src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.hmmer.HMMAlignThread;
  66 import jalview.hmmer.HMMBuildThread;
  67 import jalview.io.AlignmentProperties;
  68 import jalview.io.AnnotationFile;
  69 import jalview.io.BioJsHTMLOutput;
  70 import jalview.io.DataSourceType;
  71 import jalview.io.FileFormat;
  72 import jalview.io.FileFormatI;
  73 import jalview.io.FileFormats;
  74 import jalview.io.FileLoader;
  75 import jalview.io.FileParse;
  76 import jalview.io.FormatAdapter;
  77 import jalview.io.HtmlSvgOutput;
  78 import jalview.io.IdentifyFile;
  79 import jalview.io.JPredFile;
  80 import jalview.io.JalviewFileChooser;
  81 import jalview.io.JalviewFileView;
  82 import jalview.io.JnetAnnotationMaker;
  83 import jalview.io.NewickFile;
  84 import jalview.io.ScoreMatrixFile;
  85 import jalview.io.TCoffeeScoreFile;
  86 import jalview.jbgui.GAlignFrame;
  87 import jalview.schemes.ColourSchemeI;
  88 import jalview.schemes.ColourSchemes;
  89 import jalview.schemes.ResidueColourScheme;
  90 import jalview.schemes.TCoffeeColourScheme;
  91 import jalview.util.MessageManager;
  92 import jalview.viewmodel.AlignmentViewport;
  93 import jalview.viewmodel.ViewportRanges;
  94 import jalview.ws.DBRefFetcher;
  95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  96 import jalview.ws.jws1.Discoverer;
  97 import jalview.ws.jws2.Jws2Discoverer;
  98 import jalview.ws.jws2.jabaws2.Jws2Instance;
  99 import jalview.ws.seqfetcher.DbSourceProxy;
 100
 101 import java.awt.BorderLayout;
 102 import java.awt.Component;
 103 import java.awt.Rectangle;
 104 import java.awt.Toolkit;
 105 import java.awt.datatransfer.Clipboard;
 106 import java.awt.datatransfer.DataFlavor;
 107 import java.awt.datatransfer.StringSelection;
 108 import java.awt.datatransfer.Transferable;
 109 import java.awt.dnd.DnDConstants;
 110 import java.awt.dnd.DropTargetDragEvent;
 111 import java.awt.dnd.DropTargetDropEvent;
 112 import java.awt.dnd.DropTargetEvent;
 113 import java.awt.dnd.DropTargetListener;
 114 import java.awt.event.ActionEvent;
 115 import java.awt.event.ActionListener;
 116 import java.awt.event.FocusAdapter;
 117 import java.awt.event.FocusEvent;
 118 import java.awt.event.ItemEvent;
 119 import java.awt.event.ItemListener;
 120 import java.awt.event.KeyAdapter;
 121 import java.awt.event.KeyEvent;
 122 import java.awt.event.MouseEvent;
 123 import java.awt.print.PageFormat;
 124 import java.awt.print.PrinterJob;
 125 import java.beans.PropertyChangeEvent;
 126 import java.io.File;
 127 import java.io.FileWriter;
 128 import java.io.IOException;
 129 import java.io.PrintWriter;
 130 import java.net.URL;
 131 import java.util.ArrayList;
 132 import java.util.Arrays;
 133 import java.util.Deque;
 134 import java.util.Enumeration;
 135 import java.util.HashMap;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Map;
 139 import java.util.Vector;
 140
 141 import javax.swing.JCheckBoxMenuItem;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLayeredPane;
 145 import javax.swing.JMenu;
 146 import javax.swing.JMenuItem;
 147 import javax.swing.JOptionPane;
 148 import javax.swing.JScrollPane;
 149 import javax.swing.SwingUtilities;
 150
 151 /**
 152  * DOCUMENT ME!
 153  *
 154  * @author $author$
 155  * @version $Revision$
 156  */
 157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 158         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 159 {
 160
 161   Map<String, Float> distribution = new HashMap<>(); // temporary
 162
 163   public static final int DEFAULT_WIDTH = 700;
 164
 165   public static final int DEFAULT_HEIGHT = 500;
 166
 167   boolean autoAlignNewSequences;
 168
 169
 170   /*
 171    * The currently displayed panel (selected tabbed view if more than one)
 172    */
 173   public AlignmentPanel alignPanel;
 174
 175   AlignViewport viewport;
 176
 177   ViewportRanges vpRanges;
 178
 179   public AlignViewControllerI avc;
 180
 181   List<AlignmentPanel> alignPanels = new ArrayList<>();
 182
 183   /**
 184    * Last format used to load or save alignments in this window
 185    */
 186   FileFormatI currentFileFormat = null;
 187
 188   /**
 189    * Current filename for this alignment
 190    */
 191   String fileName = null;
 192
 193
 194   /**
 195    * Creates a new AlignFrame object with specific width and height.
 196    *
 197    * @param al
 198    * @param width
 199    * @param height
 200    */
 201   public AlignFrame(AlignmentI al, int width, int height)
 202   {
 203     this(al, null, width, height);
 204   }
 205
 206   /**
 207    * Creates a new AlignFrame object with specific width, height and
 208    * sequenceSetId
 209    *
 210    * @param al
 211    * @param width
 212    * @param height
 213    * @param sequenceSetId
 214    */
 215   public AlignFrame(AlignmentI al, int width, int height,
 216           String sequenceSetId)
 217   {
 218     this(al, null, width, height, sequenceSetId);
 219   }
 220
 221   /**
 222    * Creates a new AlignFrame object with specific width, height and
 223    * sequenceSetId
 224    *
 225    * @param al
 226    * @param width
 227    * @param height
 228    * @param sequenceSetId
 229    * @param viewId
 230    */
 231   public AlignFrame(AlignmentI al, int width, int height,
 232           String sequenceSetId, String viewId)
 233   {
 234     this(al, null, width, height, sequenceSetId, viewId);
 235   }
 236
 237   /**
 238    * new alignment window with hidden columns
 239    *
 240    * @param al
 241    *          AlignmentI
 242    * @param hiddenColumns
 243    *          ColumnSelection or null
 244    * @param width
 245    *          Width of alignment frame
 246    * @param height
 247    *          height of frame.
 248    */
 249   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 250           int width, int height)
 251   {
 252     this(al, hiddenColumns, width, height, null);
 253   }
 254
 255   /**
 256    * Create alignment frame for al with hiddenColumns, a specific width and
 257    * height, and specific sequenceId
 258    *
 259    * @param al
 260    * @param hiddenColumns
 261    * @param width
 262    * @param height
 263    * @param sequenceSetId
 264    *          (may be null)
 265    */
 266   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 267           int width, int height, String sequenceSetId)
 268   {
 269     this(al, hiddenColumns, width, height, sequenceSetId, null);
 270   }
 271
 272   /**
 273    * Create alignment frame for al with hiddenColumns, a specific width and
 274    * height, and specific sequenceId
 275    *
 276    * @param al
 277    * @param hiddenColumns
 278    * @param width
 279    * @param height
 280    * @param sequenceSetId
 281    *          (may be null)
 282    * @param viewId
 283    *          (may be null)
 284    */
 285   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 286           int width, int height, String sequenceSetId, String viewId)
 287   {
 288     setSize(width, height);
 289
 290     if (al.getDataset() == null)
 291     {
 292       al.setDataset(null);
 293     }
 294
 295     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 296
 297     alignPanel = new AlignmentPanel(this, viewport);
 298
 299     addAlignmentPanel(alignPanel, true);
 300     init();
 301   }
 302
 303   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 304           HiddenColumns hiddenColumns, int width, int height)
 305   {
 306     setSize(width, height);
 307
 308     if (al.getDataset() == null)
 309     {
 310       al.setDataset(null);
 311     }
 312
 313     viewport = new AlignViewport(al, hiddenColumns);
 314
 315     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 316     {
 317       viewport.hideSequence(hiddenSeqs);
 318     }
 319     alignPanel = new AlignmentPanel(this, viewport);
 320     addAlignmentPanel(alignPanel, true);
 321     init();
 322   }
 323
 324   /**
 325    * Make a new AlignFrame from existing alignmentPanels
 326    *
 327    * @param ap
 328    *          AlignmentPanel
 329    * @param av
 330    *          AlignViewport
 331    */
 332   public AlignFrame(AlignmentPanel ap)
 333   {
 334     viewport = ap.av;
 335     alignPanel = ap;
 336     addAlignmentPanel(ap, false);
 337     init();
 338   }
 339
 340   /**
 341    * initalise the alignframe from the underlying viewport data and the
 342    * configurations
 343    */
 344   void init()
 345   {
 346     if (!Jalview.isHeadlessMode())
 347     {
 348       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 349     }
 350
 351     vpRanges = viewport.getRanges();
 352     avc = new jalview.controller.AlignViewController(this, viewport,
 353             alignPanel);
 354     if (viewport.getAlignmentConservationAnnotation() == null)
 355     {
 356       // BLOSUM62Colour.setEnabled(false);
 357       conservationMenuItem.setEnabled(false);
 358       modifyConservation.setEnabled(false);
 359       // PIDColour.setEnabled(false);
 360       // abovePIDThreshold.setEnabled(false);
 361       // modifyPID.setEnabled(false);
 362     }
 363
 364     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 365             "No sort");
 366
 367     if (sortby.equals("Id"))
 368     {
 369       sortIDMenuItem_actionPerformed(null);
 370     }
 371     else if (sortby.equals("Pairwise Identity"))
 372     {
 373       sortPairwiseMenuItem_actionPerformed(null);
 374     }
 375
 376     this.alignPanel.av
 377             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 378
 379     setMenusFromViewport(viewport);
 380     buildSortByAnnotationScoresMenu();
 381     calculateTree.addActionListener(new ActionListener()
 382     {
 383
 384       @Override
 385       public void actionPerformed(ActionEvent e)
 386       {
 387         openTreePcaDialog();
 388       }
 389     });
 390     buildColourMenu();
 391     buildHMMERMenu();
 392
 393     if (Desktop.desktop != null)
 394     {
 395       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 396       addServiceListeners();
 397       setGUINucleotide();
 398     }
 399
 400     if (viewport.getWrapAlignment())
 401     {
 402       wrapMenuItem_actionPerformed(null);
 403     }
 404
 405     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 406     {
 407       this.overviewMenuItem_actionPerformed(null);
 408     }
 409
 410     addKeyListener();
 411
 412     final List<AlignmentPanel> selviews = new ArrayList<>();
 413     final List<AlignmentPanel> origview = new ArrayList<>();
 414     final String menuLabel = MessageManager
 415             .getString("label.copy_format_from");
 416     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 417             new ViewSetProvider()
 418             {
 419
 420               @Override
 421               public AlignmentPanel[] getAllAlignmentPanels()
 422               {
 423                 origview.clear();
 424                 origview.add(alignPanel);
 425                 // make an array of all alignment panels except for this one
 426                 List<AlignmentPanel> aps = new ArrayList<>(
 427                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 428                 aps.remove(AlignFrame.this.alignPanel);
 429                 return aps.toArray(new AlignmentPanel[aps.size()]);
 430               }
 431             }, selviews, new ItemListener()
 432             {
 433
 434               @Override
 435               public void itemStateChanged(ItemEvent e)
 436               {
 437                 if (origview.size() > 0)
 438                 {
 439                   final AlignmentPanel ap = origview.get(0);
 440
 441                   /*
 442                    * Copy the ViewStyle of the selected panel to 'this one'.
 443                    * Don't change value of 'scaleProteinAsCdna' unless copying
 444                    * from a SplitFrame.
 445                    */
 446                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 447                           .getViewStyle();
 448                   boolean fromSplitFrame = selviews.get(0)
 449                           .getAlignViewport().getCodingComplement() != null;
 450                   if (!fromSplitFrame)
 451                   {
 452                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 453                             .getViewStyle().isScaleProteinAsCdna());
 454                   }
 455                   ap.getAlignViewport().setViewStyle(vs);
 456
 457                   /*
 458                    * Also rescale ViewStyle of SplitFrame complement if there is
 459                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 460                    * the whole ViewStyle (allow cDNA protein to have different
 461                    * fonts)
 462                    */
 463                   AlignViewportI complement = ap.getAlignViewport()
 464                           .getCodingComplement();
 465                   if (complement != null && vs.isScaleProteinAsCdna())
 466                   {
 467                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 468                     ((SplitFrame) af.getSplitViewContainer())
 469                             .adjustLayout();
 470                     af.setMenusForViewport();
 471                   }
 472
 473                   ap.updateLayout();
 474                   ap.setSelected(true);
 475                   ap.alignFrame.setMenusForViewport();
 476
 477                 }
 478               }
 479             });
 480     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 481             .indexOf("devel") > -1
 482             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 483                     .indexOf("test") > -1)
 484     {
 485       formatMenu.add(vsel);
 486     }
 487     addFocusListener(new FocusAdapter()
 488     {
 489       @Override
 490       public void focusGained(FocusEvent e)
 491       {
 492         Jalview.setCurrentAlignFrame(AlignFrame.this);
 493       }
 494     });
 495
 496   }
 497
 498   private void buildHMMERMenu()
 499   {
 500     hmmerMenu.removeAll();
 501
 502     hmmerMenu.add(changeHMMERLocation);
 503     hmmerMenu.addSeparator();
 504
 505     hmmerMenu.add(autoAlignSeqs);
 506     hmmerMenu.addSeparator();
 507
 508     hmmerMenu.add(hmmAlign);
 509     hmmerMenu.add(hmmBuild);
 510     hmmerMenu.add(hmmSearch);
 511
 512   }
 513
 514   /**
 515    * Change the filename and format for the alignment, and enable the 'reload'
 516    * button functionality.
 517    *
 518    * @param file
 519    *          valid filename
 520    * @param format
 521    *          format of file
 522    */
 523   public void setFileName(String file, FileFormatI format)
 524   {
 525     fileName = file;
 526     setFileFormat(format);
 527     reload.setEnabled(true);
 528   }
 529
 530   /**
 531    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 532    * events
 533    */
 534   void addKeyListener()
 535   {
 536     addKeyListener(new KeyAdapter()
 537     {
 538       @Override
 539       public void keyPressed(KeyEvent evt)
 540       {
 541         if (viewport.cursorMode
 542                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 543                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 544                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 545                 && Character.isDigit(evt.getKeyChar()))
 546         {
 547           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 548         }
 549
 550         switch (evt.getKeyCode())
 551         {
 552
 553         case 27: // escape key
 554           deselectAllSequenceMenuItem_actionPerformed(null);
 555
 556           break;
 557
 558         case KeyEvent.VK_DOWN:
 559           if (evt.isAltDown() || !viewport.cursorMode)
 560           {
 561             moveSelectedSequences(false);
 562           }
 563           if (viewport.cursorMode)
 564           {
 565             alignPanel.getSeqPanel().moveCursor(0, 1);
 566           }
 567           break;
 568
 569         case KeyEvent.VK_UP:
 570           if (evt.isAltDown() || !viewport.cursorMode)
 571           {
 572             moveSelectedSequences(true);
 573           }
 574           if (viewport.cursorMode)
 575           {
 576             alignPanel.getSeqPanel().moveCursor(0, -1);
 577           }
 578
 579           break;
 580
 581         case KeyEvent.VK_LEFT:
 582           if (evt.isAltDown() || !viewport.cursorMode)
 583           {
 584             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 585           }
 586           else
 587           {
 588             alignPanel.getSeqPanel().moveCursor(-1, 0);
 589           }
 590
 591           break;
 592
 593         case KeyEvent.VK_RIGHT:
 594           if (evt.isAltDown() || !viewport.cursorMode)
 595           {
 596             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 597           }
 598           else
 599           {
 600             alignPanel.getSeqPanel().moveCursor(1, 0);
 601           }
 602           break;
 603
 604         case KeyEvent.VK_SPACE:
 605           if (viewport.cursorMode)
 606           {
 607             alignPanel.getSeqPanel().insertGapAtCursor(
 608                     evt.isControlDown() || evt.isShiftDown()
 609                             || evt.isAltDown());
 610           }
 611           break;
 612
 613         // case KeyEvent.VK_A:
 614         // if (viewport.cursorMode)
 615         // {
 616         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 617         // //System.out.println("A");
 618         // }
 619         // break;
 620         /*
 621          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 622          * System.out.println("closing bracket"); } break;
 623          */
 624         case KeyEvent.VK_DELETE:
 625         case KeyEvent.VK_BACK_SPACE:
 626           if (!viewport.cursorMode)
 627           {
 628             cut_actionPerformed(null);
 629           }
 630           else
 631           {
 632             alignPanel.getSeqPanel().deleteGapAtCursor(
 633                     evt.isControlDown() || evt.isShiftDown()
 634                             || evt.isAltDown());
 635           }
 636
 637           break;
 638
 639         case KeyEvent.VK_S:
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().setCursorRow();
 643           }
 644           break;
 645         case KeyEvent.VK_C:
 646           if (viewport.cursorMode && !evt.isControlDown())
 647           {
 648             alignPanel.getSeqPanel().setCursorColumn();
 649           }
 650           break;
 651         case KeyEvent.VK_P:
 652           if (viewport.cursorMode)
 653           {
 654             alignPanel.getSeqPanel().setCursorPosition();
 655           }
 656           break;
 657
 658         case KeyEvent.VK_ENTER:
 659         case KeyEvent.VK_COMMA:
 660           if (viewport.cursorMode)
 661           {
 662             alignPanel.getSeqPanel().setCursorRowAndColumn();
 663           }
 664           break;
 665
 666         case KeyEvent.VK_Q:
 667           if (viewport.cursorMode)
 668           {
 669             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 670           }
 671           break;
 672         case KeyEvent.VK_M:
 673           if (viewport.cursorMode)
 674           {
 675             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 676           }
 677           break;
 678
 679         case KeyEvent.VK_F2:
 680           viewport.cursorMode = !viewport.cursorMode;
 681           statusBar.setText(MessageManager.formatMessage(
 682                   "label.keyboard_editing_mode",
 683                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 684           if (viewport.cursorMode)
 685           {
 686             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 687                     .getStartRes();
 688             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 689                     .getStartSeq();
 690           }
 691           alignPanel.getSeqPanel().seqCanvas.repaint();
 692           break;
 693
 694         case KeyEvent.VK_F1:
 695           try
 696           {
 697             Help.showHelpWindow();
 698           } catch (Exception ex)
 699           {
 700             ex.printStackTrace();
 701           }
 702           break;
 703         case KeyEvent.VK_H:
 704         {
 705           boolean toggleSeqs = !evt.isControlDown();
 706           boolean toggleCols = !evt.isShiftDown();
 707           toggleHiddenRegions(toggleSeqs, toggleCols);
 708           break;
 709         }
 710         case KeyEvent.VK_B:
 711         {
 712           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 713           boolean modifyExisting = true; // always modify, don't clear
 714                                          // evt.isShiftDown();
 715           boolean invertHighlighted = evt.isAltDown();
 716           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 717                   toggleSel);
 718           break;
 719         }
 720         case KeyEvent.VK_PAGE_UP:
 721           if (viewport.getWrapAlignment())
 722           {
 723             vpRanges.scrollUp(true);
 724           }
 725           else
 726           {
 727             vpRanges.pageUp();
 728           }
 729           break;
 730         case KeyEvent.VK_PAGE_DOWN:
 731           if (viewport.getWrapAlignment())
 732           {
 733             vpRanges.scrollUp(false);
 734           }
 735           else
 736           {
 737             vpRanges.pageDown();
 738           }
 739           break;
 740         }
 741       }
 742
 743       @Override
 744       public void keyReleased(KeyEvent evt)
 745       {
 746         switch (evt.getKeyCode())
 747         {
 748         case KeyEvent.VK_LEFT:
 749           if (evt.isAltDown() || !viewport.cursorMode)
 750           {
 751             viewport.firePropertyChange("alignment", null, viewport
 752                     .getAlignment().getSequences());
 753           }
 754           break;
 755
 756         case KeyEvent.VK_RIGHT:
 757           if (evt.isAltDown() || !viewport.cursorMode)
 758           {
 759             viewport.firePropertyChange("alignment", null, viewport
 760                     .getAlignment().getSequences());
 761           }
 762           break;
 763         }
 764       }
 765     });
 766   }
 767
 768   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 769   {
 770     ap.alignFrame = this;
 771     avc = new jalview.controller.AlignViewController(this, viewport,
 772             alignPanel);
 773
 774     alignPanels.add(ap);
 775
 776     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 777
 778     int aSize = alignPanels.size();
 779
 780     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 781
 782     if (aSize == 1 && ap.av.viewName == null)
 783     {
 784       this.getContentPane().add(ap, BorderLayout.CENTER);
 785     }
 786     else
 787     {
 788       if (aSize == 2)
 789       {
 790         setInitialTabVisible();
 791       }
 792
 793       expandViews.setEnabled(true);
 794       gatherViews.setEnabled(true);
 795       tabbedPane.addTab(ap.av.viewName, ap);
 796
 797       ap.setVisible(false);
 798     }
 799
 800     if (newPanel)
 801     {
 802       if (ap.av.isPadGaps())
 803       {
 804         ap.av.getAlignment().padGaps();
 805       }
 806       ap.av.updateConservation(ap);
 807       ap.av.updateConsensus(ap);
 808       ap.av.updateStrucConsensus(ap);
 809       ap.av.updateInformation(ap);
 810     }
 811   }
 812
 813   public void setInitialTabVisible()
 814   {
 815     expandViews.setEnabled(true);
 816     gatherViews.setEnabled(true);
 817     tabbedPane.setVisible(true);
 818     AlignmentPanel first = alignPanels.get(0);
 819     tabbedPane.addTab(first.av.viewName, first);
 820     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 821   }
 822
 823   public AlignViewport getViewport()
 824   {
 825     return viewport;
 826   }
 827
 828   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 829   private void addServiceListeners()
 830   {
 831     final java.beans.PropertyChangeListener thisListener;
 832     Desktop.instance.addJalviewPropertyChangeListener("services",
 833             thisListener = new java.beans.PropertyChangeListener()
 834             {
 835               @Override
 836               public void propertyChange(PropertyChangeEvent evt)
 837               {
 838                 // // System.out.println("Discoverer property change.");
 839                 // if (evt.getPropertyName().equals("services"))
 840                 {
 841                   SwingUtilities.invokeLater(new Runnable()
 842                   {
 843
 844                     @Override
 845                     public void run()
 846                     {
 847                       System.err
 848                               .println("Rebuild WS Menu for service change");
 849                       BuildWebServiceMenu();
 850                     }
 851
 852                   });
 853                 }
 854               }
 855             });
 856     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 857     {
 858       @Override
 859       public void internalFrameClosed(
 860               javax.swing.event.InternalFrameEvent evt)
 861       {
 862         // System.out.println("deregistering discoverer listener");
 863         Desktop.instance.removeJalviewPropertyChangeListener("services",
 864                 thisListener);
 865         closeMenuItem_actionPerformed(true);
 866       };
 867     });
 868     // Finally, build the menu once to get current service state
 869     new Thread(new Runnable()
 870     {
 871       @Override
 872       public void run()
 873       {
 874         BuildWebServiceMenu();
 875       }
 876     }).start();
 877   }
 878
 879   /**
 880    * Configure menu items that vary according to whether the alignment is
 881    * nucleotide or protein
 882    */
 883   public void setGUINucleotide()
 884   {
 885     AlignmentI al = getViewport().getAlignment();
 886     boolean nucleotide = al.isNucleotide();
 887
 888     showTranslation.setVisible(nucleotide);
 889     showReverse.setVisible(nucleotide);
 890     showReverseComplement.setVisible(nucleotide);
 891     conservationMenuItem.setEnabled(!nucleotide);
 892     modifyConservation.setEnabled(!nucleotide
 893             && conservationMenuItem.isSelected());
 894     showGroupConservation.setEnabled(!nucleotide);
 895
 896     showComplementMenuItem.setText(nucleotide ? MessageManager
 897             .getString("label.protein") : MessageManager
 898             .getString("label.nucleotide"));
 899   }
 900
 901   /**
 902    * set up menus for the current viewport. This may be called after any
 903    * operation that affects the data in the current view (selection changed,
 904    * etc) to update the menus to reflect the new state.
