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.FeatureSettingsModelI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.ScoreModelI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.DBRefSource;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileLoader;
  72 import jalview.io.FormatAdapter;
  73 import jalview.io.HtmlSvgOutput;
  74 import jalview.io.IdentifyFile;
  75 import jalview.io.JPredFile;
  76 import jalview.io.JalviewFileChooser;
  77 import jalview.io.JalviewFileView;
  78 import jalview.io.JnetAnnotationMaker;
  79 import jalview.io.NewickFile;
  80 import jalview.io.TCoffeeScoreFile;
  81 import jalview.io.gff.SequenceOntologyI;
  82 import jalview.jbgui.GAlignFrame;
  83 import jalview.schemes.Blosum62ColourScheme;
  84 import jalview.schemes.BuriedColourScheme;
  85 import jalview.schemes.ClustalxColourScheme;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemeProperty;
  88 import jalview.schemes.HelixColourScheme;
  89 import jalview.schemes.HydrophobicColourScheme;
  90 import jalview.schemes.NucleotideColourScheme;
  91 import jalview.schemes.PIDColourScheme;
  92 import jalview.schemes.PurinePyrimidineColourScheme;
  93 import jalview.schemes.RNAHelicesColourChooser;
  94 import jalview.schemes.ResidueProperties;
  95 import jalview.schemes.StrandColourScheme;
  96 import jalview.schemes.TCoffeeColourScheme;
  97 import jalview.schemes.TaylorColourScheme;
  98 import jalview.schemes.TurnColourScheme;
  99 import jalview.schemes.UserColourScheme;
 100 import jalview.schemes.ZappoColourScheme;
 101 import jalview.structure.StructureSelectionManager;
 102 import jalview.util.MessageManager;
 103 import jalview.viewmodel.AlignmentViewport;
 104 import jalview.ws.DBRefFetcher;
 105 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 106 import jalview.ws.SequenceFetcher;
 107 import jalview.ws.jws1.Discoverer;
 108 import jalview.ws.jws2.Jws2Discoverer;
 109 import jalview.ws.jws2.jabaws2.Jws2Instance;
 110 import jalview.ws.seqfetcher.DbSourceProxy;
 111
 112 import java.awt.BorderLayout;
 113 import java.awt.Component;
 114 import java.awt.Rectangle;
 115 import java.awt.Toolkit;
 116 import java.awt.datatransfer.Clipboard;
 117 import java.awt.datatransfer.DataFlavor;
 118 import java.awt.datatransfer.StringSelection;
 119 import java.awt.datatransfer.Transferable;
 120 import java.awt.dnd.DropTargetDragEvent;
 121 import java.awt.dnd.DropTargetDropEvent;
 122 import java.awt.dnd.DropTargetEvent;
 123 import java.awt.dnd.DropTargetListener;
 124 import java.awt.event.ActionEvent;
 125 import java.awt.event.ActionListener;
 126 import java.awt.event.FocusAdapter;
 127 import java.awt.event.FocusEvent;
 128 import java.awt.event.ItemEvent;
 129 import java.awt.event.ItemListener;
 130 import java.awt.event.KeyAdapter;
 131 import java.awt.event.KeyEvent;
 132 import java.awt.event.MouseAdapter;
 133 import java.awt.event.MouseEvent;
 134 import java.awt.print.PageFormat;
 135 import java.awt.print.PrinterJob;
 136 import java.beans.PropertyChangeEvent;
 137 import java.io.File;
 138 import java.net.URL;
 139 import java.util.ArrayList;
 140 import java.util.Arrays;
 141 import java.util.Deque;
 142 import java.util.Enumeration;
 143 import java.util.Hashtable;
 144 import java.util.List;
 145 import java.util.Vector;
 146
 147 import javax.swing.JCheckBoxMenuItem;
 148 import javax.swing.JEditorPane;
 149 import javax.swing.JInternalFrame;
 150 import javax.swing.JLayeredPane;
 151 import javax.swing.JMenu;
 152 import javax.swing.JMenuItem;
 153 import javax.swing.JOptionPane;
 154 import javax.swing.JRadioButtonMenuItem;
 155 import javax.swing.JScrollPane;
 156 import javax.swing.SwingUtilities;
 157
 158 /**
 159  * DOCUMENT ME!
 160  *
 161  * @author $author$
 162  * @version $Revision$
 163  */
 164 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 165         IProgressIndicator, AlignViewControllerGuiI
 166 {
 167
 168   public static final int DEFAULT_WIDTH = 700;
 169
 170   public static final int DEFAULT_HEIGHT = 500;
 171
 172   /*
 173    * The currently displayed panel (selected tabbed view if more than one)
 174    */
 175   public AlignmentPanel alignPanel;
 176
 177   AlignViewport viewport;
 178
 179   public AlignViewControllerI avc;
 180
 181   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 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    * Creates a new AlignFrame object with specific width and height.
 195    *
 196    * @param al
 197    * @param width
 198    * @param height
 199    */
 200   public AlignFrame(AlignmentI al, int width, int height)
 201   {
 202     this(al, null, width, height);
 203   }
 204
 205   /**
 206    * Creates a new AlignFrame object with specific width, height and
 207    * sequenceSetId
 208    *
 209    * @param al
 210    * @param width
 211    * @param height
 212    * @param sequenceSetId
 213    */
 214   public AlignFrame(AlignmentI al, int width, int height,
 215           String sequenceSetId)
 216   {
 217     this(al, null, width, height, sequenceSetId);
 218   }
 219
 220   /**
 221    * Creates a new AlignFrame object with specific width, height and
 222    * sequenceSetId
 223    *
 224    * @param al
 225    * @param width
 226    * @param height
 227    * @param sequenceSetId
 228    * @param viewId
 229    */
 230   public AlignFrame(AlignmentI al, int width, int height,
 231           String sequenceSetId, String viewId)
 232   {
 233     this(al, null, width, height, sequenceSetId, viewId);
 234   }
 235
 236   /**
 237    * new alignment window with hidden columns
 238    *
 239    * @param al
 240    *          AlignmentI
 241    * @param hiddenColumns
 242    *          ColumnSelection or null
 243    * @param width
 244    *          Width of alignment frame
 245    * @param height
 246    *          height of frame.
 247    */
 248   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 249           int width, int height)
 250   {
 251     this(al, hiddenColumns, width, height, null);
 252   }
 253
 254   /**
 255    * Create alignment frame for al with hiddenColumns, a specific width and
 256    * height, and specific sequenceId
 257    *
 258    * @param al
 259    * @param hiddenColumns
 260    * @param width
 261    * @param height
 262    * @param sequenceSetId
 263    *          (may be null)
 264    */
 265   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 266           int width, int height, String sequenceSetId)
 267   {
 268     this(al, hiddenColumns, width, height, sequenceSetId, null);
 269   }
 270
 271   /**
 272    * Create alignment frame for al with hiddenColumns, a specific width and
 273    * height, and specific sequenceId
 274    *
 275    * @param al
 276    * @param hiddenColumns
 277    * @param width
 278    * @param height
 279    * @param sequenceSetId
 280    *          (may be null)
 281    * @param viewId
 282    *          (may be null)
 283    */
 284   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 285           int width, int height, String sequenceSetId, String viewId)
 286   {
 287     setSize(width, height);
 288
 289     if (al.getDataset() == null)
 290     {
 291       al.setDataset(null);
 292     }
 293
 294     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 295
 296     alignPanel = new AlignmentPanel(this, viewport);
 297
 298     addAlignmentPanel(alignPanel, true);
 299     init();
 300   }
 301
 302   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 303           ColumnSelection hiddenColumns, int width, int height)
 304   {
 305     setSize(width, height);
 306
 307     if (al.getDataset() == null)
 308     {
 309       al.setDataset(null);
 310     }
 311
 312     viewport = new AlignViewport(al, hiddenColumns);
 313
 314     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 315     {
 316       viewport.hideSequence(hiddenSeqs);
 317     }
 318     alignPanel = new AlignmentPanel(this, viewport);
 319     addAlignmentPanel(alignPanel, true);
 320     init();
 321   }
 322
 323   /**
 324    * Make a new AlignFrame from existing alignmentPanels
 325    *
 326    * @param ap
 327    *          AlignmentPanel
 328    * @param av
 329    *          AlignViewport
 330    */
 331   public AlignFrame(AlignmentPanel ap)
 332   {
 333     viewport = ap.av;
 334     alignPanel = ap;
 335     addAlignmentPanel(ap, false);
 336     init();
 337   }
 338
 339   /**
 340    * initalise the alignframe from the underlying viewport data and the
 341    * configurations
 342    */
 343   void init()
 344   {
 345     if (!Jalview.isHeadlessMode())
 346     {
 347       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 348     }
 349
 350     avc = new jalview.controller.AlignViewController(this, viewport,
 351             alignPanel);
 352     if (viewport.getAlignmentConservationAnnotation() == null)
 353     {
 354       BLOSUM62Colour.setEnabled(false);
 355       conservationMenuItem.setEnabled(false);
 356       modifyConservation.setEnabled(false);
 357       // PIDColour.setEnabled(false);
 358       // abovePIDThreshold.setEnabled(false);
 359       // modifyPID.setEnabled(false);
 360     }
 361
 362     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 363             "No sort");
 364
 365     if (sortby.equals("Id"))
 366     {
 367       sortIDMenuItem_actionPerformed(null);
 368     }
 369     else if (sortby.equals("Pairwise Identity"))
 370     {
 371       sortPairwiseMenuItem_actionPerformed(null);
 372     }
 373
 374     if (Desktop.desktop != null)
 375     {
 376       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 377       addServiceListeners();
 378       setGUINucleotide(viewport.getAlignment().isNucleotide());
 379     }
 380
 381     this.alignPanel.av
 382             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 383
 384     setMenusFromViewport(viewport);
 385     buildSortByAnnotationScoresMenu();
 386     buildTreeMenu();
 387
 388     if (viewport.getWrapAlignment())
 389     {
 390       wrapMenuItem_actionPerformed(null);
 391     }
 392
 393     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 394     {
 395       this.overviewMenuItem_actionPerformed(null);
 396     }
 397
 398     addKeyListener();
 399
 400     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 401     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 402     final String menuLabel = MessageManager
 403             .getString("label.copy_format_from");
 404     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 405             new ViewSetProvider()
 406             {
 407
 408               @Override
 409               public AlignmentPanel[] getAllAlignmentPanels()
 410               {
 411                 origview.clear();
 412                 origview.add(alignPanel);
 413                 // make an array of all alignment panels except for this one
 414                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 415                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 416                 aps.remove(AlignFrame.this.alignPanel);
 417                 return aps.toArray(new AlignmentPanel[aps.size()]);
 418               }
 419             }, selviews, new ItemListener()
 420             {
 421
 422               @Override
 423               public void itemStateChanged(ItemEvent e)
 424               {
 425                 if (origview.size() > 0)
 426                 {
 427                   final AlignmentPanel ap = origview.get(0);
 428
 429                   /*
 430                    * Copy the ViewStyle of the selected panel to 'this one'.
 431                    * Don't change value of 'scaleProteinAsCdna' unless copying
 432                    * from a SplitFrame.
 433                    */
 434                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 435                           .getViewStyle();
 436                   boolean fromSplitFrame = selviews.get(0)
 437                           .getAlignViewport().getCodingComplement() != null;
 438                   if (!fromSplitFrame)
 439                   {
 440                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 441                             .getViewStyle().isScaleProteinAsCdna());
 442                   }
 443                   ap.getAlignViewport().setViewStyle(vs);
 444
 445                   /*
 446                    * Also rescale ViewStyle of SplitFrame complement if there is
 447                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 448                    * the whole ViewStyle (allow cDNA protein to have different
 449                    * fonts)
 450                    */
 451                   AlignViewportI complement = ap.getAlignViewport()
 452                           .getCodingComplement();
 453                   if (complement != null && vs.isScaleProteinAsCdna())
 454                   {
 455                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 456                     ((SplitFrame) af.getSplitViewContainer())
 457                             .adjustLayout();
 458                     af.setMenusForViewport();
 459                   }
 460
 461                   ap.updateLayout();
 462                   ap.setSelected(true);
 463                   ap.alignFrame.setMenusForViewport();
 464
 465                 }
 466               }
 467             });
 468     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 469             .indexOf("devel") > -1
 470             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 471                     .indexOf("test") > -1)
 472     {
 473       formatMenu.add(vsel);
 474     }
 475     addFocusListener(new FocusAdapter()
 476     {
 477       @Override
 478       public void focusGained(FocusEvent e)
 479       {
 480         Jalview.setCurrentAlignFrame(AlignFrame.this);
 481       }
 482     });
 483
 484   }
 485
 486   /**
 487    * Change the filename and format for the alignment, and enable the 'reload'
 488    * button functionality.
