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.HtmlSvgOutput;
  79 import jalview.io.IdentifyFile;
  80 import jalview.io.JPredFile;
  81 import jalview.io.JalviewFileChooser;
  82 import jalview.io.JalviewFileView;
  83 import jalview.io.JnetAnnotationMaker;
  84 import jalview.io.NewickFile;
  85 import jalview.io.ScoreMatrixFile;
  86 import jalview.io.TCoffeeScoreFile;
  87 import jalview.jbgui.GAlignFrame;
  88 import jalview.schemes.ColourSchemeI;
  89 import jalview.schemes.ColourSchemes;
  90 import jalview.schemes.ResidueColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.util.MessageManager;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.ws.DBRefFetcher;
  96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Rectangle;
 105 import java.awt.Toolkit;
 106 import java.awt.datatransfer.Clipboard;
 107 import java.awt.datatransfer.DataFlavor;
 108 import java.awt.datatransfer.StringSelection;
 109 import java.awt.datatransfer.Transferable;
 110 import java.awt.dnd.DnDConstants;
 111 import java.awt.dnd.DropTargetDragEvent;
 112 import java.awt.dnd.DropTargetDropEvent;
 113 import java.awt.dnd.DropTargetEvent;
 114 import java.awt.dnd.DropTargetListener;
 115 import java.awt.event.ActionEvent;
 116 import java.awt.event.ActionListener;
 117 import java.awt.event.FocusAdapter;
 118 import java.awt.event.FocusEvent;
 119 import java.awt.event.ItemEvent;
 120 import java.awt.event.ItemListener;
 121 import java.awt.event.KeyAdapter;
 122 import java.awt.event.KeyEvent;
 123 import java.awt.event.MouseEvent;
 124 import java.awt.print.PageFormat;
 125 import java.awt.print.PrinterJob;
 126 import java.beans.PropertyChangeEvent;
 127 import java.io.File;
 128 import java.io.FileWriter;
 129 import java.io.IOException;
 130 import java.io.PrintWriter;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.HashMap;
 137 import java.util.Hashtable;
 138 import java.util.List;
 139 import java.util.Map;
 140 import java.util.Vector;
 141
 142 import javax.swing.JCheckBoxMenuItem;
 143 import javax.swing.JEditorPane;
 144 import javax.swing.JInternalFrame;
 145 import javax.swing.JLayeredPane;
 146 import javax.swing.JMenu;
 147 import javax.swing.JMenuItem;
 148 import javax.swing.JOptionPane;
 149 import javax.swing.JScrollPane;
 150 import javax.swing.SwingUtilities;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 160 {
 161
 162   Map<String, Float> distribution = new HashMap<>(); // temporary
 163
 164   public static final int DEFAULT_WIDTH = 700;
 165
 166   public static final int DEFAULT_HEIGHT = 500;
 167
 168   boolean autoAlignNewSequences;
 169
 170
 171   /*
 172    * The currently displayed panel (selected tabbed view if more than one)
 173    */
 174   public AlignmentPanel alignPanel;
 175
 176   AlignViewport viewport;
 177
 178   ViewportRanges vpRanges;
 179
 180   public AlignViewControllerI avc;
 181
 182   HiddenMarkovModel selectedHMM = null;
 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   /**
 344    * initalise the alignframe from the underlying viewport data and the
 345    * configurations
 346    */
 347   void init()
 348   {
 349     if (!Jalview.isHeadlessMode())
 350     {
 351       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 352     }
 353
 354     vpRanges = viewport.getRanges();
 355     avc = new jalview.controller.AlignViewController(this, viewport,
 356             alignPanel);
 357     if (viewport.getAlignmentConservationAnnotation() == null)
 358     {
 359       // BLOSUM62Colour.setEnabled(false);
 360       conservationMenuItem.setEnabled(false);
 361       modifyConservation.setEnabled(false);
 362       // PIDColour.setEnabled(false);
 363       // abovePIDThreshold.setEnabled(false);
 364       // modifyPID.setEnabled(false);
 365     }
 366
 367     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 368             "No sort");
 369
 370     if (sortby.equals("Id"))
 371     {
 372       sortIDMenuItem_actionPerformed(null);
 373     }
 374     else if (sortby.equals("Pairwise Identity"))
 375     {
 376       sortPairwiseMenuItem_actionPerformed(null);
 377     }
 378
 379     this.alignPanel.av
 380             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 381
 382     setMenusFromViewport(viewport);
 383     buildSortByAnnotationScoresMenu();
 384     calculateTree.addActionListener(new ActionListener()
 385     {
 386
 387       @Override
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         openTreePcaDialog();
 391       }
 392     });
 393     buildColourMenu();
 394     buildHMMERMenu();
 395
 396     if (Desktop.desktop != null)
 397     {
 398       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 399       addServiceListeners();
 400       setGUINucleotide();
 401     }
 402
 403     if (viewport.getWrapAlignment())
 404     {
 405       wrapMenuItem_actionPerformed(null);
 406     }
 407
 408     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 409     {
 410       this.overviewMenuItem_actionPerformed(null);
 411     }
 412
 413     addKeyListener();
 414
 415     final List<AlignmentPanel> selviews = new ArrayList<>();
 416     final List<AlignmentPanel> origview = new ArrayList<>();
 417     final String menuLabel = MessageManager
 418             .getString("label.copy_format_from");
 419     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 420             new ViewSetProvider()
 421             {
 422
 423               @Override
 424               public AlignmentPanel[] getAllAlignmentPanels()
 425               {
 426                 origview.clear();
 427                 origview.add(alignPanel);
 428                 // make an array of all alignment panels except for this one
 429                 List<AlignmentPanel> aps = new ArrayList<>(
 430                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 431                 aps.remove(AlignFrame.this.alignPanel);
 432                 return aps.toArray(new AlignmentPanel[aps.size()]);
 433               }
 434             }, selviews, new ItemListener()
 435             {
 436
 437               @Override
 438               public void itemStateChanged(ItemEvent e)
 439               {
 440                 if (origview.size() > 0)
 441                 {
 442                   final AlignmentPanel ap = origview.get(0);
 443
 444                   /*
 445                    * Copy the ViewStyle of the selected panel to 'this one'.
 446                    * Don't change value of 'scaleProteinAsCdna' unless copying
 447                    * from a SplitFrame.
 448                    */
 449                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 450                           .getViewStyle();
 451                   boolean fromSplitFrame = selviews.get(0)
 452                           .getAlignViewport().getCodingComplement() != null;
 453                   if (!fromSplitFrame)
 454                   {
 455                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 456                             .getViewStyle().isScaleProteinAsCdna());
 457                   }
 458                   ap.getAlignViewport().setViewStyle(vs);
 459
 460                   /*
 461                    * Also rescale ViewStyle of SplitFrame complement if there is
 462                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 463                    * the whole ViewStyle (allow cDNA protein to have different
 464                    * fonts)
 465                    */
 466                   AlignViewportI complement = ap.getAlignViewport()
 467                           .getCodingComplement();
 468                   if (complement != null && vs.isScaleProteinAsCdna())
 469                   {
 470                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 471                     ((SplitFrame) af.getSplitViewContainer())
 472                             .adjustLayout();
 473                     af.setMenusForViewport();
 474                   }
 475
 476                   ap.updateLayout();
 477                   ap.setSelected(true);
 478                   ap.alignFrame.setMenusForViewport();
 479
 480                 }
 481               }
 482             });
 483     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 484             .indexOf("devel") > -1
 485             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 486                     .indexOf("test") > -1)
 487     {
 488       formatMenu.add(vsel);
 489     }
 490     addFocusListener(new FocusAdapter()
 491     {
 492       @Override
 493       public void focusGained(FocusEvent e)
 494       {
 495         Jalview.setCurrentAlignFrame(AlignFrame.this);
 496       }
 497     });
 498
 499   }
 500
 501   private void buildHMMERMenu()
 502   {
 503     hmmerMenu.removeAll();
 504
 505     hmmerMenu.add(hmmAlign);
 506     hmmerMenu.add(hmmBuild);
 507     hmmerMenu.add(hmmSearch);
 508   }
 509
 510   /**
 511    * Change the filename and format for the alignment, and enable the 'reload'
 512    * button functionality.
 513    *
 514    * @param file
 515    *          valid filename
 516    * @param format
 517    *          format of file
 518    */
 519   public void setFileName(String file, FileFormatI format)
 520   {
 521     fileName = file;
 522     setFileFormat(format);
 523     reload.setEnabled(true);
 524   }
 525
 526   /**
 527    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 528    * events
 529    */
 530   void addKeyListener()
 531   {
 532     addKeyListener(new KeyAdapter()
 533     {
 534       @Override
 535       public void keyPressed(KeyEvent evt)
 536       {
 537         if (viewport.cursorMode
 538                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 539                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 540                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 541                 && Character.isDigit(evt.getKeyChar()))
 542         {
 543           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 544         }
 545
 546         switch (evt.getKeyCode())
 547         {
 548
 549         case 27: // escape key
 550           deselectAllSequenceMenuItem_actionPerformed(null);
 551
 552           break;
 553
 554         case KeyEvent.VK_DOWN:
 555           if (evt.isAltDown() || !viewport.cursorMode)
 556           {
 557             moveSelectedSequences(false);
 558           }
 559           if (viewport.cursorMode)
 560           {
 561             alignPanel.getSeqPanel().moveCursor(0, 1);
 562           }
 563           break;
 564
 565         case KeyEvent.VK_UP:
 566           if (evt.isAltDown() || !viewport.cursorMode)
 567           {
 568             moveSelectedSequences(true);
 569           }
 570           if (viewport.cursorMode)
 571           {
 572             alignPanel.getSeqPanel().moveCursor(0, -1);
 573           }
 574
 575           break;
 576
 577         case KeyEvent.VK_LEFT:
 578           if (evt.isAltDown() || !viewport.cursorMode)
 579           {
 580             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 581           }
 582           else
 583           {
 584             alignPanel.getSeqPanel().moveCursor(-1, 0);
 585           }
 586
 587           break;
 588
 589         case KeyEvent.VK_RIGHT:
 590           if (evt.isAltDown() || !viewport.cursorMode)
 591           {
 592             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 593           }
 594           else
 595           {
 596             alignPanel.getSeqPanel().moveCursor(1, 0);
 597           }
 598           break;
 599
 600         case KeyEvent.VK_SPACE:
 601           if (viewport.cursorMode)
 602           {
 603             alignPanel.getSeqPanel().insertGapAtCursor(
 604                     evt.isControlDown() || evt.isShiftDown()
 605                             || evt.isAltDown());
 606           }
 607           break;
 608
 609         // case KeyEvent.VK_A:
 610         // if (viewport.cursorMode)
 611         // {
 612         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 613         // //System.out.println("A");
 614         // }
 615         // break;
 616         /*
 617          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 618          * System.out.println("closing bracket"); } break;
 619          */
 620         case KeyEvent.VK_DELETE:
 621         case KeyEvent.VK_BACK_SPACE:
 622           if (!viewport.cursorMode)
 623           {
 624             cut_actionPerformed(null);
 625           }
 626           else
 627           {
 628             alignPanel.getSeqPanel().deleteGapAtCursor(
 629                     evt.isControlDown() || evt.isShiftDown()
 630                             || evt.isAltDown());
 631           }
 632
 633           break;
 634
 635         case KeyEvent.VK_S:
 636           if (viewport.cursorMode)
 637           {
 638             alignPanel.getSeqPanel().setCursorRow();
 639           }
 640           break;
 641         case KeyEvent.VK_C:
 642           if (viewport.cursorMode && !evt.isControlDown())
 643           {
 644             alignPanel.getSeqPanel().setCursorColumn();
 645           }
 646           break;
 647         case KeyEvent.VK_P:
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().setCursorPosition();
 651           }
 652           break;
 653
 654         case KeyEvent.VK_ENTER:
 655         case KeyEvent.VK_COMMA:
 656           if (viewport.cursorMode)
 657           {
 658             alignPanel.getSeqPanel().setCursorRowAndColumn();
 659           }
 660           break;
 661
 662         case KeyEvent.VK_Q:
 663           if (viewport.cursorMode)
 664           {
 665             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 666           }
 667           break;
 668         case KeyEvent.VK_M:
 669           if (viewport.cursorMode)
 670           {
 671             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 672           }
 673           break;
 674
 675         case KeyEvent.VK_F2:
 676           viewport.cursorMode = !viewport.cursorMode;
 677           statusBar.setText(MessageManager.formatMessage(
 678                   "label.keyboard_editing_mode",
 679                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 680           if (viewport.cursorMode)
 681           {
 682             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 683                     .getStartRes();
 684             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 685                     .getStartSeq();
 686           }
 687           alignPanel.getSeqPanel().seqCanvas.repaint();
 688           break;
 689
 690         case KeyEvent.VK_F1:
 691           try
 692           {
 693             Help.showHelpWindow();
 694           } catch (Exception ex)
 695           {
 696             ex.printStackTrace();
 697           }
 698           break;
 699         case KeyEvent.VK_H:
 700         {
 701           boolean toggleSeqs = !evt.isControlDown();
 702           boolean toggleCols = !evt.isShiftDown();
 703           toggleHiddenRegions(toggleSeqs, toggleCols);
 704           break;
 705         }
 706         case KeyEvent.VK_B:
 707         {
 708           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 709           boolean modifyExisting = true; // always modify, don't clear
 710                                          // evt.isShiftDown();
 711           boolean invertHighlighted = evt.isAltDown();
 712           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 713                   toggleSel);
 714           break;
 715         }
 716         case KeyEvent.VK_PAGE_UP:
 717           if (viewport.getWrapAlignment())
 718           {
 719             vpRanges.scrollUp(true);
 720           }
 721           else
 722           {
 723             vpRanges.pageUp();
 724           }
 725           break;
 726         case KeyEvent.VK_PAGE_DOWN:
 727           if (viewport.getWrapAlignment())
 728           {
 729             vpRanges.scrollUp(false);
 730           }
 731           else
 732           {
 733             vpRanges.pageDown();
 734           }
 735           break;
 736         }
 737       }
 738
 739       @Override
 740       public void keyReleased(KeyEvent evt)
 741       {
 742         switch (evt.getKeyCode())
 743         {
 744         case KeyEvent.VK_LEFT:
 745           if (evt.isAltDown() || !viewport.cursorMode)
 746           {
 747             viewport.firePropertyChange("alignment", null, viewport
 748                     .getAlignment().getSequences());
 749           }
 750           break;
 751
 752         case KeyEvent.VK_RIGHT:
 753           if (evt.isAltDown() || !viewport.cursorMode)
 754           {
 755             viewport.firePropertyChange("alignment", null, viewport
 756                     .getAlignment().getSequences());
 757           }
 758           break;
 759         }
 760       }
 761     });
 762   }
 763
 764   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 765   {
 766     ap.alignFrame = this;
 767     avc = new jalview.controller.AlignViewController(this, viewport,
 768             alignPanel);
 769
 770     alignPanels.add(ap);
 771
 772     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 773
 774     int aSize = alignPanels.size();
 775
 776     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 777
 778     if (aSize == 1 && ap.av.viewName == null)
 779     {
 780       this.getContentPane().add(ap, BorderLayout.CENTER);
 781     }
 782     else
 783     {
 784       if (aSize == 2)
 785       {
 786         setInitialTabVisible();
 787       }
 788
 789       expandViews.setEnabled(true);
 790       gatherViews.setEnabled(true);
 791       tabbedPane.addTab(ap.av.viewName, ap);
 792
 793       ap.setVisible(false);
 794     }
 795
 796     if (newPanel)
 797     {
 798       if (ap.av.isPadGaps())
 799       {
 800         ap.av.getAlignment().padGaps();
 801       }
 802       ap.av.updateConservation(ap);
 803       ap.av.updateConsensus(ap);
 804       ap.av.updateStrucConsensus(ap);
 805       ap.av.updateInformation(ap);
 806     }
 807   }
 808
 809   public void setInitialTabVisible()
 810   {
 811     expandViews.setEnabled(true);
 812     gatherViews.setEnabled(true);
 813     tabbedPane.setVisible(true);
 814     AlignmentPanel first = alignPanels.get(0);
 815     tabbedPane.addTab(first.av.viewName, first);
 816     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 817   }
 818
 819   public AlignViewport getViewport()
 820   {
 821     return viewport;
 822   }
 823
 824   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 825   private void addServiceListeners()
 826   {
 827     final java.beans.PropertyChangeListener thisListener;
 828     Desktop.instance.addJalviewPropertyChangeListener("services",
 829             thisListener = new java.beans.PropertyChangeListener()
 830             {
 831               @Override
 832               public void propertyChange(PropertyChangeEvent evt)
 833               {
 834                 // // System.out.println("Discoverer property change.");
 835                 // if (evt.getPropertyName().equals("services"))
 836                 {
 837                   SwingUtilities.invokeLater(new Runnable()
 838                   {
 839
 840                     @Override
 841                     public void run()
 842                     {
 843                       System.err
 844                               .println("Rebuild WS Menu for service change");
 845                       BuildWebServiceMenu();
 846                     }
 847
 848                   });
 849                 }
 850               }
 851             });
 852     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 853     {
 854       @Override
 855       public void internalFrameClosed(
 856               javax.swing.event.InternalFrameEvent evt)
 857       {
 858         // System.out.println("deregistering discoverer listener");
 859         Desktop.instance.removeJalviewPropertyChangeListener("services",
 860                 thisListener);
 861         closeMenuItem_actionPerformed(true);
 862       };
 863     });
 864     // Finally, build the menu once to get current service state
 865     new Thread(new Runnable()
 866     {
 867       @Override
 868       public void run()
 869       {
 870         BuildWebServiceMenu();
 871       }
 872     }).start();
 873   }
 874
 875   /**
 876    * Configure menu items that vary according to whether the alignment is
 877    * nucleotide or protein
 878    */
 879   public void setGUINucleotide()
 880   {
 881     AlignmentI al = getViewport().getAlignment();
 882     boolean nucleotide = al.isNucleotide();
 883
 884     showTranslation.setVisible(nucleotide);
 885     showReverse.setVisible(nucleotide);
 886     showReverseComplement.setVisible(nucleotide);
 887     conservationMenuItem.setEnabled(!nucleotide);
 888     modifyConservation.setEnabled(!nucleotide
 889             && conservationMenuItem.isSelected());
 890     showGroupConservation.setEnabled(!nucleotide);
 891
 892     showComplementMenuItem.setText(nucleotide ? MessageManager
 893             .getString("label.protein") : MessageManager
 894             .getString("label.nucleotide"));
 895   }
 896
 897   /**
 898    * set up menus for the current viewport. This may be called after any
 899    * operation that affects the data in the current view (selection changed,
 900    * etc) to update the menus to reflect the new state.
