManager.formatMessage(
5126                         "label.fetch_all_param",
5127                         new Object[] { src.getDbSource() }));
5128                 fetchr.addActionListener(new ActionListener()
5129                 {
5130                   @Override
5131                   public void actionPerformed(ActionEvent e)
5132                   {
5133                     new Thread(new Runnable()
5134                     {
5135
5136                       @Override
5137                       public void run()
5138                       {
5139                         boolean isNucleotide = alignPanel.alignFrame
5140                                 .getViewport().getAlignment()
5141                                 .isNucleotide();
5142                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5143                                 alignPanel.av.getSequenceSelection(),
5144                                 alignPanel.alignFrame, dassource,
5145                                 alignPanel.alignFrame.featureSettings,
5146                                 isNucleotide);
5147                         dbRefFetcher
5148                                 .addListener(new FetchFinishedListenerI()
5149                                 {
5150                                   @Override
5151                                   public void finished()
5152                                   {
5153                                     AlignFrame.this.setMenusForViewport();
5154                                   }
5155                                 });
5156                         dbRefFetcher.fetchDBRefs(false);
5157                       }
5158                     }).start();
5159                   }
5160                 });
5161
5162                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5163                         MessageManager.formatMessage(
5164                                 "label.fetch_retrieve_from_all_sources",
5165                                 new Object[] {
5166                                     Integer.valueOf(otherdb.size())
5167                                             .toString(), src.getDbSource(),
5168                                     src.getDbName() })));
5169                 dfetch.add(fetchr);
5170                 comp++;
5171                 // and then build the rest of the individual menus
5172                 ifetch = new JMenu(MessageManager.formatMessage(
5173                         "label.source_from_db_source",
5174                         new Object[] { src.getDbSource() }));
5175                 icomp = 0;
5176                 String imname = null;
5177                 int i = 0;
5178                 for (DbSourceProxy sproxy : otherdb)
5179                 {
5180                   String dbname = sproxy.getDbName();
5181                   String sname = dbname.length() > 5 ? dbname.substring(0,
5182                           5) + "..." : dbname;
5183                   String msname = dbname.length() > 10 ? dbname.substring(
5184                           0, 10) + "..." : dbname;
5185                   if (imname == null)
5186                   {
5187                     imname = MessageManager.formatMessage(
5188                             "label.from_msname", new Object[] { sname });
5189                   }
5190                   fetchr = new JMenuItem(msname);
5191                   final DbSourceProxy[] dassrc = { sproxy };
5192                   fetchr.addActionListener(new ActionListener()
5193                   {
5194
5195                     @Override
5196                     public void actionPerformed(ActionEvent e)
5197                     {
5198                       new Thread(new Runnable()
5199                       {
5200
5201                         @Override
5202                         public void run()
5203                         {
5204                           boolean isNucleotide = alignPanel.alignFrame
5205                                   .getViewport().getAlignment()
5206                                   .isNucleotide();
5207                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5208                                   alignPanel.av.getSequenceSelection(),
5209                                   alignPanel.alignFrame, dassrc,
5210                                   alignPanel.alignFrame.featureSettings,
5211                                   isNucleotide);
5212                           dbRefFetcher
5213                                   .addListener(new FetchFinishedListenerI()
5214                                   {
5215                                     @Override
5216                                     public void finished()
5217                                     {
5218                                       AlignFrame.this.setMenusForViewport();
5219                                     }
5220                                   });
5221                           dbRefFetcher.fetchDBRefs(false);
5222                         }
5223                       }).start();
5224                     }
5225
5226                   });
5227                   fetchr.setToolTipText("<html>"
5228                           + MessageManager.formatMessage(
5229                                   "label.fetch_retrieve_from", new Object[]
5230                                   { dbname }));
5231                   ifetch.add(fetchr);
5232                   ++i;
5233                   if (++icomp >= mcomp || i == (otherdb.size()))
5234                   {
5235                     ifetch.setText(MessageManager.formatMessage(
5236                             "label.source_to_target", imname, sname));
5237                     dfetch.add(ifetch);
5238                     ifetch = new JMenu();
5239                     imname = null;
5240                     icomp = 0;
5241                     comp++;
5242                   }
5243                 }
5244               }
5245               ++dbi;
5246               if (comp >= mcomp || dbi >= (dbclasses.length))
5247               {
5248                 dfetch.setText(MessageManager.formatMessage(
5249                         "label.source_to_target", mname, dbclass));
5250                 rfetch.add(dfetch);
5251                 dfetch = new JMenu();
5252                 mname = null;
5253                 comp = 0;
5254               }
5255             }
5256           }
5257         });
5258       }
5259     }).start();
5260
5261   }
5262
5263   /**
5264    * Left justify the whole alignment.