 489    *
 490    * @param file
 491    *          valid filename
 492    * @param format
 493    *          format of file
 494    */
 495   public void setFileName(String file, FileFormatI format)
 496   {
 497     fileName = file;
 498     setFileFormat(format);
 499     reload.setEnabled(true);
 500   }
 501
 502   /**
 503    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 504    * events
 505    */
 506   void addKeyListener()
 507   {
 508     addKeyListener(new KeyAdapter()
 509     {
 510       @Override
 511       public void keyPressed(KeyEvent evt)
 512       {
 513         if (viewport.cursorMode
 514                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 515                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 516                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 517                 && Character.isDigit(evt.getKeyChar()))
 518         {
 519           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 520         }
 521
 522         switch (evt.getKeyCode())
 523         {
 524
 525         case 27: // escape key
 526           deselectAllSequenceMenuItem_actionPerformed(null);
 527
 528           break;
 529
 530         case KeyEvent.VK_DOWN:
 531           if (evt.isAltDown() || !viewport.cursorMode)
 532           {
 533             moveSelectedSequences(false);
 534           }
 535           if (viewport.cursorMode)
 536           {
 537             alignPanel.getSeqPanel().moveCursor(0, 1);
 538           }
 539           break;
 540
 541         case KeyEvent.VK_UP:
 542           if (evt.isAltDown() || !viewport.cursorMode)
 543           {
 544             moveSelectedSequences(true);
 545           }
 546           if (viewport.cursorMode)
 547           {
 548             alignPanel.getSeqPanel().moveCursor(0, -1);
 549           }
 550
 551           break;
 552
 553         case KeyEvent.VK_LEFT:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555           {
 556             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 557           }
 558           else
 559           {
 560             alignPanel.getSeqPanel().moveCursor(-1, 0);
 561           }
 562
 563           break;
 564
 565         case KeyEvent.VK_RIGHT:
 566           if (evt.isAltDown() || !viewport.cursorMode)
 567           {
 568             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 569           }
 570           else
 571           {
 572             alignPanel.getSeqPanel().moveCursor(1, 0);
 573           }
 574           break;
 575
 576         case KeyEvent.VK_SPACE:
 577           if (viewport.cursorMode)
 578           {
 579             alignPanel.getSeqPanel().insertGapAtCursor(
 580                     evt.isControlDown() || evt.isShiftDown()
 581                             || evt.isAltDown());
 582           }
 583           break;
 584
 585         // case KeyEvent.VK_A:
 586         // if (viewport.cursorMode)
 587         // {
 588         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 589         // //System.out.println("A");
 590         // }
 591         // break;
 592         /*
 593          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 594          * System.out.println("closing bracket"); } break;
 595          */
 596         case KeyEvent.VK_DELETE:
 597         case KeyEvent.VK_BACK_SPACE:
 598           if (!viewport.cursorMode)
 599           {
 600             cut_actionPerformed(null);
 601           }
 602           else
 603           {
 604             alignPanel.getSeqPanel().deleteGapAtCursor(
 605                     evt.isControlDown() || evt.isShiftDown()
 606                             || evt.isAltDown());
 607           }
 608
 609           break;
 610
 611         case KeyEvent.VK_S:
 612           if (viewport.cursorMode)
 613           {
 614             alignPanel.getSeqPanel().setCursorRow();
 615           }
 616           break;
 617         case KeyEvent.VK_C:
 618           if (viewport.cursorMode && !evt.isControlDown())
 619           {
 620             alignPanel.getSeqPanel().setCursorColumn();
 621           }
 622           break;
 623         case KeyEvent.VK_P:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setCursorPosition();
 627           }
 628           break;
 629
 630         case KeyEvent.VK_ENTER:
 631         case KeyEvent.VK_COMMA:
 632           if (viewport.cursorMode)
 633           {
 634             alignPanel.getSeqPanel().setCursorRowAndColumn();
 635           }
 636           break;
 637
 638         case KeyEvent.VK_Q:
 639           if (viewport.cursorMode)
 640           {
 641             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 642           }
 643           break;
 644         case KeyEvent.VK_M:
 645           if (viewport.cursorMode)
 646           {
 647             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 648           }
 649           break;
 650
 651         case KeyEvent.VK_F2:
 652           viewport.cursorMode = !viewport.cursorMode;
 653           statusBar.setText(MessageManager.formatMessage(
 654                   "label.keyboard_editing_mode",
 655                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 656           if (viewport.cursorMode)
 657           {
 658             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 659             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 660           }
 661           alignPanel.getSeqPanel().seqCanvas.repaint();
 662           break;
 663
 664         case KeyEvent.VK_F1:
 665           try
 666           {
 667             Help.showHelpWindow();
 668           } catch (Exception ex)
 669           {
 670             ex.printStackTrace();
 671           }
 672           break;
 673         case KeyEvent.VK_H:
 674         {
 675           boolean toggleSeqs = !evt.isControlDown();
 676           boolean toggleCols = !evt.isShiftDown();
 677           toggleHiddenRegions(toggleSeqs, toggleCols);
 678           break;
 679         }
 680         case KeyEvent.VK_PAGE_UP:
 681           if (viewport.getWrapAlignment())
 682           {
 683             alignPanel.scrollUp(true);
 684           }
 685           else
 686           {
 687             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 688                     - viewport.endSeq + viewport.startSeq);
 689           }
 690           break;
 691         case KeyEvent.VK_PAGE_DOWN:
 692           if (viewport.getWrapAlignment())
 693           {
 694             alignPanel.scrollUp(false);
 695           }
 696           else
 697           {
 698             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 699                     + viewport.endSeq - viewport.startSeq);
 700           }
 701           break;
 702         }
 703       }
 704
 705       @Override
 706       public void keyReleased(KeyEvent evt)
 707       {
 708         switch (evt.getKeyCode())
 709         {
 710         case KeyEvent.VK_LEFT:
 711           if (evt.isAltDown() || !viewport.cursorMode)
 712           {
 713             viewport.firePropertyChange("alignment", null, viewport
 714                     .getAlignment().getSequences());
 715           }
 716           break;
 717
 718         case KeyEvent.VK_RIGHT:
 719           if (evt.isAltDown() || !viewport.cursorMode)
 720           {
 721             viewport.firePropertyChange("alignment", null, viewport
 722                     .getAlignment().getSequences());
 723           }
 724           break;
 725         }
 726       }
 727     });
 728   }
 729
 730   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 731   {
 732     ap.alignFrame = this;
 733     avc = new jalview.controller.AlignViewController(this, viewport,
 734             alignPanel);
 735
 736     alignPanels.add(ap);
 737
 738     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 739
 740     int aSize = alignPanels.size();
 741
 742     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 743
 744     if (aSize == 1 && ap.av.viewName == null)
 745     {
 746       this.getContentPane().add(ap, BorderLayout.CENTER);
 747     }
 748     else
 749     {
 750       if (aSize == 2)
 751       {
 752         setInitialTabVisible();
 753       }
 754
 755       expandViews.setEnabled(true);
 756       gatherViews.setEnabled(true);
 757       tabbedPane.addTab(ap.av.viewName, ap);
 758
 759       ap.setVisible(false);
 760     }
 761
 762     if (newPanel)
 763     {
 764       if (ap.av.isPadGaps())
 765       {
 766         ap.av.getAlignment().padGaps();
 767       }
 768       ap.av.updateConservation(ap);
 769       ap.av.updateConsensus(ap);
 770       ap.av.updateStrucConsensus(ap);
 771     }
 772   }
 773
 774   public void setInitialTabVisible()
 775   {
 776     expandViews.setEnabled(true);
 777     gatherViews.setEnabled(true);
 778     tabbedPane.setVisible(true);
 779     AlignmentPanel first = alignPanels.get(0);
 780     tabbedPane.addTab(first.av.viewName, first);
 781     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 782   }
 783
 784   public AlignViewport getViewport()
 785   {
 786     return viewport;
 787   }
 788
 789   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 790   private void addServiceListeners()
 791   {
 792     final java.beans.PropertyChangeListener thisListener;
 793     Desktop.instance.addJalviewPropertyChangeListener("services",
 794             thisListener = new java.beans.PropertyChangeListener()
 795             {
 796               @Override
 797               public void propertyChange(PropertyChangeEvent evt)
 798               {
 799                 // // System.out.println("Discoverer property change.");
 800                 // if (evt.getPropertyName().equals("services"))
 801                 {
 802                   SwingUtilities.invokeLater(new Runnable()
 803                   {
 804
 805                     @Override
 806                     public void run()
 807                     {
 808                       System.err
 809                               .println("Rebuild WS Menu for service change");
 810                       BuildWebServiceMenu();
 811                     }
 812
 813                   });
 814                 }
 815               }
 816             });
 817     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 818     {
 819       @Override
 820       public void internalFrameClosed(
 821               javax.swing.event.InternalFrameEvent evt)
 822       {
 823         // System.out.println("deregistering discoverer listener");
 824         Desktop.instance.removeJalviewPropertyChangeListener("services",
 825                 thisListener);
 826         closeMenuItem_actionPerformed(true);
 827       };
 828     });
 829     // Finally, build the menu once to get current service state
 830     new Thread(new Runnable()
 831     {
 832       @Override
 833       public void run()
 834       {
 835         BuildWebServiceMenu();
 836       }
 837     }).start();
 838   }
 839
 840   /**
 841    * Configure menu items that vary according to whether the alignment is
 842    * nucleotide or protein
 843    *
 844    * @param nucleotide
 845    */
 846   public void setGUINucleotide(boolean nucleotide)
 847   {
 848     showTranslation.setVisible(nucleotide);
 849     showReverse.setVisible(nucleotide);
 850     showReverseComplement.setVisible(nucleotide);
 851     conservationMenuItem.setEnabled(!nucleotide);
 852     modifyConservation.setEnabled(!nucleotide);
 853     showGroupConservation.setEnabled(!nucleotide);
 854     rnahelicesColour.setEnabled(nucleotide);
 855     purinePyrimidineColour.setEnabled(nucleotide);
 856     showComplementMenuItem.setText(MessageManager
 857             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 858     setColourSelected(jalview.bin.Cache.getDefault(
 859             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 860                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 861   }
 862
 863   /**
 864    * set up menus for the current viewport. This may be called after any
 865    * operation that affects the data in the current view (selection changed,
 866    * etc) to update the menus to reflect the new state.