 901    */
 902   @Override
 903   public void setMenusForViewport()
 904   {
 905     setMenusFromViewport(viewport);
 906   }
 907
 908   /**
 909    * Need to call this method when tabs are selected for multiple views, or when
 910    * loading from Jalview2XML.java
 911    *
 912    * @param av
 913    *          AlignViewport
 914    */
 915   void setMenusFromViewport(AlignViewport av)
 916   {
 917     padGapsMenuitem.setSelected(av.isPadGaps());
 918     colourTextMenuItem.setSelected(av.isShowColourText());
 919     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 920     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 921     conservationMenuItem.setSelected(av.getConservationSelected());
 922     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 923     seqLimits.setSelected(av.getShowJVSuffix());
 924     idRightAlign.setSelected(av.isRightAlignIds());
 925     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 926     renderGapsMenuItem.setSelected(av.isRenderGaps());
 927     wrapMenuItem.setSelected(av.getWrapAlignment());
 928     scaleAbove.setVisible(av.getWrapAlignment());
 929     scaleLeft.setVisible(av.getWrapAlignment());
 930     scaleRight.setVisible(av.getWrapAlignment());
 931     annotationPanelMenuItem.setState(av.isShowAnnotation());
 932     /*
 933      * Show/hide annotations only enabled if annotation panel is shown
 934      */
 935     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 936     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 938     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 939     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 940     viewTextMenuItem.setSelected(av.getShowText());
 941     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 942     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 943     showGroupConservation.setSelected(av.isShowGroupConservation());
 944     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 945     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 946     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 947     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 948     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 949     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 950
 951     ColourMenuHelper.setColourSelected(colourMenu,
 952             av.getGlobalColourScheme());
 953
 954     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 955     hiddenMarkers.setState(av.getShowHiddenMarkers());
 956     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 957     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 958     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 959     autoCalculate.setSelected(av.autoCalculateConsensus);
 960     sortByTree.setSelected(av.sortByTree);
 961     listenToViewSelections.setSelected(av.followSelection);
 962
 963     showProducts.setEnabled(canShowProducts());
 964     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 965
 966     updateEditMenuBar();
 967   }
 968
 969   /**
 970    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 971    *
 972    * @param b
 973    */
 974   public void setGroovyEnabled(boolean b)
 975   {
 976     runGroovy.setEnabled(b);
 977   }
 978
 979   private IProgressIndicator progressBar;
 980
 981   /*
 982    * (non-Javadoc)
 983    *
 984    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 985    */
 986   @Override
 987   public void setProgressBar(String message, long id)
 988   {
 989     progressBar.setProgressBar(message, id);
 990   }
 991
 992   @Override
 993   public void registerHandler(final long id,
 994           final IProgressIndicatorHandler handler)
 995   {
 996     progressBar.registerHandler(id, handler);
 997   }
 998
 999   /**
1000    *
1001    * @return true if any progress bars are still active
1002    */
1003   @Override
1004   public boolean operationInProgress()
1005   {
1006     return progressBar.operationInProgress();
1007   }
1008
1009   @Override
1010   public void setStatus(String text)
1011   {
1012     statusBar.setText(text);
1013   }
1014
1015   /*
1016    * Added so Castor Mapping file can obtain Jalview Version
1017    */
1018   public String getVersion()
1019   {
1020     return jalview.bin.Cache.getProperty("VERSION");
1021   }
1022
1023   public FeatureRenderer getFeatureRenderer()
1024   {
1025     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1026   }
1027
1028   @Override
1029   public void fetchSequence_actionPerformed(ActionEvent e)
1030   {
1031     new jalview.gui.SequenceFetcher(this);
1032   }
1033
1034   @Override
1035   public void addFromFile_actionPerformed(ActionEvent e)
1036   {
1037     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1038   }
1039
1040   @Override
1041   public void hmmBuild_actionPerformed(ActionEvent e)
1042           throws IOException, InterruptedException
1043   {
1044     new Thread(new HMMBuildThread(this)).start();
1045     alignPanel.repaint();
1046
1047   }
1048
1049   @Override
1050   public void hmmAlign_actionPerformed(ActionEvent e)
1051           throws IOException, InterruptedException
1052   {
1053     new Thread(new HMMAlignThread(this, true)).start();
1054     alignPanel.repaint();
1055   }
1056
1057   @Override
1058   public void changeHMMERLocation_actionPerformed(ActionEvent e)
1059   {
1060     String location = JOptionPane.showInputDialog(
1061             MessageManager.getString("label.enter_location"));
1062     Cache.setProperty(Preferences.HMMER_PATH, location);
1063   }
1064
1065   @Override
1066   public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1067   {
1068     autoAlignNewSequences = autoAlignSeqs;
1069     alignPanel.repaint();
1070   }
1071
1072   @Override
1073   public void hmmSearch_actionPerformed(ActionEvent e)
1074   {
1075     alignPanel.repaint();
1076   }
1077
1078   @Override
1079   public void reload_actionPerformed(ActionEvent e)
1080   {
1081     if (fileName != null)
1082     {
1083       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1084       // originating file's format
1085       // TODO: work out how to recover feature settings for correct view(s) when
1086       // file is reloaded.
1087       if (FileFormat.Jalview.equals(currentFileFormat))
1088       {
1089         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1090         for (int i = 0; i < frames.length; i++)
1091         {
1092           if (frames[i] instanceof AlignFrame && frames[i] != this
1093                   && ((AlignFrame) frames[i]).fileName != null
1094                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1095           {
1096             try
1097             {
1098               frames[i].setSelected(true);
1099               Desktop.instance.closeAssociatedWindows();
1100             } catch (java.beans.PropertyVetoException ex)
1101             {
1102             }
1103           }
1104
1105         }
1106         Desktop.instance.closeAssociatedWindows();
1107
1108         FileLoader loader = new FileLoader();
1109         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1110                 : DataSourceType.FILE;
1111         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1112       }
1113       else
1114       {
1115         Rectangle bounds = this.getBounds();
1116
1117         FileLoader loader = new FileLoader();
1118         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1119                 : DataSourceType.FILE;
1120         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1121                 protocol, currentFileFormat);
1122
1123         newframe.setBounds(bounds);
1124         if (featureSettings != null && featureSettings.isShowing())
1125         {
1126           final Rectangle fspos = featureSettings.frame.getBounds();
1127           // TODO: need a 'show feature settings' function that takes bounds -
1128           // need to refactor Desktop.addFrame
1129           newframe.featureSettings_actionPerformed(null);
1130           final FeatureSettings nfs = newframe.featureSettings;
1131           SwingUtilities.invokeLater(new Runnable()
1132           {
1133             @Override
1134             public void run()
1135             {
1136               nfs.frame.setBounds(fspos);
1137             }
1138           });
1139           this.featureSettings.close();
1140           this.featureSettings = null;
1141         }
1142         this.closeMenuItem_actionPerformed(true);
1143       }
1144     }
1145   }
1146
1147   @Override
1148   public void addFromText_actionPerformed(ActionEvent e)
1149   {
1150     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1151             .getAlignPanel());
1152   }
1153
1154   @Override
1155   public void addFromURL_actionPerformed(ActionEvent e)
1156   {
1157     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1158   }
1159
1160   @Override
1161   public void save_actionPerformed(ActionEvent e)
1162   {
1163     if (fileName == null || (currentFileFormat == null)
1164             || fileName.startsWith("http"))
1165     {
1166       saveAs_actionPerformed(null);
1167     }
1168     else
1169     {
1170       saveAlignment(fileName, currentFileFormat);
1171     }
1172   }
1173
1174   /**
1175    * DOCUMENT ME!
1176    *
1177    * @param e
1178    *          DOCUMENT ME!
1179    */
1180   @Override
1181   public void saveAs_actionPerformed(ActionEvent e)
1182   {
1183     String format = currentFileFormat == null ? null : currentFileFormat
1184             .getName();
1185     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1186             Cache.getProperty("LAST_DIRECTORY"), format);
1187
1188     chooser.setFileView(new JalviewFileView());
1189     chooser.setDialogTitle(MessageManager
1190             .getString("label.save_alignment_to_file"));
1191     chooser.setToolTipText(MessageManager.getString("action.save"));
1192
1193     int value = chooser.showSaveDialog(this);
1194
1195     if (value == JalviewFileChooser.APPROVE_OPTION)
1196     {
1197       currentFileFormat = chooser.getSelectedFormat();
1198       while (currentFileFormat == null)
1199       {
1200         JvOptionPane
1201                 .showInternalMessageDialog(
1202                         Desktop.desktop,
1203                         MessageManager
1204                                 .getString("label.select_file_format_before_saving"),
1205                         MessageManager
1206                                 .getString("label.file_format_not_specified"),
1207                         JvOptionPane.WARNING_MESSAGE);
1208         currentFileFormat = chooser.getSelectedFormat();
1209         value = chooser.showSaveDialog(this);
1210         if (value != JalviewFileChooser.APPROVE_OPTION)
1211         {
1212           return;
1213         }
1214       }
1215
1216       fileName = chooser.getSelectedFile().getPath();
1217
1218       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1219
1220       Cache.setProperty("LAST_DIRECTORY", fileName);
1221       saveAlignment(fileName, currentFileFormat);
1222     }
1223   }
1224
1225   public boolean saveAlignment(String file, FileFormatI format)
1226   {
1227     boolean success = true;
1228
1229     if (FileFormat.Jalview.equals(format))
1230     {
1231       String shortName = title;
1232
1233       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1234       {
1235         shortName = shortName.substring(shortName
1236                 .lastIndexOf(java.io.File.separatorChar) + 1);
1237       }
1238
1239       success = new Jalview2XML().saveAlignment(this, file, shortName);
1240
1241       statusBar.setText(MessageManager.formatMessage(
1242               "label.successfully_saved_to_file_in_format", new Object[] {
1243                   fileName, format }));
1244
1245     }
1246     else
1247     {
1248       AlignmentExportData exportData = getAlignmentForExport(format,
1249               viewport, null);
1250       if (exportData.getSettings().isCancelled())
1251       {
1252         return false;
1253       }
1254       FormatAdapter f = new FormatAdapter(alignPanel,
1255               exportData.getSettings());
1256       String output = f.formatSequences(
1257               format,
1258               exportData.getAlignment(), // class cast exceptions will
1259               // occur in the distant future
1260               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1261               f.getCacheSuffixDefault(format), viewport.getAlignment()
1262                       .getHiddenColumns());
1263
1264       if (output == null)
1265       {
1266         success = false;
1267       }
1268       else
1269       {
1270         try
1271         {
1272           PrintWriter out = new PrintWriter(new FileWriter(file));
1273
1274           out.print(output);
1275           out.close();
1276           this.setTitle(file);
1277           statusBar.setText(MessageManager.formatMessage(
1278                   "label.successfully_saved_to_file_in_format",
1279                   new Object[] { fileName, format.getName() }));
1280         } catch (Exception ex)
1281         {
1282           success = false;
1283           ex.printStackTrace();
1284         }
1285       }
1286     }
1287
1288     if (!success)
1289     {
1290       JvOptionPane.showInternalMessageDialog(this, MessageManager
1291               .formatMessage("label.couldnt_save_file",
1292                       new Object[] { fileName }), MessageManager
1293               .getString("label.error_saving_file"),
1294               JvOptionPane.WARNING_MESSAGE);
1295     }
1296
1297     return success;
1298   }
1299
1300   private void warningMessage(String warning, String title)
1301   {
1302     if (new jalview.util.Platform().isHeadless())
1303     {
1304       System.err.println("Warning: " + title + "\nWarning: " + warning);
1305
1306     }
1307     else
1308     {
1309       JvOptionPane.showInternalMessageDialog(this, warning, title,
1310               JvOptionPane.WARNING_MESSAGE);
1311     }
1312     return;
1313   }
1314
1315   /**
1316    * DOCUMENT ME!
1317    *
1318    * @param e
1319    *          DOCUMENT ME!
1320    */
1321   @Override
1322   protected void outputText_actionPerformed(ActionEvent e)
1323   {
1324     FileFormatI fileFormat = FileFormats.getInstance().forName(
1325             e.getActionCommand());
1326     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1327             viewport, null);
1328     if (exportData.getSettings().isCancelled())
1329     {
1330       return;
1331     }
1332     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1333     cap.setForInput(null);
1334     try
1335     {
1336       FileFormatI format = fileFormat;
1337       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1338               .formatSequences(format, exportData.getAlignment(),
1339                       exportData.getOmitHidden(),
1340  exportData
1341                               .getStartEndPostions(), viewport
1342                               .getAlignment().getHiddenColumns()));
1343       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1344               "label.alignment_output_command",
1345               new Object[] { e.getActionCommand() }), 600, 500);
1346     } catch (OutOfMemoryError oom)
1347     {
1348       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1349       cap.dispose();
1350     }
1351
1352   }
1353
1354   public static AlignmentExportData getAlignmentForExport(
1355           FileFormatI format, AlignViewportI viewport,
1356           AlignExportSettingI exportSettings)
1357   {
1358     AlignmentI alignmentToExport = null;
1359     AlignExportSettingI settings = exportSettings;
1360     String[] omitHidden = null;
1361
1362     HiddenSequences hiddenSeqs = viewport.getAlignment()
1363             .getHiddenSequences();
1364
1365     alignmentToExport = viewport.getAlignment();
1366
1367     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1368     if (settings == null)
1369     {
1370       settings = new AlignExportSettings(hasHiddenSeqs,
1371               viewport.hasHiddenColumns(), format);
1372     }
1373     // settings.isExportAnnotations();
1374
1375     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1376     {
1377       omitHidden = viewport.getViewAsString(false,
1378               settings.isExportHiddenSequences());
1379     }
1380
1381     int[] alignmentStartEnd = new int[2];
1382     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1383     {
1384       alignmentToExport = hiddenSeqs.getFullAlignment();
1385     }
1386     else
1387     {
1388       alignmentToExport = viewport.getAlignment();
1389     }
1390     alignmentStartEnd = alignmentToExport
1391             .getVisibleStartAndEndIndex(viewport.getAlignment()
1392                     .getHiddenColumns()
1393                     .getHiddenRegions());
1394     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1395             omitHidden, alignmentStartEnd, settings);
1396     return ed;
1397   }
1398
1399   /**
1400    * DOCUMENT ME!
1401    *
1402    * @param e
1403    *          DOCUMENT ME!
1404    */
1405   @Override
1406   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1407   {
1408     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1409     htmlSVG.exportHTML(null);
1410   }
1411
1412   @Override
1413   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1414   {
1415     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1416     bjs.exportHTML(null);
1417   }
1418
1419   public void createImageMap(File file, String image)
1420   {
1421     alignPanel.makePNGImageMap(file, image);
1422   }
1423
1424   /**
1425    * DOCUMENT ME!
1426    *
1427    * @param e
1428    *          DOCUMENT ME!
1429    */
1430   @Override
1431   public void createPNG(File f)
1432   {
1433     alignPanel.makePNG(f);
1434   }
1435
1436   /**
1437    * DOCUMENT ME!
1438    *
1439    * @param e
1440    *          DOCUMENT ME!
1441    */
1442   @Override
1443   public void createEPS(File f)
1444   {
1445     alignPanel.makeEPS(f);
1446   }
1447
1448   @Override
1449   public void createSVG(File f)
1450   {
1451     alignPanel.makeSVG(f);
1452   }
1453
1454   @Override
1455   public void pageSetup_actionPerformed(ActionEvent e)
1456   {
1457     PrinterJob printJob = PrinterJob.getPrinterJob();
1458     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1459   }
1460
1461   /**
1462    * DOCUMENT ME!
1463    *
1464    * @param e
1465    *          DOCUMENT ME!
1466    */
1467   @Override
1468   public void printMenuItem_actionPerformed(ActionEvent e)
1469   {
1470     // Putting in a thread avoids Swing painting problems
1471     PrintThread thread = new PrintThread(alignPanel);
1472     thread.start();
1473   }
1474
1475   @Override
1476   public void exportFeatures_actionPerformed(ActionEvent e)
1477   {
1478     new AnnotationExporter().exportFeatures(alignPanel);
1479   }
1480
1481   @Override
1482   public void exportAnnotations_actionPerformed(ActionEvent e)
1483   {
1484     new AnnotationExporter().exportAnnotations(alignPanel);
1485   }
1486
1487   @Override
1488   public void associatedData_actionPerformed(ActionEvent e)
1489           throws IOException, InterruptedException
1490   {
1491     // Pick the tree file
1492     JalviewFileChooser chooser = new JalviewFileChooser(
1493             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1494     chooser.setFileView(new JalviewFileView());
1495     chooser.setDialogTitle(MessageManager
1496             .getString("label.load_jalview_annotations"));
1497     chooser.setToolTipText(MessageManager
1498             .getString("label.load_jalview_annotations"));
1499
1500     int value = chooser.showOpenDialog(null);
1501
1502     if (value == JalviewFileChooser.APPROVE_OPTION)
1503     {
1504       String choice = chooser.getSelectedFile().getPath();
1505       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1506       loadJalviewDataFile(choice, null, null, null);
1507     }
1508
1509   }
1510
1511   /**
1512    * Close the current view or all views in the alignment frame. If the frame
1513    * only contains one view then the alignment will be removed from memory.
1514    *
1515    * @param closeAllTabs
1516    */
1517   @Override
1518   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1519   {
1520     if (alignPanels != null && alignPanels.size() < 2)
1521     {
1522       closeAllTabs = true;
1523     }
1524
1525     try
1526     {
1527       if (alignPanels != null)
1528       {
1529         if (closeAllTabs)
1530         {
1531           if (this.isClosed())
1532           {
1533             // really close all the windows - otherwise wait till
1534             // setClosed(true) is called
1535             for (int i = 0; i < alignPanels.size(); i++)
1536             {
1537               AlignmentPanel ap = alignPanels.get(i);
1538               ap.closePanel();
1539             }
1540           }
1541         }
1542         else
1543         {
1544           closeView(alignPanel);
1545         }
1546       }
1547
1548       if (closeAllTabs)
1549       {
1550         /*
1551          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1552          * be called recursively, with the frame now in 'closed' state
1553          */
1554         this.setClosed(true);
1555       }
1556     } catch (Exception ex)
1557     {
1558       ex.printStackTrace();
1559     }
1560   }
1561
1562   /**
1563    * Close the specified panel and close up tabs appropriately.
1564    *
1565    * @param panelToClose
1566    */
1567   public void closeView(AlignmentPanel panelToClose)
1568   {
1569     int index = tabbedPane.getSelectedIndex();
1570     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1571     alignPanels.remove(panelToClose);
1572     panelToClose.closePanel();
1573     panelToClose = null;
1574
1575     tabbedPane.removeTabAt(closedindex);
1576     tabbedPane.validate();
1577
1578     if (index > closedindex || index == tabbedPane.getTabCount())
1579     {
1580       // modify currently selected tab index if necessary.
1581       index--;
1582     }
1583
1584     this.tabSelectionChanged(index);
1585   }
1586
1587   /**
1588    * DOCUMENT ME!