 905    */
 906   @Override
 907   public void setMenusForViewport()
 908   {
 909     setMenusFromViewport(viewport);
 910   }
 911
 912   /**
 913    * Need to call this method when tabs are selected for multiple views, or when
 914    * loading from Jalview2XML.java
 915    *
 916    * @param av
 917    *          AlignViewport
 918    */
 919   void setMenusFromViewport(AlignViewport av)
 920   {
 921     padGapsMenuitem.setSelected(av.isPadGaps());
 922     colourTextMenuItem.setSelected(av.isShowColourText());
 923     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 924     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 925     conservationMenuItem.setSelected(av.getConservationSelected());
 926     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 927     seqLimits.setSelected(av.getShowJVSuffix());
 928     idRightAlign.setSelected(av.isRightAlignIds());
 929     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 930     renderGapsMenuItem.setSelected(av.isRenderGaps());
 931     wrapMenuItem.setSelected(av.getWrapAlignment());
 932     scaleAbove.setVisible(av.getWrapAlignment());
 933     scaleLeft.setVisible(av.getWrapAlignment());
 934     scaleRight.setVisible(av.getWrapAlignment());
 935     annotationPanelMenuItem.setState(av.isShowAnnotation());
 936     /*
 937      * Show/hide annotations only enabled if annotation panel is shown
 938      */
 939     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 940     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 941     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 942     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 943     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 944     viewTextMenuItem.setSelected(av.getShowText());
 945     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 946     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 947     showGroupConservation.setSelected(av.isShowGroupConservation());
 948     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 949     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 950     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 951     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 952     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 953     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 954
 955     ColourMenuHelper.setColourSelected(colourMenu,
 956             av.getGlobalColourScheme());
 957
 958     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 959     hiddenMarkers.setState(av.getShowHiddenMarkers());
 960     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 961     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 962     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 963     autoCalculate.setSelected(av.autoCalculateConsensus);
 964     sortByTree.setSelected(av.sortByTree);
 965     listenToViewSelections.setSelected(av.followSelection);
 966
 967     showProducts.setEnabled(canShowProducts());
 968     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 969
 970     updateEditMenuBar();
 971   }
 972
 973   /**
 974    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 975    *
 976    * @param b
 977    */
 978   public void setGroovyEnabled(boolean b)
 979   {
 980     runGroovy.setEnabled(b);
 981   }
 982
 983   private IProgressIndicator progressBar;
 984
 985   /*
 986    * (non-Javadoc)
 987    *
 988    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 989    */
 990   @Override
 991   public void setProgressBar(String message, long id)
 992   {
 993     progressBar.setProgressBar(message, id);
 994   }
 995
 996   @Override
 997   public void registerHandler(final long id,
 998           final IProgressIndicatorHandler handler)
 999   {
1000     progressBar.registerHandler(id, handler);
1001   }
1002
1003   /**
1004    *
1005    * @return true if any progress bars are still active
1006    */
1007   @Override
1008   public boolean operationInProgress()
1009   {
1010     return progressBar.operationInProgress();
1011   }
1012
1013   @Override
1014   public void setStatus(String text)
1015   {
1016     statusBar.setText(text);
1017   }
1018
1019   /*
1020    * Added so Castor Mapping file can obtain Jalview Version
1021    */
1022   public String getVersion()
1023   {
1024     return jalview.bin.Cache.getProperty("VERSION");
1025   }
1026
1027   public FeatureRenderer getFeatureRenderer()
1028   {
1029     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1030   }
1031
1032   @Override
1033   public void fetchSequence_actionPerformed(ActionEvent e)
1034   {
1035     new jalview.gui.SequenceFetcher(this);
1036   }
1037
1038   @Override
1039   public void addFromFile_actionPerformed(ActionEvent e)
1040   {
1041     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1042   }
1043
1044   @Override
1045   public void hmmBuild_actionPerformed(ActionEvent e)
1046           throws IOException, InterruptedException
1047   {
1048     new Thread(new HMMBuildThread(this)).start();
1049     alignPanel.repaint();
1050
1051   }
1052
1053   @Override
1054   public void hmmAlign_actionPerformed(ActionEvent e)
1055           throws IOException, InterruptedException
1056   {
1057     new Thread(new HMMAlignThread(this, true)).start();
1058     alignPanel.repaint();
1059   }
1060
1061   @Override
1062   public void changeHMMERLocation_actionPerformed(ActionEvent e)
1063   {
1064     String location = JOptionPane.showInputDialog(
1065             MessageManager.getString("label.enter_location"));
1066     Cache.setProperty(Preferences.HMMER_PATH, location);
1067   }
1068
1069   @Override
1070   public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1071   {
1072     autoAlignNewSequences = autoAlignSeqs;
1073     alignPanel.repaint();
1074   }
1075
1076   @Override
1077   public void hmmSearch_actionPerformed(ActionEvent e)
1078   {
1079     alignPanel.repaint();
1080   }
1081
1082   @Override
1083   public void reload_actionPerformed(ActionEvent e)
1084   {
1085     if (fileName != null)
1086     {
1087       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1088       // originating file's format
1089       // TODO: work out how to recover feature settings for correct view(s) when
1090       // file is reloaded.
1091       if (FileFormat.Jalview.equals(currentFileFormat))
1092       {
1093         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1094         for (int i = 0; i < frames.length; i++)
1095         {
1096           if (frames[i] instanceof AlignFrame && frames[i] != this
1097                   && ((AlignFrame) frames[i]).fileName != null
1098                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1099           {
1100             try
1101             {
1102               frames[i].setSelected(true);
1103               Desktop.instance.closeAssociatedWindows();
1104             } catch (java.beans.PropertyVetoException ex)
1105             {
1106             }
1107           }
1108
1109         }
1110         Desktop.instance.closeAssociatedWindows();
1111
1112         FileLoader loader = new FileLoader();
1113         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1114                 : DataSourceType.FILE;
1115         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1116       }
1117       else
1118       {
1119         Rectangle bounds = this.getBounds();
1120
1121         FileLoader loader = new FileLoader();
1122         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1123                 : DataSourceType.FILE;
1124         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1125                 protocol, currentFileFormat);
1126
1127         newframe.setBounds(bounds);
1128         if (featureSettings != null && featureSettings.isShowing())
1129         {
1130           final Rectangle fspos = featureSettings.frame.getBounds();
1131           // TODO: need a 'show feature settings' function that takes bounds -
1132           // need to refactor Desktop.addFrame
1133           newframe.featureSettings_actionPerformed(null);
1134           final FeatureSettings nfs = newframe.featureSettings;
1135           SwingUtilities.invokeLater(new Runnable()
1136           {
1137             @Override
1138             public void run()
1139             {
1140               nfs.frame.setBounds(fspos);
1141             }
1142           });
1143           this.featureSettings.close();
1144           this.featureSettings = null;
1145         }
1146         this.closeMenuItem_actionPerformed(true);
1147       }
1148     }
1149   }
1150
1151   @Override
1152   public void addFromText_actionPerformed(ActionEvent e)
1153   {
1154     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1155             .getAlignPanel());
1156   }
1157
1158   @Override
1159   public void addFromURL_actionPerformed(ActionEvent e)
1160   {
1161     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1162   }
1163
1164   @Override
1165   public void save_actionPerformed(ActionEvent e)
1166   {
1167     if (fileName == null || (currentFileFormat == null)
1168             || fileName.startsWith("http"))
1169     {
1170       saveAs_actionPerformed(null);
1171     }
1172     else
1173     {
1174       saveAlignment(fileName, currentFileFormat);
1175     }
1176   }
1177
1178   /**
1179    * DOCUMENT ME!
1180    *
1181    * @param e
1182    *          DOCUMENT ME!
1183    */
1184   @Override
1185   public void saveAs_actionPerformed(ActionEvent e)
1186   {
1187     String format = currentFileFormat == null ? null : currentFileFormat
1188             .getName();
1189     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1190             Cache.getProperty("LAST_DIRECTORY"), format);
1191
1192     chooser.setFileView(new JalviewFileView());
1193     chooser.setDialogTitle(MessageManager
1194             .getString("label.save_alignment_to_file"));
1195     chooser.setToolTipText(MessageManager.getString("action.save"));
1196
1197     int value = chooser.showSaveDialog(this);
1198
1199     if (value == JalviewFileChooser.APPROVE_OPTION)
1200     {
1201       currentFileFormat = chooser.getSelectedFormat();
1202       while (currentFileFormat == null)
1203       {
1204         JvOptionPane
1205                 .showInternalMessageDialog(
1206                         Desktop.desktop,
1207                         MessageManager
1208                                 .getString("label.select_file_format_before_saving"),
1209                         MessageManager
1210                                 .getString("label.file_format_not_specified"),
1211                         JvOptionPane.WARNING_MESSAGE);
1212         currentFileFormat = chooser.getSelectedFormat();
1213         value = chooser.showSaveDialog(this);
1214         if (value != JalviewFileChooser.APPROVE_OPTION)
1215         {
1216           return;
1217         }
1218       }
1219
1220       fileName = chooser.getSelectedFile().getPath();
1221
1222       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1223
1224       Cache.setProperty("LAST_DIRECTORY", fileName);
1225       saveAlignment(fileName, currentFileFormat);
1226     }
1227   }
1228
1229   public boolean saveAlignment(String file, FileFormatI format)
1230   {
1231     boolean success = true;
1232
1233     if (FileFormat.Jalview.equals(format))
1234     {
1235       String shortName = title;
1236
1237       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1238       {
1239         shortName = shortName.substring(shortName
1240                 .lastIndexOf(java.io.File.separatorChar) + 1);
1241       }
1242
1243       success = new Jalview2XML().saveAlignment(this, file, shortName);
1244
1245       statusBar.setText(MessageManager.formatMessage(
1246               "label.successfully_saved_to_file_in_format", new Object[] {
1247                   fileName, format }));
1248
1249     }
1250     else
1251     {
1252       AlignmentExportData exportData = getAlignmentForExport(format,
1253               viewport, null);
1254       if (exportData.getSettings().isCancelled())
1255       {
1256         return false;
1257       }
1258       FormatAdapter f = new FormatAdapter(alignPanel,
1259               exportData.getSettings());
1260       String output = f.formatSequences(
1261               format,
1262               exportData.getAlignment(), // class cast exceptions will
1263               // occur in the distant future
1264               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1265               f.getCacheSuffixDefault(format), viewport.getAlignment()
1266                       .getHiddenColumns());
1267
1268       if (output == null)
1269       {
1270         success = false;
1271       }
1272       else
1273       {
1274         try
1275         {
1276           PrintWriter out = new PrintWriter(new FileWriter(file));
1277
1278           out.print(output);
1279           out.close();
1280           this.setTitle(file);
1281           statusBar.setText(MessageManager.formatMessage(
1282                   "label.successfully_saved_to_file_in_format",
1283                   new Object[] { fileName, format.getName() }));
1284         } catch (Exception ex)
1285         {
1286           success = false;
1287           ex.printStackTrace();
1288         }
1289       }
1290     }
1291
1292     if (!success)
1293     {
1294       JvOptionPane.showInternalMessageDialog(this, MessageManager
1295               .formatMessage("label.couldnt_save_file",
1296                       new Object[] { fileName }), MessageManager
1297               .getString("label.error_saving_file"),
1298               JvOptionPane.WARNING_MESSAGE);
1299     }
1300
1301     return success;
1302   }
1303
1304   private void warningMessage(String warning, String title)
1305   {
1306     if (new jalview.util.Platform().isHeadless())
1307     {
1308       System.err.println("Warning: " + title + "\nWarning: " + warning);
1309
1310     }
1311     else
1312     {
1313       JvOptionPane.showInternalMessageDialog(this, warning, title,
1314               JvOptionPane.WARNING_MESSAGE);
1315     }
1316     return;
1317   }
1318
1319   /**
1320    * DOCUMENT ME!
1321    *
1322    * @param e
1323    *          DOCUMENT ME!
1324    */
1325   @Override
1326   protected void outputText_actionPerformed(ActionEvent e)
1327   {
1328     FileFormatI fileFormat = FileFormats.getInstance().forName(
1329             e.getActionCommand());
1330     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1331             viewport, null);
1332     if (exportData.getSettings().isCancelled())
1333     {
1334       return;
1335     }
1336     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1337     cap.setForInput(null);
1338     try
1339     {
1340       FileFormatI format = fileFormat;
1341       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1342               .formatSequences(format, exportData.getAlignment(),
1343                       exportData.getOmitHidden(),
1344  exportData
1345                               .getStartEndPostions(), viewport
1346                               .getAlignment().getHiddenColumns()));
1347       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1348               "label.alignment_output_command",
1349               new Object[] { e.getActionCommand() }), 600, 500);
1350     } catch (OutOfMemoryError oom)
1351     {
1352       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1353       cap.dispose();
1354     }
1355
1356   }
1357
1358   public static AlignmentExportData getAlignmentForExport(
1359           FileFormatI format, AlignViewportI viewport,
1360           AlignExportSettingI exportSettings)
1361   {
1362     AlignmentI alignmentToExport = null;
1363     AlignExportSettingI settings = exportSettings;
1364     String[] omitHidden = null;
1365
1366     HiddenSequences hiddenSeqs = viewport.getAlignment()
1367             .getHiddenSequences();
1368
1369     alignmentToExport = viewport.getAlignment();
1370
1371     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1372     if (settings == null)
1373     {
1374       settings = new AlignExportSettings(hasHiddenSeqs,
1375               viewport.hasHiddenColumns(), format);
1376     }
1377     // settings.isExportAnnotations();
1378
1379     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1380     {
1381       omitHidden = viewport.getViewAsString(false,
1382               settings.isExportHiddenSequences());
1383     }
1384
1385     int[] alignmentStartEnd = new int[2];
1386     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1387     {
1388       alignmentToExport = hiddenSeqs.getFullAlignment();
1389     }
1390     else
1391     {
1392       alignmentToExport = viewport.getAlignment();
1393     }
1394     alignmentStartEnd = alignmentToExport
1395             .getVisibleStartAndEndIndex(viewport.getAlignment()
1396                     .getHiddenColumns()
1397                     .getHiddenRegions());
1398     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1399             omitHidden, alignmentStartEnd, settings);
1400     return ed;
1401   }
1402
1403   /**
1404    * DOCUMENT ME!
1405    *
1406    * @param e
1407    *          DOCUMENT ME!
1408    */
1409   @Override
1410   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1411   {
1412     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1413     htmlSVG.exportHTML(null);
1414   }
1415
1416   @Override
1417   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1418   {
1419     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1420     bjs.exportHTML(null);
1421   }
1422
1423   public void createImageMap(File file, String image)
1424   {
1425     alignPanel.makePNGImageMap(file, image);
1426   }
1427
1428   /**
1429    * DOCUMENT ME!
1430    *
1431    * @param e
1432    *          DOCUMENT ME!
1433    */
1434   @Override
1435   public void createPNG(File f)
1436   {
1437     alignPanel.makePNG(f);
1438   }
1439
1440   /**
1441    * DOCUMENT ME!
1442    *
1443    * @param e
1444    *          DOCUMENT ME!