 867    */
 868   @Override
 869   public void setMenusForViewport()
 870   {
 871     setMenusFromViewport(viewport);
 872   }
 873
 874   /**
 875    * Need to call this method when tabs are selected for multiple views, or when
 876    * loading from Jalview2XML.java
 877    *
 878    * @param av
 879    *          AlignViewport
 880    */
 881   void setMenusFromViewport(AlignViewport av)
 882   {
 883     padGapsMenuitem.setSelected(av.isPadGaps());
 884     colourTextMenuItem.setSelected(av.isShowColourText());
 885     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 886     conservationMenuItem.setSelected(av.getConservationSelected());
 887     seqLimits.setSelected(av.getShowJVSuffix());
 888     idRightAlign.setSelected(av.isRightAlignIds());
 889     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 890     renderGapsMenuItem.setSelected(av.isRenderGaps());
 891     wrapMenuItem.setSelected(av.getWrapAlignment());
 892     scaleAbove.setVisible(av.getWrapAlignment());
 893     scaleLeft.setVisible(av.getWrapAlignment());
 894     scaleRight.setVisible(av.getWrapAlignment());
 895     annotationPanelMenuItem.setState(av.isShowAnnotation());
 896     /*
 897      * Show/hide annotations only enabled if annotation panel is shown
 898      */
 899     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 902     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 904     viewTextMenuItem.setSelected(av.getShowText());
 905     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 906     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 907     showGroupConservation.setSelected(av.isShowGroupConservation());
 908     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 909     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 910     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 911
 912     setColourSelected(ColourSchemeProperty.getColourName(av
 913             .getGlobalColourScheme()));
 914
 915     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 916     hiddenMarkers.setState(av.getShowHiddenMarkers());
 917     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 918     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 919     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 920     autoCalculate.setSelected(av.autoCalculateConsensus);
 921     sortByTree.setSelected(av.sortByTree);
 922     listenToViewSelections.setSelected(av.followSelection);
 923     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 924     rnahelicesColour
 925             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 926
 927     showProducts.setEnabled(canShowProducts());
 928     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 929
 930     updateEditMenuBar();
 931   }
 932
 933   /**
 934    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 935    *
 936    * @param b
 937    */
 938   public void setGroovyEnabled(boolean b)
 939   {
 940     runGroovy.setEnabled(b);
 941   }
 942
 943   private IProgressIndicator progressBar;
 944
 945   /*
 946    * (non-Javadoc)
 947    *
 948    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 949    */
 950   @Override
 951   public void setProgressBar(String message, long id)
 952   {
 953     progressBar.setProgressBar(message, id);
 954   }
 955
 956   @Override
 957   public void registerHandler(final long id,
 958           final IProgressIndicatorHandler handler)
 959   {
 960     progressBar.registerHandler(id, handler);
 961   }
 962
 963   /**
 964    *
 965    * @return true if any progress bars are still active
 966    */
 967   @Override
 968   public boolean operationInProgress()
 969   {
 970     return progressBar.operationInProgress();
 971   }
 972
 973   @Override
 974   public void setStatus(String text)
 975   {
 976     statusBar.setText(text);
 977   }
 978
 979   /*
 980    * Added so Castor Mapping file can obtain Jalview Version
 981    */
 982   public String getVersion()
 983   {
 984     return jalview.bin.Cache.getProperty("VERSION");
 985   }
 986
 987   public FeatureRenderer getFeatureRenderer()
 988   {
 989     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 990   }
 991
 992   @Override
 993   public void fetchSequence_actionPerformed(ActionEvent e)
 994   {
 995     new jalview.gui.SequenceFetcher(this);
 996   }
 997
 998   @Override
 999   public void addFromFile_actionPerformed(ActionEvent e)
1000   {
1001     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1002   }
1003
1004   @Override
1005   public void reload_actionPerformed(ActionEvent e)
1006   {
1007     if (fileName != null)
1008     {
1009       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010       // originating file's format
1011       // TODO: work out how to recover feature settings for correct view(s) when
1012       // file is reloaded.
1013       if (currentFileFormat == FileFormat.Jalview)
1014       {
1015         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016         for (int i = 0; i < frames.length; i++)
1017         {
1018           if (frames[i] instanceof AlignFrame && frames[i] != this
1019                   && ((AlignFrame) frames[i]).fileName != null
1020                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1021           {
1022             try
1023             {
1024               frames[i].setSelected(true);
1025               Desktop.instance.closeAssociatedWindows();
1026             } catch (java.beans.PropertyVetoException ex)
1027             {
1028             }
1029           }
1030
1031         }
1032         Desktop.instance.closeAssociatedWindows();
1033
1034         FileLoader loader = new FileLoader();
1035         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1036                 : DataSourceType.FILE;
1037         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1038       }
1039       else
1040       {
1041         Rectangle bounds = this.getBounds();
1042
1043         FileLoader loader = new FileLoader();
1044         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1045                 : DataSourceType.FILE;
1046         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1047                 protocol, currentFileFormat);
1048
1049         newframe.setBounds(bounds);
1050         if (featureSettings != null && featureSettings.isShowing())
1051         {
1052           final Rectangle fspos = featureSettings.frame.getBounds();
1053           // TODO: need a 'show feature settings' function that takes bounds -
1054           // need to refactor Desktop.addFrame
1055           newframe.featureSettings_actionPerformed(null);
1056           final FeatureSettings nfs = newframe.featureSettings;
1057           SwingUtilities.invokeLater(new Runnable()
1058           {
1059             @Override
1060             public void run()
1061             {
1062               nfs.frame.setBounds(fspos);
1063             }
1064           });
1065           this.featureSettings.close();
1066           this.featureSettings = null;
1067         }
1068         this.closeMenuItem_actionPerformed(true);
1069       }
1070     }
1071   }
1072
1073   @Override
1074   public void addFromText_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1077             .getAlignPanel());
1078   }
1079
1080   @Override
1081   public void addFromURL_actionPerformed(ActionEvent e)
1082   {
1083     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1084   }
1085
1086   @Override
1087   public void save_actionPerformed(ActionEvent e)
1088   {
1089     if (fileName == null || (currentFileFormat == null)
1090             || fileName.startsWith("http"))
1091     {
1092       saveAs_actionPerformed(null);
1093     }
1094     else
1095     {
1096       saveAlignment(fileName, currentFileFormat);
1097     }
1098   }
1099
1100   /**
1101    * DOCUMENT ME!
1102    *
1103    * @param e
1104    *          DOCUMENT ME!
1105    */
1106   @Override
1107   public void saveAs_actionPerformed(ActionEvent e)
1108   {
1109     JalviewFileChooser chooser = new JalviewFileChooser(
1110             Cache.getProperty("LAST_DIRECTORY"),
1111             // AppletFormatAdapter.WRITABLE_EXTENSIONS,
1112             // AppletFormatAdapter.WRITABLE_FNAMES,
1113             currentFileFormat, false);
1114
1115     chooser.setFileView(new JalviewFileView());
1116     chooser.setDialogTitle(MessageManager
1117             .getString("label.save_alignment_to_file"));
1118     chooser.setToolTipText(MessageManager.getString("action.save"));
1119
1120     int value = chooser.showSaveDialog(this);
1121
1122     if (value == JalviewFileChooser.APPROVE_OPTION)
1123     {
1124       currentFileFormat = chooser.getSelectedFormat();
1125       while (currentFileFormat == null)
1126       {
1127         JOptionPane
1128                 .showInternalMessageDialog(
1129                         Desktop.desktop,
1130                         MessageManager
1131                                 .getString("label.select_file_format_before_saving"),
1132                         MessageManager
1133                                 .getString("label.file_format_not_specified"),
1134                         JOptionPane.WARNING_MESSAGE);
1135         currentFileFormat = chooser.getSelectedFormat();
1136         value = chooser.showSaveDialog(this);
1137         if (value != JalviewFileChooser.APPROVE_OPTION)
1138         {
1139           return;
1140         }
1141       }
1142
1143       fileName = chooser.getSelectedFile().getPath();
1144
1145       Cache.setProperty("DEFAULT_FILE_FORMAT",
1146               currentFileFormat.toString());
1147
1148       Cache.setProperty("LAST_DIRECTORY", fileName);
1149       saveAlignment(fileName, currentFileFormat);
1150     }
1151   }
1152
1153   public boolean saveAlignment(String file, FileFormatI format)
1154   {
1155     boolean success = true;
1156
1157     if (format == FileFormat.Jalview)
1158     {
1159       String shortName = title;
1160
1161       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1162       {
1163         shortName = shortName.substring(shortName
1164                 .lastIndexOf(java.io.File.separatorChar) + 1);
1165       }
1166
1167       success = new Jalview2XML().saveAlignment(this, file, shortName);
1168
1169       statusBar.setText(MessageManager.formatMessage(
1170               "label.successfully_saved_to_file_in_format", new Object[] {
1171                   fileName, format }));
1172
1173     }
1174     else
1175     {
1176       // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1177       // {
1178       // warningMessage("Cannot save file " + fileName + " using format "
1179       // + format, "Alignment output format not supported");
1180       // if (!Jalview.isHeadlessMode())
1181       // {
1182       // saveAs_actionPerformed(null);
1183       // }
1184       // return false;
1185       // }
1186
1187       AlignmentExportData exportData = getAlignmentForExport(format,
1188               viewport, null);
1189       if (exportData.getSettings().isCancelled())
1190       {
1191         return false;
1192       }
1193       FormatAdapter f = new FormatAdapter(alignPanel,
1194               exportData.getSettings());
1195       String output = f.formatSequences(
1196               format,
1197               exportData.getAlignment(), // class cast exceptions will
1198               // occur in the distant future
1199               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1200               f.getCacheSuffixDefault(format),
1201               viewport.getColumnSelection());
1202
1203       if (output == null)
1204       {
1205         success = false;
1206       }
1207       else
1208       {
1209         try
1210         {
1211           java.io.PrintWriter out = new java.io.PrintWriter(
1212                   new java.io.FileWriter(file));
1213
1214           out.print(output);
1215           out.close();
1216           this.setTitle(file);
1217           statusBar.setText(MessageManager.formatMessage(
1218                   "label.successfully_saved_to_file_in_format",
1219                   new Object[] { fileName, format }));
1220         } catch (Exception ex)
1221         {
1222           success = false;
1223           ex.printStackTrace();
1224         }
1225       }
1226     }
1227
1228     if (!success)
1229     {
1230       JOptionPane.showInternalMessageDialog(this, MessageManager
1231               .formatMessage("label.couldnt_save_file",
1232                       new Object[] { fileName }), MessageManager
1233               .getString("label.error_saving_file"),
1234               JOptionPane.WARNING_MESSAGE);
1235     }
1236
1237     return success;
1238   }
1239
1240   private void warningMessage(String warning, String title)
1241   {
1242     if (new jalview.util.Platform().isHeadless())
1243     {
1244       System.err.println("Warning: " + title + "\nWarning: " + warning);
1245
1246     }
1247     else
1248     {
1249       JOptionPane.showInternalMessageDialog(this, warning, title,
1250               JOptionPane.WARNING_MESSAGE);
1251     }
1252     return;
1253   }
1254
1255   /**
1256    * DOCUMENT ME!
1257    *
1258    * @param e
1259    *          DOCUMENT ME!
1260    */
1261   @Override
1262   protected void outputText_actionPerformed(ActionEvent e)
1263   {
1264
1265     FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1266     AlignmentExportData exportData = getAlignmentForExport(
1267 fileFormat,
1268             viewport, null);
1269     if (exportData.getSettings().isCancelled())
1270     {
1271       return;
1272     }
1273     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1274     cap.setForInput(null);
1275     try
1276     {
1277       FileFormatI format = fileFormat;
1278       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1279               .formatSequences(format,
1280                       exportData.getAlignment(),
1281                       exportData.getOmitHidden(),
1282                       exportData.getStartEndPostions(),
1283                       viewport.getColumnSelection()));
1284       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1285               "label.alignment_output_command",
1286               new Object[] { e.getActionCommand() }), 600, 500);
1287     } catch (OutOfMemoryError oom)
1288     {
1289       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1290       cap.dispose();
1291     }
1292
1293   }
1294
1295   public static AlignmentExportData getAlignmentForExport(
1296           FileFormatI format, AlignViewportI viewport,
1297           AlignExportSettingI exportSettings)
1298   {
1299     AlignmentI alignmentToExport = null;
1300     AlignExportSettingI settings = exportSettings;
1301     String[] omitHidden = null;
1302
1303     HiddenSequences hiddenSeqs = viewport.getAlignment()
1304             .getHiddenSequences();
1305
1306     alignmentToExport = viewport.getAlignment();
1307
1308     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1309     if (settings == null)
1310     {
1311       settings = new AlignExportSettings(hasHiddenSeqs,
1312               viewport.hasHiddenColumns(), format);
1313     }
1314     // settings.isExportAnnotations();
1315
1316     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1317     {
1318       omitHidden = viewport.getViewAsString(false,
1319               settings.isExportHiddenSequences());
1320     }
1321
1322     int[] alignmentStartEnd = new int[2];
1323     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1324     {
1325       alignmentToExport = hiddenSeqs.getFullAlignment();
1326     }
1327     else
1328     {
1329       alignmentToExport = viewport.getAlignment();
1330     }
1331     alignmentStartEnd = alignmentToExport
1332             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1333                     .getHiddenColumns());
1334     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1335             omitHidden, alignmentStartEnd, settings);
1336     return ed;
1337   }
1338
1339   /**
1340    * DOCUMENT ME!