1589    */
1590   void updateEditMenuBar()
1591   {
1592
1593     if (viewport.getHistoryList().size() > 0)
1594     {
1595       undoMenuItem.setEnabled(true);
1596       CommandI command = viewport.getHistoryList().peek();
1597       undoMenuItem.setText(MessageManager.formatMessage(
1598               "label.undo_command",
1599               new Object[] { command.getDescription() }));
1600     }
1601     else
1602     {
1603       undoMenuItem.setEnabled(false);
1604       undoMenuItem.setText(MessageManager.getString("action.undo"));
1605     }
1606
1607     if (viewport.getRedoList().size() > 0)
1608     {
1609       redoMenuItem.setEnabled(true);
1610
1611       CommandI command = viewport.getRedoList().peek();
1612       redoMenuItem.setText(MessageManager.formatMessage(
1613               "label.redo_command",
1614               new Object[] { command.getDescription() }));
1615     }
1616     else
1617     {
1618       redoMenuItem.setEnabled(false);
1619       redoMenuItem.setText(MessageManager.getString("action.redo"));
1620     }
1621   }
1622
1623   @Override
1624   public void addHistoryItem(CommandI command)
1625   {
1626     if (command.getSize() > 0)
1627     {
1628       viewport.addToHistoryList(command);
1629       viewport.clearRedoList();
1630       updateEditMenuBar();
1631       viewport.updateHiddenColumns();
1632       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1633       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1634       // viewport.getColumnSelection()
1635       // .getHiddenColumns().size() > 0);
1636     }
1637   }
1638
1639   /**
1640    *
1641    * @return alignment objects for all views
1642    */
1643   AlignmentI[] getViewAlignments()
1644   {
1645     if (alignPanels != null)
1646     {
1647       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1648       int i = 0;
1649       for (AlignmentPanel ap : alignPanels)
1650       {
1651         als[i++] = ap.av.getAlignment();
1652       }
1653       return als;
1654     }
1655     if (viewport != null)
1656     {
1657       return new AlignmentI[] { viewport.getAlignment() };
1658     }
1659     return null;
1660   }
1661
1662   /**
1663    * DOCUMENT ME!
1664    *
1665    * @param e
1666    *          DOCUMENT ME!
1667    */
1668   @Override
1669   protected void undoMenuItem_actionPerformed(ActionEvent e)
1670   {
1671     if (viewport.getHistoryList().isEmpty())
1672     {
1673       return;
1674     }
1675     CommandI command = viewport.getHistoryList().pop();
1676     viewport.addToRedoList(command);
1677     command.undoCommand(getViewAlignments());
1678
1679     AlignmentViewport originalSource = getOriginatingSource(command);
1680     updateEditMenuBar();
1681
1682     if (originalSource != null)
1683     {
1684       if (originalSource != viewport)
1685       {
1686         Cache.log
1687                 .warn("Implementation worry: mismatch of viewport origin for undo");
1688       }
1689       originalSource.updateHiddenColumns();
1690       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1691       // null
1692       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1693       // viewport.getColumnSelection()
1694       // .getHiddenColumns().size() > 0);
1695       originalSource.firePropertyChange("alignment", null, originalSource
1696               .getAlignment().getSequences());
1697     }
1698   }
1699
1700   /**
1701    * DOCUMENT ME!
1702    *
1703    * @param e
1704    *          DOCUMENT ME!
1705    */
1706   @Override
1707   protected void redoMenuItem_actionPerformed(ActionEvent e)
1708   {
1709     if (viewport.getRedoList().size() < 1)
1710     {
1711       return;
1712     }
1713
1714     CommandI command = viewport.getRedoList().pop();
1715     viewport.addToHistoryList(command);
1716     command.doCommand(getViewAlignments());
1717
1718     AlignmentViewport originalSource = getOriginatingSource(command);
1719     updateEditMenuBar();
1720
1721     if (originalSource != null)
1722     {
1723
1724       if (originalSource != viewport)
1725       {
1726         Cache.log
1727                 .warn("Implementation worry: mismatch of viewport origin for redo");
1728       }
1729       originalSource.updateHiddenColumns();
1730       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1731       // null
1732       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1733       // viewport.getColumnSelection()
1734       // .getHiddenColumns().size() > 0);
1735       originalSource.firePropertyChange("alignment", null, originalSource
1736               .getAlignment().getSequences());
1737     }
1738   }
1739
1740   AlignmentViewport getOriginatingSource(CommandI command)
1741   {
1742     AlignmentViewport originalSource = null;
1743     // For sequence removal and addition, we need to fire
1744     // the property change event FROM the viewport where the
1745     // original alignment was altered
1746     AlignmentI al = null;
1747     if (command instanceof EditCommand)
1748     {
1749       EditCommand editCommand = (EditCommand) command;
1750       al = editCommand.getAlignment();
1751       List<Component> comps = PaintRefresher.components.get(viewport
1752               .getSequenceSetId());
1753
1754       for (Component comp : comps)
1755       {
1756         if (comp instanceof AlignmentPanel)
1757         {
1758           if (al == ((AlignmentPanel) comp).av.getAlignment())
1759           {
1760             originalSource = ((AlignmentPanel) comp).av;
1761             break;
1762           }
1763         }
1764       }
1765     }
1766
1767     if (originalSource == null)
1768     {
1769       // The original view is closed, we must validate
1770       // the current view against the closed view first
1771       if (al != null)
1772       {
1773         PaintRefresher.validateSequences(al, viewport.getAlignment());
1774       }
1775
1776       originalSource = viewport;
1777     }
1778
1779     return originalSource;
1780   }
1781
1782   /**
1783    * DOCUMENT ME!
1784    *
1785    * @param up
1786    *          DOCUMENT ME!
1787    */
1788   public void moveSelectedSequences(boolean up)
1789   {
1790     SequenceGroup sg = viewport.getSelectionGroup();
1791
1792     if (sg == null)
1793     {
1794       return;
1795     }
1796     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1797             viewport.getHiddenRepSequences(), up);
1798     alignPanel.paintAlignment(true);
1799   }
1800
1801   synchronized void slideSequences(boolean right, int size)
1802   {
1803     List<SequenceI> sg = new ArrayList<>();
1804     if (viewport.cursorMode)
1805     {
1806       sg.add(viewport.getAlignment().getSequenceAt(
1807               alignPanel.getSeqPanel().seqCanvas.cursorY));
1808     }
1809     else if (viewport.getSelectionGroup() != null
1810             && viewport.getSelectionGroup().getSize() != viewport
1811                     .getAlignment().getHeight())
1812     {
1813       sg = viewport.getSelectionGroup().getSequences(
1814               viewport.getHiddenRepSequences());
1815     }
1816
1817     if (sg.size() < 1)
1818     {
1819       return;
1820     }
1821
1822     List<SequenceI> invertGroup = new ArrayList<>();
1823
1824     for (SequenceI seq : viewport.getAlignment().getSequences())
1825     {
1826       if (!sg.contains(seq))
1827       {
1828         invertGroup.add(seq);
1829       }
1830     }
1831
1832     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1833
1834     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1835     for (int i = 0; i < invertGroup.size(); i++)
1836     {
1837       seqs2[i] = invertGroup.get(i);
1838     }
1839
1840     SlideSequencesCommand ssc;
1841     if (right)
1842     {
1843       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1844               size, viewport.getGapCharacter());
1845     }
1846     else
1847     {
1848       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1849               size, viewport.getGapCharacter());
1850     }
1851
1852     int groupAdjustment = 0;
1853     if (ssc.getGapsInsertedBegin() && right)
1854     {
1855       if (viewport.cursorMode)
1856       {
1857         alignPanel.getSeqPanel().moveCursor(size, 0);
1858       }
1859       else
1860       {
1861         groupAdjustment = size;
1862       }
1863     }
1864     else if (!ssc.getGapsInsertedBegin() && !right)
1865     {
1866       if (viewport.cursorMode)
1867       {
1868         alignPanel.getSeqPanel().moveCursor(-size, 0);
1869       }
1870       else
1871       {
1872         groupAdjustment = -size;
1873       }
1874     }
1875
1876     if (groupAdjustment != 0)
1877     {
1878       viewport.getSelectionGroup().setStartRes(
1879               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1880       viewport.getSelectionGroup().setEndRes(
1881               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1882     }
1883
1884     /*
1885      * just extend the last slide command if compatible; but not if in
1886      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1887      */
1888     boolean appendHistoryItem = false;
1889     Deque<CommandI> historyList = viewport.getHistoryList();
1890     boolean inSplitFrame = getSplitViewContainer() != null;
1891     if (!inSplitFrame && historyList != null && historyList.size() > 0
1892             && historyList.peek() instanceof SlideSequencesCommand)
1893     {
1894       appendHistoryItem = ssc
1895               .appendSlideCommand((SlideSequencesCommand) historyList
1896                       .peek());
1897     }
1898
1899     if (!appendHistoryItem)
1900     {
1901       addHistoryItem(ssc);
1902     }
1903
1904     repaint();
1905   }
1906
1907   /**
1908    * DOCUMENT ME!
1909    *
1910    * @param e
1911    *          DOCUMENT ME!
1912    */
1913   @Override
1914   protected void copy_actionPerformed(ActionEvent e)
1915   {
1916     System.gc();
1917     if (viewport.getSelectionGroup() == null)
1918     {
1919       return;
1920     }
1921     // TODO: preserve the ordering of displayed alignment annotation in any
1922     // internal paste (particularly sequence associated annotation)
1923     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1924     String[] omitHidden = null;
1925
1926     if (viewport.hasHiddenColumns())
1927     {
1928       omitHidden = viewport.getViewAsString(true);
1929     }
1930
1931     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1932             seqs, omitHidden, null);
1933
1934     StringSelection ss = new StringSelection(output);
1935
1936     try
1937     {
1938       jalview.gui.Desktop.internalCopy = true;
1939       // Its really worth setting the clipboard contents
1940       // to empty before setting the large StringSelection!!
1941       Toolkit.getDefaultToolkit().getSystemClipboard()
1942               .setContents(new StringSelection(""), null);
1943
1944       Toolkit.getDefaultToolkit().getSystemClipboard()
1945               .setContents(ss, Desktop.instance);
1946     } catch (OutOfMemoryError er)
1947     {
1948       new OOMWarning("copying region", er);
1949       return;
1950     }
1951
1952     ArrayList<int[]> hiddenColumns = null;
1953     if (viewport.hasHiddenColumns())
1954     {
1955       hiddenColumns = new ArrayList<>();
1956       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1957               .getSelectionGroup().getEndRes();
1958       for (int[] region : viewport.getAlignment().getHiddenColumns()
1959               .getHiddenRegions())
1960       {
1961         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1962         {
1963           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1964               region[1] - hiddenOffset });
1965         }
1966       }
1967     }
1968
1969     Desktop.jalviewClipboard = new Object[] { seqs,
1970         viewport.getAlignment().getDataset(), hiddenColumns };
1971     statusBar.setText(MessageManager.formatMessage(
1972             "label.copied_sequences_to_clipboard", new Object[] { Integer
1973                     .valueOf(seqs.length).toString() }));
1974   }
1975
1976   /**
1977    * DOCUMENT ME!
1978    *
1979    * @param e
1980    *          DOCUMENT ME!
1981    * @throws InterruptedException
1982    * @throws IOException
1983    */
1984   @Override
1985   protected void pasteNew_actionPerformed(ActionEvent e)
1986           throws IOException, InterruptedException
1987   {
1988     paste(true);
1989   }
1990
1991   /**
1992    * DOCUMENT ME!
1993    *
1994    * @param e
1995    *          DOCUMENT ME!
1996    * @throws InterruptedException
1997    * @throws IOException
1998    */
1999   @Override
2000   protected void pasteThis_actionPerformed(ActionEvent e)
2001           throws IOException, InterruptedException
2002   {
2003     paste(false);
2004   }
2005
2006   /**
2007    * Paste contents of Jalview clipboard
2008    *
2009    * @param newAlignment
2010    *          true to paste to a new alignment, otherwise add to this.
2011    * @throws InterruptedException
2012    * @throws IOException
2013    */
2014   void paste(boolean newAlignment) throws IOException, InterruptedException
2015   {
2016     boolean externalPaste = true;
2017     try
2018     {
2019       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2020       Transferable contents = c.getContents(this);
2021
2022       if (contents == null)
2023       {
2024         return;
2025       }
2026
2027       String str;
2028       FileFormatI format;
2029       try
2030       {
2031         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2032         if (str.length() < 1)
2033         {
2034           return;
2035         }
2036
2037         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2038
2039       } catch (OutOfMemoryError er)
2040       {
2041         new OOMWarning("Out of memory pasting sequences!!", er);
2042         return;
2043       }
2044
2045       SequenceI[] sequences;
2046       boolean annotationAdded = false;
2047       AlignmentI alignment = null;
2048
2049       if (Desktop.jalviewClipboard != null)
2050       {
2051         // The clipboard was filled from within Jalview, we must use the
2052         // sequences
2053         // And dataset from the copied alignment
2054         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2055         // be doubly sure that we create *new* sequence objects.
2056         sequences = new SequenceI[newseq.length];
2057         for (int i = 0; i < newseq.length; i++)
2058         {
2059           sequences[i] = new Sequence(newseq[i]);
2060         }
2061         alignment = new Alignment(sequences);
2062         externalPaste = false;
2063       }
2064       else
2065       {
2066         // parse the clipboard as an alignment.
2067         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2068                 format);
2069         sequences = alignment.getSequencesArray();
2070       }
2071
2072       int alwidth = 0;
2073       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2074       int fgroup = -1;
2075
2076       if (newAlignment)
2077       {
2078
2079         if (Desktop.jalviewClipboard != null)
2080         {
2081           // dataset is inherited
2082           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2083         }
2084         else
2085         {
2086           // new dataset is constructed
2087           alignment.setDataset(null);
2088         }
2089         alwidth = alignment.getWidth() + 1;
2090       }
2091       else
2092       {
2093         AlignmentI pastedal = alignment; // preserve pasted alignment object
2094         // Add pasted sequences and dataset into existing alignment.
2095         alignment = viewport.getAlignment();
2096         alwidth = alignment.getWidth() + 1;
2097         // decide if we need to import sequences from an existing dataset
2098         boolean importDs = Desktop.jalviewClipboard != null
2099                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2100         // importDs==true instructs us to copy over new dataset sequences from
2101         // an existing alignment
2102         Vector newDs = (importDs) ? new Vector() : null; // used to create
2103         // minimum dataset set
2104
2105         for (int i = 0; i < sequences.length; i++)
2106         {
2107           if (importDs)
2108           {
2109             newDs.addElement(null);
2110           }
2111           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2112           // paste
2113           if (importDs && ds != null)
2114           {
2115             if (!newDs.contains(ds))
2116             {
2117               newDs.setElementAt(ds, i);
2118               ds = new Sequence(ds);
2119               // update with new dataset sequence
2120               sequences[i].setDatasetSequence(ds);
2121             }
2122             else
2123             {
2124               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2125             }
2126           }
2127           else
2128           {
2129             // copy and derive new dataset sequence
2130             sequences[i] = sequences[i].deriveSequence();
2131             alignment.getDataset().addSequence(
2132                     sequences[i].getDatasetSequence());
2133             // TODO: avoid creation of duplicate dataset sequences with a
2134             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2135           }
2136           alignment.addSequence(sequences[i]); // merges dataset
2137         }
2138         if (newDs != null)
2139         {
2140           newDs.clear(); // tidy up
2141         }
2142         if (alignment.getAlignmentAnnotation() != null)
2143         {
2144           for (AlignmentAnnotation alan : alignment
2145                   .getAlignmentAnnotation())
2146           {
2147             if (alan.graphGroup > fgroup)
2148             {
2149               fgroup = alan.graphGroup;
2150             }
2151           }
2152         }
2153         if (pastedal.getAlignmentAnnotation() != null)
2154         {
2155           // Add any annotation attached to alignment.
2156           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2157           for (int i = 0; i < alann.length; i++)
2158           {
2159             annotationAdded = true;
2160             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2161             {
2162               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2163               if (newann.graphGroup > -1)
2164               {
2165                 if (newGraphGroups.size() <= newann.graphGroup
2166                         || newGraphGroups.get(newann.graphGroup) == null)
2167                 {
2168                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2169                   {
2170                     newGraphGroups.add(q, null);
2171                   }
2172                   newGraphGroups.set(newann.graphGroup, new Integer(
2173                           ++fgroup));
2174                 }
2175                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2176                         .intValue();
2177               }
2178
2179               newann.padAnnotation(alwidth);
2180               alignment.addAnnotation(newann);
2181             }
2182           }
2183         }
2184       }
2185       if (!newAlignment)
2186       {
2187         // /////
2188         // ADD HISTORY ITEM
2189         //
2190         addHistoryItem(new EditCommand(
2191                 MessageManager.getString("label.add_sequences"),
2192                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2193       }
2194       // Add any annotations attached to sequences
2195       for (int i = 0; i < sequences.length; i++)
2196       {
2197         if (sequences[i].getAnnotation() != null)
2198         {
2199           AlignmentAnnotation newann;
2200           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2201           {
2202             annotationAdded = true;
2203             newann = sequences[i].getAnnotation()[a];
2204             newann.adjustForAlignment();
2205             newann.padAnnotation(alwidth);
2206             if (newann.graphGroup > -1)
2207             {
2208               if (newann.graphGroup > -1)
2209               {
2210                 if (newGraphGroups.size() <= newann.graphGroup
2211                         || newGraphGroups.get(newann.graphGroup) == null)
2212                 {
2213                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2214                   {
2215                     newGraphGroups.add(q, null);
2216                   }
2217                   newGraphGroups.set(newann.graphGroup, new Integer(
2218                           ++fgroup));
2219                 }
2220                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2221                         .intValue();
2222               }
2223             }
2224             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2225             // was
2226             // duplicated
2227             // earlier
2228             alignment
2229                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2230           }
2231         }
2232       }
2233       if (!newAlignment)
2234       {
2235
2236         // propagate alignment changed.
2237         vpRanges.setEndSeq(alignment.getHeight());
2238         if (annotationAdded)
2239         {
2240           // Duplicate sequence annotation in all views.
2241           AlignmentI[] alview = this.getViewAlignments();
2242           for (int i = 0; i < sequences.length; i++)
2243           {
2244             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2245             if (sann == null)
2246             {
2247               continue;
2248             }
2249             for (int avnum = 0; avnum < alview.length; avnum++)
2250             {
2251               if (alview[avnum] != alignment)
2252               {
2253                 // duplicate in a view other than the one with input focus
2254                 int avwidth = alview[avnum].getWidth() + 1;
2255                 // this relies on sann being preserved after we
2256                 // modify the sequence's annotation array for each duplication
2257                 for (int a = 0; a < sann.length; a++)
2258                 {
2259                   AlignmentAnnotation newann = new AlignmentAnnotation(
2260                           sann[a]);
2261                   sequences[i].addAlignmentAnnotation(newann);
2262                   newann.padAnnotation(avwidth);
2263                   alview[avnum].addAnnotation(newann); // annotation was
2264                   // duplicated earlier
2265                   // TODO JAL-1145 graphGroups are not updated for sequence
2266                   // annotation added to several views. This may cause
2267                   // strangeness
2268                   alview[avnum].setAnnotationIndex(newann, a);
2269                 }
2270               }
2271             }
2272           }
2273           buildSortByAnnotationScoresMenu();
2274         }
2275         viewport.firePropertyChange("alignment", null,
2276                 alignment.getSequences());
2277         if (alignPanels != null)
2278         {
2279           for (AlignmentPanel ap : alignPanels)
2280           {
2281             ap.validateAnnotationDimensions(false);
2282           }
2283         }
2284         else
2285         {
2286           alignPanel.validateAnnotationDimensions(false);
2287         }
2288
2289       }
2290       else
2291       {
2292         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2293                 DEFAULT_HEIGHT);
2294         String newtitle = new String("Copied sequences");
2295
2296         if (Desktop.jalviewClipboard != null
2297                 && Desktop.jalviewClipboard[2] != null)
2298         {
2299           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2300           for (int[] region : hc)
2301           {
2302             af.viewport.hideColumns(region[0], region[1]);
2303           }
2304         }
2305
2306         // >>>This is a fix for the moment, until a better solution is
2307         // found!!<<<
2308         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2309                 .transferSettings(
2310                         alignPanel.getSeqPanel().seqCanvas
2311                                 .getFeatureRenderer());
2312
2313         // TODO: maintain provenance of an alignment, rather than just make the
2314         // title a concatenation of operations.