1445    */
1446   @Override
1447   public void createEPS(File f)
1448   {
1449     alignPanel.makeEPS(f);
1450   }
1451
1452   @Override
1453   public void createSVG(File f)
1454   {
1455     alignPanel.makeSVG(f);
1456   }
1457
1458   @Override
1459   public void pageSetup_actionPerformed(ActionEvent e)
1460   {
1461     PrinterJob printJob = PrinterJob.getPrinterJob();
1462     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1463   }
1464
1465   /**
1466    * DOCUMENT ME!
1467    *
1468    * @param e
1469    *          DOCUMENT ME!
1470    */
1471   @Override
1472   public void printMenuItem_actionPerformed(ActionEvent e)
1473   {
1474     // Putting in a thread avoids Swing painting problems
1475     PrintThread thread = new PrintThread(alignPanel);
1476     thread.start();
1477   }
1478
1479   @Override
1480   public void exportFeatures_actionPerformed(ActionEvent e)
1481   {
1482     new AnnotationExporter().exportFeatures(alignPanel);
1483   }
1484
1485   @Override
1486   public void exportAnnotations_actionPerformed(ActionEvent e)
1487   {
1488     new AnnotationExporter().exportAnnotations(alignPanel);
1489   }
1490
1491   @Override
1492   public void associatedData_actionPerformed(ActionEvent e)
1493           throws IOException, InterruptedException
1494   {
1495     // Pick the tree file
1496     JalviewFileChooser chooser = new JalviewFileChooser(
1497             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1498     chooser.setFileView(new JalviewFileView());
1499     chooser.setDialogTitle(MessageManager
1500             .getString("label.load_jalview_annotations"));
1501     chooser.setToolTipText(MessageManager
1502             .getString("label.load_jalview_annotations"));
1503
1504     int value = chooser.showOpenDialog(null);
1505
1506     if (value == JalviewFileChooser.APPROVE_OPTION)
1507     {
1508       String choice = chooser.getSelectedFile().getPath();
1509       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1510       loadJalviewDataFile(choice, null, null, null);
1511     }
1512
1513   }
1514
1515   /**
1516    * Close the current view or all views in the alignment frame. If the frame
1517    * only contains one view then the alignment will be removed from memory.
1518    *
1519    * @param closeAllTabs
1520    */
1521   @Override
1522   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1523   {
1524     if (alignPanels != null && alignPanels.size() < 2)
1525     {
1526       closeAllTabs = true;
1527     }
1528
1529     try
1530     {
1531       if (alignPanels != null)
1532       {
1533         if (closeAllTabs)
1534         {
1535           if (this.isClosed())
1536           {
1537             // really close all the windows - otherwise wait till
1538             // setClosed(true) is called
1539             for (int i = 0; i < alignPanels.size(); i++)
1540             {
1541               AlignmentPanel ap = alignPanels.get(i);
1542               ap.closePanel();
1543             }
1544           }
1545         }
1546         else
1547         {
1548           closeView(alignPanel);
1549         }
1550       }
1551
1552       if (closeAllTabs)
1553       {
1554         /*
1555          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1556          * be called recursively, with the frame now in 'closed' state
1557          */
1558         this.setClosed(true);
1559       }
1560     } catch (Exception ex)
1561     {
1562       ex.printStackTrace();
1563     }
1564   }
1565
1566   /**
1567    * Close the specified panel and close up tabs appropriately.
1568    *
1569    * @param panelToClose
1570    */
1571   public void closeView(AlignmentPanel panelToClose)
1572   {
1573     int index = tabbedPane.getSelectedIndex();
1574     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1575     alignPanels.remove(panelToClose);
1576     panelToClose.closePanel();
1577     panelToClose = null;
1578
1579     tabbedPane.removeTabAt(closedindex);
1580     tabbedPane.validate();
1581
1582     if (index > closedindex || index == tabbedPane.getTabCount())
1583     {
1584       // modify currently selected tab index if necessary.
1585       index--;
1586     }
1587
1588     this.tabSelectionChanged(index);
1589   }
1590
1591   /**
1592    * DOCUMENT ME!
1593    */
1594   void updateEditMenuBar()
1595   {
1596
1597     if (viewport.getHistoryList().size() > 0)
1598     {
1599       undoMenuItem.setEnabled(true);
1600       CommandI command = viewport.getHistoryList().peek();
1601       undoMenuItem.setText(MessageManager.formatMessage(
1602               "label.undo_command",
1603               new Object[] { command.getDescription() }));
1604     }
1605     else
1606     {
1607       undoMenuItem.setEnabled(false);
1608       undoMenuItem.setText(MessageManager.getString("action.undo"));
1609     }
1610
1611     if (viewport.getRedoList().size() > 0)
1612     {
1613       redoMenuItem.setEnabled(true);
1614
1615       CommandI command = viewport.getRedoList().peek();
1616       redoMenuItem.setText(MessageManager.formatMessage(
1617               "label.redo_command",
1618               new Object[] { command.getDescription() }));
1619     }
1620     else
1621     {
1622       redoMenuItem.setEnabled(false);
1623       redoMenuItem.setText(MessageManager.getString("action.redo"));
1624     }
1625   }
1626
1627   @Override
1628   public void addHistoryItem(CommandI command)
1629   {
1630     if (command.getSize() > 0)
1631     {
1632       viewport.addToHistoryList(command);
1633       viewport.clearRedoList();
1634       updateEditMenuBar();
1635       viewport.updateHiddenColumns();
1636       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1637       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1638       // viewport.getColumnSelection()
1639       // .getHiddenColumns().size() > 0);
1640     }
1641   }
1642
1643   /**
1644    *
1645    * @return alignment objects for all views
1646    */
1647   AlignmentI[] getViewAlignments()
1648   {
1649     if (alignPanels != null)
1650     {
1651       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1652       int i = 0;
1653       for (AlignmentPanel ap : alignPanels)
1654       {
1655         als[i++] = ap.av.getAlignment();
1656       }
1657       return als;
1658     }
1659     if (viewport != null)
1660     {
1661       return new AlignmentI[] { viewport.getAlignment() };
1662     }
1663     return null;
1664   }
1665
1666   /**
1667    * DOCUMENT ME!
1668    *
1669    * @param e
1670    *          DOCUMENT ME!
1671    */
1672   @Override
1673   protected void undoMenuItem_actionPerformed(ActionEvent e)
1674   {
1675     if (viewport.getHistoryList().isEmpty())
1676     {
1677       return;
1678     }
1679     CommandI command = viewport.getHistoryList().pop();
1680     viewport.addToRedoList(command);
1681     command.undoCommand(getViewAlignments());
1682
1683     AlignmentViewport originalSource = getOriginatingSource(command);
1684     updateEditMenuBar();
1685
1686     if (originalSource != null)
1687     {
1688       if (originalSource != viewport)
1689       {
1690         Cache.log
1691                 .warn("Implementation worry: mismatch of viewport origin for undo");
1692       }
1693       originalSource.updateHiddenColumns();
1694       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1695       // null
1696       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1697       // viewport.getColumnSelection()
1698       // .getHiddenColumns().size() > 0);
1699       originalSource.firePropertyChange("alignment", null, originalSource
1700               .getAlignment().getSequences());
1701     }
1702   }
1703
1704   /**
1705    * DOCUMENT ME!
1706    *
1707    * @param e
1708    *          DOCUMENT ME!
1709    */
1710   @Override
1711   protected void redoMenuItem_actionPerformed(ActionEvent e)
1712   {
1713     if (viewport.getRedoList().size() < 1)
1714     {
1715       return;
1716     }
1717
1718     CommandI command = viewport.getRedoList().pop();
1719     viewport.addToHistoryList(command);
1720     command.doCommand(getViewAlignments());
1721
1722     AlignmentViewport originalSource = getOriginatingSource(command);
1723     updateEditMenuBar();
1724
1725     if (originalSource != null)
1726     {
1727
1728       if (originalSource != viewport)
1729       {
1730         Cache.log
1731                 .warn("Implementation worry: mismatch of viewport origin for redo");
1732       }
1733       originalSource.updateHiddenColumns();
1734       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1735       // null
1736       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1737       // viewport.getColumnSelection()
1738       // .getHiddenColumns().size() > 0);
1739       originalSource.firePropertyChange("alignment", null, originalSource
1740               .getAlignment().getSequences());
1741     }
1742   }
1743
1744   AlignmentViewport getOriginatingSource(CommandI command)
1745   {
1746     AlignmentViewport originalSource = null;
1747     // For sequence removal and addition, we need to fire
1748     // the property change event FROM the viewport where the
1749     // original alignment was altered
1750     AlignmentI al = null;
1751     if (command instanceof EditCommand)
1752     {
1753       EditCommand editCommand = (EditCommand) command;
1754       al = editCommand.getAlignment();
1755       List<Component> comps = PaintRefresher.components.get(viewport
1756               .getSequenceSetId());
1757
1758       for (Component comp : comps)
1759       {
1760         if (comp instanceof AlignmentPanel)
1761         {
1762           if (al == ((AlignmentPanel) comp).av.getAlignment())
1763           {
1764             originalSource = ((AlignmentPanel) comp).av;
1765             break;
1766           }
1767         }
1768       }
1769     }
1770
1771     if (originalSource == null)
1772     {
1773       // The original view is closed, we must validate
1774       // the current view against the closed view first
1775       if (al != null)
1776       {
1777         PaintRefresher.validateSequences(al, viewport.getAlignment());
1778       }
1779
1780       originalSource = viewport;
1781     }
1782
1783     return originalSource;
1784   }
1785
1786   /**
1787    * DOCUMENT ME!
1788    *
1789    * @param up
1790    *          DOCUMENT ME!
1791    */
1792   public void moveSelectedSequences(boolean up)
1793   {
1794     SequenceGroup sg = viewport.getSelectionGroup();
1795
1796     if (sg == null)
1797     {
1798       return;
1799     }
1800     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1801             viewport.getHiddenRepSequences(), up);
1802     alignPanel.paintAlignment(true);
1803   }
1804
1805   synchronized void slideSequences(boolean right, int size)
1806   {
1807     List<SequenceI> sg = new ArrayList<>();
1808     if (viewport.cursorMode)
1809     {
1810       sg.add(viewport.getAlignment().getSequenceAt(
1811               alignPanel.getSeqPanel().seqCanvas.cursorY));
1812     }
1813     else if (viewport.getSelectionGroup() != null
1814             && viewport.getSelectionGroup().getSize() != viewport
1815                     .getAlignment().getHeight())
1816     {
1817       sg = viewport.getSelectionGroup().getSequences(
1818               viewport.getHiddenRepSequences());
1819     }
1820
1821     if (sg.size() < 1)
1822     {
1823       return;
1824     }
1825
1826     List<SequenceI> invertGroup = new ArrayList<>();
1827
1828     for (SequenceI seq : viewport.getAlignment().getSequences())
1829     {
1830       if (!sg.contains(seq))
1831       {
1832         invertGroup.add(seq);
1833       }
1834     }
1835
1836     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1837
1838     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1839     for (int i = 0; i < invertGroup.size(); i++)
1840     {
1841       seqs2[i] = invertGroup.get(i);
1842     }
1843
1844     SlideSequencesCommand ssc;
1845     if (right)
1846     {
1847       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1848               size, viewport.getGapCharacter());
1849     }
1850     else
1851     {
1852       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1853               size, viewport.getGapCharacter());
1854     }
1855
1856     int groupAdjustment = 0;
1857     if (ssc.getGapsInsertedBegin() && right)
1858     {
1859       if (viewport.cursorMode)
1860       {
1861         alignPanel.getSeqPanel().moveCursor(size, 0);
1862       }
1863       else
1864       {
1865         groupAdjustment = size;
1866       }
1867     }
1868     else if (!ssc.getGapsInsertedBegin() && !right)
1869     {
1870       if (viewport.cursorMode)
1871       {
1872         alignPanel.getSeqPanel().moveCursor(-size, 0);
1873       }
1874       else
1875       {
1876         groupAdjustment = -size;
1877       }
1878     }
1879
1880     if (groupAdjustment != 0)
1881     {
1882       viewport.getSelectionGroup().setStartRes(
1883               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1884       viewport.getSelectionGroup().setEndRes(
1885               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1886     }
1887
1888     /*
1889      * just extend the last slide command if compatible; but not if in
1890      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1891      */
1892     boolean appendHistoryItem = false;
1893     Deque<CommandI> historyList = viewport.getHistoryList();
1894     boolean inSplitFrame = getSplitViewContainer() != null;
1895     if (!inSplitFrame && historyList != null && historyList.size() > 0
1896             && historyList.peek() instanceof SlideSequencesCommand)
1897     {
1898       appendHistoryItem = ssc
1899               .appendSlideCommand((SlideSequencesCommand) historyList
1900                       .peek());
1901     }
1902
1903     if (!appendHistoryItem)
1904     {
1905       addHistoryItem(ssc);
1906     }
1907
1908     repaint();
1909   }
1910
1911   /**
1912    * DOCUMENT ME!
1913    *
1914    * @param e
1915    *          DOCUMENT ME!
1916    */
1917   @Override
1918   protected void copy_actionPerformed(ActionEvent e)
1919   {
1920     System.gc();
1921     if (viewport.getSelectionGroup() == null)
1922     {
1923       return;
1924     }
1925     // TODO: preserve the ordering of displayed alignment annotation in any
1926     // internal paste (particularly sequence associated annotation)
1927     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1928     String[] omitHidden = null;
1929
1930     if (viewport.hasHiddenColumns())
1931     {
1932       omitHidden = viewport.getViewAsString(true);
1933     }
1934
1935     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1936             seqs, omitHidden, null);
1937
1938     StringSelection ss = new StringSelection(output);
1939
1940     try
1941     {
1942       jalview.gui.Desktop.internalCopy = true;
1943       // Its really worth setting the clipboard contents
1944       // to empty before setting the large StringSelection!!
1945       Toolkit.getDefaultToolkit().getSystemClipboard()
1946               .setContents(new StringSelection(""), null);
1947
1948       Toolkit.getDefaultToolkit().getSystemClipboard()
1949               .setContents(ss, Desktop.instance);
1950     } catch (OutOfMemoryError er)
1951     {
1952       new OOMWarning("copying region", er);
1953       return;
1954     }
1955
1956     ArrayList<int[]> hiddenColumns = null;
1957     if (viewport.hasHiddenColumns())
1958     {
1959       hiddenColumns = new ArrayList<>();
1960       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1961               .getSelectionGroup().getEndRes();
1962       for (int[] region : viewport.getAlignment().getHiddenColumns()
1963               .getHiddenRegions())
1964       {
1965         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1966         {
1967           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1968               region[1] - hiddenOffset });
1969         }
1970       }
1971     }
1972
1973     Desktop.jalviewClipboard = new Object[] { seqs,
1974         viewport.getAlignment().getDataset(), hiddenColumns };
1975     statusBar.setText(MessageManager.formatMessage(
1976             "label.copied_sequences_to_clipboard", new Object[] { Integer
1977                     .valueOf(seqs.length).toString() }));
1978   }
1979
1980   /**
1981    * DOCUMENT ME!
1982    *
1983    * @param e
1984    *          DOCUMENT ME!
1985    * @throws InterruptedException
1986    * @throws IOException
1987    */
1988   @Override
1989   protected void pasteNew_actionPerformed(ActionEvent e)
1990           throws IOException, InterruptedException
1991   {
1992     paste(true);
1993   }
1994
1995   /**
1996    * DOCUMENT ME!
1997    *
1998    * @param e
1999    *          DOCUMENT ME!
2000    * @throws InterruptedException
2001    * @throws IOException
2002    */
2003   @Override
2004   protected void pasteThis_actionPerformed(ActionEvent e)
2005           throws IOException, InterruptedException
2006   {
2007     paste(false);
2008   }
2009
2010   /**
2011    * Paste contents of Jalview clipboard
2012    *
2013    * @param newAlignment
2014    *          true to paste to a new alignment, otherwise add to this.
2015    * @throws InterruptedException
2016    * @throws IOException
2017    */
2018   void paste(boolean newAlignment) throws IOException, InterruptedException
2019   {
2020     boolean externalPaste = true;
2021     try
2022     {
2023       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2024       Transferable contents = c.getContents(this);
2025
2026       if (contents == null)
2027       {
2028         return;
2029       }
2030
2031       String str;
2032       FileFormatI format;
2033       try
2034       {
2035         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2036         if (str.length() < 1)
2037         {
2038           return;
2039         }
2040
2041         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2042
2043       } catch (OutOfMemoryError er)
2044       {
2045         new OOMWarning("Out of memory pasting sequences!!", er);
2046         return;
2047       }
2048
2049       SequenceI[] sequences;
2050       boolean annotationAdded = false;
2051       AlignmentI alignment = null;
2052
2053       if (Desktop.jalviewClipboard != null)
2054       {
2055         // The clipboard was filled from within Jalview, we must use the
2056         // sequences
2057         // And dataset from the copied alignment
2058         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2059         // be doubly sure that we create *new* sequence objects.
2060         sequences = new SequenceI[newseq.length];
2061         for (int i = 0; i < newseq.length; i++)
2062         {
2063           sequences[i] = new Sequence(newseq[i]);
2064         }
2065         alignment = new Alignment(sequences);
2066         externalPaste = false;
2067       }
2068       else
2069       {
2070         // parse the clipboard as an alignment.
2071         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2072                 format);
2073         sequences = alignment.getSequencesArray();
2074       }
2075
2076       int alwidth = 0;
2077       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2078       int fgroup = -1;
2079
2080       if (newAlignment)
2081       {
2082
2083         if (Desktop.jalviewClipboard != null)
2084         {
2085           // dataset is inherited
2086           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2087         }
2088         else
2089         {
2090           // new dataset is constructed
2091           alignment.setDataset(null);
2092         }
2093         alwidth = alignment.getWidth() + 1;
2094       }
2095       else
2096       {
2097         AlignmentI pastedal = alignment; // preserve pasted alignment object
2098         // Add pasted sequences and dataset into existing alignment.
2099         alignment = viewport.getAlignment();
2100         alwidth = alignment.getWidth() + 1;
2101         // decide if we need to import sequences from an existing dataset
2102         boolean importDs = Desktop.jalviewClipboard != null
2103                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2104         // importDs==true instructs us to copy over new dataset sequences from
2105         // an existing alignment
2106         Vector newDs = (importDs) ? new Vector() : null; // used to create
2107         // minimum dataset set
2108
2109         for (int i = 0; i < sequences.length; i++)
2110         {
2111           if (importDs)
2112           {
2113             newDs.addElement(null);
2114           }
2115           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2116           // paste
2117           if (importDs && ds != null)
2118           {
2119             if (!newDs.contains(ds))
2120             {
2121               newDs.setElementAt(ds, i);
2122               ds = new Sequence(ds);
2123               // update with new dataset sequence
2124               sequences[i].setDatasetSequence(ds);
2125             }
2126             else
2127             {
2128               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2129             }
2130           }
2131           else
2132           {
2133             // copy and derive new dataset sequence
2134             sequences[i] = sequences[i].deriveSequence();
2135             alignment.getDataset().addSequence(
2136                     sequences[i].getDatasetSequence());
2137             // TODO: avoid creation of duplicate dataset sequences with a
2138             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2139           }
2140           alignment.addSequence(sequences[i]); // merges dataset
2141         }
2142         if (newDs != null)
2143         {
2144           newDs.clear(); // tidy up
2145         }
2146         if (alignment.getAlignmentAnnotation() != null)
2147         {
2148           for (AlignmentAnnotation alan : alignment
2149                   .getAlignmentAnnotation())
2150           {
2151             if (alan.graphGroup > fgroup)
2152             {
2153               fgroup = alan.graphGroup;
2154             }
2155           }
2156         }
2157         if (pastedal.getAlignmentAnnotation() != null)
2158         {
2159           // Add any annotation attached to alignment.