1341    *
1342    * @param e
1343    *          DOCUMENT ME!
1344    */
1345   @Override
1346   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1347   {
1348     new HtmlSvgOutput(null, alignPanel);
1349   }
1350
1351   @Override
1352   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1353   {
1354     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1355     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1356   }
1357
1358   public void createImageMap(File file, String image)
1359   {
1360     alignPanel.makePNGImageMap(file, image);
1361   }
1362
1363   /**
1364    * DOCUMENT ME!
1365    *
1366    * @param e
1367    *          DOCUMENT ME!
1368    */
1369   @Override
1370   public void createPNG(File f)
1371   {
1372     alignPanel.makePNG(f);
1373   }
1374
1375   /**
1376    * DOCUMENT ME!
1377    *
1378    * @param e
1379    *          DOCUMENT ME!
1380    */
1381   @Override
1382   public void createEPS(File f)
1383   {
1384     alignPanel.makeEPS(f);
1385   }
1386
1387   @Override
1388   public void createSVG(File f)
1389   {
1390     alignPanel.makeSVG(f);
1391   }
1392
1393   @Override
1394   public void pageSetup_actionPerformed(ActionEvent e)
1395   {
1396     PrinterJob printJob = PrinterJob.getPrinterJob();
1397     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1398   }
1399
1400   /**
1401    * DOCUMENT ME!
1402    *
1403    * @param e
1404    *          DOCUMENT ME!
1405    */
1406   @Override
1407   public void printMenuItem_actionPerformed(ActionEvent e)
1408   {
1409     // Putting in a thread avoids Swing painting problems
1410     PrintThread thread = new PrintThread(alignPanel);
1411     thread.start();
1412   }
1413
1414   @Override
1415   public void exportFeatures_actionPerformed(ActionEvent e)
1416   {
1417     new AnnotationExporter().exportFeatures(alignPanel);
1418   }
1419
1420   @Override
1421   public void exportAnnotations_actionPerformed(ActionEvent e)
1422   {
1423     new AnnotationExporter().exportAnnotations(alignPanel);
1424   }
1425
1426   @Override
1427   public void associatedData_actionPerformed(ActionEvent e)
1428   {
1429     // Pick the tree file
1430     JalviewFileChooser chooser = new JalviewFileChooser(
1431             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1432     chooser.setFileView(new JalviewFileView());
1433     chooser.setDialogTitle(MessageManager
1434             .getString("label.load_jalview_annotations"));
1435     chooser.setToolTipText(MessageManager
1436             .getString("label.load_jalview_annotations"));
1437
1438     int value = chooser.showOpenDialog(null);
1439
1440     if (value == JalviewFileChooser.APPROVE_OPTION)
1441     {
1442       String choice = chooser.getSelectedFile().getPath();
1443       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1444       loadJalviewDataFile(choice, null, null, null);
1445     }
1446
1447   }
1448
1449   /**
1450    * Close the current view or all views in the alignment frame. If the frame
1451    * only contains one view then the alignment will be removed from memory.
1452    *
1453    * @param closeAllTabs
1454    */
1455   @Override
1456   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1457   {
1458     if (alignPanels != null && alignPanels.size() < 2)
1459     {
1460       closeAllTabs = true;
1461     }
1462
1463     try
1464     {
1465       if (alignPanels != null)
1466       {
1467         if (closeAllTabs)
1468         {
1469           if (this.isClosed())
1470           {
1471             // really close all the windows - otherwise wait till
1472             // setClosed(true) is called
1473             for (int i = 0; i < alignPanels.size(); i++)
1474             {
1475               AlignmentPanel ap = alignPanels.get(i);
1476               ap.closePanel();
1477             }
1478           }
1479         }
1480         else
1481         {
1482           closeView(alignPanel);
1483         }
1484       }
1485
1486       if (closeAllTabs)
1487       {
1488         /*
1489          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1490          * be called recursively, with the frame now in 'closed' state
1491          */
1492         this.setClosed(true);
1493       }
1494     } catch (Exception ex)
1495     {
1496       ex.printStackTrace();
1497     }
1498   }
1499
1500   /**
1501    * Close the specified panel and close up tabs appropriately.
1502    *
1503    * @param panelToClose
1504    */
1505   public void closeView(AlignmentPanel panelToClose)
1506   {
1507     int index = tabbedPane.getSelectedIndex();
1508     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1509     alignPanels.remove(panelToClose);
1510     panelToClose.closePanel();
1511     panelToClose = null;
1512
1513     tabbedPane.removeTabAt(closedindex);
1514     tabbedPane.validate();
1515
1516     if (index > closedindex || index == tabbedPane.getTabCount())
1517     {
1518       // modify currently selected tab index if necessary.
1519       index--;
1520     }
1521
1522     this.tabSelectionChanged(index);
1523   }
1524
1525   /**
1526    * DOCUMENT ME!
1527    */
1528   void updateEditMenuBar()
1529   {
1530
1531     if (viewport.getHistoryList().size() > 0)
1532     {
1533       undoMenuItem.setEnabled(true);
1534       CommandI command = viewport.getHistoryList().peek();
1535       undoMenuItem.setText(MessageManager.formatMessage(
1536               "label.undo_command",
1537               new Object[] { command.getDescription() }));
1538     }
1539     else
1540     {
1541       undoMenuItem.setEnabled(false);
1542       undoMenuItem.setText(MessageManager.getString("action.undo"));
1543     }
1544
1545     if (viewport.getRedoList().size() > 0)
1546     {
1547       redoMenuItem.setEnabled(true);
1548
1549       CommandI command = viewport.getRedoList().peek();
1550       redoMenuItem.setText(MessageManager.formatMessage(
1551               "label.redo_command",
1552               new Object[] { command.getDescription() }));
1553     }
1554     else
1555     {
1556       redoMenuItem.setEnabled(false);
1557       redoMenuItem.setText(MessageManager.getString("action.redo"));
1558     }
1559   }
1560
1561   @Override
1562   public void addHistoryItem(CommandI command)
1563   {
1564     if (command.getSize() > 0)
1565     {
1566       viewport.addToHistoryList(command);
1567       viewport.clearRedoList();
1568       updateEditMenuBar();
1569       viewport.updateHiddenColumns();
1570       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1571       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1572       // viewport.getColumnSelection()
1573       // .getHiddenColumns().size() > 0);
1574     }
1575   }
1576
1577   /**
1578    *
1579    * @return alignment objects for all views
1580    */
1581   AlignmentI[] getViewAlignments()
1582   {
1583     if (alignPanels != null)
1584     {
1585       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1586       int i = 0;
1587       for (AlignmentPanel ap : alignPanels)
1588       {
1589         als[i++] = ap.av.getAlignment();
1590       }
1591       return als;
1592     }
1593     if (viewport != null)
1594     {
1595       return new AlignmentI[] { viewport.getAlignment() };
1596     }
1597     return null;
1598   }
1599
1600   /**
1601    * DOCUMENT ME!
1602    *
1603    * @param e
1604    *          DOCUMENT ME!
1605    */
1606   @Override
1607   protected void undoMenuItem_actionPerformed(ActionEvent e)
1608   {
1609     if (viewport.getHistoryList().isEmpty())
1610     {
1611       return;
1612     }
1613     CommandI command = viewport.getHistoryList().pop();
1614     viewport.addToRedoList(command);
1615     command.undoCommand(getViewAlignments());
1616
1617     AlignmentViewport originalSource = getOriginatingSource(command);
1618     updateEditMenuBar();
1619
1620     if (originalSource != null)
1621     {
1622       if (originalSource != viewport)
1623       {
1624         Cache.log
1625                 .warn("Implementation worry: mismatch of viewport origin for undo");
1626       }
1627       originalSource.updateHiddenColumns();
1628       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1629       // null
1630       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1631       // viewport.getColumnSelection()
1632       // .getHiddenColumns().size() > 0);
1633       originalSource.firePropertyChange("alignment", null, originalSource
1634               .getAlignment().getSequences());
1635     }
1636   }
1637
1638   /**
1639    * DOCUMENT ME!
1640    *
1641    * @param e
1642    *          DOCUMENT ME!
1643    */
1644   @Override
1645   protected void redoMenuItem_actionPerformed(ActionEvent e)
1646   {
1647     if (viewport.getRedoList().size() < 1)
1648     {
1649       return;
1650     }
1651
1652     CommandI command = viewport.getRedoList().pop();
1653     viewport.addToHistoryList(command);
1654     command.doCommand(getViewAlignments());
1655
1656     AlignmentViewport originalSource = getOriginatingSource(command);
1657     updateEditMenuBar();
1658
1659     if (originalSource != null)
1660     {
1661
1662       if (originalSource != viewport)
1663       {
1664         Cache.log
1665                 .warn("Implementation worry: mismatch of viewport origin for redo");
1666       }
1667       originalSource.updateHiddenColumns();
1668       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1669       // null
1670       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1671       // viewport.getColumnSelection()
1672       // .getHiddenColumns().size() > 0);
1673       originalSource.firePropertyChange("alignment", null, originalSource
1674               .getAlignment().getSequences());
1675     }
1676   }
1677
1678   AlignmentViewport getOriginatingSource(CommandI command)
1679   {
1680     AlignmentViewport originalSource = null;
1681     // For sequence removal and addition, we need to fire
1682     // the property change event FROM the viewport where the
1683     // original alignment was altered
1684     AlignmentI al = null;
1685     if (command instanceof EditCommand)
1686     {
1687       EditCommand editCommand = (EditCommand) command;
1688       al = editCommand.getAlignment();
1689       List<Component> comps = PaintRefresher.components.get(viewport
1690               .getSequenceSetId());
1691
1692       for (Component comp : comps)
1693       {
1694         if (comp instanceof AlignmentPanel)
1695         {
1696           if (al == ((AlignmentPanel) comp).av.getAlignment())
1697           {
1698             originalSource = ((AlignmentPanel) comp).av;
1699             break;
1700           }
1701         }
1702       }
1703     }
1704
1705     if (originalSource == null)
1706     {
1707       // The original view is closed, we must validate
1708       // the current view against the closed view first
1709       if (al != null)
1710       {
1711         PaintRefresher.validateSequences(al, viewport.getAlignment());
1712       }
1713
1714       originalSource = viewport;
1715     }
1716
1717     return originalSource;
1718   }
1719
1720   /**
1721    * DOCUMENT ME!
1722    *
1723    * @param up
1724    *          DOCUMENT ME!