2315         if (!externalPaste)
2316         {
2317           if (title.startsWith("Copied sequences"))
2318           {
2319             newtitle = title;
2320           }
2321           else
2322           {
2323             newtitle = newtitle.concat("- from " + title);
2324           }
2325         }
2326         else
2327         {
2328           newtitle = new String("Pasted sequences");
2329         }
2330
2331         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2332                 DEFAULT_HEIGHT);
2333
2334       }
2335
2336     } catch (Exception ex)
2337     {
2338       ex.printStackTrace();
2339       System.out.println("Exception whilst pasting: " + ex);
2340       // could be anything being pasted in here
2341     }
2342   }
2343
2344   @Override
2345   protected void expand_newalign(ActionEvent e)
2346   {
2347     try
2348     {
2349       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2350               .getAlignment(), -1);
2351       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2352               DEFAULT_HEIGHT);
2353       String newtitle = new String("Flanking alignment");
2354
2355       if (Desktop.jalviewClipboard != null
2356               && Desktop.jalviewClipboard[2] != null)
2357       {
2358         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2359         for (int region[] : hc)
2360         {
2361           af.viewport.hideColumns(region[0], region[1]);
2362         }
2363       }
2364
2365       // >>>This is a fix for the moment, until a better solution is
2366       // found!!<<<
2367       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2368               .transferSettings(
2369                       alignPanel.getSeqPanel().seqCanvas
2370                               .getFeatureRenderer());
2371
2372       // TODO: maintain provenance of an alignment, rather than just make the
2373       // title a concatenation of operations.
2374       {
2375         if (title.startsWith("Copied sequences"))
2376         {
2377           newtitle = title;
2378         }
2379         else
2380         {
2381           newtitle = newtitle.concat("- from " + title);
2382         }
2383       }
2384
2385       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2386
2387     } catch (Exception ex)
2388     {
2389       ex.printStackTrace();
2390       System.out.println("Exception whilst pasting: " + ex);
2391       // could be anything being pasted in here
2392     } catch (OutOfMemoryError oom)
2393     {
2394       new OOMWarning("Viewing flanking region of alignment", oom);
2395     }
2396   }
2397
2398   /**
2399    * DOCUMENT ME!
2400    *
2401    * @param e
2402    *          DOCUMENT ME!
2403    */
2404   @Override
2405   protected void cut_actionPerformed(ActionEvent e)
2406   {
2407     copy_actionPerformed(null);
2408     delete_actionPerformed(null);
2409   }
2410
2411   /**
2412    * DOCUMENT ME!
2413    *
2414    * @param e
2415    *          DOCUMENT ME!
2416    */
2417   @Override
2418   protected void delete_actionPerformed(ActionEvent evt)
2419   {
2420
2421     SequenceGroup sg = viewport.getSelectionGroup();
2422     if (sg == null)
2423     {
2424       return;
2425     }
2426
2427     /*
2428      * If the cut affects all sequences, warn, remove highlighted columns
2429      */
2430     if (sg.getSize() == viewport.getAlignment().getHeight())
2431     {
2432       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2433               .getAlignment().getWidth()) ? true : false;
2434       if (isEntireAlignWidth)
2435       {
2436         int confirm = JvOptionPane.showConfirmDialog(this,
2437                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2438                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2439                 JvOptionPane.OK_CANCEL_OPTION);
2440
2441         if (confirm == JvOptionPane.CANCEL_OPTION
2442                 || confirm == JvOptionPane.CLOSED_OPTION)
2443         {
2444           return;
2445         }
2446       }
2447       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2448               sg.getEndRes() + 1);
2449     }
2450     SequenceI[] cut = sg.getSequences()
2451             .toArray(new SequenceI[sg.getSize()]);
2452
2453     addHistoryItem(new EditCommand(
2454             MessageManager.getString("label.cut_sequences"), Action.CUT,
2455             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2456             viewport.getAlignment()));
2457
2458     viewport.setSelectionGroup(null);
2459     viewport.sendSelection();
2460     viewport.getAlignment().deleteGroup(sg);
2461
2462     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2463             .getSequences());
2464     if (viewport.getAlignment().getHeight() < 1)
2465     {
2466       try
2467       {
2468         this.setClosed(true);
2469       } catch (Exception ex)
2470       {
2471       }
2472     }
2473   }
2474
2475   /**
2476    * DOCUMENT ME!
2477    *
2478    * @param e
2479    *          DOCUMENT ME!
2480    */
2481   @Override
2482   protected void deleteGroups_actionPerformed(ActionEvent e)
2483   {
2484     if (avc.deleteGroups())
2485     {
2486       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2487       alignPanel.updateAnnotation();
2488       alignPanel.paintAlignment(true);
2489     }
2490   }
2491
2492   /**
2493    * DOCUMENT ME!
2494    *
2495    * @param e
2496    *          DOCUMENT ME!
2497    */
2498   @Override
2499   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2500   {
2501     SequenceGroup sg = new SequenceGroup();
2502
2503     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2504     {
2505       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2506     }
2507
2508     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2509     viewport.setSelectionGroup(sg);
2510     viewport.sendSelection();
2511     // JAL-2034 - should delegate to
2512     // alignPanel to decide if overview needs
2513     // updating.
2514     alignPanel.paintAlignment(false);
2515     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2516   }
2517
2518   /**
2519    * DOCUMENT ME!
2520    *
2521    * @param e
2522    *          DOCUMENT ME!
2523    */
2524   @Override
2525   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2526   {
2527     if (viewport.cursorMode)
2528     {
2529       alignPanel.getSeqPanel().keyboardNo1 = null;
2530       alignPanel.getSeqPanel().keyboardNo2 = null;
2531     }
2532     viewport.setSelectionGroup(null);
2533     viewport.getColumnSelection().clear();
2534     viewport.setSelectionGroup(null);
2535     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2536     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2537     // JAL-2034 - should delegate to
2538     // alignPanel to decide if overview needs
2539     // updating.
2540     alignPanel.paintAlignment(false);
2541     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2542     viewport.sendSelection();
2543   }
2544
2545   /**
2546    * DOCUMENT ME!
2547    *
2548    * @param e
2549    *          DOCUMENT ME!
2550    */
2551   @Override
2552   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2553   {
2554     SequenceGroup sg = viewport.getSelectionGroup();
2555
2556     if (sg == null)
2557     {
2558       selectAllSequenceMenuItem_actionPerformed(null);
2559
2560       return;
2561     }
2562
2563     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2564     {
2565       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2566     }
2567     // JAL-2034 - should delegate to
2568     // alignPanel to decide if overview needs
2569     // updating.
2570
2571     alignPanel.paintAlignment(true);
2572     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2573     viewport.sendSelection();
2574   }
2575
2576   @Override
2577   public void invertColSel_actionPerformed(ActionEvent e)
2578   {
2579     viewport.invertColumnSelection();
2580     alignPanel.paintAlignment(true);
2581     viewport.sendSelection();
2582   }
2583
2584   /**
2585    * DOCUMENT ME!
2586    *
2587    * @param e
2588    *          DOCUMENT ME!
2589    */
2590   @Override
2591   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2592   {
2593     trimAlignment(true);
2594   }
2595
2596   /**
2597    * DOCUMENT ME!
2598    *
2599    * @param e
2600    *          DOCUMENT ME!
2601    */
2602   @Override
2603   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2604   {
2605     trimAlignment(false);
2606   }
2607
2608   void trimAlignment(boolean trimLeft)
2609   {
2610     ColumnSelection colSel = viewport.getColumnSelection();
2611     int column;
2612
2613     if (!colSel.isEmpty())
2614     {
2615       if (trimLeft)
2616       {
2617         column = colSel.getMin();
2618       }
2619       else
2620       {
2621         column = colSel.getMax();
2622       }
2623
2624       SequenceI[] seqs;
2625       if (viewport.getSelectionGroup() != null)
2626       {
2627         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2628                 viewport.getHiddenRepSequences());
2629       }
2630       else
2631       {
2632         seqs = viewport.getAlignment().getSequencesArray();
2633       }
2634
2635       TrimRegionCommand trimRegion;
2636       if (trimLeft)
2637       {
2638         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2639                 column, viewport.getAlignment());
2640         vpRanges.setStartRes(0);
2641       }
2642       else
2643       {
2644         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2645                 column, viewport.getAlignment());
2646       }
2647
2648       statusBar.setText(MessageManager.formatMessage(
2649               "label.removed_columns",
2650               new String[] { Integer.valueOf(trimRegion.getSize())
2651                       .toString() }));
2652
2653       addHistoryItem(trimRegion);
2654
2655       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2656       {
2657         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2658                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2659         {
2660           viewport.getAlignment().deleteGroup(sg);
2661         }
2662       }
2663
2664       viewport.firePropertyChange("alignment", null, viewport
2665               .getAlignment().getSequences());
2666     }
2667   }
2668
2669   /**
2670    * DOCUMENT ME!
2671    *
2672    * @param e
2673    *          DOCUMENT ME!
2674    */
2675   @Override
2676   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2677   {
2678     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2679
2680     SequenceI[] seqs;
2681     if (viewport.getSelectionGroup() != null)
2682     {
2683       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2684               viewport.getHiddenRepSequences());
2685       start = viewport.getSelectionGroup().getStartRes();
2686       end = viewport.getSelectionGroup().getEndRes();
2687     }
2688     else
2689     {
2690       seqs = viewport.getAlignment().getSequencesArray();
2691     }
2692
2693     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2694             "Remove Gapped Columns", seqs, start, end,
2695             viewport.getAlignment());
2696
2697     addHistoryItem(removeGapCols);
2698
2699     statusBar.setText(MessageManager.formatMessage(
2700             "label.removed_empty_columns",
2701             new Object[] { Integer.valueOf(removeGapCols.getSize())
2702                     .toString() }));
2703
2704     // This is to maintain viewport position on first residue
2705     // of first sequence
2706     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2707     int startRes = seq.findPosition(vpRanges.getStartRes());
2708     // ShiftList shifts;
2709     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2710     // edit.alColumnChanges=shifts.getInverse();
2711     // if (viewport.hasHiddenColumns)
2712     // viewport.getColumnSelection().compensateForEdits(shifts);
2713     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2714     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2715             .getSequences());
2716
2717   }
2718
2719   /**
2720    * DOCUMENT ME!
2721    *
2722    * @param e
2723    *          DOCUMENT ME!
2724    */
2725   @Override
2726   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2727   {
2728     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2729
2730     SequenceI[] seqs;
2731     if (viewport.getSelectionGroup() != null)
2732     {
2733       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2734               viewport.getHiddenRepSequences());
2735       start = viewport.getSelectionGroup().getStartRes();
2736       end = viewport.getSelectionGroup().getEndRes();
2737     }
2738     else
2739     {
2740       seqs = viewport.getAlignment().getSequencesArray();
2741     }
2742
2743     // This is to maintain viewport position on first residue
2744     // of first sequence
2745     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2746     int startRes = seq.findPosition(vpRanges.getStartRes());
2747
2748     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2749             viewport.getAlignment()));
2750
2751     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2752
2753     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2754             .getSequences());
2755
2756   }
2757
2758   /**
2759    * DOCUMENT ME!
2760    *
2761    * @param e
2762    *          DOCUMENT ME!
2763    */
2764   @Override
2765   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2766   {
2767     viewport.setPadGaps(padGapsMenuitem.isSelected());
2768     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2769             .getSequences());
2770   }
2771
2772   /**
2773    * DOCUMENT ME!
2774    *
2775    * @param e
2776    *          DOCUMENT ME!
2777    */
2778   @Override
2779   public void findMenuItem_actionPerformed(ActionEvent e)
2780   {
2781     new Finder();
2782   }
2783
2784   /**
2785    * Create a new view of the current alignment.
2786    */
2787   @Override
2788   public void newView_actionPerformed(ActionEvent e)
2789   {
2790     newView(null, true);
2791   }
2792
2793   /**
2794    * Creates and shows a new view of the current alignment.
2795    *
2796    * @param viewTitle
2797    *          title of newly created view; if null, one will be generated
2798    * @param copyAnnotation
2799    *          if true then duplicate all annnotation, groups and settings
2800    * @return new alignment panel, already displayed.
2801    */
2802   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2803   {
2804     /*
2805      * Create a new AlignmentPanel (with its own, new Viewport)
2806      */
2807     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2808             true);
2809     if (!copyAnnotation)
2810     {
2811       /*
2812        * remove all groups and annotation except for the automatic stuff
2813        */
2814       newap.av.getAlignment().deleteAllGroups();
2815       newap.av.getAlignment().deleteAllAnnotations(false);
2816     }
2817
2818     newap.av.setGatherViewsHere(false);
2819
2820     if (viewport.viewName == null)
2821     {
2822       viewport.viewName = MessageManager
2823               .getString("label.view_name_original");
2824     }
2825
2826     /*
2827      * Views share the same edits undo and redo stacks
2828      */
2829     newap.av.setHistoryList(viewport.getHistoryList());
2830     newap.av.setRedoList(viewport.getRedoList());
2831
2832     /*
2833      * Views share the same mappings; need to deregister any new mappings
2834      * created by copyAlignPanel, and register the new reference to the shared
2835      * mappings
2836      */
2837     newap.av.replaceMappings(viewport.getAlignment());
2838
2839     /*
2840      * start up cDNA consensus (if applicable) now mappings are in place
2841      */
2842     if (newap.av.initComplementConsensus())
2843     {
2844       newap.refresh(true); // adjust layout of annotations
2845     }
2846
2847     newap.av.viewName = getNewViewName(viewTitle);
2848
2849     addAlignmentPanel(newap, true);
2850     newap.alignmentChanged();
2851
2852     if (alignPanels.size() == 2)
2853     {
2854       viewport.setGatherViewsHere(true);
2855     }
2856     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2857     return newap;
2858   }
2859
2860   /**
2861    * Make a new name for the view, ensuring it is unique within the current
2862    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2863    * these now use viewId. Unique view names are still desirable for usability.)
2864    *
2865    * @param viewTitle
2866    * @return
2867    */
2868   protected String getNewViewName(String viewTitle)
2869   {
2870     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2871     boolean addFirstIndex = false;
2872     if (viewTitle == null || viewTitle.trim().length() == 0)
2873     {
2874       viewTitle = MessageManager.getString("action.view");
2875       addFirstIndex = true;
2876     }
2877     else
2878     {
2879       index = 1;// we count from 1 if given a specific name
2880     }
2881     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2882
2883     List<Component> comps = PaintRefresher.components.get(viewport
2884             .getSequenceSetId());
2885
2886     List<String> existingNames = getExistingViewNames(comps);
2887
2888     while (existingNames.contains(newViewName))
2889     {
2890       newViewName = viewTitle + " " + (++index);
2891     }
2892     return newViewName;
2893   }
2894
2895   /**
2896    * Returns a list of distinct view names found in the given list of
2897    * components. View names are held on the viewport of an AlignmentPanel.
2898    *
2899    * @param comps
2900    * @return
2901    */
2902   protected List<String> getExistingViewNames(List<Component> comps)
2903   {
2904     List<String> existingNames = new ArrayList<>();
2905     for (Component comp : comps)
2906     {
2907       if (comp instanceof AlignmentPanel)
2908       {
2909         AlignmentPanel ap = (AlignmentPanel) comp;
2910         if (!existingNames.contains(ap.av.viewName))
2911         {
2912           existingNames.add(ap.av.viewName);
2913         }
2914       }
2915     }
2916     return existingNames;
2917   }
2918
2919   /**
2920    * Explode tabbed views into separate windows.
2921    */
2922   @Override
2923   public void expandViews_actionPerformed(ActionEvent e)
2924   {
2925     Desktop.explodeViews(this);
2926   }
2927
2928   /**
2929    * Gather views in separate windows back into a tabbed presentation.
2930    */
2931   @Override
2932   public void gatherViews_actionPerformed(ActionEvent e)
2933   {
2934     Desktop.instance.gatherViews(this);
2935   }
2936
2937   /**
2938    * DOCUMENT ME!
2939    *
2940    * @param e
2941    *          DOCUMENT ME!
2942    */
2943   @Override
2944   public void font_actionPerformed(ActionEvent e)
2945   {
2946     new FontChooser(alignPanel);
2947   }
2948
2949   /**
2950    * DOCUMENT ME!
2951    *
2952    * @param e
2953    *          DOCUMENT ME!
2954    */
2955   @Override
2956   protected void seqLimit_actionPerformed(ActionEvent e)
2957   {
2958     viewport.setShowJVSuffix(seqLimits.isSelected());
2959
2960     alignPanel.getIdPanel().getIdCanvas()
2961             .setPreferredSize(alignPanel.calculateIdWidth());
2962     alignPanel.paintAlignment(true);
2963   }
2964
2965   @Override
2966   public void idRightAlign_actionPerformed(ActionEvent e)
2967   {
2968     viewport.setRightAlignIds(idRightAlign.isSelected());
2969     alignPanel.paintAlignment(true);
2970   }
2971
2972   @Override
2973   public void centreColumnLabels_actionPerformed(ActionEvent e)
2974   {
2975     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2976     alignPanel.paintAlignment(true);
2977   }
2978
2979   /*
2980    * (non-Javadoc)
2981    *
2982    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2983    */
2984   @Override
2985   protected void followHighlight_actionPerformed()
2986   {
2987     /*
2988      * Set the 'follow' flag on the Viewport (and scroll to position if now
2989      * true).
2990      */
2991     final boolean state = this.followHighlightMenuItem.getState();
2992     viewport.setFollowHighlight(state);
2993     if (state)
2994     {
2995       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2996     }
2997   }
2998
2999   /**
3000    * DOCUMENT ME!
3001    *
3002    * @param e
3003    *          DOCUMENT ME!
3004    */
3005   @Override
3006   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3007   {
3008     viewport.setColourText(colourTextMenuItem.isSelected());
3009     alignPanel.paintAlignment(true);
3010   }
3011
3012   /**
3013    * DOCUMENT ME!
3014    *
3015    * @param e
3016    *          DOCUMENT ME!