2160           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2161           for (int i = 0; i < alann.length; i++)
2162           {
2163             annotationAdded = true;
2164             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2165             {
2166               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2167               if (newann.graphGroup > -1)
2168               {
2169                 if (newGraphGroups.size() <= newann.graphGroup
2170                         || newGraphGroups.get(newann.graphGroup) == null)
2171                 {
2172                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2173                   {
2174                     newGraphGroups.add(q, null);
2175                   }
2176                   newGraphGroups.set(newann.graphGroup, new Integer(
2177                           ++fgroup));
2178                 }
2179                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2180                         .intValue();
2181               }
2182
2183               newann.padAnnotation(alwidth);
2184               alignment.addAnnotation(newann);
2185             }
2186           }
2187         }
2188       }
2189       if (!newAlignment)
2190       {
2191         // /////
2192         // ADD HISTORY ITEM
2193         //
2194         addHistoryItem(new EditCommand(
2195                 MessageManager.getString("label.add_sequences"),
2196                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2197       }
2198       // Add any annotations attached to sequences
2199       for (int i = 0; i < sequences.length; i++)
2200       {
2201         if (sequences[i].getAnnotation() != null)
2202         {
2203           AlignmentAnnotation newann;
2204           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2205           {
2206             annotationAdded = true;
2207             newann = sequences[i].getAnnotation()[a];
2208             newann.adjustForAlignment();
2209             newann.padAnnotation(alwidth);
2210             if (newann.graphGroup > -1)
2211             {
2212               if (newann.graphGroup > -1)
2213               {
2214                 if (newGraphGroups.size() <= newann.graphGroup
2215                         || newGraphGroups.get(newann.graphGroup) == null)
2216                 {
2217                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2218                   {
2219                     newGraphGroups.add(q, null);
2220                   }
2221                   newGraphGroups.set(newann.graphGroup, new Integer(
2222                           ++fgroup));
2223                 }
2224                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2225                         .intValue();
2226               }
2227             }
2228             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2229             // was
2230             // duplicated
2231             // earlier
2232             alignment
2233                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2234           }
2235         }
2236       }
2237       if (!newAlignment)
2238       {
2239
2240         // propagate alignment changed.
2241         vpRanges.setEndSeq(alignment.getHeight());
2242         if (annotationAdded)
2243         {
2244           // Duplicate sequence annotation in all views.
2245           AlignmentI[] alview = this.getViewAlignments();
2246           for (int i = 0; i < sequences.length; i++)
2247           {
2248             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2249             if (sann == null)
2250             {
2251               continue;
2252             }
2253             for (int avnum = 0; avnum < alview.length; avnum++)
2254             {
2255               if (alview[avnum] != alignment)
2256               {
2257                 // duplicate in a view other than the one with input focus
2258                 int avwidth = alview[avnum].getWidth() + 1;
2259                 // this relies on sann being preserved after we
2260                 // modify the sequence's annotation array for each duplication
2261                 for (int a = 0; a < sann.length; a++)
2262                 {
2263                   AlignmentAnnotation newann = new AlignmentAnnotation(
2264                           sann[a]);
2265                   sequences[i].addAlignmentAnnotation(newann);
2266                   newann.padAnnotation(avwidth);
2267                   alview[avnum].addAnnotation(newann); // annotation was
2268                   // duplicated earlier
2269                   // TODO JAL-1145 graphGroups are not updated for sequence
2270                   // annotation added to several views. This may cause
2271                   // strangeness
2272                   alview[avnum].setAnnotationIndex(newann, a);
2273                 }
2274               }
2275             }
2276           }
2277           buildSortByAnnotationScoresMenu();
2278         }
2279         viewport.firePropertyChange("alignment", null,
2280                 alignment.getSequences());
2281         if (alignPanels != null)
2282         {
2283           for (AlignmentPanel ap : alignPanels)
2284           {
2285             ap.validateAnnotationDimensions(false);
2286           }
2287         }
2288         else
2289         {
2290           alignPanel.validateAnnotationDimensions(false);
2291         }
2292
2293       }
2294       else
2295       {
2296         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2297                 DEFAULT_HEIGHT);
2298         String newtitle = new String("Copied sequences");
2299
2300         if (Desktop.jalviewClipboard != null
2301                 && Desktop.jalviewClipboard[2] != null)
2302         {
2303           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2304           for (int[] region : hc)
2305           {
2306             af.viewport.hideColumns(region[0], region[1]);
2307           }
2308         }
2309
2310         // >>>This is a fix for the moment, until a better solution is
2311         // found!!<<<
2312         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2313                 .transferSettings(
2314                         alignPanel.getSeqPanel().seqCanvas
2315                                 .getFeatureRenderer());
2316
2317         // TODO: maintain provenance of an alignment, rather than just make the
2318         // title a concatenation of operations.
2319         if (!externalPaste)
2320         {
2321           if (title.startsWith("Copied sequences"))
2322           {
2323             newtitle = title;
2324           }
2325           else
2326           {
2327             newtitle = newtitle.concat("- from " + title);
2328           }
2329         }
2330         else
2331         {
2332           newtitle = new String("Pasted sequences");
2333         }
2334
2335         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2336                 DEFAULT_HEIGHT);
2337
2338       }
2339
2340     } catch (Exception ex)
2341     {
2342       ex.printStackTrace();
2343       System.out.println("Exception whilst pasting: " + ex);
2344       // could be anything being pasted in here
2345     }
2346   }
2347
2348   @Override
2349   protected void expand_newalign(ActionEvent e)
2350   {
2351     try
2352     {
2353       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2354               .getAlignment(), -1);
2355       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2356               DEFAULT_HEIGHT);
2357       String newtitle = new String("Flanking alignment");
2358
2359       if (Desktop.jalviewClipboard != null
2360               && Desktop.jalviewClipboard[2] != null)
2361       {
2362         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2363         for (int region[] : hc)
2364         {
2365           af.viewport.hideColumns(region[0], region[1]);
2366         }
2367       }
2368
2369       // >>>This is a fix for the moment, until a better solution is
2370       // found!!<<<
2371       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2372               .transferSettings(
2373                       alignPanel.getSeqPanel().seqCanvas
2374                               .getFeatureRenderer());
2375
2376       // TODO: maintain provenance of an alignment, rather than just make the
2377       // title a concatenation of operations.
2378       {
2379         if (title.startsWith("Copied sequences"))
2380         {
2381           newtitle = title;
2382         }
2383         else
2384         {
2385           newtitle = newtitle.concat("- from " + title);
2386         }
2387       }
2388
2389       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2390
2391     } catch (Exception ex)
2392     {
2393       ex.printStackTrace();
2394       System.out.println("Exception whilst pasting: " + ex);
2395       // could be anything being pasted in here
2396     } catch (OutOfMemoryError oom)
2397     {
2398       new OOMWarning("Viewing flanking region of alignment", oom);
2399     }
2400   }
2401
2402   /**
2403    * DOCUMENT ME!
2404    *
2405    * @param e
2406    *          DOCUMENT ME!
2407    */
2408   @Override
2409   protected void cut_actionPerformed(ActionEvent e)
2410   {
2411     copy_actionPerformed(null);
2412     delete_actionPerformed(null);
2413   }
2414
2415   /**
2416    * DOCUMENT ME!
2417    *
2418    * @param e
2419    *          DOCUMENT ME!
2420    */
2421   @Override
2422   protected void delete_actionPerformed(ActionEvent evt)
2423   {
2424
2425     SequenceGroup sg = viewport.getSelectionGroup();
2426     if (sg == null)
2427     {
2428       return;
2429     }
2430
2431     /*
2432      * If the cut affects all sequences, warn, remove highlighted columns
2433      */
2434     if (sg.getSize() == viewport.getAlignment().getHeight())
2435     {
2436       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2437               .getAlignment().getWidth()) ? true : false;
2438       if (isEntireAlignWidth)
2439       {
2440         int confirm = JvOptionPane.showConfirmDialog(this,
2441                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2442                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2443                 JvOptionPane.OK_CANCEL_OPTION);
2444
2445         if (confirm == JvOptionPane.CANCEL_OPTION
2446                 || confirm == JvOptionPane.CLOSED_OPTION)
2447         {
2448           return;
2449         }
2450       }
2451       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2452               sg.getEndRes() + 1);
2453     }
2454     SequenceI[] cut = sg.getSequences()
2455             .toArray(new SequenceI[sg.getSize()]);
2456
2457     addHistoryItem(new EditCommand(
2458             MessageManager.getString("label.cut_sequences"), Action.CUT,
2459             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2460             viewport.getAlignment()));
2461
2462     viewport.setSelectionGroup(null);
2463     viewport.sendSelection();
2464     viewport.getAlignment().deleteGroup(sg);
2465
2466     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2467             .getSequences());
2468     if (viewport.getAlignment().getHeight() < 1)
2469     {
2470       try
2471       {
2472         this.setClosed(true);
2473       } catch (Exception ex)
2474       {
2475       }
2476     }
2477   }
2478
2479   /**
2480    * DOCUMENT ME!
2481    *
2482    * @param e
2483    *          DOCUMENT ME!
2484    */
2485   @Override
2486   protected void deleteGroups_actionPerformed(ActionEvent e)
2487   {
2488     if (avc.deleteGroups())
2489     {
2490       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2491       alignPanel.updateAnnotation();
2492       alignPanel.paintAlignment(true);
2493     }
2494   }
2495
2496   /**
2497    * DOCUMENT ME!
2498    *
2499    * @param e
2500    *          DOCUMENT ME!
2501    */
2502   @Override
2503   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2504   {
2505     SequenceGroup sg = new SequenceGroup();
2506
2507     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2508     {
2509       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2510     }
2511
2512     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2513     viewport.setSelectionGroup(sg);
2514     viewport.sendSelection();
2515     // JAL-2034 - should delegate to
2516     // alignPanel to decide if overview needs
2517     // updating.
2518     alignPanel.paintAlignment(false);
2519     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2520   }
2521
2522   /**
2523    * DOCUMENT ME!
2524    *
2525    * @param e
2526    *          DOCUMENT ME!
2527    */
2528   @Override
2529   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2530   {
2531     if (viewport.cursorMode)
2532     {
2533       alignPanel.getSeqPanel().keyboardNo1 = null;
2534       alignPanel.getSeqPanel().keyboardNo2 = null;
2535     }
2536     viewport.setSelectionGroup(null);
2537     viewport.getColumnSelection().clear();
2538     viewport.setSelectionGroup(null);
2539     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2540     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2541     // JAL-2034 - should delegate to
2542     // alignPanel to decide if overview needs
2543     // updating.
2544     alignPanel.paintAlignment(false);
2545     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2546     viewport.sendSelection();
2547   }
2548
2549   /**
2550    * DOCUMENT ME!
2551    *
2552    * @param e
2553    *          DOCUMENT ME!
2554    */
2555   @Override
2556   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2557   {
2558     SequenceGroup sg = viewport.getSelectionGroup();
2559
2560     if (sg == null)
2561     {
2562       selectAllSequenceMenuItem_actionPerformed(null);
2563
2564       return;
2565     }
2566
2567     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2568     {
2569       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2570     }
2571     // JAL-2034 - should delegate to
2572     // alignPanel to decide if overview needs
2573     // updating.
2574
2575     alignPanel.paintAlignment(true);
2576     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2577     viewport.sendSelection();
2578   }
2579
2580   @Override
2581   public void invertColSel_actionPerformed(ActionEvent e)
2582   {
2583     viewport.invertColumnSelection();
2584     alignPanel.paintAlignment(true);
2585     viewport.sendSelection();
2586   }
2587
2588   /**
2589    * DOCUMENT ME!
2590    *
2591    * @param e
2592    *          DOCUMENT ME!
2593    */
2594   @Override
2595   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2596   {
2597     trimAlignment(true);
2598   }
2599
2600   /**
2601    * DOCUMENT ME!
2602    *
2603    * @param e
2604    *          DOCUMENT ME!
2605    */
2606   @Override
2607   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2608   {
2609     trimAlignment(false);
2610   }
2611
2612   void trimAlignment(boolean trimLeft)
2613   {
2614     ColumnSelection colSel = viewport.getColumnSelection();
2615     int column;
2616
2617     if (!colSel.isEmpty())
2618     {
2619       if (trimLeft)
2620       {
2621         column = colSel.getMin();
2622       }
2623       else
2624       {
2625         column = colSel.getMax();
2626       }
2627
2628       SequenceI[] seqs;
2629       if (viewport.getSelectionGroup() != null)
2630       {
2631         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2632                 viewport.getHiddenRepSequences());
2633       }
2634       else
2635       {
2636         seqs = viewport.getAlignment().getSequencesArray();
2637       }
2638
2639       TrimRegionCommand trimRegion;
2640       if (trimLeft)
2641       {
2642         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2643                 column, viewport.getAlignment());
2644         vpRanges.setStartRes(0);
2645       }
2646       else
2647       {
2648         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2649                 column, viewport.getAlignment());
2650       }
2651
2652       statusBar.setText(MessageManager.formatMessage(
2653               "label.removed_columns",
2654               new String[] { Integer.valueOf(trimRegion.getSize())
2655                       .toString() }));
2656
2657       addHistoryItem(trimRegion);
2658
2659       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2660       {
2661         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2662                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2663         {
2664           viewport.getAlignment().deleteGroup(sg);
2665         }
2666       }
2667
2668       viewport.firePropertyChange("alignment", null, viewport
2669               .getAlignment().getSequences());
2670     }
2671   }
2672
2673   /**
2674    * DOCUMENT ME!
2675    *
2676    * @param e
2677    *          DOCUMENT ME!
2678    */
2679   @Override
2680   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2681   {
2682     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2683
2684     SequenceI[] seqs;
2685     if (viewport.getSelectionGroup() != null)
2686     {
2687       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2688               viewport.getHiddenRepSequences());
2689       start = viewport.getSelectionGroup().getStartRes();
2690       end = viewport.getSelectionGroup().getEndRes();
2691     }
2692     else
2693     {
2694       seqs = viewport.getAlignment().getSequencesArray();
2695     }
2696
2697     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2698             "Remove Gapped Columns", seqs, start, end,
2699             viewport.getAlignment());
2700
2701     addHistoryItem(removeGapCols);
2702
2703     statusBar.setText(MessageManager.formatMessage(
2704             "label.removed_empty_columns",
2705             new Object[] { Integer.valueOf(removeGapCols.getSize())
2706                     .toString() }));
2707
2708     // This is to maintain viewport position on first residue
2709     // of first sequence
2710     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2711     int startRes = seq.findPosition(vpRanges.getStartRes());
2712     // ShiftList shifts;
2713     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2714     // edit.alColumnChanges=shifts.getInverse();
2715     // if (viewport.hasHiddenColumns)
2716     // viewport.getColumnSelection().compensateForEdits(shifts);
2717     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2718     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2719             .getSequences());
2720
2721   }
2722
2723   /**
2724    * DOCUMENT ME!
2725    *
2726    * @param e
2727    *          DOCUMENT ME!
2728    */
2729   @Override
2730   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2731   {
2732     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2733
2734     SequenceI[] seqs;
2735     if (viewport.getSelectionGroup() != null)
2736     {
2737       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2738               viewport.getHiddenRepSequences());
2739       start = viewport.getSelectionGroup().getStartRes();
2740       end = viewport.getSelectionGroup().getEndRes();
2741     }
2742     else
2743     {
2744       seqs = viewport.getAlignment().getSequencesArray();
2745     }
2746
2747     // This is to maintain viewport position on first residue
2748     // of first sequence
2749     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2750     int startRes = seq.findPosition(vpRanges.getStartRes());
2751
2752     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2753             viewport.getAlignment()));
2754
2755     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2756
2757     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2758             .getSequences());
2759
2760   }
2761
2762   /**
2763    * DOCUMENT ME!
2764    *
2765    * @param e
2766    *          DOCUMENT ME!
2767    */
2768   @Override
2769   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2770   {
2771     viewport.setPadGaps(padGapsMenuitem.isSelected());
2772     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2773             .getSequences());
2774   }
2775
2776   /**
2777    * DOCUMENT ME!
2778    *
2779    * @param e
2780    *          DOCUMENT ME!
2781    */
2782   @Override
2783   public void findMenuItem_actionPerformed(ActionEvent e)
2784   {
2785     new Finder();
2786   }
2787
2788   /**
2789    * Create a new view of the current alignment.
2790    */
2791   @Override
2792   public void newView_actionPerformed(ActionEvent e)
2793   {
2794     newView(null, true);
2795   }
2796
2797   /**
2798    * Creates and shows a new view of the current alignment.
2799    *
2800    * @param viewTitle
2801    *          title of newly created view; if null, one will be generated
2802    * @param copyAnnotation
2803    *          if true then duplicate all annnotation, groups and settings
2804    * @return new alignment panel, already displayed.
2805    */
2806   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2807   {
2808     /*
2809      * Create a new AlignmentPanel (with its own, new Viewport)
2810      */
2811     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2812             true);
2813     if (!copyAnnotation)
2814     {
2815       /*
2816        * remove all groups and annotation except for the automatic stuff
2817        */
2818       newap.av.getAlignment().deleteAllGroups();
2819       newap.av.getAlignment().deleteAllAnnotations(false);
2820     }
2821
2822     newap.av.setGatherViewsHere(false);
2823
2824     if (viewport.viewName == null)
2825     {
2826       viewport.viewName = MessageManager
2827               .getString("label.view_name_original");
2828     }
2829
2830     /*
2831      * Views share the same edits undo and redo stacks
2832      */
2833     newap.av.setHistoryList(viewport.getHistoryList());
2834     newap.av.setRedoList(viewport.getRedoList());
2835
2836     /*
2837      * Views share the same mappings; need to deregister any new mappings
2838      * created by copyAlignPanel, and register the new reference to the shared
2839      * mappings
2840      */
2841     newap.av.replaceMappings(viewport.getAlignment());
2842
2843     /*
2844      * start up cDNA consensus (if applicable) now mappings are in place
2845      */
2846     if (newap.av.initComplementConsensus())
2847     {
2848       newap.refresh(true); // adjust layout of annotations
2849     }
2850
2851     newap.av.viewName = getNewViewName(viewTitle);
2852
2853     addAlignmentPanel(newap, true);
2854     newap.alignmentChanged();
2855
2856     if (alignPanels.size() == 2)
2857     {
2858       viewport.setGatherViewsHere(true);
2859     }
2860     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2861     return newap;
2862   }
2863
2864   /**
2865    * Make a new name for the view, ensuring it is unique within the current
2866    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2867    * these now use viewId. Unique view names are still desirable for usability.)
2868    *
2869    * @param viewTitle
2870    * @return
2871    */
2872   protected String getNewViewName(String viewTitle)
2873   {
2874     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2875     boolean addFirstIndex = false;
2876     if (viewTitle == null || viewTitle.trim().length() == 0)
2877     {
2878       viewTitle = MessageManager.getString("action.view");
2879       addFirstIndex = true;
2880     }
2881     else
2882     {
2883       index = 1;// we count from 1 if given a specific name
2884     }
2885     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2886
2887     List<Component> comps = PaintRefresher.components.get(viewport
2888             .getSequenceSetId());
2889
2890     List<String> existingNames = getExistingViewNames(comps);
2891
2892     while (existingNames.contains(newViewName))
2893     {
2894       newViewName = viewTitle + " " + (++index);
2895     }
2896     return newViewName;
2897   }
2898
2899   /**
2900    * Returns a list of distinct view names found in the given list of
2901    * components. View names are held on the viewport of an AlignmentPanel.