1725    */
1726   public void moveSelectedSequences(boolean up)
1727   {
1728     SequenceGroup sg = viewport.getSelectionGroup();
1729
1730     if (sg == null)
1731     {
1732       return;
1733     }
1734     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1735             viewport.getHiddenRepSequences(), up);
1736     alignPanel.paintAlignment(true);
1737   }
1738
1739   synchronized void slideSequences(boolean right, int size)
1740   {
1741     List<SequenceI> sg = new ArrayList<SequenceI>();
1742     if (viewport.cursorMode)
1743     {
1744       sg.add(viewport.getAlignment().getSequenceAt(
1745               alignPanel.getSeqPanel().seqCanvas.cursorY));
1746     }
1747     else if (viewport.getSelectionGroup() != null
1748             && viewport.getSelectionGroup().getSize() != viewport
1749                     .getAlignment().getHeight())
1750     {
1751       sg = viewport.getSelectionGroup().getSequences(
1752               viewport.getHiddenRepSequences());
1753     }
1754
1755     if (sg.size() < 1)
1756     {
1757       return;
1758     }
1759
1760     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1761
1762     for (SequenceI seq : viewport.getAlignment().getSequences())
1763     {
1764       if (!sg.contains(seq))
1765       {
1766         invertGroup.add(seq);
1767       }
1768     }
1769
1770     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1771
1772     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1773     for (int i = 0; i < invertGroup.size(); i++)
1774     {
1775       seqs2[i] = invertGroup.get(i);
1776     }
1777
1778     SlideSequencesCommand ssc;
1779     if (right)
1780     {
1781       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1782               size, viewport.getGapCharacter());
1783     }
1784     else
1785     {
1786       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1787               size, viewport.getGapCharacter());
1788     }
1789
1790     int groupAdjustment = 0;
1791     if (ssc.getGapsInsertedBegin() && right)
1792     {
1793       if (viewport.cursorMode)
1794       {
1795         alignPanel.getSeqPanel().moveCursor(size, 0);
1796       }
1797       else
1798       {
1799         groupAdjustment = size;
1800       }
1801     }
1802     else if (!ssc.getGapsInsertedBegin() && !right)
1803     {
1804       if (viewport.cursorMode)
1805       {
1806         alignPanel.getSeqPanel().moveCursor(-size, 0);
1807       }
1808       else
1809       {
1810         groupAdjustment = -size;
1811       }
1812     }
1813
1814     if (groupAdjustment != 0)
1815     {
1816       viewport.getSelectionGroup().setStartRes(
1817               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1818       viewport.getSelectionGroup().setEndRes(
1819               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1820     }
1821
1822     /*
1823      * just extend the last slide command if compatible; but not if in
1824      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1825      */
1826     boolean appendHistoryItem = false;
1827     Deque<CommandI> historyList = viewport.getHistoryList();
1828     boolean inSplitFrame = getSplitViewContainer() != null;
1829     if (!inSplitFrame && historyList != null && historyList.size() > 0
1830             && historyList.peek() instanceof SlideSequencesCommand)
1831     {
1832       appendHistoryItem = ssc
1833               .appendSlideCommand((SlideSequencesCommand) historyList
1834                       .peek());
1835     }
1836
1837     if (!appendHistoryItem)
1838     {
1839       addHistoryItem(ssc);
1840     }
1841
1842     repaint();
1843   }
1844
1845   /**
1846    * DOCUMENT ME!
1847    *
1848    * @param e
1849    *          DOCUMENT ME!
1850    */
1851   @Override
1852   protected void copy_actionPerformed(ActionEvent e)
1853   {
1854     System.gc();
1855     if (viewport.getSelectionGroup() == null)
1856     {
1857       return;
1858     }
1859     // TODO: preserve the ordering of displayed alignment annotation in any
1860     // internal paste (particularly sequence associated annotation)
1861     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1862     String[] omitHidden = null;
1863
1864     if (viewport.hasHiddenColumns())
1865     {
1866       omitHidden = viewport.getViewAsString(true);
1867     }
1868
1869     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1870             omitHidden, null);
1871
1872     StringSelection ss = new StringSelection(output);
1873
1874     try
1875     {
1876       jalview.gui.Desktop.internalCopy = true;
1877       // Its really worth setting the clipboard contents
1878       // to empty before setting the large StringSelection!!
1879       Toolkit.getDefaultToolkit().getSystemClipboard()
1880               .setContents(new StringSelection(""), null);
1881
1882       Toolkit.getDefaultToolkit().getSystemClipboard()
1883               .setContents(ss, Desktop.instance);
1884     } catch (OutOfMemoryError er)
1885     {
1886       new OOMWarning("copying region", er);
1887       return;
1888     }
1889
1890     ArrayList<int[]> hiddenColumns = null;
1891     if (viewport.hasHiddenColumns())
1892     {
1893       hiddenColumns = new ArrayList<int[]>();
1894       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1895               .getSelectionGroup().getEndRes();
1896       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1897       {
1898         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1899         {
1900           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1901               region[1] - hiddenOffset });
1902         }
1903       }
1904     }
1905
1906     Desktop.jalviewClipboard = new Object[] { seqs,
1907         viewport.getAlignment().getDataset(), hiddenColumns };
1908     statusBar.setText(MessageManager.formatMessage(
1909             "label.copied_sequences_to_clipboard", new Object[] { Integer
1910                     .valueOf(seqs.length).toString() }));
1911   }
1912
1913   /**
1914    * DOCUMENT ME!
1915    *
1916    * @param e
1917    *          DOCUMENT ME!
1918    */
1919   @Override
1920   protected void pasteNew_actionPerformed(ActionEvent e)
1921   {
1922     paste(true);
1923   }
1924
1925   /**
1926    * DOCUMENT ME!
1927    *
1928    * @param e
1929    *          DOCUMENT ME!
1930    */
1931   @Override
1932   protected void pasteThis_actionPerformed(ActionEvent e)
1933   {
1934     paste(false);
1935   }
1936
1937   /**
1938    * Paste contents of Jalview clipboard
1939    *
1940    * @param newAlignment
1941    *          true to paste to a new alignment, otherwise add to this.
1942    */
1943   void paste(boolean newAlignment)
1944   {
1945     boolean externalPaste = true;
1946     try
1947     {
1948       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1949       Transferable contents = c.getContents(this);
1950
1951       if (contents == null)
1952       {
1953         return;
1954       }
1955
1956       String str;
1957       FileFormatI format;
1958       try
1959       {
1960         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1961         if (str.length() < 1)
1962         {
1963           return;
1964         }
1965
1966         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1967
1968       } catch (OutOfMemoryError er)
1969       {
1970         new OOMWarning("Out of memory pasting sequences!!", er);
1971         return;
1972       }
1973
1974       SequenceI[] sequences;
1975       boolean annotationAdded = false;
1976       AlignmentI alignment = null;
1977
1978       if (Desktop.jalviewClipboard != null)
1979       {
1980         // The clipboard was filled from within Jalview, we must use the
1981         // sequences
1982         // And dataset from the copied alignment
1983         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1984         // be doubly sure that we create *new* sequence objects.
1985         sequences = new SequenceI[newseq.length];
1986         for (int i = 0; i < newseq.length; i++)
1987         {
1988           sequences[i] = new Sequence(newseq[i]);
1989         }
1990         alignment = new Alignment(sequences);
1991         externalPaste = false;
1992       }
1993       else
1994       {
1995         // parse the clipboard as an alignment.
1996         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1997                 format);
1998         sequences = alignment.getSequencesArray();
1999       }
2000
2001       int alwidth = 0;
2002       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2003       int fgroup = -1;
2004
2005       if (newAlignment)
2006       {
2007
2008         if (Desktop.jalviewClipboard != null)
2009         {
2010           // dataset is inherited
2011           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2012         }
2013         else
2014         {
2015           // new dataset is constructed
2016           alignment.setDataset(null);
2017         }
2018         alwidth = alignment.getWidth() + 1;
2019       }
2020       else
2021       {
2022         AlignmentI pastedal = alignment; // preserve pasted alignment object
2023         // Add pasted sequences and dataset into existing alignment.
2024         alignment = viewport.getAlignment();
2025         alwidth = alignment.getWidth() + 1;
2026         // decide if we need to import sequences from an existing dataset
2027         boolean importDs = Desktop.jalviewClipboard != null
2028                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2029         // importDs==true instructs us to copy over new dataset sequences from
2030         // an existing alignment
2031         Vector newDs = (importDs) ? new Vector() : null; // used to create
2032         // minimum dataset set
2033
2034         for (int i = 0; i < sequences.length; i++)
2035         {
2036           if (importDs)
2037           {
2038             newDs.addElement(null);
2039           }
2040           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2041           // paste
2042           if (importDs && ds != null)
2043           {
2044             if (!newDs.contains(ds))
2045             {
2046               newDs.setElementAt(ds, i);
2047               ds = new Sequence(ds);
2048               // update with new dataset sequence
2049               sequences[i].setDatasetSequence(ds);
2050             }
2051             else
2052             {
2053               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2054             }
2055           }
2056           else
2057           {
2058             // copy and derive new dataset sequence
2059             sequences[i] = sequences[i].deriveSequence();
2060             alignment.getDataset().addSequence(
2061                     sequences[i].getDatasetSequence());
2062             // TODO: avoid creation of duplicate dataset sequences with a
2063             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2064           }
2065           alignment.addSequence(sequences[i]); // merges dataset
2066         }
2067         if (newDs != null)
2068         {
2069           newDs.clear(); // tidy up
2070         }
2071         if (alignment.getAlignmentAnnotation() != null)
2072         {
2073           for (AlignmentAnnotation alan : alignment
2074                   .getAlignmentAnnotation())
2075           {
2076             if (alan.graphGroup > fgroup)
2077             {
2078               fgroup = alan.graphGroup;
2079             }
2080           }
2081         }
2082         if (pastedal.getAlignmentAnnotation() != null)
2083         {
2084           // Add any annotation attached to alignment.
2085           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2086           for (int i = 0; i < alann.length; i++)
2087           {
2088             annotationAdded = true;
2089             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2090             {
2091               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2092               if (newann.graphGroup > -1)
2093               {
2094                 if (newGraphGroups.size() <= newann.graphGroup
2095                         || newGraphGroups.get(newann.graphGroup) == null)
2096                 {
2097                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2098                   {
2099                     newGraphGroups.add(q, null);
2100                   }
2101                   newGraphGroups.set(newann.graphGroup, new Integer(
2102                           ++fgroup));
2103                 }
2104                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2105                         .intValue();
2106               }
2107
2108               newann.padAnnotation(alwidth);
2109               alignment.addAnnotation(newann);
2110             }
2111           }
2112         }
2113       }
2114       if (!newAlignment)
2115       {
2116         // /////
2117         // ADD HISTORY ITEM
2118         //
2119         addHistoryItem(new EditCommand(
2120                 MessageManager.getString("label.add_sequences"),
2121                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2122       }
2123       // Add any annotations attached to sequences
2124       for (int i = 0; i < sequences.length; i++)
2125       {
2126         if (sequences[i].getAnnotation() != null)
2127         {
2128           AlignmentAnnotation newann;
2129           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2130           {
2131             annotationAdded = true;
2132             newann = sequences[i].getAnnotation()[a];
2133             newann.adjustForAlignment();
2134             newann.padAnnotation(alwidth);
2135             if (newann.graphGroup > -1)
2136             {
2137               if (newann.graphGroup > -1)
2138               {
2139                 if (newGraphGroups.size() <= newann.graphGroup
2140                         || newGraphGroups.get(newann.graphGroup) == null)
2141                 {
2142                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2143                   {
2144                     newGraphGroups.add(q, null);
2145                   }
2146                   newGraphGroups.set(newann.graphGroup, new Integer(
2147                           ++fgroup));
2148                 }
2149                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2150                         .intValue();
2151               }
2152             }
2153             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2154             // was
2155             // duplicated
2156             // earlier
2157             alignment
2158                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2159           }
2160         }
2161       }
2162       if (!newAlignment)
2163       {
2164
2165         // propagate alignment changed.
2166         viewport.setEndSeq(alignment.getHeight());
2167         if (annotationAdded)
2168         {
2169           // Duplicate sequence annotation in all views.