3017    */
3018   @Override
3019   public void wrapMenuItem_actionPerformed(ActionEvent e)
3020   {
3021     scaleAbove.setVisible(wrapMenuItem.isSelected());
3022     scaleLeft.setVisible(wrapMenuItem.isSelected());
3023     scaleRight.setVisible(wrapMenuItem.isSelected());
3024     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3025     alignPanel.updateLayout();
3026   }
3027
3028   @Override
3029   public void showAllSeqs_actionPerformed(ActionEvent e)
3030   {
3031     viewport.showAllHiddenSeqs();
3032   }
3033
3034   @Override
3035   public void showAllColumns_actionPerformed(ActionEvent e)
3036   {
3037     viewport.showAllHiddenColumns();
3038     repaint();
3039     viewport.sendSelection();
3040   }
3041
3042   @Override
3043   public void hideSelSequences_actionPerformed(ActionEvent e)
3044   {
3045     viewport.hideAllSelectedSeqs();
3046     // alignPanel.paintAlignment(true);
3047   }
3048
3049   /**
3050    * called by key handler and the hide all/show all menu items
3051    *
3052    * @param toggleSeqs
3053    * @param toggleCols
3054    */
3055   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3056   {
3057
3058     boolean hide = false;
3059     SequenceGroup sg = viewport.getSelectionGroup();
3060     if (!toggleSeqs && !toggleCols)
3061     {
3062       // Hide everything by the current selection - this is a hack - we do the
3063       // invert and then hide
3064       // first check that there will be visible columns after the invert.
3065       if (viewport.hasSelectedColumns()
3066               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3067                       .getEndRes()))
3068       {
3069         // now invert the sequence set, if required - empty selection implies
3070         // that no hiding is required.
3071         if (sg != null)
3072         {
3073           invertSequenceMenuItem_actionPerformed(null);
3074           sg = viewport.getSelectionGroup();
3075           toggleSeqs = true;
3076
3077         }
3078         viewport.expandColSelection(sg, true);
3079         // finally invert the column selection and get the new sequence
3080         // selection.
3081         invertColSel_actionPerformed(null);
3082         toggleCols = true;
3083       }
3084     }
3085
3086     if (toggleSeqs)
3087     {
3088       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3089       {
3090         hideSelSequences_actionPerformed(null);
3091         hide = true;
3092       }
3093       else if (!(toggleCols && viewport.hasSelectedColumns()))
3094       {
3095         showAllSeqs_actionPerformed(null);
3096       }
3097     }
3098
3099     if (toggleCols)
3100     {
3101       if (viewport.hasSelectedColumns())
3102       {
3103         hideSelColumns_actionPerformed(null);
3104         if (!toggleSeqs)
3105         {
3106           viewport.setSelectionGroup(sg);
3107         }
3108       }
3109       else if (!hide)
3110       {
3111         showAllColumns_actionPerformed(null);
3112       }
3113     }
3114   }
3115
3116   /*
3117    * (non-Javadoc)
3118    *
3119    * @see
3120    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3121    * event.ActionEvent)
3122    */
3123   @Override
3124   public void hideAllButSelection_actionPerformed(ActionEvent e)
3125   {
3126     toggleHiddenRegions(false, false);
3127     viewport.sendSelection();
3128   }
3129
3130   /*
3131    * (non-Javadoc)
3132    *
3133    * @see
3134    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3135    * .ActionEvent)
3136    */
3137   @Override
3138   public void hideAllSelection_actionPerformed(ActionEvent e)
3139   {
3140     SequenceGroup sg = viewport.getSelectionGroup();
3141     viewport.expandColSelection(sg, false);
3142     viewport.hideAllSelectedSeqs();
3143     viewport.hideSelectedColumns();
3144     alignPanel.paintAlignment(true);
3145     viewport.sendSelection();
3146   }
3147
3148   /*
3149    * (non-Javadoc)
3150    *
3151    * @see
3152    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3153    * ActionEvent)
3154    */
3155   @Override
3156   public void showAllhidden_actionPerformed(ActionEvent e)
3157   {
3158     viewport.showAllHiddenColumns();
3159     viewport.showAllHiddenSeqs();
3160     alignPanel.paintAlignment(true);
3161     viewport.sendSelection();
3162   }
3163
3164   @Override
3165   public void hideSelColumns_actionPerformed(ActionEvent e)
3166   {
3167     viewport.hideSelectedColumns();
3168     alignPanel.paintAlignment(true);
3169     viewport.sendSelection();
3170   }
3171
3172   @Override
3173   public void hiddenMarkers_actionPerformed(ActionEvent e)
3174   {
3175     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3176     repaint();
3177   }
3178
3179   /**
3180    * DOCUMENT ME!
3181    *
3182    * @param e
3183    *          DOCUMENT ME!
3184    */
3185   @Override
3186   protected void scaleAbove_actionPerformed(ActionEvent e)
3187   {
3188     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3189     alignPanel.paintAlignment(true);
3190   }
3191
3192   /**
3193    * DOCUMENT ME!
3194    *
3195    * @param e
3196    *          DOCUMENT ME!
3197    */
3198   @Override
3199   protected void scaleLeft_actionPerformed(ActionEvent e)
3200   {
3201     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3202     alignPanel.paintAlignment(true);
3203   }
3204
3205   /**
3206    * DOCUMENT ME!
3207    *
3208    * @param e
3209    *          DOCUMENT ME!
3210    */
3211   @Override
3212   protected void scaleRight_actionPerformed(ActionEvent e)
3213   {
3214     viewport.setScaleRightWrapped(scaleRight.isSelected());
3215     alignPanel.paintAlignment(true);
3216   }
3217
3218   /**
3219    * DOCUMENT ME!
3220    *
3221    * @param e
3222    *          DOCUMENT ME!
3223    */
3224   @Override
3225   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3226   {
3227     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3228     alignPanel.paintAlignment(true);
3229   }
3230
3231   /**
3232    * DOCUMENT ME!
3233    *
3234    * @param e
3235    *          DOCUMENT ME!
3236    */
3237   @Override
3238   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3239   {
3240     viewport.setShowText(viewTextMenuItem.isSelected());
3241     alignPanel.paintAlignment(true);
3242   }
3243
3244   /**
3245    * DOCUMENT ME!
3246    *
3247    * @param e
3248    *          DOCUMENT ME!
3249    */
3250   @Override
3251   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3252   {
3253     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3254     alignPanel.paintAlignment(true);
3255   }
3256
3257   public FeatureSettings featureSettings;
3258
3259   @Override
3260   public FeatureSettingsControllerI getFeatureSettingsUI()
3261   {
3262     return featureSettings;
3263   }
3264
3265   @Override
3266   public void featureSettings_actionPerformed(ActionEvent e)
3267   {
3268     if (featureSettings != null)
3269     {
3270       featureSettings.close();
3271       featureSettings = null;
3272     }
3273     if (!showSeqFeatures.isSelected())
3274     {
3275       // make sure features are actually displayed
3276       showSeqFeatures.setSelected(true);
3277       showSeqFeatures_actionPerformed(null);
3278     }
3279     featureSettings = new FeatureSettings(this);
3280   }
3281
3282   /**
3283    * Set or clear 'Show Sequence Features'
3284    *
3285    * @param evt
3286    *          DOCUMENT ME!
3287    */
3288   @Override
3289   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3290   {
3291     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3292     alignPanel.paintAlignment(true);
3293     if (alignPanel.getOverviewPanel() != null)
3294     {
3295       alignPanel.getOverviewPanel().updateOverviewImage();
3296     }
3297   }
3298
3299   /**
3300    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3301    * the annotations panel as a whole.
3302    *
3303    * The options to show/hide all annotations should be enabled when the panel
3304    * is shown, and disabled when the panel is hidden.
3305    *
3306    * @param e
3307    */
3308   @Override
3309   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3310   {
3311     final boolean setVisible = annotationPanelMenuItem.isSelected();
3312     viewport.setShowAnnotation(setVisible);
3313     this.showAllSeqAnnotations.setEnabled(setVisible);
3314     this.hideAllSeqAnnotations.setEnabled(setVisible);
3315     this.showAllAlAnnotations.setEnabled(setVisible);
3316     this.hideAllAlAnnotations.setEnabled(setVisible);
3317     alignPanel.updateLayout();
3318   }
3319
3320   @Override
3321   public void alignmentProperties()
3322   {
3323     JEditorPane editPane = new JEditorPane("text/html", "");
3324     editPane.setEditable(false);
3325     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3326             .formatAsHtml();
3327     editPane.setText(MessageManager.formatMessage("label.html_content",
3328             new Object[] { contents.toString() }));
3329     JInternalFrame frame = new JInternalFrame();
3330     frame.getContentPane().add(new JScrollPane(editPane));
3331
3332     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3333             "label.alignment_properties", new Object[] { getTitle() }),
3334             500, 400);
3335   }
3336
3337   /**
3338    * DOCUMENT ME!
3339    *
3340    * @param e
3341    *          DOCUMENT ME!
3342    */
3343   @Override
3344   public void overviewMenuItem_actionPerformed(ActionEvent e)
3345   {
3346     if (alignPanel.overviewPanel != null)
3347     {
3348       return;
3349     }
3350
3351     JInternalFrame frame = new JInternalFrame();
3352     OverviewPanel overview = new OverviewPanel(alignPanel);
3353     frame.setContentPane(overview);
3354     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3355             "label.overview_params", new Object[] { this.getTitle() }),
3356             true, frame.getWidth(), frame.getHeight(), true, true);
3357     frame.pack();
3358     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3359     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3360     {
3361       @Override
3362       public void internalFrameClosed(
3363               javax.swing.event.InternalFrameEvent evt)
3364       {
3365         alignPanel.setOverviewPanel(null);
3366       };
3367     });
3368
3369     alignPanel.setOverviewPanel(overview);
3370   }
3371
3372   @Override
3373   public void textColour_actionPerformed()
3374   {
3375     new TextColourChooser().chooseColour(alignPanel, null);
3376   }
3377
3378   /*
3379    * public void covariationColour_actionPerformed() {
3380    * changeColour(new
3381    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3382    * ()[0])); }
3383    */
3384   @Override
3385   public void annotationColour_actionPerformed()
3386   {
3387     new AnnotationColourChooser(viewport, alignPanel);
3388   }
3389
3390   @Override
3391   public void annotationColumn_actionPerformed(ActionEvent e)
3392   {
3393     new AnnotationColumnChooser(viewport, alignPanel);
3394   }
3395
3396   /**
3397    * Action on the user checking or unchecking the option to apply the selected
3398    * colour scheme to all groups. If unchecked, groups may have their own
3399    * independent colour schemes.
3400    *
3401    * @param selected
3402    */
3403   @Override
3404   public void applyToAllGroups_actionPerformed(boolean selected)
3405   {
3406     viewport.setColourAppliesToAllGroups(selected);
3407   }
3408
3409   /**
3410    * Action on user selecting a colour from the colour menu
3411    *
3412    * @param name
3413    *          the name (not the menu item label!) of the colour scheme
3414    */
3415   @Override
3416   public void changeColour_actionPerformed(String name)
3417   {
3418     /*
3419      * 'User Defined' opens a panel to configure or load a
3420      * user-defined colour scheme
3421      */
3422     if (ResidueColourScheme.USER_DEFINED.equals(name))
3423     {
3424       new UserDefinedColours(alignPanel);
3425       return;
3426     }
3427
3428     /*
3429      * otherwise set the chosen colour scheme (or null for 'None')
3430      */
3431     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3432             viewport.getAlignment(), viewport.getHiddenRepSequences());
3433     changeColour(cs);
3434   }
3435
3436   /**
3437    * Actions on setting or changing the alignment colour scheme
3438    *
3439    * @param cs
3440    */
3441   @Override
3442   public void changeColour(ColourSchemeI cs)
3443   {
3444     // TODO: pull up to controller method
3445     ColourMenuHelper.setColourSelected(colourMenu, cs);
3446
3447     viewport.setGlobalColourScheme(cs);
3448
3449     alignPanel.paintAlignment(true);
3450   }
3451
3452   /**
3453    * Show the PID threshold slider panel
3454    */
3455   @Override
3456   protected void modifyPID_actionPerformed()
3457   {
3458     SliderPanel.setPIDSliderSource(alignPanel,
3459             viewport.getResidueShading(), alignPanel.getViewName());
3460     SliderPanel.showPIDSlider();
3461   }
3462
3463   /**
3464    * Show the Conservation slider panel
3465    */
3466   @Override
3467   protected void modifyConservation_actionPerformed()
3468   {
3469     SliderPanel.setConservationSlider(alignPanel,
3470             viewport.getResidueShading(), alignPanel.getViewName());
3471     SliderPanel.showConservationSlider();
3472   }
3473
3474   /**
3475    * Action on selecting or deselecting (Colour) By Conservation
3476    */
3477   @Override
3478   public void conservationMenuItem_actionPerformed(boolean selected)
3479   {
3480     modifyConservation.setEnabled(selected);
3481     viewport.setConservationSelected(selected);
3482     viewport.getResidueShading().setConservationApplied(selected);
3483
3484     changeColour(viewport.getGlobalColourScheme());
3485     if (selected)
3486     {
3487       modifyConservation_actionPerformed();
3488     }
3489     else
3490     {
3491       SliderPanel.hideConservationSlider();
3492     }
3493   }
3494
3495   /**
3496    * Action on selecting or deselecting (Colour) Above PID Threshold
3497    */
3498   @Override
3499   public void abovePIDThreshold_actionPerformed(boolean selected)
3500   {
3501     modifyPID.setEnabled(selected);
3502     viewport.setAbovePIDThreshold(selected);
3503     if (!selected)
3504     {
3505       viewport.getResidueShading().setThreshold(0,
3506               viewport.isIgnoreGapsConsensus());
3507     }
3508
3509     changeColour(viewport.getGlobalColourScheme());
3510     if (selected)
3511     {
3512       modifyPID_actionPerformed();
3513     }
3514     else
3515     {
3516       SliderPanel.hidePIDSlider();
3517     }
3518   }
3519
3520   /**
3521    * DOCUMENT ME!
3522    *
3523    * @param e
3524    *          DOCUMENT ME!
3525    */
3526   @Override
3527   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3528   {
3529     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3530     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3531             .getAlignment().getSequenceAt(0));
3532     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3533             viewport.getAlignment()));
3534     alignPanel.paintAlignment(true);
3535   }
3536
3537   /**
3538    * DOCUMENT ME!
3539    *
3540    * @param e
3541    *          DOCUMENT ME!
3542    */
3543   @Override
3544   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3545   {
3546     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3547     AlignmentSorter.sortByID(viewport.getAlignment());
3548     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3549             viewport.getAlignment()));
3550     alignPanel.paintAlignment(true);
3551   }
3552
3553   /**
3554    * DOCUMENT ME!
3555    *
3556    * @param e
3557    *          DOCUMENT ME!
3558    */
3559   @Override
3560   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3561   {
3562     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3563     AlignmentSorter.sortByLength(viewport.getAlignment());
3564     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3565             viewport.getAlignment()));
3566     alignPanel.paintAlignment(true);
3567   }
3568
3569   /**
3570    * DOCUMENT ME!
3571    *
3572    * @param e
3573    *          DOCUMENT ME!
3574    */
3575   @Override
3576   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3577   {
3578     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3579     AlignmentSorter.sortByGroup(viewport.getAlignment());
3580     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3581             viewport.getAlignment()));
3582
3583     alignPanel.paintAlignment(true);
3584   }
3585
3586   /**
3587    * DOCUMENT ME!
3588    *
3589    * @param e
3590    *          DOCUMENT ME!
3591    */
3592   @Override
3593   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3594   {
3595     new RedundancyPanel(alignPanel, this);
3596   }
3597
3598   /**
3599    * DOCUMENT ME!
3600    *
3601    * @param e
3602    *          DOCUMENT ME!
3603    */
3604   @Override
3605   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3606   {
3607     if ((viewport.getSelectionGroup() == null)
3608             || (viewport.getSelectionGroup().getSize() < 2))
3609     {
3610       JvOptionPane.showInternalMessageDialog(this, MessageManager
3611               .getString("label.you_must_select_least_two_sequences"),
3612               MessageManager.getString("label.invalid_selection"),
3613               JvOptionPane.WARNING_MESSAGE);
3614     }
3615     else
3616     {
3617       JInternalFrame frame = new JInternalFrame();
3618       frame.setContentPane(new PairwiseAlignPanel(viewport));
3619       Desktop.addInternalFrame(frame,
3620               MessageManager.getString("action.pairwise_alignment"), 600,
3621               500);
3622     }
3623   }
3624
3625   @Override
3626   public void autoCalculate_actionPerformed(ActionEvent e)
3627   {
3628     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3629     if (viewport.autoCalculateConsensus)
3630     {
3631       viewport.firePropertyChange("alignment", null, viewport
3632               .getAlignment().getSequences());
3633     }
3634   }
3635
3636   @Override
3637   public void sortByTreeOption_actionPerformed(ActionEvent e)
3638   {
3639     viewport.sortByTree = sortByTree.isSelected();
3640   }
3641
3642   @Override
3643   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3644   {
3645     viewport.followSelection = listenToViewSelections.isSelected();
3646   }
3647
3648   /**
3649    * Constructs a tree panel and adds it to the desktop
3650    *
3651    * @param type
3652    *          tree type (NJ or AV)
3653    * @param modelName
3654    *          name of score model used to compute the tree
3655    * @param options
3656    *          parameters for the distance or similarity calculation
3657    */
3658   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3659   {
3660     String frameTitle = "";
3661     TreePanel tp;
3662
3663     boolean onSelection = false;
3664     if (viewport.getSelectionGroup() != null
3665             && viewport.getSelectionGroup().getSize() > 0)
3666     {
3667       SequenceGroup sg = viewport.getSelectionGroup();
3668
3669       /* Decide if the selection is a column region */
3670       for (SequenceI _s : sg.getSequences())
3671       {
3672         if (_s.getLength() < sg.getEndRes())
3673         {
3674           JvOptionPane
3675                   .showMessageDialog(
3676                           Desktop.desktop,
3677                           MessageManager
3678                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3679                           MessageManager
3680                                   .getString("label.sequences_selection_not_aligned"),
3681                           JvOptionPane.WARNING_MESSAGE);
3682
3683           return;
3684         }
3685       }
3686       onSelection = true;
3687     }
3688     else
3689     {
3690       if (viewport.getAlignment().getHeight() < 2)
3691       {
3692         return;
3693       }
3694     }
3695
3696     tp = new TreePanel(alignPanel, type, modelName, options);
3697     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3698
3699     frameTitle += " from ";
3700
3701     if (viewport.viewName != null)
3702     {
3703       frameTitle += viewport.viewName + " of ";
3704     }
3705
3706     frameTitle += this.title;
3707
3708     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3709   }
3710
3711   /**
3712    * DOCUMENT ME!
3713    *
3714    * @param title
3715    *          DOCUMENT ME!
3716    * @param order
3717    *          DOCUMENT ME!