2902    *
2903    * @param comps
2904    * @return
2905    */
2906   protected List<String> getExistingViewNames(List<Component> comps)
2907   {
2908     List<String> existingNames = new ArrayList<>();
2909     for (Component comp : comps)
2910     {
2911       if (comp instanceof AlignmentPanel)
2912       {
2913         AlignmentPanel ap = (AlignmentPanel) comp;
2914         if (!existingNames.contains(ap.av.viewName))
2915         {
2916           existingNames.add(ap.av.viewName);
2917         }
2918       }
2919     }
2920     return existingNames;
2921   }
2922
2923   /**
2924    * Explode tabbed views into separate windows.
2925    */
2926   @Override
2927   public void expandViews_actionPerformed(ActionEvent e)
2928   {
2929     Desktop.explodeViews(this);
2930   }
2931
2932   /**
2933    * Gather views in separate windows back into a tabbed presentation.
2934    */
2935   @Override
2936   public void gatherViews_actionPerformed(ActionEvent e)
2937   {
2938     Desktop.instance.gatherViews(this);
2939   }
2940
2941   /**
2942    * DOCUMENT ME!
2943    *
2944    * @param e
2945    *          DOCUMENT ME!
2946    */
2947   @Override
2948   public void font_actionPerformed(ActionEvent e)
2949   {
2950     new FontChooser(alignPanel);
2951   }
2952
2953   /**
2954    * DOCUMENT ME!
2955    *
2956    * @param e
2957    *          DOCUMENT ME!
2958    */
2959   @Override
2960   protected void seqLimit_actionPerformed(ActionEvent e)
2961   {
2962     viewport.setShowJVSuffix(seqLimits.isSelected());
2963
2964     alignPanel.getIdPanel().getIdCanvas()
2965             .setPreferredSize(alignPanel.calculateIdWidth());
2966     alignPanel.paintAlignment(true);
2967   }
2968
2969   @Override
2970   public void idRightAlign_actionPerformed(ActionEvent e)
2971   {
2972     viewport.setRightAlignIds(idRightAlign.isSelected());
2973     alignPanel.paintAlignment(true);
2974   }
2975
2976   @Override
2977   public void centreColumnLabels_actionPerformed(ActionEvent e)
2978   {
2979     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2980     alignPanel.paintAlignment(true);
2981   }
2982
2983   /*
2984    * (non-Javadoc)
2985    *
2986    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2987    */
2988   @Override
2989   protected void followHighlight_actionPerformed()
2990   {
2991     /*
2992      * Set the 'follow' flag on the Viewport (and scroll to position if now
2993      * true).
2994      */
2995     final boolean state = this.followHighlightMenuItem.getState();
2996     viewport.setFollowHighlight(state);
2997     if (state)
2998     {
2999       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3000     }
3001   }
3002
3003   /**
3004    * DOCUMENT ME!
3005    *
3006    * @param e
3007    *          DOCUMENT ME!
3008    */
3009   @Override
3010   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3011   {
3012     viewport.setColourText(colourTextMenuItem.isSelected());
3013     alignPanel.paintAlignment(true);
3014   }
3015
3016   /**
3017    * DOCUMENT ME!
3018    *
3019    * @param e
3020    *          DOCUMENT ME!
3021    */
3022   @Override
3023   public void wrapMenuItem_actionPerformed(ActionEvent e)
3024   {
3025     scaleAbove.setVisible(wrapMenuItem.isSelected());
3026     scaleLeft.setVisible(wrapMenuItem.isSelected());
3027     scaleRight.setVisible(wrapMenuItem.isSelected());
3028     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3029     alignPanel.updateLayout();
3030   }
3031
3032   @Override
3033   public void showAllSeqs_actionPerformed(ActionEvent e)
3034   {
3035     viewport.showAllHiddenSeqs();
3036   }
3037
3038   @Override
3039   public void showAllColumns_actionPerformed(ActionEvent e)
3040   {
3041     viewport.showAllHiddenColumns();
3042     repaint();
3043     viewport.sendSelection();
3044   }
3045
3046   @Override
3047   public void hideSelSequences_actionPerformed(ActionEvent e)
3048   {
3049     viewport.hideAllSelectedSeqs();
3050     // alignPanel.paintAlignment(true);
3051   }
3052
3053   /**
3054    * called by key handler and the hide all/show all menu items
3055    *
3056    * @param toggleSeqs
3057    * @param toggleCols
3058    */
3059   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3060   {
3061
3062     boolean hide = false;
3063     SequenceGroup sg = viewport.getSelectionGroup();
3064     if (!toggleSeqs && !toggleCols)
3065     {
3066       // Hide everything by the current selection - this is a hack - we do the
3067       // invert and then hide
3068       // first check that there will be visible columns after the invert.
3069       if (viewport.hasSelectedColumns()
3070               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3071                       .getEndRes()))
3072       {
3073         // now invert the sequence set, if required - empty selection implies
3074         // that no hiding is required.
3075         if (sg != null)
3076         {
3077           invertSequenceMenuItem_actionPerformed(null);
3078           sg = viewport.getSelectionGroup();
3079           toggleSeqs = true;
3080
3081         }
3082         viewport.expandColSelection(sg, true);
3083         // finally invert the column selection and get the new sequence
3084         // selection.
3085         invertColSel_actionPerformed(null);
3086         toggleCols = true;
3087       }
3088     }
3089
3090     if (toggleSeqs)
3091     {
3092       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3093       {
3094         hideSelSequences_actionPerformed(null);
3095         hide = true;
3096       }
3097       else if (!(toggleCols && viewport.hasSelectedColumns()))
3098       {
3099         showAllSeqs_actionPerformed(null);
3100       }
3101     }
3102
3103     if (toggleCols)
3104     {
3105       if (viewport.hasSelectedColumns())
3106       {
3107         hideSelColumns_actionPerformed(null);
3108         if (!toggleSeqs)
3109         {
3110           viewport.setSelectionGroup(sg);
3111         }
3112       }
3113       else if (!hide)
3114       {
3115         showAllColumns_actionPerformed(null);
3116       }
3117     }
3118   }
3119
3120   /*
3121    * (non-Javadoc)
3122    *
3123    * @see
3124    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3125    * event.ActionEvent)
3126    */
3127   @Override
3128   public void hideAllButSelection_actionPerformed(ActionEvent e)
3129   {
3130     toggleHiddenRegions(false, false);
3131     viewport.sendSelection();
3132   }
3133
3134   /*
3135    * (non-Javadoc)
3136    *
3137    * @see
3138    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3139    * .ActionEvent)
3140    */
3141   @Override
3142   public void hideAllSelection_actionPerformed(ActionEvent e)
3143   {
3144     SequenceGroup sg = viewport.getSelectionGroup();
3145     viewport.expandColSelection(sg, false);
3146     viewport.hideAllSelectedSeqs();
3147     viewport.hideSelectedColumns();
3148     alignPanel.paintAlignment(true);
3149     viewport.sendSelection();
3150   }
3151
3152   /*
3153    * (non-Javadoc)
3154    *
3155    * @see
3156    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3157    * ActionEvent)
3158    */
3159   @Override
3160   public void showAllhidden_actionPerformed(ActionEvent e)
3161   {
3162     viewport.showAllHiddenColumns();
3163     viewport.showAllHiddenSeqs();
3164     alignPanel.paintAlignment(true);
3165     viewport.sendSelection();
3166   }
3167
3168   @Override
3169   public void hideSelColumns_actionPerformed(ActionEvent e)
3170   {
3171     viewport.hideSelectedColumns();
3172     alignPanel.paintAlignment(true);
3173     viewport.sendSelection();
3174   }
3175
3176   @Override
3177   public void hiddenMarkers_actionPerformed(ActionEvent e)
3178   {
3179     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3180     repaint();
3181   }
3182
3183   /**
3184    * DOCUMENT ME!
3185    *
3186    * @param e
3187    *          DOCUMENT ME!
3188    */
3189   @Override
3190   protected void scaleAbove_actionPerformed(ActionEvent e)
3191   {
3192     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3193     alignPanel.paintAlignment(true);
3194   }
3195
3196   /**
3197    * DOCUMENT ME!
3198    *
3199    * @param e
3200    *          DOCUMENT ME!
3201    */
3202   @Override
3203   protected void scaleLeft_actionPerformed(ActionEvent e)
3204   {
3205     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3206     alignPanel.paintAlignment(true);
3207   }
3208
3209   /**
3210    * DOCUMENT ME!
3211    *
3212    * @param e
3213    *          DOCUMENT ME!
3214    */
3215   @Override
3216   protected void scaleRight_actionPerformed(ActionEvent e)
3217   {
3218     viewport.setScaleRightWrapped(scaleRight.isSelected());
3219     alignPanel.paintAlignment(true);
3220   }
3221
3222   /**
3223    * DOCUMENT ME!
3224    *
3225    * @param e
3226    *          DOCUMENT ME!
3227    */
3228   @Override
3229   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3230   {
3231     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3232     alignPanel.paintAlignment(true);
3233   }
3234
3235   /**
3236    * DOCUMENT ME!
3237    *
3238    * @param e
3239    *          DOCUMENT ME!
3240    */
3241   @Override
3242   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3243   {
3244     viewport.setShowText(viewTextMenuItem.isSelected());
3245     alignPanel.paintAlignment(true);
3246   }
3247
3248   /**
3249    * DOCUMENT ME!
3250    *
3251    * @param e
3252    *          DOCUMENT ME!
3253    */
3254   @Override
3255   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3256   {
3257     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3258     alignPanel.paintAlignment(true);
3259   }
3260
3261   public FeatureSettings featureSettings;
3262
3263   @Override
3264   public FeatureSettingsControllerI getFeatureSettingsUI()
3265   {
3266     return featureSettings;
3267   }
3268
3269   @Override
3270   public void featureSettings_actionPerformed(ActionEvent e)
3271   {
3272     if (featureSettings != null)
3273     {
3274       featureSettings.close();
3275       featureSettings = null;
3276     }
3277     if (!showSeqFeatures.isSelected())
3278     {
3279       // make sure features are actually displayed
3280       showSeqFeatures.setSelected(true);
3281       showSeqFeatures_actionPerformed(null);
3282     }
3283     featureSettings = new FeatureSettings(this);
3284   }
3285
3286   /**
3287    * Set or clear 'Show Sequence Features'
3288    *
3289    * @param evt
3290    *          DOCUMENT ME!
3291    */
3292   @Override
3293   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3294   {
3295     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3296     alignPanel.paintAlignment(true);
3297     if (alignPanel.getOverviewPanel() != null)
3298     {
3299       alignPanel.getOverviewPanel().updateOverviewImage();
3300     }
3301   }
3302
3303   /**
3304    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3305    * the annotations panel as a whole.
3306    *
3307    * The options to show/hide all annotations should be enabled when the panel
3308    * is shown, and disabled when the panel is hidden.
3309    *
3310    * @param e
3311    */
3312   @Override
3313   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3314   {
3315     final boolean setVisible = annotationPanelMenuItem.isSelected();
3316     viewport.setShowAnnotation(setVisible);
3317     this.showAllSeqAnnotations.setEnabled(setVisible);
3318     this.hideAllSeqAnnotations.setEnabled(setVisible);
3319     this.showAllAlAnnotations.setEnabled(setVisible);
3320     this.hideAllAlAnnotations.setEnabled(setVisible);
3321     alignPanel.updateLayout();
3322   }
3323
3324   @Override
3325   public void alignmentProperties()
3326   {
3327     JEditorPane editPane = new JEditorPane("text/html", "");
3328     editPane.setEditable(false);
3329     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3330             .formatAsHtml();
3331     editPane.setText(MessageManager.formatMessage("label.html_content",
3332             new Object[] { contents.toString() }));
3333     JInternalFrame frame = new JInternalFrame();
3334     frame.getContentPane().add(new JScrollPane(editPane));
3335
3336     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3337             "label.alignment_properties", new Object[] { getTitle() }),
3338             500, 400);
3339   }
3340
3341   /**
3342    * DOCUMENT ME!
3343    *
3344    * @param e
3345    *          DOCUMENT ME!
3346    */
3347   @Override
3348   public void overviewMenuItem_actionPerformed(ActionEvent e)
3349   {
3350     if (alignPanel.overviewPanel != null)
3351     {
3352       return;
3353     }
3354
3355     JInternalFrame frame = new JInternalFrame();
3356     OverviewPanel overview = new OverviewPanel(alignPanel);
3357     frame.setContentPane(overview);
3358     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3359             "label.overview_params", new Object[] { this.getTitle() }),
3360             true, frame.getWidth(), frame.getHeight(), true, true);
3361     frame.pack();
3362     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3363     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3364     {
3365       @Override
3366       public void internalFrameClosed(
3367               javax.swing.event.InternalFrameEvent evt)
3368       {
3369         alignPanel.setOverviewPanel(null);
3370       };
3371     });
3372
3373     alignPanel.setOverviewPanel(overview);
3374   }
3375
3376   @Override
3377   public void textColour_actionPerformed()
3378   {
3379     new TextColourChooser().chooseColour(alignPanel, null);
3380   }
3381
3382   /*
3383    * public void covariationColour_actionPerformed() {
3384    * changeColour(new
3385    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3386    * ()[0])); }
3387    */
3388   @Override
3389   public void annotationColour_actionPerformed()
3390   {
3391     new AnnotationColourChooser(viewport, alignPanel);
3392   }
3393
3394   @Override
3395   public void annotationColumn_actionPerformed(ActionEvent e)
3396   {
3397     new AnnotationColumnChooser(viewport, alignPanel);
3398   }
3399
3400   /**
3401    * Action on the user checking or unchecking the option to apply the selected
3402    * colour scheme to all groups. If unchecked, groups may have their own
3403    * independent colour schemes.
3404    *
3405    * @param selected
3406    */
3407   @Override
3408   public void applyToAllGroups_actionPerformed(boolean selected)
3409   {
3410     viewport.setColourAppliesToAllGroups(selected);
3411   }
3412
3413   /**
3414    * Action on user selecting a colour from the colour menu
3415    *
3416    * @param name
3417    *          the name (not the menu item label!) of the colour scheme
3418    */
3419   @Override
3420   public void changeColour_actionPerformed(String name)
3421   {
3422     /*
3423      * 'User Defined' opens a panel to configure or load a
3424      * user-defined colour scheme
3425      */
3426     if (ResidueColourScheme.USER_DEFINED.equals(name))
3427     {
3428       new UserDefinedColours(alignPanel);
3429       return;
3430     }
3431
3432     /*
3433      * otherwise set the chosen colour scheme (or null for 'None')
3434      */
3435     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3436             viewport.getAlignment(), viewport.getHiddenRepSequences());
3437     changeColour(cs);
3438   }
3439
3440   /**
3441    * Actions on setting or changing the alignment colour scheme
3442    *
3443    * @param cs
3444    */
3445   @Override
3446   public void changeColour(ColourSchemeI cs)
3447   {
3448     // TODO: pull up to controller method
3449     ColourMenuHelper.setColourSelected(colourMenu, cs);
3450
3451     viewport.setGlobalColourScheme(cs);
3452
3453     alignPanel.paintAlignment(true);
3454   }
3455
3456   /**
3457    * Show the PID threshold slider panel
3458    */
3459   @Override
3460   protected void modifyPID_actionPerformed()
3461   {
3462     SliderPanel.setPIDSliderSource(alignPanel,
3463             viewport.getResidueShading(), alignPanel.getViewName());
3464     SliderPanel.showPIDSlider();
3465   }
3466
3467   /**
3468    * Show the Conservation slider panel
3469    */
3470   @Override
3471   protected void modifyConservation_actionPerformed()
3472   {
3473     SliderPanel.setConservationSlider(alignPanel,
3474             viewport.getResidueShading(), alignPanel.getViewName());
3475     SliderPanel.showConservationSlider();
3476   }
3477
3478   /**
3479    * Action on selecting or deselecting (Colour) By Conservation
3480    */
3481   @Override
3482   public void conservationMenuItem_actionPerformed(boolean selected)
3483   {
3484     modifyConservation.setEnabled(selected);
3485     viewport.setConservationSelected(selected);
3486     viewport.getResidueShading().setConservationApplied(selected);
3487
3488     changeColour(viewport.getGlobalColourScheme());
3489     if (selected)
3490     {
3491       modifyConservation_actionPerformed();
3492     }
3493     else
3494     {
3495       SliderPanel.hideConservationSlider();
3496     }
3497   }
3498
3499   /**
3500    * Action on selecting or deselecting (Colour) Above PID Threshold
3501    */
3502   @Override
3503   public void abovePIDThreshold_actionPerformed(boolean selected)
3504   {
3505     modifyPID.setEnabled(selected);
3506     viewport.setAbovePIDThreshold(selected);
3507     if (!selected)
3508     {
3509       viewport.getResidueShading().setThreshold(0,
3510               viewport.isIgnoreGapsConsensus());
3511     }
3512
3513     changeColour(viewport.getGlobalColourScheme());
3514     if (selected)
3515     {
3516       modifyPID_actionPerformed();
3517     }
3518     else
3519     {
3520       SliderPanel.hidePIDSlider();
3521     }
3522   }
3523
3524   /**
3525    * DOCUMENT ME!
3526    *
3527    * @param e
3528    *          DOCUMENT ME!
3529    */
3530   @Override
3531   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3532   {
3533     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3534     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3535             .getAlignment().getSequenceAt(0));
3536     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3537             viewport.getAlignment()));
3538     alignPanel.paintAlignment(true);
3539   }
3540
3541   /**
3542    * DOCUMENT ME!
3543    *
3544    * @param e
3545    *          DOCUMENT ME!
3546    */
3547   @Override
3548   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3549   {
3550     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3551     AlignmentSorter.sortByID(viewport.getAlignment());
3552     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3553             viewport.getAlignment()));
3554     alignPanel.paintAlignment(true);
3555   }
3556
3557   /**
3558    * DOCUMENT ME!
3559    *
3560    * @param e
3561    *          DOCUMENT ME!
3562    */
3563   @Override
3564   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3565   {
3566     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3567     AlignmentSorter.sortByLength(viewport.getAlignment());
3568     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3569             viewport.getAlignment()));
3570     alignPanel.paintAlignment(true);
3571   }
3572
3573   /**
3574    * DOCUMENT ME!
3575    *
3576    * @param e
3577    *          DOCUMENT ME!
3578    */
3579   @Override
3580   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3581   {
3582     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3583     AlignmentSorter.sortByGroup(viewport.getAlignment());
3584     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3585             viewport.getAlignment()));
3586
3587     alignPanel.paintAlignment(true);
3588   }
3589
3590   /**
3591    * DOCUMENT ME!
3592    *
3593    * @param e
3594    *          DOCUMENT ME!
3595    */
3596   @Override
3597   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3598   {
3599     new RedundancyPanel(alignPanel, this);
3600   }
3601
3602   /**
3603    * DOCUMENT ME!
3604    *
3605    * @param e
3606    *          DOCUMENT ME!