2170           AlignmentI[] alview = this.getViewAlignments();
2171           for (int i = 0; i < sequences.length; i++)
2172           {
2173             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2174             if (sann == null)
2175             {
2176               continue;
2177             }
2178             for (int avnum = 0; avnum < alview.length; avnum++)
2179             {
2180               if (alview[avnum] != alignment)
2181               {
2182                 // duplicate in a view other than the one with input focus
2183                 int avwidth = alview[avnum].getWidth() + 1;
2184                 // this relies on sann being preserved after we
2185                 // modify the sequence's annotation array for each duplication
2186                 for (int a = 0; a < sann.length; a++)
2187                 {
2188                   AlignmentAnnotation newann = new AlignmentAnnotation(
2189                           sann[a]);
2190                   sequences[i].addAlignmentAnnotation(newann);
2191                   newann.padAnnotation(avwidth);
2192                   alview[avnum].addAnnotation(newann); // annotation was
2193                   // duplicated earlier
2194                   // TODO JAL-1145 graphGroups are not updated for sequence
2195                   // annotation added to several views. This may cause
2196                   // strangeness
2197                   alview[avnum].setAnnotationIndex(newann, a);
2198                 }
2199               }
2200             }
2201           }
2202           buildSortByAnnotationScoresMenu();
2203         }
2204         viewport.firePropertyChange("alignment", null,
2205                 alignment.getSequences());
2206         if (alignPanels != null)
2207         {
2208           for (AlignmentPanel ap : alignPanels)
2209           {
2210             ap.validateAnnotationDimensions(false);
2211           }
2212         }
2213         else
2214         {
2215           alignPanel.validateAnnotationDimensions(false);
2216         }
2217
2218       }
2219       else
2220       {
2221         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2222                 DEFAULT_HEIGHT);
2223         String newtitle = new String("Copied sequences");
2224
2225         if (Desktop.jalviewClipboard != null
2226                 && Desktop.jalviewClipboard[2] != null)
2227         {
2228           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2229           for (int[] region : hc)
2230           {
2231             af.viewport.hideColumns(region[0], region[1]);
2232           }
2233         }
2234
2235         // >>>This is a fix for the moment, until a better solution is
2236         // found!!<<<
2237         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2238                 .transferSettings(
2239                         alignPanel.getSeqPanel().seqCanvas
2240                                 .getFeatureRenderer());
2241
2242         // TODO: maintain provenance of an alignment, rather than just make the
2243         // title a concatenation of operations.
2244         if (!externalPaste)
2245         {
2246           if (title.startsWith("Copied sequences"))
2247           {
2248             newtitle = title;
2249           }
2250           else
2251           {
2252             newtitle = newtitle.concat("- from " + title);
2253           }
2254         }
2255         else
2256         {
2257           newtitle = new String("Pasted sequences");
2258         }
2259
2260         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2261                 DEFAULT_HEIGHT);
2262
2263       }
2264
2265     } catch (Exception ex)
2266     {
2267       ex.printStackTrace();
2268       System.out.println("Exception whilst pasting: " + ex);
2269       // could be anything being pasted in here
2270     }
2271
2272   }
2273
2274   @Override
2275   protected void expand_newalign(ActionEvent e)
2276   {
2277     try
2278     {
2279       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2280               .getAlignment(), -1);
2281       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2282               DEFAULT_HEIGHT);
2283       String newtitle = new String("Flanking alignment");
2284
2285       if (Desktop.jalviewClipboard != null
2286               && Desktop.jalviewClipboard[2] != null)
2287       {
2288         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2289         for (int region[] : hc)
2290         {
2291           af.viewport.hideColumns(region[0], region[1]);
2292         }
2293       }
2294
2295       // >>>This is a fix for the moment, until a better solution is
2296       // found!!<<<
2297       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2298               .transferSettings(
2299                       alignPanel.getSeqPanel().seqCanvas
2300                               .getFeatureRenderer());
2301
2302       // TODO: maintain provenance of an alignment, rather than just make the
2303       // title a concatenation of operations.
2304       {
2305         if (title.startsWith("Copied sequences"))
2306         {
2307           newtitle = title;
2308         }
2309         else
2310         {
2311           newtitle = newtitle.concat("- from " + title);
2312         }
2313       }
2314
2315       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2316
2317     } catch (Exception ex)
2318     {
2319       ex.printStackTrace();
2320       System.out.println("Exception whilst pasting: " + ex);
2321       // could be anything being pasted in here
2322     } catch (OutOfMemoryError oom)
2323     {
2324       new OOMWarning("Viewing flanking region of alignment", oom);
2325     }
2326   }
2327
2328   /**
2329    * DOCUMENT ME!
2330    *
2331    * @param e
2332    *          DOCUMENT ME!
2333    */
2334   @Override
2335   protected void cut_actionPerformed(ActionEvent e)
2336   {
2337     copy_actionPerformed(null);
2338     delete_actionPerformed(null);
2339   }
2340
2341   /**
2342    * DOCUMENT ME!
2343    *
2344    * @param e
2345    *          DOCUMENT ME!
2346    */
2347   @Override
2348   protected void delete_actionPerformed(ActionEvent evt)
2349   {
2350
2351     SequenceGroup sg = viewport.getSelectionGroup();
2352     if (sg == null)
2353     {
2354       return;
2355     }
2356
2357     /*
2358      * If the cut affects all sequences, warn, remove highlighted columns
2359      */
2360     if (sg.getSize() == viewport.getAlignment().getHeight())
2361     {
2362       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2363               .getAlignment().getWidth()) ? true : false;
2364       if (isEntireAlignWidth)
2365       {
2366         int confirm = JOptionPane.showConfirmDialog(this,
2367                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2368                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2369                 JOptionPane.OK_CANCEL_OPTION);
2370
2371         if (confirm == JOptionPane.CANCEL_OPTION
2372                 || confirm == JOptionPane.CLOSED_OPTION)
2373         {
2374           return;
2375         }
2376       }
2377       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2378               sg.getEndRes() + 1);
2379     }
2380     SequenceI[] cut = sg.getSequences()
2381             .toArray(new SequenceI[sg.getSize()]);
2382
2383     addHistoryItem(new EditCommand(
2384             MessageManager.getString("label.cut_sequences"), Action.CUT,
2385             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2386             viewport.getAlignment()));
2387
2388     viewport.setSelectionGroup(null);
2389     viewport.sendSelection();
2390     viewport.getAlignment().deleteGroup(sg);
2391
2392     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2393             .getSequences());
2394     if (viewport.getAlignment().getHeight() < 1)
2395     {
2396       try
2397       {
2398         this.setClosed(true);
2399       } catch (Exception ex)
2400       {
2401       }
2402     }
2403   }
2404
2405   /**
2406    * DOCUMENT ME!
2407    *
2408    * @param e
2409    *          DOCUMENT ME!
2410    */
2411   @Override
2412   protected void deleteGroups_actionPerformed(ActionEvent e)
2413   {
2414     if (avc.deleteGroups())
2415     {
2416       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2417       alignPanel.updateAnnotation();
2418       alignPanel.paintAlignment(true);
2419     }
2420   }
2421
2422   /**
2423    * DOCUMENT ME!
2424    *
2425    * @param e
2426    *          DOCUMENT ME!
2427    */
2428   @Override
2429   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2430   {
2431     SequenceGroup sg = new SequenceGroup();
2432
2433     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2434     {
2435       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2436     }
2437
2438     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2439     viewport.setSelectionGroup(sg);
2440     viewport.sendSelection();
2441     alignPanel.paintAlignment(true);
2442     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2443   }
2444
2445   /**
2446    * DOCUMENT ME!
2447    *
2448    * @param e
2449    *          DOCUMENT ME!
2450    */
2451   @Override
2452   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2453   {
2454     if (viewport.cursorMode)
2455     {
2456       alignPanel.getSeqPanel().keyboardNo1 = null;
2457       alignPanel.getSeqPanel().keyboardNo2 = null;
2458     }
2459     viewport.setSelectionGroup(null);
2460     viewport.getColumnSelection().clear();
2461     viewport.setSelectionGroup(null);
2462     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2463     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2464     alignPanel.paintAlignment(true);
2465     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466     viewport.sendSelection();
2467   }
2468
2469   /**
2470    * DOCUMENT ME!
2471    *
2472    * @param e
2473    *          DOCUMENT ME!
2474    */
2475   @Override
2476   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2477   {
2478     SequenceGroup sg = viewport.getSelectionGroup();
2479
2480     if (sg == null)
2481     {
2482       selectAllSequenceMenuItem_actionPerformed(null);
2483
2484       return;
2485     }
2486
2487     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2488     {
2489       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2490     }
2491
2492     alignPanel.paintAlignment(true);
2493     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2494     viewport.sendSelection();
2495   }
2496
2497   @Override
2498   public void invertColSel_actionPerformed(ActionEvent e)
2499   {
2500     viewport.invertColumnSelection();
2501     alignPanel.paintAlignment(true);
2502     viewport.sendSelection();
2503   }
2504
2505   /**
2506    * DOCUMENT ME!
2507    *
2508    * @param e
2509    *          DOCUMENT ME!
2510    */
2511   @Override
2512   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2513   {
2514     trimAlignment(true);
2515   }
2516
2517   /**
2518    * DOCUMENT ME!
2519    *
2520    * @param e
2521    *          DOCUMENT ME!
2522    */
2523   @Override
2524   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2525   {
2526     trimAlignment(false);
2527   }
2528
2529   void trimAlignment(boolean trimLeft)
2530   {
2531     ColumnSelection colSel = viewport.getColumnSelection();
2532     int column;
2533
2534     if (!colSel.isEmpty())
2535     {
2536       if (trimLeft)
2537       {
2538         column = colSel.getMin();
2539       }
2540       else
2541       {
2542         column = colSel.getMax();
2543       }
2544
2545       SequenceI[] seqs;
2546       if (viewport.getSelectionGroup() != null)
2547       {
2548         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2549                 viewport.getHiddenRepSequences());
2550       }
2551       else
2552       {
2553         seqs = viewport.getAlignment().getSequencesArray();
2554       }
2555
2556       TrimRegionCommand trimRegion;
2557       if (trimLeft)
2558       {
2559         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2560                 column, viewport.getAlignment());
2561         viewport.setStartRes(0);
2562       }
2563       else
2564       {
2565         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2566                 column, viewport.getAlignment());
2567       }
2568
2569       statusBar.setText(MessageManager.formatMessage(
2570               "label.removed_columns",
2571               new String[] { Integer.valueOf(trimRegion.getSize())
2572                       .toString() }));
2573
2574       addHistoryItem(trimRegion);
2575
2576       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2577       {
2578         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2579                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2580         {
2581           viewport.getAlignment().deleteGroup(sg);
2582         }
2583       }
2584
2585       viewport.firePropertyChange("alignment", null, viewport
2586               .getAlignment().getSequences());
2587     }
2588   }
2589
2590   /**
2591    * DOCUMENT ME!
2592    *
2593    * @param e
2594    *          DOCUMENT ME!
2595    */
2596   @Override
2597   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2598   {
2599     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2600
2601     SequenceI[] seqs;
2602     if (viewport.getSelectionGroup() != null)
2603     {
2604       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2605               viewport.getHiddenRepSequences());
2606       start = viewport.getSelectionGroup().getStartRes();
2607       end = viewport.getSelectionGroup().getEndRes();
2608     }
2609     else
2610     {
2611       seqs = viewport.getAlignment().getSequencesArray();
2612     }
2613
2614     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2615             "Remove Gapped Columns", seqs, start, end,
2616             viewport.getAlignment());
2617
2618     addHistoryItem(removeGapCols);
2619
2620     statusBar.setText(MessageManager.formatMessage(
2621             "label.removed_empty_columns",
2622             new Object[] { Integer.valueOf(removeGapCols.getSize())
2623                     .toString() }));
2624
2625     // This is to maintain viewport position on first residue
2626     // of first sequence
2627     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2628     int startRes = seq.findPosition(viewport.startRes);
2629     // ShiftList shifts;
2630     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2631     // edit.alColumnChanges=shifts.getInverse();
2632     // if (viewport.hasHiddenColumns)
2633     // viewport.getColumnSelection().compensateForEdits(shifts);
2634     viewport.setStartRes(seq.findIndex(startRes) - 1);
2635     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2636             .getSequences());
2637
2638   }
2639
2640   /**
2641    * DOCUMENT ME!
2642    *
2643    * @param e
2644    *          DOCUMENT ME!