3718    */
3719   public void addSortByOrderMenuItem(String title,
3720           final AlignmentOrder order)
3721   {
3722     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3723             "action.by_title_param", new Object[] { title }));
3724     sort.add(item);
3725     item.addActionListener(new java.awt.event.ActionListener()
3726     {
3727       @Override
3728       public void actionPerformed(ActionEvent e)
3729       {
3730         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3731
3732         // TODO: JBPNote - have to map order entries to curent SequenceI
3733         // pointers
3734         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3735
3736         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3737                 .getAlignment()));
3738
3739         alignPanel.paintAlignment(true);
3740       }
3741     });
3742   }
3743
3744   /**
3745    * Add a new sort by annotation score menu item
3746    *
3747    * @param sort
3748    *          the menu to add the option to
3749    * @param scoreLabel
3750    *          the label used to retrieve scores for each sequence on the
3751    *          alignment
3752    */
3753   public void addSortByAnnotScoreMenuItem(JMenu sort,
3754           final String scoreLabel)
3755   {
3756     final JMenuItem item = new JMenuItem(scoreLabel);
3757     sort.add(item);
3758     item.addActionListener(new java.awt.event.ActionListener()
3759     {
3760       @Override
3761       public void actionPerformed(ActionEvent e)
3762       {
3763         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3764         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3765                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3766         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3767                 viewport.getAlignment()));
3768         alignPanel.paintAlignment(true);
3769       }
3770     });
3771   }
3772
3773   /**
3774    * last hash for alignment's annotation array - used to minimise cost of
3775    * rebuild.
3776    */
3777   protected int _annotationScoreVectorHash;
3778
3779   /**
3780    * search the alignment and rebuild the sort by annotation score submenu the
3781    * last alignment annotation vector hash is stored to minimize cost of
3782    * rebuilding in subsequence calls.
3783    *
3784    */
3785   @Override
3786   public void buildSortByAnnotationScoresMenu()
3787   {
3788     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3789     {
3790       return;
3791     }
3792
3793     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3794     {
3795       sortByAnnotScore.removeAll();
3796       // almost certainly a quicker way to do this - but we keep it simple
3797       Hashtable scoreSorts = new Hashtable();
3798       AlignmentAnnotation aann[];
3799       for (SequenceI sqa : viewport.getAlignment().getSequences())
3800       {
3801         aann = sqa.getAnnotation();
3802         for (int i = 0; aann != null && i < aann.length; i++)
3803         {
3804           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3805           {
3806             scoreSorts.put(aann[i].label, aann[i].label);
3807           }
3808         }
3809       }
3810       Enumeration labels = scoreSorts.keys();
3811       while (labels.hasMoreElements())
3812       {
3813         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3814                 (String) labels.nextElement());
3815       }
3816       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3817       scoreSorts.clear();
3818
3819       _annotationScoreVectorHash = viewport.getAlignment()
3820               .getAlignmentAnnotation().hashCode();
3821     }
3822   }
3823
3824   /**
3825    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3826    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3827    * call. Listeners are added to remove the menu item when the treePanel is
3828    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3829    * modified.
3830    */
3831   @Override
3832   public void buildTreeSortMenu()
3833   {
3834     sortByTreeMenu.removeAll();
3835
3836     List<Component> comps = PaintRefresher.components.get(viewport
3837             .getSequenceSetId());
3838     List<TreePanel> treePanels = new ArrayList<>();
3839     for (Component comp : comps)
3840     {
3841       if (comp instanceof TreePanel)
3842       {
3843         treePanels.add((TreePanel) comp);
3844       }
3845     }
3846
3847     if (treePanels.size() < 1)
3848     {
3849       sortByTreeMenu.setVisible(false);
3850       return;
3851     }
3852
3853     sortByTreeMenu.setVisible(true);
3854
3855     for (final TreePanel tp : treePanels)
3856     {
3857       final JMenuItem item = new JMenuItem(tp.getTitle());
3858       item.addActionListener(new java.awt.event.ActionListener()
3859       {
3860         @Override
3861         public void actionPerformed(ActionEvent e)
3862         {
3863           tp.sortByTree_actionPerformed();
3864           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3865
3866         }
3867       });
3868
3869       sortByTreeMenu.add(item);
3870     }
3871   }
3872
3873   public boolean sortBy(AlignmentOrder alorder, String undoname)
3874   {
3875     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3876     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3877     if (undoname != null)
3878     {
3879       addHistoryItem(new OrderCommand(undoname, oldOrder,
3880               viewport.getAlignment()));
3881     }
3882     alignPanel.paintAlignment(true);
3883     return true;
3884   }
3885
3886   /**
3887    * Work out whether the whole set of sequences or just the selected set will
3888    * be submitted for multiple alignment.
3889    *
3890    */
3891   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3892   {
3893     // Now, check we have enough sequences
3894     AlignmentView msa = null;
3895
3896     if ((viewport.getSelectionGroup() != null)
3897             && (viewport.getSelectionGroup().getSize() > 1))
3898     {
3899       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3900       // some common interface!
3901       /*
3902        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3903        * SequenceI[sz = seqs.getSize(false)];
3904        *
3905        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3906        * seqs.getSequenceAt(i); }
3907        */
3908       msa = viewport.getAlignmentView(true);
3909     }
3910     else if (viewport.getSelectionGroup() != null
3911             && viewport.getSelectionGroup().getSize() == 1)
3912     {
3913       int option = JvOptionPane.showConfirmDialog(this,
3914               MessageManager.getString("warn.oneseq_msainput_selection"),
3915               MessageManager.getString("label.invalid_selection"),
3916               JvOptionPane.OK_CANCEL_OPTION);
3917       if (option == JvOptionPane.OK_OPTION)
3918       {
3919         msa = viewport.getAlignmentView(false);
3920       }
3921     }
3922     else
3923     {
3924       msa = viewport.getAlignmentView(false);
3925     }
3926     return msa;
3927   }
3928
3929   /**
3930    * Decides what is submitted to a secondary structure prediction service: the
3931    * first sequence in the alignment, or in the current selection, or, if the
3932    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3933    * region or the whole alignment. (where the first sequence in the set is the
3934    * one that the prediction will be for).
3935    */
3936   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3937   {
3938     AlignmentView seqs = null;
3939
3940     if ((viewport.getSelectionGroup() != null)
3941             && (viewport.getSelectionGroup().getSize() > 0))
3942     {
3943       seqs = viewport.getAlignmentView(true);
3944     }
3945     else
3946     {
3947       seqs = viewport.getAlignmentView(false);
3948     }
3949     // limit sequences - JBPNote in future - could spawn multiple prediction
3950     // jobs
3951     // TODO: viewport.getAlignment().isAligned is a global state - the local
3952     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3953     if (!viewport.getAlignment().isAligned(false))
3954     {
3955       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3956       // TODO: if seqs.getSequences().length>1 then should really have warned
3957       // user!
3958
3959     }
3960     return seqs;
3961   }
3962
3963   /**
3964    * DOCUMENT ME!
3965    *
3966    * @param e
3967    *          DOCUMENT ME!
3968    */
3969   @Override
3970   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3971   {
3972     // Pick the tree file
3973     JalviewFileChooser chooser = new JalviewFileChooser(
3974             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3975     chooser.setFileView(new JalviewFileView());
3976     chooser.setDialogTitle(MessageManager
3977             .getString("label.select_newick_like_tree_file"));
3978     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3979
3980     int value = chooser.showOpenDialog(null);
3981
3982     if (value == JalviewFileChooser.APPROVE_OPTION)
3983     {
3984       String filePath = chooser.getSelectedFile().getPath();
3985       Cache.setProperty("LAST_DIRECTORY", filePath);
3986       NewickFile fin = null;
3987       try
3988       {
3989         fin = new NewickFile(filePath, DataSourceType.FILE);
3990         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3991       } catch (Exception ex)
3992       {
3993         JvOptionPane
3994                 .showMessageDialog(
3995                         Desktop.desktop,
3996                         ex.getMessage(),
3997                         MessageManager
3998                                 .getString("label.problem_reading_tree_file"),
3999                         JvOptionPane.WARNING_MESSAGE);
4000         ex.printStackTrace();
4001       }
4002       if (fin != null && fin.hasWarningMessage())
4003       {
4004         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4005                 .getWarningMessage(), MessageManager
4006                 .getString("label.possible_problem_with_tree_file"),
4007                 JvOptionPane.WARNING_MESSAGE);
4008       }
4009     }
4010   }
4011
4012   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4013   {
4014     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4015   }
4016
4017   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4018           int h, int x, int y)
4019   {
4020     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4021   }
4022
4023   /**
4024    * Add a treeviewer for the tree extracted from a Newick file object to the
4025    * current alignment view
4026    *
4027    * @param nf
4028    *          the tree
4029    * @param title
4030    *          tree viewer title
4031    * @param input
4032    *          Associated alignment input data (or null)
4033    * @param w
4034    *          width
4035    * @param h
4036    *          height
4037    * @param x
4038    *          position
4039    * @param y
4040    *          position
4041    * @return TreePanel handle
4042    */
4043   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4044           AlignmentView input, int w, int h, int x, int y)
4045   {
4046     TreePanel tp = null;
4047
4048     try
4049     {
4050       nf.parse();
4051
4052       if (nf.getTree() != null)
4053       {
4054         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4055
4056         tp.setSize(w, h);
4057
4058         if (x > 0 && y > 0)
4059         {
4060           tp.setLocation(x, y);
4061         }
4062
4063         Desktop.addInternalFrame(tp, treeTitle, w, h);
4064       }
4065     } catch (Exception ex)
4066     {
4067       ex.printStackTrace();
4068     }
4069
4070     return tp;
4071   }
4072
4073   private boolean buildingMenu = false;
4074
4075   /**
4076    * Generates menu items and listener event actions for web service clients
4077    *
4078    */
4079   public void BuildWebServiceMenu()
4080   {
4081     while (buildingMenu)
4082     {
4083       try
4084       {
4085         System.err.println("Waiting for building menu to finish.");
4086         Thread.sleep(10);
4087       } catch (Exception e)
4088       {
4089       }
4090     }
4091     final AlignFrame me = this;
4092     buildingMenu = true;
4093     new Thread(new Runnable()
4094     {
4095       @Override
4096       public void run()
4097       {
4098         final List<JMenuItem> legacyItems = new ArrayList<>();
4099         try
4100         {
4101           // System.err.println("Building ws menu again "
4102           // + Thread.currentThread());
4103           // TODO: add support for context dependent disabling of services based
4104           // on
4105           // alignment and current selection
4106           // TODO: add additional serviceHandle parameter to specify abstract
4107           // handler
4108           // class independently of AbstractName
4109           // TODO: add in rediscovery GUI function to restart discoverer
4110           // TODO: group services by location as well as function and/or
4111           // introduce
4112           // object broker mechanism.
4113           final Vector<JMenu> wsmenu = new Vector<>();
4114           final IProgressIndicator af = me;
4115
4116           /*
4117            * do not i18n these strings - they are hard-coded in class
4118            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4119            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4120            */
4121           final JMenu msawsmenu = new JMenu("Alignment");
4122           final JMenu secstrmenu = new JMenu(
4123                   "Secondary Structure Prediction");
4124           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4125           final JMenu analymenu = new JMenu("Analysis");
4126           final JMenu dismenu = new JMenu("Protein Disorder");
4127           // JAL-940 - only show secondary structure prediction services from
4128           // the legacy server
4129           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4130               // &&
4131           Discoverer.services != null && (Discoverer.services.size() > 0))
4132           {
4133             // TODO: refactor to allow list of AbstractName/Handler bindings to
4134             // be
4135             // stored or retrieved from elsewhere
4136             // No MSAWS used any more:
4137             // Vector msaws = null; // (Vector)
4138             // Discoverer.services.get("MsaWS");
4139             Vector secstrpr = (Vector) Discoverer.services
4140                     .get("SecStrPred");
4141             if (secstrpr != null)
4142             {
4143               // Add any secondary structure prediction services
4144               for (int i = 0, j = secstrpr.size(); i < j; i++)
4145               {
4146                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4147                         .get(i);
4148                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4149                         .getServiceClient(sh);
4150                 int p = secstrmenu.getItemCount();
4151                 impl.attachWSMenuEntry(secstrmenu, me);
4152                 int q = secstrmenu.getItemCount();
4153                 for (int litm = p; litm < q; litm++)
4154                 {
4155                   legacyItems.add(secstrmenu.getItem(litm));
4156                 }
4157               }
4158             }
4159           }
4160
4161           // Add all submenus in the order they should appear on the web
4162           // services menu
4163           wsmenu.add(msawsmenu);
4164           wsmenu.add(secstrmenu);
4165           wsmenu.add(dismenu);
4166           wsmenu.add(analymenu);
4167           // No search services yet
4168           // wsmenu.add(seqsrchmenu);
4169
4170           javax.swing.SwingUtilities.invokeLater(new Runnable()
4171           {
4172             @Override
4173             public void run()
4174             {
4175               try
4176               {
4177                 webService.removeAll();
4178                 // first, add discovered services onto the webservices menu
4179                 if (wsmenu.size() > 0)
4180                 {
4181                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4182                   {
4183                     webService.add(wsmenu.get(i));
4184                   }
4185                 }
4186                 else
4187                 {
4188                   webService.add(me.webServiceNoServices);
4189                 }
4190                 // TODO: move into separate menu builder class.
4191                 boolean new_sspred = false;
4192                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4193                 {
4194                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4195                   if (jws2servs != null)
4196                   {
4197                     if (jws2servs.hasServices())
4198                     {
4199                       jws2servs.attachWSMenuEntry(webService, me);
4200                       for (Jws2Instance sv : jws2servs.getServices())
4201                       {
4202                         if (sv.description.toLowerCase().contains("jpred"))
4203                         {
4204                           for (JMenuItem jmi : legacyItems)
4205                           {
4206                             jmi.setVisible(false);
4207                           }
4208                         }
4209                       }
4210
4211                     }
4212                     if (jws2servs.isRunning())
4213                     {
4214                       JMenuItem tm = new JMenuItem(
4215                               "Still discovering JABA Services");
4216                       tm.setEnabled(false);
4217                       webService.add(tm);
4218                     }
4219                   }
4220                 }
4221                 build_urlServiceMenu(me.webService);
4222                 build_fetchdbmenu(webService);
4223                 for (JMenu item : wsmenu)
4224                 {
4225                   if (item.getItemCount() == 0)
4226                   {
4227                     item.setEnabled(false);
4228                   }
4229                   else
4230                   {
4231                     item.setEnabled(true);
4232                   }
4233                 }
4234               } catch (Exception e)
4235               {
4236                 Cache.log
4237                         .debug("Exception during web service menu building process.",
4238                                 e);
4239               }
4240             }
4241           });
4242         } catch (Exception e)
4243         {
4244         }
4245         buildingMenu = false;
4246       }
4247     }).start();
4248
4249   }
4250
4251   /**
4252    * construct any groupURL type service menu entries.
4253    *
4254    * @param webService
4255    */
4256   private void build_urlServiceMenu(JMenu webService)
4257   {
4258     // TODO: remove this code when 2.7 is released
4259     // DEBUG - alignmentView
4260     /*
4261      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4262      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4263      *
4264      * @Override public void actionPerformed(ActionEvent e) {
4265      * jalview.datamodel.AlignmentView
4266      * .testSelectionViews(af.viewport.getAlignment(),
4267      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4268      *
4269      * }); webService.add(testAlView);
4270      */
4271     // TODO: refactor to RestClient discoverer and merge menu entries for
4272     // rest-style services with other types of analysis/calculation service
4273     // SHmmr test client - still being implemented.
4274     // DEBUG - alignmentView
4275
4276     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4277             .getRestClients())
4278     {
4279       client.attachWSMenuEntry(
4280               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4281               this);
4282     }
4283   }
4284
4285   /**
4286    * Searches the alignment sequences for xRefs and builds the Show
4287    * Cross-References menu (formerly called Show Products), with database
4288    * sources for which cross-references are found (protein sources for a
4289    * nucleotide alignment and vice versa)
4290    *
4291    * @return true if Show Cross-references menu should be enabled
4292    */
4293   public boolean canShowProducts()
4294   {
4295     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4296     AlignmentI dataset = viewport.getAlignment().getDataset();
4297
4298     showProducts.removeAll();
4299     final boolean dna = viewport.getAlignment().isNucleotide();
4300
4301     if (seqs == null || seqs.length == 0)
4302     {
4303       // nothing to see here.
4304       return false;
4305     }
4306
4307     boolean showp = false;
4308     try
4309     {
4310       List<String> ptypes = new CrossRef(seqs, dataset)
4311               .findXrefSourcesForSequences(dna);
4312
4313       for (final String source : ptypes)
4314       {
4315         showp = true;
4316         final AlignFrame af = this;
4317         JMenuItem xtype = new JMenuItem(source);
4318         xtype.addActionListener(new ActionListener()
4319         {
4320           @Override
4321           public void actionPerformed(ActionEvent e)
4322           {
4323             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4324           }
4325         });
4326         showProducts.add(xtype);
4327       }
4328       showProducts.setVisible(showp);
4329       showProducts.setEnabled(showp);
4330     } catch (Exception e)
4331     {
4332       Cache.log
4333               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4334                       e);
4335       return false;
4336     }
4337     return showp;
4338   }
4339
4340   /**
4341    * Finds and displays cross-references for the selected sequences (protein
4342    * products for nucleotide sequences, dna coding sequences for peptides).
4343    *
4344    * @param sel
4345    *          the sequences to show cross-references for
4346    * @param dna
4347    *          true if from a nucleotide alignment (so showing proteins)
4348    * @param source
4349    *          the database to show cross-references for
4350    */
4351   protected void showProductsFor(final SequenceI[] sel,
4352           final boolean _odna, final String source)
4353   {
4354     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4355             .start();
4356   }
4357
4358   /**
4359    * Construct and display a new frame containing the translation of this
4360    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4361    */
4362   @Override
4363   public void showTranslation_actionPerformed(ActionEvent e)
4364   {
4365     AlignmentI al = null;
4366     try
4367     {
4368       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4369
4370       al = dna.translateCdna();
4371     } catch (Exception ex)
4372     {
4373       jalview.bin.Cache.log.error(
4374               "Exception during translation. Please report this !", ex);
4375       final String msg = MessageManager
4376               .getString("label.error_when_translating_sequences_submit_bug_report");
4377       final String errorTitle = MessageManager
4378               .getString("label.implementation_error")
4379               + MessageManager.getString("label.translation_failed");
4380       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4381               JvOptionPane.ERROR_MESSAGE);
4382       return;
4383     }
4384     if (al == null || al.getHeight() == 0)
4385     {
4386       final String msg = MessageManager
4387               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4388       final String errorTitle = MessageManager
4389               .getString("label.translation_failed");
4390       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4391               JvOptionPane.WARNING_MESSAGE);
4392     }
4393     else
4394     {
4395       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4396       af.setFileFormat(this.currentFileFormat);
4397       final String newTitle = MessageManager.formatMessage(
4398               "label.translation_of_params",
4399               new Object[] { this.getTitle() });
4400       af.setTitle(newTitle);
4401       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4402       {
4403         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4404         viewport.openSplitFrame(af, new Alignment(seqs));
4405       }
4406       else
4407       {
4408         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4409                 DEFAULT_HEIGHT);
4410       }
4411     }
4412   }
4413
4414   /**
4415    * Set the file format
4416    *
4417    * @param format
4418    */
4419   public void setFileFormat(FileFormatI format)
4420   {
4421     this.currentFileFormat = format;
4422   }
4423
4424   /**
4425    * Try to load a features file onto the alignment.