3607    */
3608   @Override
3609   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3610   {
3611     if ((viewport.getSelectionGroup() == null)
3612             || (viewport.getSelectionGroup().getSize() < 2))
3613     {
3614       JvOptionPane.showInternalMessageDialog(this, MessageManager
3615               .getString("label.you_must_select_least_two_sequences"),
3616               MessageManager.getString("label.invalid_selection"),
3617               JvOptionPane.WARNING_MESSAGE);
3618     }
3619     else
3620     {
3621       JInternalFrame frame = new JInternalFrame();
3622       frame.setContentPane(new PairwiseAlignPanel(viewport));
3623       Desktop.addInternalFrame(frame,
3624               MessageManager.getString("action.pairwise_alignment"), 600,
3625               500);
3626     }
3627   }
3628
3629   @Override
3630   public void autoCalculate_actionPerformed(ActionEvent e)
3631   {
3632     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3633     if (viewport.autoCalculateConsensus)
3634     {
3635       viewport.firePropertyChange("alignment", null, viewport
3636               .getAlignment().getSequences());
3637     }
3638   }
3639
3640   @Override
3641   public void sortByTreeOption_actionPerformed(ActionEvent e)
3642   {
3643     viewport.sortByTree = sortByTree.isSelected();
3644   }
3645
3646   @Override
3647   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3648   {
3649     viewport.followSelection = listenToViewSelections.isSelected();
3650   }
3651
3652   /**
3653    * Constructs a tree panel and adds it to the desktop
3654    *
3655    * @param type
3656    *          tree type (NJ or AV)
3657    * @param modelName
3658    *          name of score model used to compute the tree
3659    * @param options
3660    *          parameters for the distance or similarity calculation
3661    */
3662   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3663   {
3664     String frameTitle = "";
3665     TreePanel tp;
3666
3667     boolean onSelection = false;
3668     if (viewport.getSelectionGroup() != null
3669             && viewport.getSelectionGroup().getSize() > 0)
3670     {
3671       SequenceGroup sg = viewport.getSelectionGroup();
3672
3673       /* Decide if the selection is a column region */
3674       for (SequenceI _s : sg.getSequences())
3675       {
3676         if (_s.getLength() < sg.getEndRes())
3677         {
3678           JvOptionPane
3679                   .showMessageDialog(
3680                           Desktop.desktop,
3681                           MessageManager
3682                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3683                           MessageManager
3684                                   .getString("label.sequences_selection_not_aligned"),
3685                           JvOptionPane.WARNING_MESSAGE);
3686
3687           return;
3688         }
3689       }
3690       onSelection = true;
3691     }
3692     else
3693     {
3694       if (viewport.getAlignment().getHeight() < 2)
3695       {
3696         return;
3697       }
3698     }
3699
3700     tp = new TreePanel(alignPanel, type, modelName, options);
3701     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3702
3703     frameTitle += " from ";
3704
3705     if (viewport.viewName != null)
3706     {
3707       frameTitle += viewport.viewName + " of ";
3708     }
3709
3710     frameTitle += this.title;
3711
3712     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3713   }
3714
3715   /**
3716    * DOCUMENT ME!
3717    *
3718    * @param title
3719    *          DOCUMENT ME!
3720    * @param order
3721    *          DOCUMENT ME!
3722    */
3723   public void addSortByOrderMenuItem(String title,
3724           final AlignmentOrder order)
3725   {
3726     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3727             "action.by_title_param", new Object[] { title }));
3728     sort.add(item);
3729     item.addActionListener(new java.awt.event.ActionListener()
3730     {
3731       @Override
3732       public void actionPerformed(ActionEvent e)
3733       {
3734         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3735
3736         // TODO: JBPNote - have to map order entries to curent SequenceI
3737         // pointers
3738         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3739
3740         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3741                 .getAlignment()));
3742
3743         alignPanel.paintAlignment(true);
3744       }
3745     });
3746   }
3747
3748   /**
3749    * Add a new sort by annotation score menu item
3750    *
3751    * @param sort
3752    *          the menu to add the option to
3753    * @param scoreLabel
3754    *          the label used to retrieve scores for each sequence on the
3755    *          alignment
3756    */
3757   public void addSortByAnnotScoreMenuItem(JMenu sort,
3758           final String scoreLabel)
3759   {
3760     final JMenuItem item = new JMenuItem(scoreLabel);
3761     sort.add(item);
3762     item.addActionListener(new java.awt.event.ActionListener()
3763     {
3764       @Override
3765       public void actionPerformed(ActionEvent e)
3766       {
3767         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3768         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3769                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3770         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3771                 viewport.getAlignment()));
3772         alignPanel.paintAlignment(true);
3773       }
3774     });
3775   }
3776
3777   /**
3778    * last hash for alignment's annotation array - used to minimise cost of
3779    * rebuild.
3780    */
3781   protected int _annotationScoreVectorHash;
3782
3783   /**
3784    * search the alignment and rebuild the sort by annotation score submenu the
3785    * last alignment annotation vector hash is stored to minimize cost of
3786    * rebuilding in subsequence calls.
3787    *
3788    */
3789   @Override
3790   public void buildSortByAnnotationScoresMenu()
3791   {
3792     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3793     {
3794       return;
3795     }
3796
3797     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3798     {
3799       sortByAnnotScore.removeAll();
3800       // almost certainly a quicker way to do this - but we keep it simple
3801       Hashtable scoreSorts = new Hashtable();
3802       AlignmentAnnotation aann[];
3803       for (SequenceI sqa : viewport.getAlignment().getSequences())
3804       {
3805         aann = sqa.getAnnotation();
3806         for (int i = 0; aann != null && i < aann.length; i++)
3807         {
3808           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3809           {
3810             scoreSorts.put(aann[i].label, aann[i].label);
3811           }
3812         }
3813       }
3814       Enumeration labels = scoreSorts.keys();
3815       while (labels.hasMoreElements())
3816       {
3817         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3818                 (String) labels.nextElement());
3819       }
3820       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3821       scoreSorts.clear();
3822
3823       _annotationScoreVectorHash = viewport.getAlignment()
3824               .getAlignmentAnnotation().hashCode();
3825     }
3826   }
3827
3828   /**
3829    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3830    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3831    * call. Listeners are added to remove the menu item when the treePanel is
3832    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3833    * modified.
3834    */
3835   @Override
3836   public void buildTreeSortMenu()
3837   {
3838     sortByTreeMenu.removeAll();
3839
3840     List<Component> comps = PaintRefresher.components.get(viewport
3841             .getSequenceSetId());
3842     List<TreePanel> treePanels = new ArrayList<>();
3843     for (Component comp : comps)
3844     {
3845       if (comp instanceof TreePanel)
3846       {
3847         treePanels.add((TreePanel) comp);
3848       }
3849     }
3850
3851     if (treePanels.size() < 1)
3852     {
3853       sortByTreeMenu.setVisible(false);
3854       return;
3855     }
3856
3857     sortByTreeMenu.setVisible(true);
3858
3859     for (final TreePanel tp : treePanels)
3860     {
3861       final JMenuItem item = new JMenuItem(tp.getTitle());
3862       item.addActionListener(new java.awt.event.ActionListener()
3863       {
3864         @Override
3865         public void actionPerformed(ActionEvent e)
3866         {
3867           tp.sortByTree_actionPerformed();
3868           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3869
3870         }
3871       });
3872
3873       sortByTreeMenu.add(item);
3874     }
3875   }
3876
3877   public boolean sortBy(AlignmentOrder alorder, String undoname)
3878   {
3879     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3880     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3881     if (undoname != null)
3882     {
3883       addHistoryItem(new OrderCommand(undoname, oldOrder,
3884               viewport.getAlignment()));
3885     }
3886     alignPanel.paintAlignment(true);
3887     return true;
3888   }
3889
3890   /**
3891    * Work out whether the whole set of sequences or just the selected set will
3892    * be submitted for multiple alignment.
3893    *
3894    */
3895   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3896   {
3897     // Now, check we have enough sequences
3898     AlignmentView msa = null;
3899
3900     if ((viewport.getSelectionGroup() != null)
3901             && (viewport.getSelectionGroup().getSize() > 1))
3902     {
3903       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3904       // some common interface!
3905       /*
3906        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3907        * SequenceI[sz = seqs.getSize(false)];
3908        *
3909        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3910        * seqs.getSequenceAt(i); }
3911        */
3912       msa = viewport.getAlignmentView(true);
3913     }
3914     else if (viewport.getSelectionGroup() != null
3915             && viewport.getSelectionGroup().getSize() == 1)
3916     {
3917       int option = JvOptionPane.showConfirmDialog(this,
3918               MessageManager.getString("warn.oneseq_msainput_selection"),
3919               MessageManager.getString("label.invalid_selection"),
3920               JvOptionPane.OK_CANCEL_OPTION);
3921       if (option == JvOptionPane.OK_OPTION)
3922       {
3923         msa = viewport.getAlignmentView(false);
3924       }
3925     }
3926     else
3927     {
3928       msa = viewport.getAlignmentView(false);
3929     }
3930     return msa;
3931   }
3932
3933   /**
3934    * Decides what is submitted to a secondary structure prediction service: the
3935    * first sequence in the alignment, or in the current selection, or, if the
3936    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3937    * region or the whole alignment. (where the first sequence in the set is the
3938    * one that the prediction will be for).
3939    */
3940   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3941   {
3942     AlignmentView seqs = null;
3943
3944     if ((viewport.getSelectionGroup() != null)
3945             && (viewport.getSelectionGroup().getSize() > 0))
3946     {
3947       seqs = viewport.getAlignmentView(true);
3948     }
3949     else
3950     {
3951       seqs = viewport.getAlignmentView(false);
3952     }
3953     // limit sequences - JBPNote in future - could spawn multiple prediction
3954     // jobs
3955     // TODO: viewport.getAlignment().isAligned is a global state - the local
3956     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3957     if (!viewport.getAlignment().isAligned(false))
3958     {
3959       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3960       // TODO: if seqs.getSequences().length>1 then should really have warned
3961       // user!
3962
3963     }
3964     return seqs;
3965   }
3966
3967   /**
3968    * DOCUMENT ME!
3969    *
3970    * @param e
3971    *          DOCUMENT ME!
3972    */
3973   @Override
3974   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3975   {
3976     // Pick the tree file
3977     JalviewFileChooser chooser = new JalviewFileChooser(
3978             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3979     chooser.setFileView(new JalviewFileView());
3980     chooser.setDialogTitle(MessageManager
3981             .getString("label.select_newick_like_tree_file"));
3982     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3983
3984     int value = chooser.showOpenDialog(null);
3985
3986     if (value == JalviewFileChooser.APPROVE_OPTION)
3987     {
3988       String filePath = chooser.getSelectedFile().getPath();
3989       Cache.setProperty("LAST_DIRECTORY", filePath);
3990       NewickFile fin = null;
3991       try
3992       {
3993         fin = new NewickFile(filePath, DataSourceType.FILE);
3994         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3995       } catch (Exception ex)
3996       {
3997         JvOptionPane
3998                 .showMessageDialog(
3999                         Desktop.desktop,
4000                         ex.getMessage(),
4001                         MessageManager
4002                                 .getString("label.problem_reading_tree_file"),
4003                         JvOptionPane.WARNING_MESSAGE);
4004         ex.printStackTrace();
4005       }
4006       if (fin != null && fin.hasWarningMessage())
4007       {
4008         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4009                 .getWarningMessage(), MessageManager
4010                 .getString("label.possible_problem_with_tree_file"),
4011                 JvOptionPane.WARNING_MESSAGE);
4012       }
4013     }
4014   }
4015
4016   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4017   {
4018     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4019   }
4020
4021   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4022           int h, int x, int y)
4023   {
4024     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4025   }
4026
4027   /**
4028    * Add a treeviewer for the tree extracted from a Newick file object to the
4029    * current alignment view
4030    *
4031    * @param nf
4032    *          the tree
4033    * @param title
4034    *          tree viewer title
4035    * @param input
4036    *          Associated alignment input data (or null)
4037    * @param w
4038    *          width
4039    * @param h
4040    *          height
4041    * @param x
4042    *          position
4043    * @param y
4044    *          position
4045    * @return TreePanel handle
4046    */
4047   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4048           AlignmentView input, int w, int h, int x, int y)
4049   {
4050     TreePanel tp = null;
4051
4052     try
4053     {
4054       nf.parse();
4055
4056       if (nf.getTree() != null)
4057       {
4058         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4059
4060         tp.setSize(w, h);
4061
4062         if (x > 0 && y > 0)
4063         {
4064           tp.setLocation(x, y);
4065         }
4066
4067         Desktop.addInternalFrame(tp, treeTitle, w, h);
4068       }
4069     } catch (Exception ex)
4070     {
4071       ex.printStackTrace();
4072     }
4073
4074     return tp;
4075   }
4076
4077   private boolean buildingMenu = false;
4078
4079   /**
4080    * Generates menu items and listener event actions for web service clients
4081    *
4082    */
4083   public void BuildWebServiceMenu()
4084   {
4085     while (buildingMenu)
4086     {
4087       try
4088       {
4089         System.err.println("Waiting for building menu to finish.");
4090         Thread.sleep(10);
4091       } catch (Exception e)
4092       {
4093       }
4094     }
4095     final AlignFrame me = this;
4096     buildingMenu = true;
4097     new Thread(new Runnable()
4098     {
4099       @Override
4100       public void run()
4101       {
4102         final List<JMenuItem> legacyItems = new ArrayList<>();
4103         try
4104         {
4105           // System.err.println("Building ws menu again "
4106           // + Thread.currentThread());
4107           // TODO: add support for context dependent disabling of services based
4108           // on
4109           // alignment and current selection
4110           // TODO: add additional serviceHandle parameter to specify abstract
4111           // handler
4112           // class independently of AbstractName
4113           // TODO: add in rediscovery GUI function to restart discoverer
4114           // TODO: group services by location as well as function and/or
4115           // introduce
4116           // object broker mechanism.
4117           final Vector<JMenu> wsmenu = new Vector<>();
4118           final IProgressIndicator af = me;
4119
4120           /*
4121            * do not i18n these strings - they are hard-coded in class
4122            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4123            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4124            */
4125           final JMenu msawsmenu = new JMenu("Alignment");
4126           final JMenu secstrmenu = new JMenu(
4127                   "Secondary Structure Prediction");
4128           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4129           final JMenu analymenu = new JMenu("Analysis");
4130           final JMenu dismenu = new JMenu("Protein Disorder");
4131           // JAL-940 - only show secondary structure prediction services from
4132           // the legacy server
4133           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4134               // &&
4135           Discoverer.services != null && (Discoverer.services.size() > 0))
4136           {
4137             // TODO: refactor to allow list of AbstractName/Handler bindings to
4138             // be
4139             // stored or retrieved from elsewhere
4140             // No MSAWS used any more:
4141             // Vector msaws = null; // (Vector)
4142             // Discoverer.services.get("MsaWS");
4143             Vector secstrpr = (Vector) Discoverer.services
4144                     .get("SecStrPred");
4145             if (secstrpr != null)
4146             {
4147               // Add any secondary structure prediction services
4148               for (int i = 0, j = secstrpr.size(); i < j; i++)
4149               {
4150                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4151                         .get(i);
4152                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4153                         .getServiceClient(sh);
4154                 int p = secstrmenu.getItemCount();
4155                 impl.attachWSMenuEntry(secstrmenu, me);
4156                 int q = secstrmenu.getItemCount();
4157                 for (int litm = p; litm < q; litm++)
4158                 {
4159                   legacyItems.add(secstrmenu.getItem(litm));
4160                 }
4161               }
4162             }
4163           }
4164
4165           // Add all submenus in the order they should appear on the web
4166           // services menu
4167           wsmenu.add(msawsmenu);
4168           wsmenu.add(secstrmenu);
4169           wsmenu.add(dismenu);
4170           wsmenu.add(analymenu);
4171           // No search services yet
4172           // wsmenu.add(seqsrchmenu);
4173
4174           javax.swing.SwingUtilities.invokeLater(new Runnable()
4175           {
4176             @Override
4177             public void run()
4178             {
4179               try
4180               {
4181                 webService.removeAll();
4182                 // first, add discovered services onto the webservices menu
4183                 if (wsmenu.size() > 0)
4184                 {
4185                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4186                   {
4187                     webService.add(wsmenu.get(i));
4188                   }
4189                 }
4190                 else
4191                 {
4192                   webService.add(me.webServiceNoServices);
4193                 }
4194                 // TODO: move into separate menu builder class.
4195                 boolean new_sspred = false;
4196                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4197                 {
4198                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4199                   if (jws2servs != null)
4200                   {
4201                     if (jws2servs.hasServices())
4202                     {
4203                       jws2servs.attachWSMenuEntry(webService, me);
4204                       for (Jws2Instance sv : jws2servs.getServices())
4205                       {
4206                         if (sv.description.toLowerCase().contains("jpred"))
4207                         {
4208                           for (JMenuItem jmi : legacyItems)
4209                           {
4210                             jmi.setVisible(false);
4211                           }
4212                         }
4213                       }
4214
4215                     }
4216                     if (jws2servs.isRunning())
4217                     {
4218                       JMenuItem tm = new JMenuItem(
4219                               "Still discovering JABA Services");
4220                       tm.setEnabled(false);
4221                       webService.add(tm);
4222                     }
4223                   }
4224                 }
4225                 build_urlServiceMenu(me.webService);
4226                 build_fetchdbmenu(webService);
4227                 for (JMenu item : wsmenu)
4228                 {
4229                   if (item.getItemCount() == 0)
4230                   {
4231                     item.setEnabled(false);
4232                   }
4233                   else
4234                   {
4235                     item.setEnabled(true);
4236                   }
4237                 }
4238               } catch (Exception e)
4239               {
4240                 Cache.log
4241                         .debug("Exception during web service menu building process.",
4242                                 e);
4243               }
4244             }
4245           });
4246         } catch (Exception e)
4247         {
4248         }
4249         buildingMenu = false;
4250       }
4251     }).start();
4252
4253   }
4254
4255   /**
4256    * construct any groupURL type service menu entries.
4257    *
4258    * @param webService
4259    */
4260   private void build_urlServiceMenu(JMenu webService)
4261   {
4262     // TODO: remove this code when 2.7 is released
4263     // DEBUG - alignmentView
4264     /*
4265      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4266      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4267      *
4268      * @Override public void actionPerformed(ActionEvent e) {
4269      * jalview.datamodel.AlignmentView
4270      * .testSelectionViews(af.viewport.getAlignment(),
4271      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4272      *
4273      * }); webService.add(testAlView);
4274      */
4275     // TODO: refactor to RestClient discoverer and merge menu entries for
4276     // rest-style services with other types of analysis/calculation service
4277     // SHmmr test client - still being implemented.
4278     // DEBUG - alignmentView
4279
4280     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4281             .getRestClients())
4282     {
4283       client.attachWSMenuEntry(
4284               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4285               this);
4286     }
4287   }
4288
4289   /**
4290    * Searches the alignment sequences for xRefs and builds the Show
4291    * Cross-References menu (formerly called Show Products), with database
4292    * sources for which cross-references are found (protein sources for a
4293    * nucleotide alignment and vice versa)
4294    *
4295    * @return true if Show Cross-references menu should be enabled
4296    */
4297   public boolean canShowProducts()
4298   {
4299     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4300     AlignmentI dataset = viewport.getAlignment().getDataset();
4301
4302     showProducts.removeAll();
4303     final boolean dna = viewport.getAlignment().isNucleotide();
4304
4305     if (seqs == null || seqs.length == 0)
4306     {
4307       // nothing to see here.
4308       return false;
4309     }
4310
4311     boolean showp = false;
4312     try
4313     {
4314       List<String> ptypes = new CrossRef(seqs, dataset)
4315               .findXrefSourcesForSequences(dna);
4316
4317       for (final String source : ptypes)
4318       {
4319         showp = true;
4320         final AlignFrame af = this;
4321         JMenuItem xtype = new JMenuItem(source);
4322         xtype.addActionListener(new ActionListener()
4323         {
4324           @Override
4325           public void actionPerformed(ActionEvent e)
4326           {
4327             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4328           }
4329         });
4330         showProducts.add(xtype);
4331       }
4332       showProducts.setVisible(showp);
4333       showProducts.setEnabled(showp);
4334     } catch (Exception e)
4335     {
4336       Cache.log
4337               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4338                       e);
4339       return false;
4340     }
4341     return showp;
4342   }
4343
4344   /**
4345    * Finds and displays cross-references for the selected sequences (protein
4346    * products for nucleotide sequences, dna coding sequences for peptides).