2645    */
2646   @Override
2647   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2648   {
2649     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2650
2651     SequenceI[] seqs;
2652     if (viewport.getSelectionGroup() != null)
2653     {
2654       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2655               viewport.getHiddenRepSequences());
2656       start = viewport.getSelectionGroup().getStartRes();
2657       end = viewport.getSelectionGroup().getEndRes();
2658     }
2659     else
2660     {
2661       seqs = viewport.getAlignment().getSequencesArray();
2662     }
2663
2664     // This is to maintain viewport position on first residue
2665     // of first sequence
2666     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2667     int startRes = seq.findPosition(viewport.startRes);
2668
2669     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2670             viewport.getAlignment()));
2671
2672     viewport.setStartRes(seq.findIndex(startRes) - 1);
2673
2674     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2675             .getSequences());
2676
2677   }
2678
2679   /**
2680    * DOCUMENT ME!
2681    *
2682    * @param e
2683    *          DOCUMENT ME!
2684    */
2685   @Override
2686   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2687   {
2688     viewport.setPadGaps(padGapsMenuitem.isSelected());
2689     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2690             .getSequences());
2691   }
2692
2693   /**
2694    * DOCUMENT ME!
2695    *
2696    * @param e
2697    *          DOCUMENT ME!
2698    */
2699   @Override
2700   public void findMenuItem_actionPerformed(ActionEvent e)
2701   {
2702     new Finder();
2703   }
2704
2705   /**
2706    * Create a new view of the current alignment.
2707    */
2708   @Override
2709   public void newView_actionPerformed(ActionEvent e)
2710   {
2711     newView(null, true);
2712   }
2713
2714   /**
2715    * Creates and shows a new view of the current alignment.
2716    *
2717    * @param viewTitle
2718    *          title of newly created view; if null, one will be generated
2719    * @param copyAnnotation
2720    *          if true then duplicate all annnotation, groups and settings
2721    * @return new alignment panel, already displayed.
2722    */
2723   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2724   {
2725     /*
2726      * Create a new AlignmentPanel (with its own, new Viewport)
2727      */
2728     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2729             true);
2730     if (!copyAnnotation)
2731     {
2732       /*
2733        * remove all groups and annotation except for the automatic stuff
2734        */
2735       newap.av.getAlignment().deleteAllGroups();
2736       newap.av.getAlignment().deleteAllAnnotations(false);
2737     }
2738
2739     newap.av.setGatherViewsHere(false);
2740
2741     if (viewport.viewName == null)
2742     {
2743       viewport.viewName = MessageManager
2744               .getString("label.view_name_original");
2745     }
2746
2747     /*
2748      * Views share the same edits undo and redo stacks
2749      */
2750     newap.av.setHistoryList(viewport.getHistoryList());
2751     newap.av.setRedoList(viewport.getRedoList());
2752
2753     /*
2754      * Views share the same mappings; need to deregister any new mappings
2755      * created by copyAlignPanel, and register the new reference to the shared
2756      * mappings
2757      */
2758     newap.av.replaceMappings(viewport.getAlignment());
2759
2760     newap.av.viewName = getNewViewName(viewTitle);
2761
2762     addAlignmentPanel(newap, true);
2763     newap.alignmentChanged();
2764
2765     if (alignPanels.size() == 2)
2766     {
2767       viewport.setGatherViewsHere(true);
2768     }
2769     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2770     return newap;
2771   }
2772
2773   /**
2774    * Make a new name for the view, ensuring it is unique within the current
2775    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2776    * these now use viewId. Unique view names are still desirable for usability.)
2777    *
2778    * @param viewTitle
2779    * @return
2780    */
2781   protected String getNewViewName(String viewTitle)
2782   {
2783     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2784     boolean addFirstIndex = false;
2785     if (viewTitle == null || viewTitle.trim().length() == 0)
2786     {
2787       viewTitle = MessageManager.getString("action.view");
2788       addFirstIndex = true;
2789     }
2790     else
2791     {
2792       index = 1;// we count from 1 if given a specific name
2793     }
2794     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2795
2796     List<Component> comps = PaintRefresher.components.get(viewport
2797             .getSequenceSetId());
2798
2799     List<String> existingNames = getExistingViewNames(comps);
2800
2801     while (existingNames.contains(newViewName))
2802     {
2803       newViewName = viewTitle + " " + (++index);
2804     }
2805     return newViewName;
2806   }
2807
2808   /**
2809    * Returns a list of distinct view names found in the given list of
2810    * components. View names are held on the viewport of an AlignmentPanel.
2811    *
2812    * @param comps
2813    * @return
2814    */
2815   protected List<String> getExistingViewNames(List<Component> comps)
2816   {
2817     List<String> existingNames = new ArrayList<String>();
2818     for (Component comp : comps)
2819     {
2820       if (comp instanceof AlignmentPanel)
2821       {
2822         AlignmentPanel ap = (AlignmentPanel) comp;
2823         if (!existingNames.contains(ap.av.viewName))
2824         {
2825           existingNames.add(ap.av.viewName);
2826         }
2827       }
2828     }
2829     return existingNames;
2830   }
2831
2832   /**
2833    * Explode tabbed views into separate windows.
2834    */
2835   @Override
2836   public void expandViews_actionPerformed(ActionEvent e)
2837   {
2838     Desktop.instance.explodeViews(this);
2839   }
2840
2841   /**
2842    * Gather views in separate windows back into a tabbed presentation.
2843    */
2844   @Override
2845   public void gatherViews_actionPerformed(ActionEvent e)
2846   {
2847     Desktop.instance.gatherViews(this);
2848   }
2849
2850   /**
2851    * DOCUMENT ME!
2852    *
2853    * @param e
2854    *          DOCUMENT ME!
2855    */
2856   @Override
2857   public void font_actionPerformed(ActionEvent e)
2858   {
2859     new FontChooser(alignPanel);
2860   }
2861
2862   /**
2863    * DOCUMENT ME!
2864    *
2865    * @param e
2866    *          DOCUMENT ME!
2867    */
2868   @Override
2869   protected void seqLimit_actionPerformed(ActionEvent e)
2870   {
2871     viewport.setShowJVSuffix(seqLimits.isSelected());
2872
2873     alignPanel.getIdPanel().getIdCanvas()
2874             .setPreferredSize(alignPanel.calculateIdWidth());
2875     alignPanel.paintAlignment(true);
2876   }
2877
2878   @Override
2879   public void idRightAlign_actionPerformed(ActionEvent e)
2880   {
2881     viewport.setRightAlignIds(idRightAlign.isSelected());
2882     alignPanel.paintAlignment(true);
2883   }
2884
2885   @Override
2886   public void centreColumnLabels_actionPerformed(ActionEvent e)
2887   {
2888     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2889     alignPanel.paintAlignment(true);
2890   }
2891
2892   /*
2893    * (non-Javadoc)
2894    *
2895    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2896    */
2897   @Override
2898   protected void followHighlight_actionPerformed()
2899   {
2900     /*
2901      * Set the 'follow' flag on the Viewport (and scroll to position if now
2902      * true).
2903      */
2904     final boolean state = this.followHighlightMenuItem.getState();
2905     viewport.setFollowHighlight(state);
2906     if (state)
2907     {
2908       alignPanel.scrollToPosition(
2909               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2910     }
2911   }
2912
2913   /**
2914    * DOCUMENT ME!
2915    *
2916    * @param e
2917    *          DOCUMENT ME!
2918    */
2919   @Override
2920   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2921   {
2922     viewport.setColourText(colourTextMenuItem.isSelected());
2923     alignPanel.paintAlignment(true);
2924   }
2925
2926   /**
2927    * DOCUMENT ME!
2928    *
2929    * @param e
2930    *          DOCUMENT ME!
2931    */
2932   @Override
2933   public void wrapMenuItem_actionPerformed(ActionEvent e)
2934   {
2935     scaleAbove.setVisible(wrapMenuItem.isSelected());
2936     scaleLeft.setVisible(wrapMenuItem.isSelected());
2937     scaleRight.setVisible(wrapMenuItem.isSelected());
2938     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2939     alignPanel.updateLayout();
2940   }
2941
2942   @Override
2943   public void showAllSeqs_actionPerformed(ActionEvent e)
2944   {
2945     viewport.showAllHiddenSeqs();
2946   }
2947
2948   @Override
2949   public void showAllColumns_actionPerformed(ActionEvent e)
2950   {
2951     viewport.showAllHiddenColumns();
2952     repaint();
2953     viewport.sendSelection();
2954   }
2955
2956   @Override
2957   public void hideSelSequences_actionPerformed(ActionEvent e)
2958   {
2959     viewport.hideAllSelectedSeqs();
2960     // alignPanel.paintAlignment(true);
2961   }
2962
2963   /**
2964    * called by key handler and the hide all/show all menu items
2965    *
2966    * @param toggleSeqs
2967    * @param toggleCols
2968    */
2969   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2970   {
2971
2972     boolean hide = false;
2973     SequenceGroup sg = viewport.getSelectionGroup();
2974     if (!toggleSeqs && !toggleCols)
2975     {
2976       // Hide everything by the current selection - this is a hack - we do the
2977       // invert and then hide
2978       // first check that there will be visible columns after the invert.
2979       if ((viewport.getColumnSelection() != null
2980               && viewport.getColumnSelection().getSelected() != null && viewport
2981               .getColumnSelection().getSelected().size() > 0)
2982               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2983                       .getEndRes()))
2984       {
2985         // now invert the sequence set, if required - empty selection implies
2986         // that no hiding is required.
2987         if (sg != null)
2988         {
2989           invertSequenceMenuItem_actionPerformed(null);
2990           sg = viewport.getSelectionGroup();
2991           toggleSeqs = true;
2992
2993         }
2994         viewport.expandColSelection(sg, true);
2995         // finally invert the column selection and get the new sequence
2996         // selection.
2997         invertColSel_actionPerformed(null);
2998         toggleCols = true;
2999       }
3000     }
3001
3002     if (toggleSeqs)
3003     {
3004       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3005       {
3006         hideSelSequences_actionPerformed(null);
3007         hide = true;
3008       }
3009       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3010               .size() > 0))
3011       {
3012         showAllSeqs_actionPerformed(null);
3013       }
3014     }
3015
3016     if (toggleCols)
3017     {
3018       if (viewport.getColumnSelection().getSelected().size() > 0)
3019       {
3020         hideSelColumns_actionPerformed(null);
3021         if (!toggleSeqs)
3022         {
3023           viewport.setSelectionGroup(sg);
3024         }
3025       }
3026       else if (!hide)
3027       {
3028         showAllColumns_actionPerformed(null);
3029       }
3030     }
3031   }
3032
3033   /*
3034    * (non-Javadoc)
3035    *
3036    * @see
3037    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3038    * event.ActionEvent)
3039    */
3040   @Override
3041   public void hideAllButSelection_actionPerformed(ActionEvent e)
3042   {
3043     toggleHiddenRegions(false, false);
3044     viewport.sendSelection();
3045   }
3046
3047   /*
3048    * (non-Javadoc)
3049    *
3050    * @see
3051    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3052    * .ActionEvent)
3053    */
3054   @Override
3055   public void hideAllSelection_actionPerformed(ActionEvent e)
3056   {
3057     SequenceGroup sg = viewport.getSelectionGroup();
3058     viewport.expandColSelection(sg, false);
3059     viewport.hideAllSelectedSeqs();
3060     viewport.hideSelectedColumns();
3061     alignPanel.paintAlignment(true);
3062     viewport.sendSelection();
3063   }
3064
3065   /*
3066    * (non-Javadoc)
3067    *
3068    * @see
3069    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3070    * ActionEvent)
3071    */
3072   @Override
3073   public void showAllhidden_actionPerformed(ActionEvent e)
3074   {
3075     viewport.showAllHiddenColumns();
3076     viewport.showAllHiddenSeqs();
3077     alignPanel.paintAlignment(true);
3078     viewport.sendSelection();
3079   }
3080
3081   @Override
3082   public void hideSelColumns_actionPerformed(ActionEvent e)
3083   {
3084     viewport.hideSelectedColumns();
3085     alignPanel.paintAlignment(true);
3086     viewport.sendSelection();
3087   }
3088
3089   @Override
3090   public void hiddenMarkers_actionPerformed(ActionEvent e)
3091   {
3092     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3093     repaint();
3094   }
3095
3096   /**
3097    * DOCUMENT ME!
3098    *
3099    * @param e
3100    *          DOCUMENT ME!