4426    *
4427    * @param file
4428    *          contents or path to retrieve file
4429    * @param sourceType
4430    *          access mode of file (see jalview.io.AlignFile)
4431    * @return true if features file was parsed correctly.
4432    */
4433   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4434   {
4435     return avc.parseFeaturesFile(file, sourceType,
4436             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4437
4438   }
4439
4440   @Override
4441   public void refreshFeatureUI(boolean enableIfNecessary)
4442   {
4443     // note - currently this is only still here rather than in the controller
4444     // because of the featureSettings hard reference that is yet to be
4445     // abstracted
4446     if (enableIfNecessary)
4447     {
4448       viewport.setShowSequenceFeatures(true);
4449       showSeqFeatures.setSelected(true);
4450     }
4451
4452   }
4453
4454   @Override
4455   public void dragEnter(DropTargetDragEvent evt)
4456   {
4457   }
4458
4459   @Override
4460   public void dragExit(DropTargetEvent evt)
4461   {
4462   }
4463
4464   @Override
4465   public void dragOver(DropTargetDragEvent evt)
4466   {
4467   }
4468
4469   @Override
4470   public void dropActionChanged(DropTargetDragEvent evt)
4471   {
4472   }
4473
4474   @Override
4475   public void drop(DropTargetDropEvent evt)
4476   {
4477     // JAL-1552 - acceptDrop required before getTransferable call for
4478     // Java's Transferable for native dnd
4479     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4480     Transferable t = evt.getTransferable();
4481     List<String> files = new ArrayList<>();
4482     List<DataSourceType> protocols = new ArrayList<>();
4483
4484     try
4485     {
4486       Desktop.transferFromDropTarget(files, protocols, evt, t);
4487     } catch (Exception e)
4488     {
4489       e.printStackTrace();
4490     }
4491     if (files != null)
4492     {
4493       try
4494       {
4495         // check to see if any of these files have names matching sequences in
4496         // the alignment
4497         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4498                 .getAlignment().getSequencesArray());
4499         /**
4500          * Object[] { String,SequenceI}
4501          */
4502         ArrayList<Object[]> filesmatched = new ArrayList<>();
4503         ArrayList<String> filesnotmatched = new ArrayList<>();
4504         for (int i = 0; i < files.size(); i++)
4505         {
4506           String file = files.get(i).toString();
4507           String pdbfn = "";
4508           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4509           if (protocol == DataSourceType.FILE)
4510           {
4511             File fl = new File(file);
4512             pdbfn = fl.getName();
4513           }
4514           else if (protocol == DataSourceType.URL)
4515           {
4516             URL url = new URL(file);
4517             pdbfn = url.getFile();
4518           }
4519           if (pdbfn.length() > 0)
4520           {
4521             // attempt to find a match in the alignment
4522             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4523             int l = 0, c = pdbfn.indexOf(".");
4524             while (mtch == null && c != -1)
4525             {
4526               do
4527               {
4528                 l = c;
4529               } while ((c = pdbfn.indexOf(".", l)) > l);
4530               if (l > -1)
4531               {
4532                 pdbfn = pdbfn.substring(0, l);
4533               }
4534               mtch = idm.findAllIdMatches(pdbfn);
4535             }
4536             if (mtch != null)
4537             {
4538               FileFormatI type = null;
4539               try
4540               {
4541                 type = new IdentifyFile().identify(file, protocol);
4542               } catch (Exception ex)
4543               {
4544                 type = null;
4545               }
4546               if (type != null && type.isStructureFile())
4547               {
4548                 filesmatched.add(new Object[] { file, protocol, mtch });
4549                 continue;
4550               }
4551             }
4552             // File wasn't named like one of the sequences or wasn't a PDB file.
4553             filesnotmatched.add(file);
4554           }
4555         }
4556         int assocfiles = 0;
4557         if (filesmatched.size() > 0)
4558         {
4559           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4560                   || JvOptionPane
4561                           .showConfirmDialog(
4562                                   this,
4563                                   MessageManager
4564                                           .formatMessage(
4565                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4566                                                   new Object[] { Integer
4567                                                           .valueOf(
4568                                                                   filesmatched
4569                                                                           .size())
4570                                                           .toString() }),
4571                                   MessageManager
4572                                           .getString("label.automatically_associate_structure_files_by_name"),
4573                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4574
4575           {
4576             for (Object[] fm : filesmatched)
4577             {
4578               // try and associate
4579               // TODO: may want to set a standard ID naming formalism for
4580               // associating PDB files which have no IDs.
4581               for (SequenceI toassoc : (SequenceI[]) fm[2])
4582               {
4583                 PDBEntry pe = new AssociatePdbFileWithSeq()
4584                         .associatePdbWithSeq((String) fm[0],
4585                                 (DataSourceType) fm[1], toassoc, false,
4586                                 Desktop.instance);
4587                 if (pe != null)
4588                 {
4589                   System.err.println("Associated file : "
4590                           + ((String) fm[0]) + " with "
4591                           + toassoc.getDisplayId(true));
4592                   assocfiles++;
4593                 }
4594               }
4595               alignPanel.paintAlignment(true);
4596             }
4597           }
4598         }
4599         if (filesnotmatched.size() > 0)
4600         {
4601           if (assocfiles > 0
4602                   && (Cache.getDefault(
4603                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4604                           .showConfirmDialog(
4605                                   this,
4606                                   "<html>"
4607                                           + MessageManager
4608                                                   .formatMessage(
4609                                                           "label.ignore_unmatched_dropped_files_info",
4610                                                           new Object[] { Integer
4611                                                                   .valueOf(
4612                                                                           filesnotmatched
4613                                                                                   .size())
4614                                                                   .toString() })
4615                                           + "</html>",
4616                                   MessageManager
4617                                           .getString("label.ignore_unmatched_dropped_files"),
4618                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4619           {
4620             return;
4621           }
4622           for (String fn : filesnotmatched)
4623           {
4624             loadJalviewDataFile(fn, null, null, null);
4625           }
4626
4627         }
4628       } catch (Exception ex)
4629       {
4630         ex.printStackTrace();
4631       }
4632     }
4633   }
4634
4635   /**
4636    * Attempt to load a "dropped" file or URL string, by testing in turn for
4637    * <ul>
4638    * <li>an Annotation file</li>
4639    * <li>a JNet file</li>
4640    * <li>a features file</li>
4641    * <li>else try to interpret as an alignment file</li>
4642    * </ul>
4643    *
4644    * @param file
4645    *          either a filename or a URL string.
4646    * @throws InterruptedException
4647    * @throws IOException
4648    */
4649   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4650           FileFormatI format, SequenceI assocSeq)
4651   {
4652     try
4653     {
4654       if (sourceType == null)
4655       {
4656         sourceType = FormatAdapter.checkProtocol(file);
4657       }
4658       // if the file isn't identified, or not positively identified as some
4659       // other filetype (PFAM is default unidentified alignment file type) then
4660       // try to parse as annotation.
4661       boolean isAnnotation = (format == null || FileFormat.Pfam
4662               .equals(format)) ? new AnnotationFile()
4663               .annotateAlignmentView(viewport, file, sourceType) : false;
4664
4665       if (!isAnnotation)
4666       {
4667         // first see if its a T-COFFEE score file
4668         TCoffeeScoreFile tcf = null;
4669         try
4670         {
4671           tcf = new TCoffeeScoreFile(file, sourceType);
4672           if (tcf.isValid())
4673           {
4674             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4675             {
4676               buildColourMenu();
4677               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4678               isAnnotation = true;
4679               statusBar
4680                       .setText(MessageManager
4681                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4682             }
4683             else
4684             {
4685               // some problem - if no warning its probable that the ID matching
4686               // process didn't work
4687               JvOptionPane
4688                       .showMessageDialog(
4689                               Desktop.desktop,
4690                               tcf.getWarningMessage() == null ? MessageManager
4691                                       .getString("label.check_file_matches_sequence_ids_alignment")
4692                                       : tcf.getWarningMessage(),
4693                               MessageManager
4694                                       .getString("label.problem_reading_tcoffee_score_file"),
4695                               JvOptionPane.WARNING_MESSAGE);
4696             }
4697           }
4698           else
4699           {
4700             tcf = null;
4701           }
4702         } catch (Exception x)
4703         {
4704           Cache.log
4705                   .debug("Exception when processing data source as T-COFFEE score file",
4706                           x);
4707           tcf = null;
4708         }
4709         if (tcf == null)
4710         {
4711           // try to see if its a JNet 'concise' style annotation file *before*
4712           // we
4713           // try to parse it as a features file
4714           if (format == null)
4715           {
4716             format = new IdentifyFile().identify(file, sourceType);
4717           }
4718           if (FileFormat.ScoreMatrix == format)
4719           {
4720             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4721                     sourceType));
4722             sm.parse();
4723             // todo: i18n this message
4724             statusBar
4725                     .setText(MessageManager.formatMessage(
4726                             "label.successfully_loaded_matrix",
4727                             sm.getMatrixName()));
4728           }
4729           else if (FileFormat.Jnet.equals(format))
4730           {
4731             JPredFile predictions = new JPredFile(file, sourceType);
4732             new JnetAnnotationMaker();
4733             JnetAnnotationMaker.add_annotation(predictions,
4734                     viewport.getAlignment(), 0, false);
4735             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4736             viewport.getAlignment().setSeqrep(repseq);
4737             HiddenColumns cs = new HiddenColumns();
4738             cs.hideInsertionsFor(repseq);
4739             viewport.getAlignment().setHiddenColumns(cs);
4740             isAnnotation = true;
4741           }
4742           // else if (IdentifyFile.FeaturesFile.equals(format))
4743           else if (FileFormat.Features.equals(format))
4744           {
4745             if (parseFeaturesFile(file, sourceType))
4746             {
4747               alignPanel.paintAlignment(true);
4748             }
4749           }
4750           else
4751           {
4752             new FileLoader().LoadFile(viewport, file, sourceType, format);
4753           }
4754         }
4755       }
4756       if (isAnnotation)
4757       {
4758         alignPanel.adjustAnnotationHeight();
4759         viewport.updateSequenceIdColours();
4760         buildSortByAnnotationScoresMenu();
4761         alignPanel.paintAlignment(true);
4762       }
4763     } catch (Exception ex)
4764     {
4765       ex.printStackTrace();
4766     } catch (OutOfMemoryError oom)
4767     {
4768       try
4769       {
4770         System.gc();
4771       } catch (Exception x)
4772       {
4773       }
4774       new OOMWarning(
4775               "loading data "
4776                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4777                               : "using " + sourceType + " from " + file)
4778                               : ".")
4779                       + (format != null ? "(parsing as '" + format
4780                               + "' file)" : ""), oom, Desktop.desktop);
4781     }
4782   }
4783
4784   /**
4785    * Method invoked by the ChangeListener on the tabbed pane, in other words
4786    * when a different tabbed pane is selected by the user or programmatically.
4787    */
4788   @Override
4789   public void tabSelectionChanged(int index)
4790   {
4791     if (index > -1)
4792     {
4793       alignPanel = alignPanels.get(index);
4794       viewport = alignPanel.av;
4795       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4796       setMenusFromViewport(viewport);
4797     }
4798
4799     /*
4800      * 'focus' any colour slider that is open to the selected viewport
4801      */
4802     if (viewport.getConservationSelected())
4803     {
4804       SliderPanel.setConservationSlider(alignPanel,
4805               viewport.getResidueShading(), alignPanel.getViewName());
4806     }
4807     else
4808     {
4809       SliderPanel.hideConservationSlider();
4810     }
4811     if (viewport.getAbovePIDThreshold())
4812     {
4813       SliderPanel.setPIDSliderSource(alignPanel,
4814               viewport.getResidueShading(), alignPanel.getViewName());
4815     }
4816     else
4817     {
4818       SliderPanel.hidePIDSlider();
4819     }
4820
4821     /*
4822      * If there is a frame linked to this one in a SplitPane, switch it to the
4823      * same view tab index. No infinite recursion of calls should happen, since
4824      * tabSelectionChanged() should not get invoked on setting the selected
4825      * index to an unchanged value. Guard against setting an invalid index
4826      * before the new view peer tab has been created.
4827      */
4828     final AlignViewportI peer = viewport.getCodingComplement();
4829     if (peer != null)
4830     {
4831       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4832       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4833       {
4834         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4835       }
4836     }
4837   }
4838
4839   /**
4840    * On right mouse click on view tab, prompt for and set new view name.
4841    */
4842   @Override
4843   public void tabbedPane_mousePressed(MouseEvent e)
4844   {
4845     if (e.isPopupTrigger())
4846     {
4847       String msg = MessageManager.getString("label.enter_view_name");
4848       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4849               JvOptionPane.QUESTION_MESSAGE);
4850
4851       if (reply != null)
4852       {
4853         viewport.viewName = reply;
4854         // TODO warn if reply is in getExistingViewNames()?
4855         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4856       }
4857     }
4858   }
4859
4860   public AlignViewport getCurrentView()
4861   {
4862     return viewport;
4863   }
4864
4865   /**
4866    * Open the dialog for regex description parsing.
4867    */
4868   @Override
4869   protected void extractScores_actionPerformed(ActionEvent e)
4870   {
4871     ParseProperties pp = new jalview.analysis.ParseProperties(
4872             viewport.getAlignment());
4873     // TODO: verify regex and introduce GUI dialog for version 2.5
4874     // if (pp.getScoresFromDescription("col", "score column ",
4875     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4876     // true)>0)
4877     if (pp.getScoresFromDescription("description column",
4878             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4879     {
4880       buildSortByAnnotationScoresMenu();
4881     }
4882   }
4883
4884   /*
4885    * (non-Javadoc)
4886    *
4887    * @see
4888    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4889    * )
4890    */
4891   @Override
4892   protected void showDbRefs_actionPerformed(ActionEvent e)
4893   {
4894     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4895   }
4896
4897   /*
4898    * (non-Javadoc)
4899    *
4900    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4901    * ActionEvent)
4902    */
4903   @Override
4904   protected void showNpFeats_actionPerformed(ActionEvent e)
4905   {
4906     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4907   }
4908
4909   /**
4910    * find the viewport amongst the tabs in this alignment frame and close that
4911    * tab
4912    *
4913    * @param av
4914    */
4915   public boolean closeView(AlignViewportI av)
4916   {
4917     if (viewport == av)
4918     {
4919       this.closeMenuItem_actionPerformed(false);
4920       return true;
4921     }
4922     Component[] comp = tabbedPane.getComponents();
4923     for (int i = 0; comp != null && i < comp.length; i++)
4924     {
4925       if (comp[i] instanceof AlignmentPanel)
4926       {
4927         if (((AlignmentPanel) comp[i]).av == av)
4928         {
4929           // close the view.
4930           closeView((AlignmentPanel) comp[i]);
4931           return true;
4932         }
4933       }
4934     }
4935     return false;
4936   }
4937
4938   protected void build_fetchdbmenu(JMenu webService)
4939   {
4940     // Temporary hack - DBRef Fetcher always top level ws entry.