4347    *
4348    * @param sel
4349    *          the sequences to show cross-references for
4350    * @param dna
4351    *          true if from a nucleotide alignment (so showing proteins)
4352    * @param source
4353    *          the database to show cross-references for
4354    */
4355   protected void showProductsFor(final SequenceI[] sel,
4356           final boolean _odna, final String source)
4357   {
4358     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4359             .start();
4360   }
4361
4362   /**
4363    * Construct and display a new frame containing the translation of this
4364    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4365    */
4366   @Override
4367   public void showTranslation_actionPerformed(ActionEvent e)
4368   {
4369     AlignmentI al = null;
4370     try
4371     {
4372       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4373
4374       al = dna.translateCdna();
4375     } catch (Exception ex)
4376     {
4377       jalview.bin.Cache.log.error(
4378               "Exception during translation. Please report this !", ex);
4379       final String msg = MessageManager
4380               .getString("label.error_when_translating_sequences_submit_bug_report");
4381       final String errorTitle = MessageManager
4382               .getString("label.implementation_error")
4383               + MessageManager.getString("label.translation_failed");
4384       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4385               JvOptionPane.ERROR_MESSAGE);
4386       return;
4387     }
4388     if (al == null || al.getHeight() == 0)
4389     {
4390       final String msg = MessageManager
4391               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4392       final String errorTitle = MessageManager
4393               .getString("label.translation_failed");
4394       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4395               JvOptionPane.WARNING_MESSAGE);
4396     }
4397     else
4398     {
4399       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4400       af.setFileFormat(this.currentFileFormat);
4401       final String newTitle = MessageManager.formatMessage(
4402               "label.translation_of_params",
4403               new Object[] { this.getTitle() });
4404       af.setTitle(newTitle);
4405       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4406       {
4407         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4408         viewport.openSplitFrame(af, new Alignment(seqs));
4409       }
4410       else
4411       {
4412         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4413                 DEFAULT_HEIGHT);
4414       }
4415     }
4416   }
4417
4418   /**
4419    * Set the file format
4420    *
4421    * @param format
4422    */
4423   public void setFileFormat(FileFormatI format)
4424   {
4425     this.currentFileFormat = format;
4426   }
4427
4428   /**
4429    * Try to load a features file onto the alignment.
4430    *
4431    * @param file
4432    *          contents or path to retrieve file
4433    * @param sourceType
4434    *          access mode of file (see jalview.io.AlignFile)
4435    * @return true if features file was parsed correctly.
4436    */
4437   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4438   {
4439     return avc.parseFeaturesFile(file, sourceType,
4440             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4441
4442   }
4443
4444   @Override
4445   public void refreshFeatureUI(boolean enableIfNecessary)
4446   {
4447     // note - currently this is only still here rather than in the controller
4448     // because of the featureSettings hard reference that is yet to be
4449     // abstracted
4450     if (enableIfNecessary)
4451     {
4452       viewport.setShowSequenceFeatures(true);
4453       showSeqFeatures.setSelected(true);
4454     }
4455
4456   }
4457
4458   @Override
4459   public void dragEnter(DropTargetDragEvent evt)
4460   {
4461   }
4462
4463   @Override
4464   public void dragExit(DropTargetEvent evt)
4465   {
4466   }
4467
4468   @Override
4469   public void dragOver(DropTargetDragEvent evt)
4470   {
4471   }
4472
4473   @Override
4474   public void dropActionChanged(DropTargetDragEvent evt)
4475   {
4476   }
4477
4478   @Override
4479   public void drop(DropTargetDropEvent evt)
4480   {
4481     // JAL-1552 - acceptDrop required before getTransferable call for
4482     // Java's Transferable for native dnd
4483     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4484     Transferable t = evt.getTransferable();
4485     List<String> files = new ArrayList<>();
4486     List<DataSourceType> protocols = new ArrayList<>();
4487
4488     try
4489     {
4490       Desktop.transferFromDropTarget(files, protocols, evt, t);
4491     } catch (Exception e)
4492     {
4493       e.printStackTrace();
4494     }
4495     if (files != null)
4496     {
4497       try
4498       {
4499         // check to see if any of these files have names matching sequences in
4500         // the alignment
4501         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4502                 .getAlignment().getSequencesArray());
4503         /**
4504          * Object[] { String,SequenceI}
4505          */
4506         ArrayList<Object[]> filesmatched = new ArrayList<>();
4507         ArrayList<String> filesnotmatched = new ArrayList<>();
4508         for (int i = 0; i < files.size(); i++)
4509         {
4510           String file = files.get(i).toString();
4511           String pdbfn = "";
4512           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4513           if (protocol == DataSourceType.FILE)
4514           {
4515             File fl = new File(file);
4516             pdbfn = fl.getName();
4517           }
4518           else if (protocol == DataSourceType.URL)
4519           {
4520             URL url = new URL(file);
4521             pdbfn = url.getFile();
4522           }
4523           if (pdbfn.length() > 0)
4524           {
4525             // attempt to find a match in the alignment
4526             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4527             int l = 0, c = pdbfn.indexOf(".");
4528             while (mtch == null && c != -1)
4529             {
4530               do
4531               {
4532                 l = c;
4533               } while ((c = pdbfn.indexOf(".", l)) > l);
4534               if (l > -1)
4535               {
4536                 pdbfn = pdbfn.substring(0, l);
4537               }
4538               mtch = idm.findAllIdMatches(pdbfn);
4539             }
4540             if (mtch != null)
4541             {
4542               FileFormatI type = null;
4543               try
4544               {
4545                 type = new IdentifyFile().identify(file, protocol);
4546               } catch (Exception ex)
4547               {
4548                 type = null;
4549               }
4550               if (type != null && type.isStructureFile())
4551               {
4552                 filesmatched.add(new Object[] { file, protocol, mtch });
4553                 continue;
4554               }
4555             }
4556             // File wasn't named like one of the sequences or wasn't a PDB file.
4557             filesnotmatched.add(file);
4558           }
4559         }
4560         int assocfiles = 0;
4561         if (filesmatched.size() > 0)
4562         {
4563           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4564                   || JvOptionPane
4565                           .showConfirmDialog(
4566                                   this,
4567                                   MessageManager
4568                                           .formatMessage(
4569                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4570                                                   new Object[] { Integer
4571                                                           .valueOf(
4572                                                                   filesmatched
4573                                                                           .size())
4574                                                           .toString() }),
4575                                   MessageManager
4576                                           .getString("label.automatically_associate_structure_files_by_name"),
4577                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4578
4579           {
4580             for (Object[] fm : filesmatched)
4581             {
4582               // try and associate
4583               // TODO: may want to set a standard ID naming formalism for
4584               // associating PDB files which have no IDs.
4585               for (SequenceI toassoc : (SequenceI[]) fm[2])
4586               {
4587                 PDBEntry pe = new AssociatePdbFileWithSeq()
4588                         .associatePdbWithSeq((String) fm[0],
4589                                 (DataSourceType) fm[1], toassoc, false,
4590                                 Desktop.instance);
4591                 if (pe != null)
4592                 {
4593                   System.err.println("Associated file : "
4594                           + ((String) fm[0]) + " with "
4595                           + toassoc.getDisplayId(true));
4596                   assocfiles++;
4597                 }
4598               }
4599               alignPanel.paintAlignment(true);
4600             }
4601           }
4602         }
4603         if (filesnotmatched.size() > 0)
4604         {
4605           if (assocfiles > 0
4606                   && (Cache.getDefault(
4607                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4608                           .showConfirmDialog(
4609                                   this,
4610                                   "<html>"
4611                                           + MessageManager
4612                                                   .formatMessage(
4613                                                           "label.ignore_unmatched_dropped_files_info",
4614                                                           new Object[] { Integer
4615                                                                   .valueOf(
4616                                                                           filesnotmatched
4617                                                                                   .size())
4618                                                                   .toString() })
4619                                           + "</html>",
4620                                   MessageManager
4621                                           .getString("label.ignore_unmatched_dropped_files"),
4622                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4623           {
4624             return;
4625           }
4626           for (String fn : filesnotmatched)
4627           {
4628             loadJalviewDataFile(fn, null, null, null);
4629           }
4630
4631         }
4632       } catch (Exception ex)
4633       {
4634         ex.printStackTrace();
4635       }
4636     }
4637   }
4638
4639   /**
4640    * Attempt to load a "dropped" file or URL string, by testing in turn for
4641    * <ul>
4642    * <li>an Annotation file</li>
4643    * <li>a JNet file</li>
4644    * <li>a features file</li>
4645    * <li>else try to interpret as an alignment file</li>
4646    * </ul>
4647    *
4648    * @param file
4649    *          either a filename or a URL string.
4650    * @throws InterruptedException
4651    * @throws IOException
4652    */
4653   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4654           FileFormatI format, SequenceI assocSeq)
4655   {
4656     try
4657     {
4658       if (sourceType == null)
4659       {
4660         sourceType = FormatAdapter.checkProtocol(file);
4661       }
4662       // if the file isn't identified, or not positively identified as some
4663       // other filetype (PFAM is default unidentified alignment file type) then
4664       // try to parse as annotation.
4665       boolean isAnnotation = (format == null || FileFormat.Pfam
4666               .equals(format)) ? new AnnotationFile()
4667               .annotateAlignmentView(viewport, file, sourceType) : false;
4668
4669       if (!isAnnotation)
4670       {
4671         // first see if its a T-COFFEE score file
4672         TCoffeeScoreFile tcf = null;
4673         try
4674         {
4675           tcf = new TCoffeeScoreFile(file, sourceType);
4676           if (tcf.isValid())
4677           {
4678             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4679             {
4680               buildColourMenu();
4681               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4682               isAnnotation = true;
4683               statusBar
4684                       .setText(MessageManager
4685                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4686             }
4687             else
4688             {
4689               // some problem - if no warning its probable that the ID matching
4690               // process didn't work
4691               JvOptionPane
4692                       .showMessageDialog(
4693                               Desktop.desktop,
4694                               tcf.getWarningMessage() == null ? MessageManager
4695                                       .getString("label.check_file_matches_sequence_ids_alignment")
4696                                       : tcf.getWarningMessage(),
4697                               MessageManager
4698                                       .getString("label.problem_reading_tcoffee_score_file"),
4699                               JvOptionPane.WARNING_MESSAGE);
4700             }
4701           }
4702           else
4703           {
4704             tcf = null;
4705           }
4706         } catch (Exception x)
4707         {
4708           Cache.log
4709                   .debug("Exception when processing data source as T-COFFEE score file",
4710                           x);
4711           tcf = null;
4712         }
4713         if (tcf == null)
4714         {
4715           // try to see if its a JNet 'concise' style annotation file *before*
4716           // we
4717           // try to parse it as a features file
4718           if (format == null)
4719           {
4720             format = new IdentifyFile().identify(file, sourceType);
4721           }
4722           if (FileFormat.ScoreMatrix == format)
4723           {
4724             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4725                     sourceType));
4726             sm.parse();
4727             // todo: i18n this message
4728             statusBar
4729                     .setText(MessageManager.formatMessage(
4730                             "label.successfully_loaded_matrix",
4731                             sm.getMatrixName()));
4732           }
4733           else if (FileFormat.Jnet.equals(format))
4734           {
4735             JPredFile predictions = new JPredFile(file, sourceType);
4736             new JnetAnnotationMaker();
4737             JnetAnnotationMaker.add_annotation(predictions,
4738                     viewport.getAlignment(), 0, false);
4739             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4740             viewport.getAlignment().setSeqrep(repseq);
4741             HiddenColumns cs = new HiddenColumns();
4742             cs.hideInsertionsFor(repseq);
4743             viewport.getAlignment().setHiddenColumns(cs);
4744             isAnnotation = true;
4745           }
4746           // else if (IdentifyFile.FeaturesFile.equals(format))
4747           else if (FileFormat.Features.equals(format))
4748           {
4749             if (parseFeaturesFile(file, sourceType))
4750             {
4751               alignPanel.paintAlignment(true);
4752             }
4753           }
4754           else
4755           {
4756             new FileLoader().LoadFile(viewport, file, sourceType, format);
4757           }
4758         }
4759       }
4760       if (isAnnotation)
4761       {
4762         alignPanel.adjustAnnotationHeight();
4763         viewport.updateSequenceIdColours();
4764         buildSortByAnnotationScoresMenu();
4765         alignPanel.paintAlignment(true);
4766       }
4767     } catch (Exception ex)
4768     {
4769       ex.printStackTrace();
4770     } catch (OutOfMemoryError oom)
4771     {
4772       try
4773       {
4774         System.gc();
4775       } catch (Exception x)
4776       {
4777       }
4778       new OOMWarning(
4779               "loading data "
4780                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4781                               : "using " + sourceType + " from " + file)
4782                               : ".")
4783                       + (format != null ? "(parsing as '" + format
4784                               + "' file)" : ""), oom, Desktop.desktop);
4785     }
4786   }
4787
4788   /**
4789    * Method invoked by the ChangeListener on the tabbed pane, in other words
4790    * when a different tabbed pane is selected by the user or programmatically.
4791    */
4792   @Override
4793   public void tabSelectionChanged(int index)
4794   {
4795     if (index > -1)
4796     {
4797       alignPanel = alignPanels.get(index);
4798       viewport = alignPanel.av;
4799       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4800       setMenusFromViewport(viewport);
4801     }
4802
4803     /*
4804      * 'focus' any colour slider that is open to the selected viewport
4805      */
4806     if (viewport.getConservationSelected())
4807     {
4808       SliderPanel.setConservationSlider(alignPanel,
4809               viewport.getResidueShading(), alignPanel.getViewName());
4810     }
4811     else
4812     {
4813       SliderPanel.hideConservationSlider();
4814     }
4815     if (viewport.getAbovePIDThreshold())
4816     {
4817       SliderPanel.setPIDSliderSource(alignPanel,
4818               viewport.getResidueShading(), alignPanel.getViewName());
4819     }
4820     else
4821     {
4822       SliderPanel.hidePIDSlider();
4823     }
4824
4825     /*
4826      * If there is a frame linked to this one in a SplitPane, switch it to the
4827      * same view tab index. No infinite recursion of calls should happen, since
4828      * tabSelectionChanged() should not get invoked on setting the selected
4829      * index to an unchanged value. Guard against setting an invalid index
4830      * before the new view peer tab has been created.
4831      */
4832     final AlignViewportI peer = viewport.getCodingComplement();
4833     if (peer != null)
4834     {
4835       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4836       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4837       {
4838         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4839       }
4840     }
4841   }
4842
4843   /**
4844    * On right mouse click on view tab, prompt for and set new view name.
4845    */
4846   @Override
4847   public void tabbedPane_mousePressed(MouseEvent e)
4848   {
4849     if (e.isPopupTrigger())
4850     {
4851       String msg = MessageManager.getString("label.enter_view_name");
4852       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4853               JvOptionPane.QUESTION_MESSAGE);
4854
4855       if (reply != null)
4856       {
4857         viewport.viewName = reply;
4858         // TODO warn if reply is in getExistingViewNames()?
4859         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4860       }
4861     }
4862   }
4863
4864   public AlignViewport getCurrentView()
4865   {
4866     return viewport;
4867   }
4868
4869   /**
4870    * Open the dialog for regex description parsing.
4871    */
4872   @Override
4873   protected void extractScores_actionPerformed(ActionEvent e)
4874   {
4875     ParseProperties pp = new jalview.analysis.ParseProperties(
4876             viewport.getAlignment());
4877     // TODO: verify regex and introduce GUI dialog for version 2.5
4878     // if (pp.getScoresFromDescription("col", "score column ",
4879     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4880     // true)>0)
4881     if (pp.getScoresFromDescription("description column",
4882             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4883     {
4884       buildSortByAnnotationScoresMenu();
4885     }
4886   }
4887
4888   /*
4889    * (non-Javadoc)
4890    *
4891    * @see
4892    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4893    * )
4894    */
4895   @Override
4896   protected void showDbRefs_actionPerformed(ActionEvent e)
4897   {
4898     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4899   }
4900
4901   /*
4902    * (non-Javadoc)
4903    *
4904    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4905    * ActionEvent)
4906    */
4907   @Override
4908   protected void showNpFeats_actionPerformed(ActionEvent e)
4909   {
4910     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4911   }
4912
4913   /**
4914    * find the viewport amongst the tabs in this alignment frame and close that
4915    * tab
4916    *
4917    * @param av
4918    */
4919   public boolean closeView(AlignViewportI av)
4920   {
4921     if (viewport == av)
4922     {
4923       this.closeMenuItem_actionPerformed(false);
4924       return true;
4925     }
4926     Component[] comp = tabbedPane.getComponents();
4927     for (int i = 0; comp != null && i < comp.length; i++)
4928     {
4929       if (comp[i] instanceof AlignmentPanel)
4930       {
4931         if (((AlignmentPanel) comp[i]).av == av)
4932         {
4933           // close the view.
4934           closeView((AlignmentPanel) comp[i]);
4935           return true;
4936         }
4937       }
4938     }
4939     return false;
4940   }
4941
4942   protected void build_fetchdbmenu(JMenu webService)
4943   {
4944     // Temporary hack - DBRef Fetcher always top level ws entry.