5265    */
5266   @Override
5267   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5268   {
5269     AlignmentI al = viewport.getAlignment();
5270     al.justify(false);
5271     viewport.firePropertyChange("alignment", null, al);
5272   }
5273
5274   /**
5275    * Right justify the whole alignment.
5276    */
5277   @Override
5278   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5279   {
5280     AlignmentI al = viewport.getAlignment();
5281     al.justify(true);
5282     viewport.firePropertyChange("alignment", null, al);
5283   }
5284
5285   @Override
5286   public void setShowSeqFeatures(boolean b)
5287   {
5288     showSeqFeatures.setSelected(b);
5289     viewport.setShowSequenceFeatures(b);
5290   }
5291
5292   /*
5293    * (non-Javadoc)
5294    *
5295    * @see
5296    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5297    * awt.event.ActionEvent)
5298    */
5299   @Override
5300   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5301   {
5302     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5303     alignPanel.paintAlignment(true);
5304   }
5305
5306   /*
5307    * (non-Javadoc)
5308    *
5309    * @see
5310    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5311    * .ActionEvent)
5312    */
5313   @Override
5314   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5315   {
5316     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5317     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5318
5319   }
5320
5321   /*
5322    * (non-Javadoc)
5323    *
5324    * @see
5325    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5326    * .event.ActionEvent)
5327    */
5328   @Override
5329   protected void showGroupConservation_actionPerformed(ActionEvent e)
5330   {
5331     viewport.setShowGroupConservation(showGroupConservation.getState());
5332     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5333   }
5334
5335   /*
5336    * (non-Javadoc)
5337    *
5338    * @see
5339    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5340    * .event.ActionEvent)
5341    */
5342   @Override
5343   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5344   {
5345     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5346     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5347   }
5348
5349   /*
5350    * (non-Javadoc)
5351    *
5352    * @see
5353    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5354    * .event.ActionEvent)
5355    */
5356   @Override
5357   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5358   {
5359     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5360     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361   }
5362
5363   @Override
5364   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5365   {
5366     showSequenceLogo.setState(true);
5367     viewport.setShowSequenceLogo(true);
5368     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5369     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5370   }
5371
5372   @Override
5373   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5374   {
5375     viewport.setShowInformationHistogram(
5376             showInformationHistogram.getState());
5377     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5378   }
5379
5380   @Override
5381   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5382   {
5383     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5384     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5385   }
5386
5387   @Override
5388   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5389   {
5390     showHMMSequenceLogo.setState(true);
5391     viewport.setShowHMMSequenceLogo(true);
5392     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5393     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5394   }
5395
5396   @Override
5397   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5398   {
5399     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5400   }
5401
5402   /*
5403    * (non-Javadoc)
5404    *
5405    * @see
5406    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5407    * .event.ActionEvent)
5408    */
5409   @Override
5410   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5411   {
5412     if (avc.makeGroupsFromSelection())
5413     {
5414       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5415       alignPanel.updateAnnotation();
5416       alignPanel.paintAlignment(true);
5417     }
5418   }
5419
5420   public void clearAlignmentSeqRep()
5421   {
5422     // TODO refactor alignmentseqrep to controller
5423     if (viewport.getAlignment().hasSeqrep())
5424     {
5425       viewport.getAlignment().setSeqrep(null);
5426       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5427       alignPanel.updateAnnotation();
5428       alignPanel.paintAlignment(true);
5429     }
5430   }
5431
5432   @Override
5433   protected void createGroup_actionPerformed(ActionEvent e)
5434   {
5435     if (avc.createGroup())
5436     {
5437       alignPanel.alignmentChanged();
5438     }
5439   }
5440
5441   @Override
5442   protected void unGroup_actionPerformed(ActionEvent e)
5443   {
5444     if (avc.unGroup())
5445     {
5446       alignPanel.alignmentChanged();
5447     }
5448   }
5449
5450   /**
5451    * make the given alignmentPanel the currently selected tab
5452    *
5453    * @param alignmentPanel
5454    */
5455   public void setDisplayedView(AlignmentPanel alignmentPanel)
5456   {
5457     if (!viewport.getSequenceSetId().equals(
5458             alignmentPanel.av.getSequenceSetId()))
5459     {
5460       throw new Error(
5461               MessageManager
5462                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5463     }
5464     if (tabbedPane != null
5465             && tabbedPane.getTabCount() > 0
5466             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5467                     .getSelectedIndex())
5468     {
5469       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5470     }
5471   }
5472
5473   /**
5474    * Action on selection of menu options to Show or Hide annotations.