4941     // TODO We probably want to store a sequence database checklist in
4942     // preferences and have checkboxes.. rather than individual sources selected
4943     // here
4944     final JMenu rfetch = new JMenu(
4945             MessageManager.getString("action.fetch_db_references"));
4946     rfetch.setToolTipText(MessageManager
4947             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4948     webService.add(rfetch);
4949
4950     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4951             MessageManager.getString("option.trim_retrieved_seqs"));
4952     trimrs.setToolTipText(MessageManager
4953             .getString("label.trim_retrieved_sequences"));
4954     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4955     trimrs.addActionListener(new ActionListener()
4956     {
4957       @Override
4958       public void actionPerformed(ActionEvent e)
4959       {
4960         trimrs.setSelected(trimrs.isSelected());
4961         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4962                 Boolean.valueOf(trimrs.isSelected()).toString());
4963       };
4964     });
4965     rfetch.add(trimrs);
4966     JMenuItem fetchr = new JMenuItem(
4967             MessageManager.getString("label.standard_databases"));
4968     fetchr.setToolTipText(MessageManager
4969             .getString("label.fetch_embl_uniprot"));
4970     fetchr.addActionListener(new ActionListener()
4971     {
4972
4973       @Override
4974       public void actionPerformed(ActionEvent e)
4975       {
4976         new Thread(new Runnable()
4977         {
4978           @Override
4979           public void run()
4980           {
4981             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4982                     .getAlignment().isNucleotide();
4983             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4984                     .getSequenceSelection(), alignPanel.alignFrame, null,
4985                     alignPanel.alignFrame.featureSettings, isNucleotide);
4986             dbRefFetcher.addListener(new FetchFinishedListenerI()
4987             {
4988               @Override
4989               public void finished()
4990               {
4991                 AlignFrame.this.setMenusForViewport();
4992               }
4993             });
4994             dbRefFetcher.fetchDBRefs(false);
4995           }
4996         }).start();
4997
4998       }
4999
5000     });
5001     rfetch.add(fetchr);
5002     final AlignFrame me = this;
5003     new Thread(new Runnable()
5004     {
5005       @Override
5006       public void run()
5007       {
5008         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5009                 .getSequenceFetcherSingleton(me);
5010         javax.swing.SwingUtilities.invokeLater(new Runnable()
5011         {
5012           @Override
5013           public void run()
5014           {
5015             String[] dbclasses = sf.getOrderedSupportedSources();
5016             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5017             // jalview.util.QuickSort.sort(otherdb, otherdb);
5018             List<DbSourceProxy> otherdb;
5019             JMenu dfetch = new JMenu();
5020             JMenu ifetch = new JMenu();
5021             JMenuItem fetchr = null;
5022             int comp = 0, icomp = 0, mcomp = 15;
5023             String mname = null;
5024             int dbi = 0;
5025             for (String dbclass : dbclasses)
5026             {
5027               otherdb = sf.getSourceProxy(dbclass);
5028               // add a single entry for this class, or submenu allowing 'fetch
5029               // all' or pick one
5030               if (otherdb == null || otherdb.size() < 1)
5031               {
5032                 continue;
5033               }
5034               // List<DbSourceProxy> dbs=otherdb;
5035               // otherdb=new ArrayList<DbSourceProxy>();
5036               // for (DbSourceProxy db:dbs)
5037               // {
5038               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5039               // }
5040               if (mname == null)
5041               {
5042                 mname = "From " + dbclass;
5043               }
5044               if (otherdb.size() == 1)
5045               {
5046                 final DbSourceProxy[] dassource = otherdb
5047                         .toArray(new DbSourceProxy[0]);
5048                 DbSourceProxy src = otherdb.get(0);
5049                 fetchr = new JMenuItem(src.getDbSource());
5050                 fetchr.addActionListener(new ActionListener()
5051                 {
5052
5053                   @Override
5054                   public void actionPerformed(ActionEvent e)
5055                   {
5056                     new Thread(new Runnable()
5057                     {
5058
5059                       @Override
5060                       public void run()
5061                       {
5062                         boolean isNucleotide = alignPanel.alignFrame
5063                                 .getViewport().getAlignment()
5064                                 .isNucleotide();
5065                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5066                                 alignPanel.av.getSequenceSelection(),
5067                                 alignPanel.alignFrame, dassource,
5068                                 alignPanel.alignFrame.featureSettings,
5069                                 isNucleotide);
5070                         dbRefFetcher
5071                                 .addListener(new FetchFinishedListenerI()
5072                                 {
5073                                   @Override
5074                                   public void finished()
5075                                   {
5076                                     AlignFrame.this.setMenusForViewport();
5077                                   }
5078                                 });
5079                         dbRefFetcher.fetchDBRefs(false);
5080                       }
5081                     }).start();
5082                   }
5083
5084                 });
5085                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5086                         MessageManager.formatMessage(
5087                                 "label.fetch_retrieve_from",
5088                                 new Object[] { src.getDbName() })));
5089                 dfetch.add(fetchr);
5090                 comp++;
5091               }
5092               else
5093               {
5094                 final DbSourceProxy[] dassource = otherdb
5095                         .toArray(new DbSourceProxy[0]);
5096                 // fetch all entry
5097                 DbSourceProxy src = otherdb.get(0);
5098                 fetchr = new JMenuItem(MessageManager.formatMessage(
5099                         "label.fetch_all_param",
5100                         new Object[] { src.getDbSource() }));
5101                 fetchr.addActionListener(new ActionListener()
5102                 {
5103                   @Override
5104                   public void actionPerformed(ActionEvent e)
5105                   {
5106                     new Thread(new Runnable()
5107                     {
5108
5109                       @Override
5110                       public void run()
5111                       {
5112                         boolean isNucleotide = alignPanel.alignFrame
5113                                 .getViewport().getAlignment()
5114                                 .isNucleotide();
5115                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5116                                 alignPanel.av.getSequenceSelection(),
5117                                 alignPanel.alignFrame, dassource,
5118                                 alignPanel.alignFrame.featureSettings,
5119                                 isNucleotide);
5120                         dbRefFetcher
5121                                 .addListener(new FetchFinishedListenerI()
5122                                 {
5123                                   @Override
5124                                   public void finished()
5125                                   {
5126                                     AlignFrame.this.setMenusForViewport();
5127                                   }
5128                                 });
5129                         dbRefFetcher.fetchDBRefs(false);
5130                       }
5131                     }).start();
5132                   }
5133                 });
5134
5135                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5136                         MessageManager.formatMessage(
5137                                 "label.fetch_retrieve_from_all_sources",
5138                                 new Object[] {
5139                                     Integer.valueOf(otherdb.size())
5140                                             .toString(), src.getDbSource(),
5141                                     src.getDbName() })));
5142                 dfetch.add(fetchr);
5143                 comp++;
5144                 // and then build the rest of the individual menus
5145                 ifetch = new JMenu(MessageManager.formatMessage(
5146                         "label.source_from_db_source",
5147                         new Object[] { src.getDbSource() }));
5148                 icomp = 0;
5149                 String imname = null;
5150                 int i = 0;
5151                 for (DbSourceProxy sproxy : otherdb)
5152                 {
5153                   String dbname = sproxy.getDbName();
5154                   String sname = dbname.length() > 5 ? dbname.substring(0,
5155                           5) + "..." : dbname;
5156                   String msname = dbname.length() > 10 ? dbname.substring(
5157                           0, 10) + "..." : dbname;
5158                   if (imname == null)
5159                   {
5160                     imname = MessageManager.formatMessage(
5161                             "label.from_msname", new Object[] { sname });
5162                   }
5163                   fetchr = new JMenuItem(msname);
5164                   final DbSourceProxy[] dassrc = { sproxy };
5165                   fetchr.addActionListener(new ActionListener()
5166                   {
5167
5168                     @Override
5169                     public void actionPerformed(ActionEvent e)
5170                     {
5171                       new Thread(new Runnable()
5172                       {
5173
5174                         @Override
5175                         public void run()
5176                         {
5177                           boolean isNucleotide = alignPanel.alignFrame
5178                                   .getViewport().getAlignment()
5179                                   .isNucleotide();
5180                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5181                                   alignPanel.av.getSequenceSelection(),
5182                                   alignPanel.alignFrame, dassrc,
5183                                   alignPanel.alignFrame.featureSettings,
5184                                   isNucleotide);
5185                           dbRefFetcher
5186                                   .addListener(new FetchFinishedListenerI()
5187                                   {
5188                                     @Override
5189                                     public void finished()
5190                                     {
5191                                       AlignFrame.this.setMenusForViewport();
5192                                     }
5193                                   });
5194                           dbRefFetcher.fetchDBRefs(false);
5195                         }
5196                       }).start();
5197                     }
5198
5199                   });
5200                   fetchr.setToolTipText("<html>"
5201                           + MessageManager.formatMessage(
5202                                   "label.fetch_retrieve_from", new Object[]
5203                                   { dbname }));
5204                   ifetch.add(fetchr);
5205                   ++i;
5206                   if (++icomp >= mcomp || i == (otherdb.size()))
5207                   {
5208                     ifetch.setText(MessageManager.formatMessage(
5209                             "label.source_to_target", imname, sname));
5210                     dfetch.add(ifetch);
5211                     ifetch = new JMenu();
5212                     imname = null;
5213                     icomp = 0;
5214                     comp++;
5215                   }
5216                 }
5217               }
5218               ++dbi;
5219               if (comp >= mcomp || dbi >= (dbclasses.length))
5220               {
5221                 dfetch.setText(MessageManager.formatMessage(
5222                         "label.source_to_target", mname, dbclass));
5223                 rfetch.add(dfetch);
5224                 dfetch = new JMenu();
5225                 mname = null;
5226                 comp = 0;
5227               }
5228             }
5229           }
5230         });
5231       }
5232     }).start();
5233
5234   }
5235
5236   /**
5237    * Left justify the whole alignment.
5238    */
5239   @Override
5240   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5241   {
5242     AlignmentI al = viewport.getAlignment();
5243     al.justify(false);
5244     viewport.firePropertyChange("alignment", null, al);
5245   }
5246
5247   /**
5248    * Right justify the whole alignment.
5249    */
5250   @Override
5251   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5252   {
5253     AlignmentI al = viewport.getAlignment();
5254     al.justify(true);
5255     viewport.firePropertyChange("alignment", null, al);
5256   }
5257
5258   @Override
5259   public void setShowSeqFeatures(boolean b)
5260   {
5261     showSeqFeatures.setSelected(b);
5262     viewport.setShowSequenceFeatures(b);
5263   }
5264
5265   /*
5266    * (non-Javadoc)
5267    *
5268    * @see
5269    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5270    * awt.event.ActionEvent)
5271    */
5272   @Override
5273   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5274   {
5275     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5276     alignPanel.paintAlignment(true);
5277   }
5278
5279   /*
5280    * (non-Javadoc)
5281    *
5282    * @see
5283    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5284    * .ActionEvent)
5285    */
5286   @Override
5287   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5288   {
5289     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5290     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5291
5292   }
5293
5294   /*
5295    * (non-Javadoc)
5296    *
5297    * @see
5298    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5299    * .event.ActionEvent)
5300    */
5301   @Override
5302   protected void showGroupConservation_actionPerformed(ActionEvent e)
5303   {
5304     viewport.setShowGroupConservation(showGroupConservation.getState());
5305     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5306   }
5307
5308   /*
5309    * (non-Javadoc)
5310    *
5311    * @see
5312    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5313    * .event.ActionEvent)
5314    */
5315   @Override
5316   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5317   {
5318     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5319     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5320   }
5321
5322   /*
5323    * (non-Javadoc)
5324    *
5325    * @see
5326    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5327    * .event.ActionEvent)
5328    */
5329   @Override
5330   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5331   {
5332     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5333     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5334   }
5335
5336   @Override
5337   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5338   {
5339     showSequenceLogo.setState(true);
5340     viewport.setShowSequenceLogo(true);
5341     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5342     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5343   }
5344
5345   @Override
5346   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5347   {
5348     viewport.setShowInformationHistogram(
5349             showInformationHistogram.getState());
5350     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5351   }
5352
5353   @Override
5354   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5355   {
5356     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5357     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5358   }
5359
5360   @Override
5361   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5362   {
5363     showHMMSequenceLogo.setState(true);
5364     viewport.setShowHMMSequenceLogo(true);
5365     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5366     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5367   }
5368
5369   @Override
5370   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5371   {
5372     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5373   }
5374
5375   /*
5376    * (non-Javadoc)
5377    *
5378    * @see
5379    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5380    * .event.ActionEvent)
5381    */
5382   @Override
5383   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5384   {
5385     if (avc.makeGroupsFromSelection())
5386     {
5387       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5388       alignPanel.updateAnnotation();
5389       alignPanel.paintAlignment(true);
5390     }
5391   }
5392
5393   public void clearAlignmentSeqRep()
5394   {
5395     // TODO refactor alignmentseqrep to controller
5396     if (viewport.getAlignment().hasSeqrep())
5397     {
5398       viewport.getAlignment().setSeqrep(null);
5399       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5400       alignPanel.updateAnnotation();
5401       alignPanel.paintAlignment(true);
5402     }
5403   }
5404
5405   @Override
5406   protected void createGroup_actionPerformed(ActionEvent e)
5407   {
5408     if (avc.createGroup())
5409     {
5410       alignPanel.alignmentChanged();
5411     }
5412   }
5413
5414   @Override
5415   protected void unGroup_actionPerformed(ActionEvent e)
5416   {
5417     if (avc.unGroup())
5418     {
5419       alignPanel.alignmentChanged();
5420     }
5421   }
5422
5423   /**
5424    * make the given alignmentPanel the currently selected tab
5425    *
5426    * @param alignmentPanel
5427    */
5428   public void setDisplayedView(AlignmentPanel alignmentPanel)
5429   {
5430     if (!viewport.getSequenceSetId().equals(
5431             alignmentPanel.av.getSequenceSetId()))
5432     {
5433       throw new Error(
5434               MessageManager
5435                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5436     }
5437     if (tabbedPane != null
5438             && tabbedPane.getTabCount() > 0
5439             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5440                     .getSelectedIndex())
5441     {
5442       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5443     }
5444   }
5445
5446   /**
5447    * Action on selection of menu options to Show or Hide annotations.
5448    *
5449    * @param visible
5450    * @param forSequences
5451    *          update sequence-related annotations
5452    * @param forAlignment
5453    *          update non-sequence-related annotations
5454    */
5455   @Override
5456   protected void setAnnotationsVisibility(boolean visible,
5457           boolean forSequences, boolean forAlignment)
5458   {
5459     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5460             .getAlignmentAnnotation();
5461     if (anns == null)
5462     {
5463       return;
5464     }
5465     for (AlignmentAnnotation aa : anns)
5466     {
5467       /*
5468        * don't display non-positional annotations on an alignment
5469        */
5470       if (aa.annotations == null)
5471       {
5472         continue;
5473       }
5474       boolean apply = (aa.sequenceRef == null && forAlignment)
5475               || (aa.sequenceRef != null && forSequences);
5476       if (apply)
5477       {
5478         aa.visible = visible;
5479       }
5480     }
5481     alignPanel.validateAnnotationDimensions(true);
5482     alignPanel.alignmentChanged();
5483   }
5484
5485   /**
5486    * Store selected annotation sort order for the view and repaint.
5487    */
5488   @Override
5489   protected void sortAnnotations_actionPerformed()
5490   {
5491     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5492     this.alignPanel.av
5493             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5494     alignPanel.paintAlignment(true);
5495   }
5496
5497   /**
5498    *
5499    * @return alignment panels in this alignment frame
5500    */
5501   public List<? extends AlignmentViewPanel> getAlignPanels()
5502   {
5503     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5504   }
5505
5506   /**
5507    * Open a new alignment window, with the cDNA associated with this (protein)
5508    * alignment, aligned as is the protein.
5509    */
5510   protected void viewAsCdna_actionPerformed()
5511   {
5512     // TODO no longer a menu action - refactor as required
5513     final AlignmentI alignment = getViewport().getAlignment();
5514     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5515     if (mappings == null)
5516     {
5517       return;
5518     }
5519     List<SequenceI> cdnaSeqs = new ArrayList<>();
5520     for (SequenceI aaSeq : alignment.getSequences())
5521     {
5522       for (AlignedCodonFrame acf : mappings)
5523       {
5524         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5525         if (dnaSeq != null)
5526         {
5527           /*
5528            * There is a cDNA mapping for this protein sequence - add to new
5529            * alignment. It will share the same dataset sequence as other mapped
5530            * cDNA (no new mappings need to be created).
5531            */
5532           final Sequence newSeq = new Sequence(dnaSeq);
5533           newSeq.setDatasetSequence(dnaSeq);
5534           cdnaSeqs.add(newSeq);
5535         }
5536       }
5537     }
5538     if (cdnaSeqs.size() == 0)
5539     {
5540       // show a warning dialog no mapped cDNA
5541       return;
5542     }
5543     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5544             .size()]));
5545     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5546             AlignFrame.DEFAULT_HEIGHT);
5547     cdna.alignAs(alignment);
5548     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5549             + this.title;
5550     Desktop.addInternalFrame(alignFrame, newtitle,
5551             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5552   }
5553
5554   /**
5555    * Set visibility of dna/protein complement view (available when shown in a
5556    * split frame).
5557    *
5558    * @param show
5559    */
5560   @Override
5561   protected void showComplement_actionPerformed(boolean show)
5562   {
5563     SplitContainerI sf = getSplitViewContainer();
5564     if (sf != null)
5565     {
5566       sf.setComplementVisible(this, show);
5567     }
5568   }
5569
5570   /**
5571    * Generate the reverse (optionally complemented) of the selected sequences,
5572    * and add them to the alignment
5573    */
5574   @Override
5575   protected void showReverse_actionPerformed(boolean complement)
5576   {
5577     AlignmentI al = null;
5578     try
5579     {
5580       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5581       al = dna.reverseCdna(complement);
5582       viewport.addAlignment(al, "");
5583       addHistoryItem(new EditCommand(
5584               MessageManager.getString("label.add_sequences"),
5585               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5586               viewport.getAlignment()));
5587     } catch (Exception ex)
5588     {
5589       System.err.println(ex.getMessage());
5590       return;
5591     }
5592   }
5593
5594   /**
5595    * Try to run a script in the Groovy console, having first ensured that this
5596    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5597    * be targeted at this alignment.
5598    */
5599   @Override
5600   protected void runGroovy_actionPerformed()
5601   {
5602     Jalview.setCurrentAlignFrame(this);
5603     groovy.ui.Console console = Desktop.getGroovyConsole();
5604     if (console != null)
5605     {
5606       try
5607       {
5608         console.runScript();
5609       } catch (Exception ex)
5610       {
5611         System.err.println((ex.toString()));
5612         JvOptionPane
5613                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5614                         .getString("label.couldnt_run_groovy_script"),
5615                         MessageManager
5616                                 .getString("label.groovy_support_failed"),
5617                         JvOptionPane.ERROR_MESSAGE);
5618       }
5619     }
5620     else
5621     {
5622       System.err.println("Can't run Groovy script as console not found");
5623     }
5624   }
5625
5626   /**
5627    * Hides columns containing (or not containing) a specified feature, provided
5628    * that would not leave all columns hidden
5629    *
5630    * @param featureType
5631    * @param columnsContaining
5632    * @return
5633    */
5634   public boolean hideFeatureColumns(String featureType,
5635           boolean columnsContaining)
5636   {
5637     boolean notForHiding = avc.markColumnsContainingFeatures(
5638             columnsContaining, false, false, featureType);
5639     if (notForHiding)
5640     {
5641       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5642               false, featureType))
5643       {
5644         getViewport().hideSelectedColumns();
5645         return true;
5646       }
5647     }
5648     return false;
5649   }
5650
5651   @Override
5652   protected void selectHighlightedColumns_actionPerformed(
5653           ActionEvent actionEvent)
5654   {
5655     // include key modifier check in case user selects from menu
5656     avc.markHighlightedColumns(
5657             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5658             true,
5659             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5660   }
5661
5662   /**
5663    * Rebuilds the Colour menu, including any user-defined colours which have
5664    * been loaded either on startup or during the session
5665    */
5666   public void buildColourMenu()
5667   {
5668     colourMenu.removeAll();
5669
5670     colourMenu.add(applyToAllGroups);
5671     colourMenu.add(textColour);
5672     colourMenu.addSeparator();
5673
5674     ColourMenuHelper.addMenuItems(colourMenu, this,
5675             viewport.getAlignment(), false);
5676
5677     colourMenu.addSeparator();
5678     colourMenu.add(conservationMenuItem);
5679     colourMenu.add(modifyConservation);
5680     colourMenu.add(abovePIDThreshold);
5681     colourMenu.add(modifyPID);
5682     colourMenu.add(annotationColour);
5683
5684     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5685     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5686   }
5687
5688   /**
5689    * Open a dialog (if not already open) that allows the user to select and
5690    * calculate PCA or Tree analysis
5691    */
5692   protected void openTreePcaDialog()
5693   {
5694     if (alignPanel.getCalculationDialog() == null)
5695     {
5696       new CalculationChooser(AlignFrame.this);
5697     }
5698   }
5699
5700   public void updateHMMERStatus(boolean status)
5701   {
5702     hmmerMenu.setEnabled(status);
5703   }
5704
5705   public HiddenMarkovModel getSelectedHMM()
5706   {
5707     return selectedHMM;
5708   }
5709
5710   /**
5711    * Sets the selected hidden Markov model
5712    *
5713    * @param selectedHMM
5714    */
5715   public void setSelectedHMM(HiddenMarkovModel selectedHMM)
5716   {
5717     this.selectedHMM = selectedHMM;
5718     hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5719             + selectedHMM.getName() + "_HMM");
5720     hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5721             + selectedHMM.getName() + "_HMM");
5722   }
5723
5724   @Override
5725   public void hmmerMenu_actionPerformed(ActionEvent e)
5726   {
5727     SequenceGroup grp = getViewport().getSelectionGroup();
5728     if (grp != null)
5729     {
5730       hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5731               + grp.getName());
5732     }
5733     else
5734     {
5735       hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5736               + " from Alignment");
5737     }
5738   }
5739
5740 }
5741
5742 class PrintThread extends Thread
5743 {
5744   AlignmentPanel ap;
5745
5746   public PrintThread(AlignmentPanel ap)
5747   {
5748     this.ap = ap;
5749   }
5750
5751   static PageFormat pf;
5752
5753   @Override
5754   public void run()
5755   {
5756     PrinterJob printJob = PrinterJob.getPrinterJob();
5757
5758     if (pf != null)
5759     {
5760       printJob.setPrintable(ap, pf);
5761     }
5762     else
5763     {
5764       printJob.setPrintable(ap);
5765     }
5766
5767     if (printJob.printDialog())
5768     {
5769       try
5770       {
5771         printJob.print();
5772       } catch (Exception PrintException)
5773       {
5774         PrintException.printStackTrace();
5775       }
5776     }
5777   }
5778 }