4945     // TODO We probably want to store a sequence database checklist in
4946     // preferences and have checkboxes.. rather than individual sources selected
4947     // here
4948     final JMenu rfetch = new JMenu(
4949             MessageManager.getString("action.fetch_db_references"));
4950     rfetch.setToolTipText(MessageManager
4951             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4952     webService.add(rfetch);
4953
4954     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4955             MessageManager.getString("option.trim_retrieved_seqs"));
4956     trimrs.setToolTipText(MessageManager
4957             .getString("label.trim_retrieved_sequences"));
4958     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4959     trimrs.addActionListener(new ActionListener()
4960     {
4961       @Override
4962       public void actionPerformed(ActionEvent e)
4963       {
4964         trimrs.setSelected(trimrs.isSelected());
4965         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4966                 Boolean.valueOf(trimrs.isSelected()).toString());
4967       };
4968     });
4969     rfetch.add(trimrs);
4970     JMenuItem fetchr = new JMenuItem(
4971             MessageManager.getString("label.standard_databases"));
4972     fetchr.setToolTipText(MessageManager
4973             .getString("label.fetch_embl_uniprot"));
4974     fetchr.addActionListener(new ActionListener()
4975     {
4976
4977       @Override
4978       public void actionPerformed(ActionEvent e)
4979       {
4980         new Thread(new Runnable()
4981         {
4982           @Override
4983           public void run()
4984           {
4985             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4986                     .getAlignment().isNucleotide();
4987             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4988                     .getSequenceSelection(), alignPanel.alignFrame, null,
4989                     alignPanel.alignFrame.featureSettings, isNucleotide);
4990             dbRefFetcher.addListener(new FetchFinishedListenerI()
4991             {
4992               @Override
4993               public void finished()
4994               {
4995                 AlignFrame.this.setMenusForViewport();
4996               }
4997             });
4998             dbRefFetcher.fetchDBRefs(false);
4999           }
5000         }).start();
5001
5002       }
5003
5004     });
5005     rfetch.add(fetchr);
5006     final AlignFrame me = this;
5007     new Thread(new Runnable()
5008     {
5009       @Override
5010       public void run()
5011       {
5012         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5013                 .getSequenceFetcherSingleton(me);
5014         javax.swing.SwingUtilities.invokeLater(new Runnable()
5015         {
5016           @Override
5017           public void run()
5018           {
5019             String[] dbclasses = sf.getOrderedSupportedSources();
5020             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5021             // jalview.util.QuickSort.sort(otherdb, otherdb);
5022             List<DbSourceProxy> otherdb;
5023             JMenu dfetch = new JMenu();
5024             JMenu ifetch = new JMenu();
5025             JMenuItem fetchr = null;
5026             int comp = 0, icomp = 0, mcomp = 15;
5027             String mname = null;
5028             int dbi = 0;
5029             for (String dbclass : dbclasses)
5030             {
5031               otherdb = sf.getSourceProxy(dbclass);
5032               // add a single entry for this class, or submenu allowing 'fetch
5033               // all' or pick one
5034               if (otherdb == null || otherdb.size() < 1)
5035               {
5036                 continue;
5037               }
5038               // List<DbSourceProxy> dbs=otherdb;
5039               // otherdb=new ArrayList<DbSourceProxy>();
5040               // for (DbSourceProxy db:dbs)
5041               // {
5042               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5043               // }
5044               if (mname == null)
5045               {
5046                 mname = "From " + dbclass;
5047               }
5048               if (otherdb.size() == 1)
5049               {
5050                 final DbSourceProxy[] dassource = otherdb
5051                         .toArray(new DbSourceProxy[0]);
5052                 DbSourceProxy src = otherdb.get(0);
5053                 fetchr = new JMenuItem(src.getDbSource());
5054                 fetchr.addActionListener(new ActionListener()
5055                 {
5056
5057                   @Override
5058                   public void actionPerformed(ActionEvent e)
5059                   {
5060                     new Thread(new Runnable()
5061                     {
5062
5063                       @Override
5064                       public void run()
5065                       {
5066                         boolean isNucleotide = alignPanel.alignFrame
5067                                 .getViewport().getAlignment()
5068                                 .isNucleotide();
5069                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5070                                 alignPanel.av.getSequenceSelection(),
5071                                 alignPanel.alignFrame, dassource,
5072                                 alignPanel.alignFrame.featureSettings,
5073                                 isNucleotide);
5074                         dbRefFetcher
5075                                 .addListener(new FetchFinishedListenerI()
5076                                 {
5077                                   @Override
5078                                   public void finished()
5079                                   {
5080                                     AlignFrame.this.setMenusForViewport();
5081                                   }
5082                                 });
5083                         dbRefFetcher.fetchDBRefs(false);
5084                       }
5085                     }).start();
5086                   }
5087
5088                 });
5089                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5090                         MessageManager.formatMessage(
5091                                 "label.fetch_retrieve_from",
5092                                 new Object[] { src.getDbName() })));
5093                 dfetch.add(fetchr);
5094                 comp++;
5095               }
5096               else
5097               {
5098                 final DbSourceProxy[] dassource = otherdb
5099                         .toArray(new DbSourceProxy[0]);
5100                 // fetch all entry
5101                 DbSourceProxy src = otherdb.get(0);
5102                 fetchr = new JMenuItem(MessageManager.formatMessage(
5103                         "label.fetch_all_param",
5104                         new Object[] { src.getDbSource() }));
5105                 fetchr.addActionListener(new ActionListener()
5106                 {
5107                   @Override
5108                   public void actionPerformed(ActionEvent e)
5109                   {
5110                     new Thread(new Runnable()
5111                     {
5112
5113                       @Override
5114                       public void run()
5115                       {
5116                         boolean isNucleotide = alignPanel.alignFrame
5117                                 .getViewport().getAlignment()
5118                                 .isNucleotide();
5119                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5120                                 alignPanel.av.getSequenceSelection(),
5121                                 alignPanel.alignFrame, dassource,
5122                                 alignPanel.alignFrame.featureSettings,
5123                                 isNucleotide);
5124                         dbRefFetcher
5125                                 .addListener(new FetchFinishedListenerI()
5126                                 {
5127                                   @Override
5128                                   public void finished()
5129                                   {
5130                                     AlignFrame.this.setMenusForViewport();
5131                                   }
5132                                 });
5133                         dbRefFetcher.fetchDBRefs(false);
5134                       }
5135                     }).start();
5136                   }
5137                 });
5138
5139                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5140                         MessageManager.formatMessage(
5141                                 "label.fetch_retrieve_from_all_sources",
5142                                 new Object[] {
5143                                     Integer.valueOf(otherdb.size())
5144                                             .toString(), src.getDbSource(),
5145                                     src.getDbName() })));
5146                 dfetch.add(fetchr);
5147                 comp++;
5148                 // and then build the rest of the individual menus
5149                 ifetch = new JMenu(MessageManager.formatMessage(
5150                         "label.source_from_db_source",
5151                         new Object[] { src.getDbSource() }));
5152                 icomp = 0;
5153                 String imname = null;
5154                 int i = 0;
5155                 for (DbSourceProxy sproxy : otherdb)
5156                 {
5157                   String dbname = sproxy.getDbName();
5158                   String sname = dbname.length() > 5 ? dbname.substring(0,
5159                           5) + "..." : dbname;
5160                   String msname = dbname.length() > 10 ? dbname.substring(
5161                           0, 10) + "..." : dbname;
5162                   if (imname == null)
5163                   {
5164                     imname = MessageManager.formatMessage(
5165                             "label.from_msname", new Object[] { sname });
5166                   }
5167                   fetchr = new JMenuItem(msname);
5168                   final DbSourceProxy[] dassrc = { sproxy };
5169                   fetchr.addActionListener(new ActionListener()
5170                   {
5171
5172                     @Override
5173                     public void actionPerformed(ActionEvent e)
5174                     {
5175                       new Thread(new Runnable()
5176                       {
5177
5178                         @Override
5179                         public void run()
5180                         {
5181                           boolean isNucleotide = alignPanel.alignFrame
5182                                   .getViewport().getAlignment()
5183                                   .isNucleotide();
5184                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5185                                   alignPanel.av.getSequenceSelection(),
5186                                   alignPanel.alignFrame, dassrc,
5187                                   alignPanel.alignFrame.featureSettings,
5188                                   isNucleotide);
5189                           dbRefFetcher
5190                                   .addListener(new FetchFinishedListenerI()
5191                                   {
5192                                     @Override
5193                                     public void finished()
5194                                     {
5195                                       AlignFrame.this.setMenusForViewport();
5196                                     }
5197                                   });
5198                           dbRefFetcher.fetchDBRefs(false);
5199                         }
5200                       }).start();
5201                     }
5202
5203                   });
5204                   fetchr.setToolTipText("<html>"
5205                           + MessageManager.formatMessage(
5206                                   "label.fetch_retrieve_from", new Object[]
5207                                   { dbname }));
5208                   ifetch.add(fetchr);
5209                   ++i;
5210                   if (++icomp >= mcomp || i == (otherdb.size()))
5211                   {
5212                     ifetch.setText(MessageManager.formatMessage(
5213                             "label.source_to_target", imname, sname));
5214                     dfetch.add(ifetch);
5215                     ifetch = new JMenu();
5216                     imname = null;
5217                     icomp = 0;
5218                     comp++;
5219                   }
5220                 }
5221               }
5222               ++dbi;
5223               if (comp >= mcomp || dbi >= (dbclasses.length))
5224               {
5225                 dfetch.setText(MessageManager.formatMessage(
5226                         "label.source_to_target", mname, dbclass));
5227                 rfetch.add(dfetch);
5228                 dfetch = new JMenu();
5229                 mname = null;
5230                 comp = 0;
5231               }
5232             }
5233           }
5234         });
5235       }
5236     }).start();
5237
5238   }
5239
5240   /**
5241    * Left justify the whole alignment.
5242    */
5243   @Override
5244   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5245   {
5246     AlignmentI al = viewport.getAlignment();
5247     al.justify(false);
5248     viewport.firePropertyChange("alignment", null, al);
5249   }
5250
5251   /**
5252    * Right justify the whole alignment.
5253    */
5254   @Override
5255   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5256   {
5257     AlignmentI al = viewport.getAlignment();
5258     al.justify(true);
5259     viewport.firePropertyChange("alignment", null, al);
5260   }
5261
5262   @Override
5263   public void setShowSeqFeatures(boolean b)
5264   {
5265     showSeqFeatures.setSelected(b);
5266     viewport.setShowSequenceFeatures(b);
5267   }
5268
5269   /*
5270    * (non-Javadoc)
5271    *
5272    * @see
5273    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5274    * awt.event.ActionEvent)
5275    */
5276   @Override
5277   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5278   {
5279     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5280     alignPanel.paintAlignment(true);
5281   }
5282
5283   /*
5284    * (non-Javadoc)
5285    *
5286    * @see
5287    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5288    * .ActionEvent)
5289    */
5290   @Override
5291   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5292   {
5293     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5294     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5295
5296   }
5297
5298   /*
5299    * (non-Javadoc)
5300    *
5301    * @see
5302    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5303    * .event.ActionEvent)
5304    */
5305   @Override
5306   protected void showGroupConservation_actionPerformed(ActionEvent e)
5307   {
5308     viewport.setShowGroupConservation(showGroupConservation.getState());
5309     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310   }
5311
5312   /*
5313    * (non-Javadoc)
5314    *
5315    * @see
5316    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5317    * .event.ActionEvent)
5318    */
5319   @Override
5320   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5321   {
5322     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5323     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5324   }
5325
5326   /*
5327    * (non-Javadoc)
5328    *
5329    * @see
5330    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5331    * .event.ActionEvent)
5332    */
5333   @Override
5334   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5335   {
5336     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5337     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5338   }
5339
5340   @Override
5341   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5342   {
5343     showSequenceLogo.setState(true);
5344     viewport.setShowSequenceLogo(true);
5345     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5346     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5347   }
5348
5349   @Override
5350   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5351   {
5352     viewport.setShowInformationHistogram(
5353             showInformationHistogram.getState());
5354     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5355   }
5356
5357   @Override
5358   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5359   {
5360     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5361     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5362   }
5363
5364   @Override
5365   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5366   {
5367     showHMMSequenceLogo.setState(true);
5368     viewport.setShowHMMSequenceLogo(true);
5369     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5370     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5371   }
5372
5373   @Override
5374   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5375   {
5376     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5377   }
5378
5379   /*
5380    * (non-Javadoc)
5381    *
5382    * @see
5383    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5384    * .event.ActionEvent)
5385    */
5386   @Override
5387   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5388   {
5389     if (avc.makeGroupsFromSelection())
5390     {
5391       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5392       alignPanel.updateAnnotation();
5393       alignPanel.paintAlignment(true);
5394     }
5395   }
5396
5397   public void clearAlignmentSeqRep()
5398   {
5399     // TODO refactor alignmentseqrep to controller
5400     if (viewport.getAlignment().hasSeqrep())
5401     {
5402       viewport.getAlignment().setSeqrep(null);
5403       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5404       alignPanel.updateAnnotation();
5405       alignPanel.paintAlignment(true);
5406     }
5407   }
5408
5409   @Override
5410   protected void createGroup_actionPerformed(ActionEvent e)
5411   {
5412     if (avc.createGroup())
5413     {
5414       alignPanel.alignmentChanged();
5415     }
5416   }
5417
5418   @Override
5419   protected void unGroup_actionPerformed(ActionEvent e)
5420   {
5421     if (avc.unGroup())
5422     {
5423       alignPanel.alignmentChanged();
5424     }
5425   }
5426
5427   /**
5428    * make the given alignmentPanel the currently selected tab
5429    *
5430    * @param alignmentPanel
5431    */
5432   public void setDisplayedView(AlignmentPanel alignmentPanel)
5433   {
5434     if (!viewport.getSequenceSetId().equals(
5435             alignmentPanel.av.getSequenceSetId()))
5436     {
5437       throw new Error(
5438               MessageManager
5439                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5440     }
5441     if (tabbedPane != null
5442             && tabbedPane.getTabCount() > 0
5443             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5444                     .getSelectedIndex())
5445     {
5446       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5447     }
5448   }
5449
5450   /**
5451    * Action on selection of menu options to Show or Hide annotations.
5452    *
5453    * @param visible
5454    * @param forSequences
5455    *          update sequence-related annotations
5456    * @param forAlignment
5457    *          update non-sequence-related annotations
5458    */
5459   @Override
5460   protected void setAnnotationsVisibility(boolean visible,
5461           boolean forSequences, boolean forAlignment)
5462   {
5463     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5464             .getAlignmentAnnotation();
5465     if (anns == null)
5466     {
5467       return;
5468     }
5469     for (AlignmentAnnotation aa : anns)
5470     {
5471       /*
5472        * don't display non-positional annotations on an alignment
5473        */
5474       if (aa.annotations == null)
5475       {
5476         continue;
5477       }
5478       boolean apply = (aa.sequenceRef == null && forAlignment)
5479               || (aa.sequenceRef != null && forSequences);
5480       if (apply)
5481       {
5482         aa.visible = visible;
5483       }
5484     }
5485     alignPanel.validateAnnotationDimensions(true);
5486     alignPanel.alignmentChanged();
5487   }
5488
5489   /**
5490    * Store selected annotation sort order for the view and repaint.
5491    */
5492   @Override
5493   protected void sortAnnotations_actionPerformed()
5494   {
5495     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5496     this.alignPanel.av
5497             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5498     alignPanel.paintAlignment(true);
5499   }
5500
5501   /**
5502    *
5503    * @return alignment panels in this alignment frame
5504    */
5505   public List<? extends AlignmentViewPanel> getAlignPanels()
5506   {
5507     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5508   }
5509
5510   /**
5511    * Open a new alignment window, with the cDNA associated with this (protein)
5512    * alignment, aligned as is the protein.
5513    */
5514   protected void viewAsCdna_actionPerformed()
5515   {
5516     // TODO no longer a menu action - refactor as required
5517     final AlignmentI alignment = getViewport().getAlignment();
5518     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5519     if (mappings == null)
5520     {
5521       return;
5522     }
5523     List<SequenceI> cdnaSeqs = new ArrayList<>();
5524     for (SequenceI aaSeq : alignment.getSequences())
5525     {
5526       for (AlignedCodonFrame acf : mappings)
5527       {
5528         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5529         if (dnaSeq != null)
5530         {
5531           /*
5532            * There is a cDNA mapping for this protein sequence - add to new
5533            * alignment. It will share the same dataset sequence as other mapped
5534            * cDNA (no new mappings need to be created).
5535            */
5536           final Sequence newSeq = new Sequence(dnaSeq);
5537           newSeq.setDatasetSequence(dnaSeq);
5538           cdnaSeqs.add(newSeq);
5539         }
5540       }
5541     }
5542     if (cdnaSeqs.size() == 0)
5543     {
5544       // show a warning dialog no mapped cDNA
5545       return;
5546     }
5547     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5548             .size()]));
5549     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5550             AlignFrame.DEFAULT_HEIGHT);
5551     cdna.alignAs(alignment);
5552     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5553             + this.title;
5554     Desktop.addInternalFrame(alignFrame, newtitle,
5555             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5556   }
5557
5558   /**
5559    * Set visibility of dna/protein complement view (available when shown in a
5560    * split frame).
5561    *
5562    * @param show
5563    */
5564   @Override
5565   protected void showComplement_actionPerformed(boolean show)
5566   {
5567     SplitContainerI sf = getSplitViewContainer();
5568     if (sf != null)
5569     {
5570       sf.setComplementVisible(this, show);
5571     }
5572   }
5573
5574   /**
5575    * Generate the reverse (optionally complemented) of the selected sequences,
5576    * and add them to the alignment
5577    */
5578   @Override
5579   protected void showReverse_actionPerformed(boolean complement)
5580   {
5581     AlignmentI al = null;
5582     try
5583     {
5584       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5585       al = dna.reverseCdna(complement);
5586       viewport.addAlignment(al, "");
5587       addHistoryItem(new EditCommand(
5588               MessageManager.getString("label.add_sequences"),
5589               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5590               viewport.getAlignment()));
5591     } catch (Exception ex)
5592     {
5593       System.err.println(ex.getMessage());
5594       return;
5595     }
5596   }
5597
5598   /**
5599    * Try to run a script in the Groovy console, having first ensured that this
5600    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5601    * be targeted at this alignment.
5602    */
5603   @Override
5604   protected void runGroovy_actionPerformed()
5605   {
5606     Jalview.setCurrentAlignFrame(this);
5607     groovy.ui.Console console = Desktop.getGroovyConsole();
5608     if (console != null)
5609     {
5610       try
5611       {
5612         console.runScript();
5613       } catch (Exception ex)
5614       {
5615         System.err.println((ex.toString()));
5616         JvOptionPane
5617                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5618                         .getString("label.couldnt_run_groovy_script"),
5619                         MessageManager
5620                                 .getString("label.groovy_support_failed"),
5621                         JvOptionPane.ERROR_MESSAGE);
5622       }
5623     }
5624     else
5625     {
5626       System.err.println("Can't run Groovy script as console not found");
5627     }
5628   }
5629
5630   /**
5631    * Hides columns containing (or not containing) a specified feature, provided
5632    * that would not leave all columns hidden
5633    *
5634    * @param featureType
5635    * @param columnsContaining
5636    * @return
5637    */
5638   public boolean hideFeatureColumns(String featureType,
5639           boolean columnsContaining)
5640   {
5641     boolean notForHiding = avc.markColumnsContainingFeatures(
5642             columnsContaining, false, false, featureType);
5643     if (notForHiding)
5644     {
5645       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5646               false, featureType))
5647       {
5648         getViewport().hideSelectedColumns();
5649         return true;
5650       }
5651     }
5652     return false;
5653   }
5654
5655   @Override
5656   protected void selectHighlightedColumns_actionPerformed(
5657           ActionEvent actionEvent)
5658   {
5659     // include key modifier check in case user selects from menu
5660     avc.markHighlightedColumns(
5661             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5662             true,
5663             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5664   }
5665
5666   /**
5667    * Rebuilds the Colour menu, including any user-defined colours which have
5668    * been loaded either on startup or during the session
5669    */
5670   public void buildColourMenu()
5671   {
5672     colourMenu.removeAll();
5673
5674     colourMenu.add(applyToAllGroups);
5675     colourMenu.add(textColour);
5676     colourMenu.addSeparator();
5677
5678     ColourMenuHelper.addMenuItems(colourMenu, this,
5679             viewport.getAlignment(), false);
5680
5681     colourMenu.addSeparator();
5682     colourMenu.add(conservationMenuItem);
5683     colourMenu.add(modifyConservation);
5684     colourMenu.add(abovePIDThreshold);
5685     colourMenu.add(modifyPID);
5686     colourMenu.add(annotationColour);
5687
5688     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5689     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5690   }
5691
5692   /**
5693    * Open a dialog (if not already open) that allows the user to select and
5694    * calculate PCA or Tree analysis
5695    */
5696   protected void openTreePcaDialog()
5697   {
5698     if (alignPanel.getCalculationDialog() == null)
5699     {
5700       new CalculationChooser(AlignFrame.this);
5701     }
5702   }
5703 }
5704
5705 class PrintThread extends Thread
5706 {
5707   AlignmentPanel ap;
5708
5709   public PrintThread(AlignmentPanel ap)
5710   {
5711     this.ap = ap;
5712   }
5713
5714   static PageFormat pf;
5715
5716   @Override
5717   public void run()
5718   {
5719     PrinterJob printJob = PrinterJob.getPrinterJob();
5720
5721     if (pf != null)
5722     {
5723       printJob.setPrintable(ap, pf);
5724     }
5725     else
5726     {
5727       printJob.setPrintable(ap);
5728     }
5729
5730     if (printJob.printDialog())
5731     {
5732       try
5733       {
5734         printJob.print();
5735       } catch (Exception PrintException)
5736       {
5737         PrintException.printStackTrace();
5738       }
5739     }
5740   }
5741
5742
5743 }