5475    *
5476    * @param visible
5477    * @param forSequences
5478    *          update sequence-related annotations
5479    * @param forAlignment
5480    *          update non-sequence-related annotations
5481    */
5482   @Override
5483   protected void setAnnotationsVisibility(boolean visible,
5484           boolean forSequences, boolean forAlignment)
5485   {
5486     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5487             .getAlignmentAnnotation();
5488     if (anns == null)
5489     {
5490       return;
5491     }
5492     for (AlignmentAnnotation aa : anns)
5493     {
5494       /*
5495        * don't display non-positional annotations on an alignment
5496        */
5497       if (aa.annotations == null)
5498       {
5499         continue;
5500       }
5501       boolean apply = (aa.sequenceRef == null && forAlignment)
5502               || (aa.sequenceRef != null && forSequences);
5503       if (apply)
5504       {
5505         aa.visible = visible;
5506       }
5507     }
5508     alignPanel.validateAnnotationDimensions(true);
5509     alignPanel.alignmentChanged();
5510   }
5511
5512   /**
5513    * Store selected annotation sort order for the view and repaint.
5514    */
5515   @Override
5516   protected void sortAnnotations_actionPerformed()
5517   {
5518     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5519     this.alignPanel.av
5520             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5521     alignPanel.paintAlignment(true);
5522   }
5523
5524   /**
5525    *
5526    * @return alignment panels in this alignment frame
5527    */
5528   public List<? extends AlignmentViewPanel> getAlignPanels()
5529   {
5530     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5531   }
5532
5533   /**
5534    * Open a new alignment window, with the cDNA associated with this (protein)
5535    * alignment, aligned as is the protein.
5536    */
5537   protected void viewAsCdna_actionPerformed()
5538   {
5539     // TODO no longer a menu action - refactor as required
5540     final AlignmentI alignment = getViewport().getAlignment();
5541     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5542     if (mappings == null)
5543     {
5544       return;
5545     }
5546     List<SequenceI> cdnaSeqs = new ArrayList<>();
5547     for (SequenceI aaSeq : alignment.getSequences())
5548     {
5549       for (AlignedCodonFrame acf : mappings)
5550       {
5551         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5552         if (dnaSeq != null)
5553         {
5554           /*
5555            * There is a cDNA mapping for this protein sequence - add to new
5556            * alignment. It will share the same dataset sequence as other mapped
5557            * cDNA (no new mappings need to be created).
5558            */
5559           final Sequence newSeq = new Sequence(dnaSeq);
5560           newSeq.setDatasetSequence(dnaSeq);
5561           cdnaSeqs.add(newSeq);
5562         }
5563       }
5564     }
5565     if (cdnaSeqs.size() == 0)
5566     {
5567       // show a warning dialog no mapped cDNA
5568       return;
5569     }
5570     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5571             .size()]));
5572     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5573             AlignFrame.DEFAULT_HEIGHT);
5574     cdna.alignAs(alignment);
5575     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5576             + this.title;
5577     Desktop.addInternalFrame(alignFrame, newtitle,
5578             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5579   }
5580
5581   /**
5582    * Set visibility of dna/protein complement view (available when shown in a
5583    * split frame).
5584    *
5585    * @param show
5586    */
5587   @Override
5588   protected void showComplement_actionPerformed(boolean show)
5589   {
5590     SplitContainerI sf = getSplitViewContainer();
5591     if (sf != null)
5592     {
5593       sf.setComplementVisible(this, show);
5594     }
5595   }
5596
5597   /**
5598    * Generate the reverse (optionally complemented) of the selected sequences,
5599    * and add them to the alignment
5600    */
5601   @Override
5602   protected void showReverse_actionPerformed(boolean complement)
5603   {
5604     AlignmentI al = null;
5605     try
5606     {
5607       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5608       al = dna.reverseCdna(complement);
5609       viewport.addAlignment(al, "");
5610       addHistoryItem(new EditCommand(
5611               MessageManager.getString("label.add_sequences"),
5612               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5613               viewport.getAlignment()));
5614     } catch (Exception ex)
5615     {
5616       System.err.println(ex.getMessage());
5617       return;
5618     }
5619   }
5620
5621   /**
5622    * Try to run a script in the Groovy console, having first ensured that this
5623    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5624    * be targeted at this alignment.
5625    */
5626   @Override
5627   protected void runGroovy_actionPerformed()
5628   {
5629     Jalview.setCurrentAlignFrame(this);
5630     groovy.ui.Console console = Desktop.getGroovyConsole();
5631     if (console != null)
5632     {
5633       try
5634       {
5635         console.runScript();
5636       } catch (Exception ex)
5637       {
5638         System.err.println((ex.toString()));
5639         JvOptionPane
5640                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5641                         .getString("label.couldnt_run_groovy_script"),
5642                         MessageManager
5643                                 .getString("label.groovy_support_failed"),
5644                         JvOptionPane.ERROR_MESSAGE);
5645       }
5646     }
5647     else
5648     {
5649       System.err.println("Can't run Groovy script as console not found");
5650     }
5651   }
5652
5653   /**
5654    * Hides columns containing (or not containing) a specified feature, provided
5655    * that would not leave all columns hidden
5656    *
5657    * @param featureType
5658    * @param columnsContaining
5659    * @return
5660    */
5661   public boolean hideFeatureColumns(String featureType,
5662           boolean columnsContaining)
5663   {
5664     boolean notForHiding = avc.markColumnsContainingFeatures(
5665             columnsContaining, false, false, featureType);
5666     if (notForHiding)
5667     {
5668       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5669               false, featureType))
5670       {
5671         getViewport().hideSelectedColumns();
5672         return true;
5673       }
5674     }
5675     return false;
5676   }
5677
5678   @Override
5679   protected void selectHighlightedColumns_actionPerformed(
5680           ActionEvent actionEvent)
5681   {
5682     // include key modifier check in case user selects from menu
5683     avc.markHighlightedColumns(
5684             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5685             true,
5686             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5687   }
5688
5689   /**
5690    * Rebuilds the Colour menu, including any user-defined colours which have
5691    * been loaded either on startup or during the session
5692    */
5693   public void buildColourMenu()
5694   {
5695     colourMenu.removeAll();
5696
5697     colourMenu.add(applyToAllGroups);
5698     colourMenu.add(textColour);
5699     colourMenu.addSeparator();
5700
5701     ColourMenuHelper.addMenuItems(colourMenu, this,
5702             viewport.getAlignment(), false);
5703
5704     colourMenu.addSeparator();
5705     colourMenu.add(conservationMenuItem);
5706     colourMenu.add(modifyConservation);
5707     colourMenu.add(abovePIDThreshold);
5708     colourMenu.add(modifyPID);
5709     colourMenu.add(annotationColour);
5710
5711     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5712     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5713   }
5714
5715   /**
5716    * Open a dialog (if not already open) that allows the user to select and
5717    * calculate PCA or Tree analysis
5718    */
5719   protected void openTreePcaDialog()
5720   {
5721     if (alignPanel.getCalculationDialog() == null)
5722     {
5723       new CalculationChooser(AlignFrame.this);
5724     }
5725   }
5726 }
5727
5728 class PrintThread extends Thread
5729 {
5730   AlignmentPanel ap;
5731
5732   public PrintThread(AlignmentPanel ap)
5733   {
5734     this.ap = ap;
5735   }
5736
5737   static PageFormat pf;
5738
5739   @Override
5740   public void run()
5741   {
5742     PrinterJob printJob = PrinterJob.getPrinterJob();
5743
5744     if (pf != null)
5745     {
5746       printJob.setPrintable(ap, pf);
5747     }
5748     else
5749     {
5750       printJob.setPrintable(ap);
5751     }
5752
5753     if (printJob.printDialog())
5754     {
5755       try
5756       {
5757         printJob.print();
5758       } catch (Exception PrintException)
5759       {
5760         PrintException.printStackTrace();
5761       }
5762     }
5763   }
5764
5765
5766 }