3101    */
3102   @Override
3103   protected void scaleAbove_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3106     alignPanel.paintAlignment(true);
3107   }
3108
3109   /**
3110    * DOCUMENT ME!
3111    *
3112    * @param e
3113    *          DOCUMENT ME!
3114    */
3115   @Override
3116   protected void scaleLeft_actionPerformed(ActionEvent e)
3117   {
3118     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3119     alignPanel.paintAlignment(true);
3120   }
3121
3122   /**
3123    * DOCUMENT ME!
3124    *
3125    * @param e
3126    *          DOCUMENT ME!
3127    */
3128   @Override
3129   protected void scaleRight_actionPerformed(ActionEvent e)
3130   {
3131     viewport.setScaleRightWrapped(scaleRight.isSelected());
3132     alignPanel.paintAlignment(true);
3133   }
3134
3135   /**
3136    * DOCUMENT ME!
3137    *
3138    * @param e
3139    *          DOCUMENT ME!
3140    */
3141   @Override
3142   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3143   {
3144     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3145     alignPanel.paintAlignment(true);
3146   }
3147
3148   /**
3149    * DOCUMENT ME!
3150    *
3151    * @param e
3152    *          DOCUMENT ME!
3153    */
3154   @Override
3155   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3156   {
3157     viewport.setShowText(viewTextMenuItem.isSelected());
3158     alignPanel.paintAlignment(true);
3159   }
3160
3161   /**
3162    * DOCUMENT ME!
3163    *
3164    * @param e
3165    *          DOCUMENT ME!
3166    */
3167   @Override
3168   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3169   {
3170     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3171     alignPanel.paintAlignment(true);
3172   }
3173
3174   public FeatureSettings featureSettings;
3175
3176   @Override
3177   public FeatureSettingsControllerI getFeatureSettingsUI()
3178   {
3179     return featureSettings;
3180   }
3181
3182   @Override
3183   public void featureSettings_actionPerformed(ActionEvent e)
3184   {
3185     if (featureSettings != null)
3186     {
3187       featureSettings.close();
3188       featureSettings = null;
3189     }
3190     if (!showSeqFeatures.isSelected())
3191     {
3192       // make sure features are actually displayed
3193       showSeqFeatures.setSelected(true);
3194       showSeqFeatures_actionPerformed(null);
3195     }
3196     featureSettings = new FeatureSettings(this);
3197   }
3198
3199   /**
3200    * Set or clear 'Show Sequence Features'
3201    *
3202    * @param evt
3203    *          DOCUMENT ME!
3204    */
3205   @Override
3206   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3207   {
3208     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3209     alignPanel.paintAlignment(true);
3210     if (alignPanel.getOverviewPanel() != null)
3211     {
3212       alignPanel.getOverviewPanel().updateOverviewImage();
3213     }
3214   }
3215
3216   /**
3217    * Set or clear 'Show Sequence Features'
3218    *
3219    * @param evt
3220    *          DOCUMENT ME!
3221    */
3222   @Override
3223   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3224   {
3225     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3226             .isSelected());
3227     if (viewport.isShowSequenceFeaturesHeight())
3228     {
3229       // ensure we're actually displaying features
3230       viewport.setShowSequenceFeatures(true);
3231       showSeqFeatures.setSelected(true);
3232     }
3233     alignPanel.paintAlignment(true);
3234     if (alignPanel.getOverviewPanel() != null)
3235     {
3236       alignPanel.getOverviewPanel().updateOverviewImage();
3237     }
3238   }
3239
3240   /**
3241    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3242    * the annotations panel as a whole.
3243    *
3244    * The options to show/hide all annotations should be enabled when the panel
3245    * is shown, and disabled when the panel is hidden.
3246    *
3247    * @param e
3248    */
3249   @Override
3250   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3251   {
3252     final boolean setVisible = annotationPanelMenuItem.isSelected();
3253     viewport.setShowAnnotation(setVisible);
3254     this.showAllSeqAnnotations.setEnabled(setVisible);
3255     this.hideAllSeqAnnotations.setEnabled(setVisible);
3256     this.showAllAlAnnotations.setEnabled(setVisible);
3257     this.hideAllAlAnnotations.setEnabled(setVisible);
3258     alignPanel.updateLayout();
3259   }
3260
3261   @Override
3262   public void alignmentProperties()
3263   {
3264     JEditorPane editPane = new JEditorPane("text/html", "");
3265     editPane.setEditable(false);
3266     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3267             .formatAsHtml();
3268     editPane.setText(MessageManager.formatMessage("label.html_content",
3269             new Object[] { contents.toString() }));
3270     JInternalFrame frame = new JInternalFrame();
3271     frame.getContentPane().add(new JScrollPane(editPane));
3272
3273     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3274             "label.alignment_properties", new Object[] { getTitle() }),
3275             500, 400);
3276   }
3277
3278   /**
3279    * DOCUMENT ME!
3280    *
3281    * @param e
3282    *          DOCUMENT ME!
3283    */
3284   @Override
3285   public void overviewMenuItem_actionPerformed(ActionEvent e)
3286   {
3287     if (alignPanel.overviewPanel != null)
3288     {
3289       return;
3290     }
3291
3292     JInternalFrame frame = new JInternalFrame();
3293     OverviewPanel overview = new OverviewPanel(alignPanel);
3294     frame.setContentPane(overview);
3295     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3296             "label.overview_params", new Object[] { this.getTitle() }),
3297             frame.getWidth(), frame.getHeight());
3298     frame.pack();
3299     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3300     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3301     {
3302       @Override
3303       public void internalFrameClosed(
3304               javax.swing.event.InternalFrameEvent evt)
3305       {
3306         alignPanel.setOverviewPanel(null);
3307       };
3308     });
3309
3310     alignPanel.setOverviewPanel(overview);
3311   }
3312
3313   @Override
3314   public void textColour_actionPerformed(ActionEvent e)
3315   {
3316     new TextColourChooser().chooseColour(alignPanel, null);
3317   }
3318
3319   /**
3320    * DOCUMENT ME!
3321    *
3322    * @param e
3323    *          DOCUMENT ME!
3324    */
3325   @Override
3326   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3327   {
3328     changeColour(null);
3329   }
3330
3331   /**
3332    * DOCUMENT ME!
3333    *
3334    * @param e
3335    *          DOCUMENT ME!
3336    */
3337   @Override
3338   public void clustalColour_actionPerformed(ActionEvent e)
3339   {
3340     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3341             viewport.getHiddenRepSequences()));
3342   }
3343
3344   /**
3345    * DOCUMENT ME!
3346    *
3347    * @param e
3348    *          DOCUMENT ME!
3349    */
3350   @Override
3351   public void zappoColour_actionPerformed(ActionEvent e)
3352   {
3353     changeColour(new ZappoColourScheme());
3354   }
3355
3356   /**
3357    * DOCUMENT ME!
3358    *
3359    * @param e
3360    *          DOCUMENT ME!
3361    */
3362   @Override
3363   public void taylorColour_actionPerformed(ActionEvent e)
3364   {
3365     changeColour(new TaylorColourScheme());
3366   }
3367
3368   /**
3369    * DOCUMENT ME!
3370    *
3371    * @param e
3372    *          DOCUMENT ME!
3373    */
3374   @Override
3375   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3376   {
3377     changeColour(new HydrophobicColourScheme());
3378   }
3379
3380   /**
3381    * DOCUMENT ME!
3382    *
3383    * @param e
3384    *          DOCUMENT ME!
3385    */
3386   @Override
3387   public void helixColour_actionPerformed(ActionEvent e)
3388   {
3389     changeColour(new HelixColourScheme());
3390   }
3391
3392   /**
3393    * DOCUMENT ME!
3394    *
3395    * @param e
3396    *          DOCUMENT ME!
3397    */
3398   @Override
3399   public void strandColour_actionPerformed(ActionEvent e)
3400   {
3401     changeColour(new StrandColourScheme());
3402   }
3403
3404   /**
3405    * DOCUMENT ME!
3406    *
3407    * @param e
3408    *          DOCUMENT ME!
3409    */
3410   @Override
3411   public void turnColour_actionPerformed(ActionEvent e)
3412   {
3413     changeColour(new TurnColourScheme());
3414   }
3415
3416   /**
3417    * DOCUMENT ME!
3418    *
3419    * @param e
3420    *          DOCUMENT ME!
3421    */
3422   @Override
3423   public void buriedColour_actionPerformed(ActionEvent e)
3424   {
3425     changeColour(new BuriedColourScheme());
3426   }
3427
3428   /**
3429    * DOCUMENT ME!
3430    *
3431    * @param e
3432    *          DOCUMENT ME!
3433    */
3434   @Override
3435   public void nucleotideColour_actionPerformed(ActionEvent e)
3436   {
3437     changeColour(new NucleotideColourScheme());
3438   }
3439
3440   @Override
3441   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3442   {
3443     changeColour(new PurinePyrimidineColourScheme());
3444   }
3445
3446   /*
3447    * public void covariationColour_actionPerformed(ActionEvent e) {
3448    * changeColour(new
3449    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3450    * ()[0])); }
3451    */
3452   @Override
3453   public void annotationColour_actionPerformed(ActionEvent e)
3454   {
3455     new AnnotationColourChooser(viewport, alignPanel);
3456   }
3457
3458   @Override
3459   public void annotationColumn_actionPerformed(ActionEvent e)
3460   {
3461     new AnnotationColumnChooser(viewport, alignPanel);
3462   }
3463
3464   @Override
3465   public void rnahelicesColour_actionPerformed(ActionEvent e)
3466   {
3467     new RNAHelicesColourChooser(viewport, alignPanel);
3468   }
3469
3470   /**
3471    * DOCUMENT ME!
3472    *
3473    * @param e
3474    *          DOCUMENT ME!
3475    */
3476   @Override
3477   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3478   {
3479     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3480   }
3481
3482   /**
3483    * DOCUMENT ME!
3484    *
3485    * @param cs
3486    *          DOCUMENT ME!
3487    */
3488   @Override
3489   public void changeColour(ColourSchemeI cs)
3490   {
3491     // TODO: pull up to controller method
3492
3493     if (cs != null)
3494     {
3495       // Make sure viewport is up to date w.r.t. any sliders
3496       if (viewport.getAbovePIDThreshold())
3497       {
3498         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3499                 "Background");
3500         viewport.setThreshold(threshold);
3501       }
3502
3503       if (viewport.getConservationSelected())
3504       {
3505         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3506                 cs, "Background"));
3507       }
3508       if (cs instanceof TCoffeeColourScheme)
3509       {
3510         tcoffeeColour.setEnabled(true);
3511         tcoffeeColour.setSelected(true);
3512       }
3513     }
3514
3515     viewport.setGlobalColourScheme(cs);
3516
3517     alignPanel.paintAlignment(true);
3518   }
3519
3520   /**
3521    * DOCUMENT ME!
3522    *
3523    * @param e
3524    *          DOCUMENT ME!
3525    */
3526   @Override
3527   protected void modifyPID_actionPerformed(ActionEvent e)
3528   {
3529     if (viewport.getAbovePIDThreshold()
3530             && viewport.getGlobalColourScheme() != null)
3531     {
3532       SliderPanel.setPIDSliderSource(alignPanel,
3533               viewport.getGlobalColourScheme(), "Background");
3534       SliderPanel.showPIDSlider();
3535     }
3536   }
3537
3538   /**
3539    * DOCUMENT ME!
3540    *
3541    * @param e
3542    *          DOCUMENT ME!
3543    */
3544   @Override
3545   protected void modifyConservation_actionPerformed(ActionEvent e)
3546   {
3547     if (viewport.getConservationSelected()
3548             && viewport.getGlobalColourScheme() != null)
3549     {
3550       SliderPanel.setConservationSlider(alignPanel,
3551               viewport.getGlobalColourScheme(), "Background");
3552       SliderPanel.showConservationSlider();
3553     }
3554   }
3555
3556   /**
3557    * DOCUMENT ME!
3558    *
3559    * @param e
3560    *          DOCUMENT ME!
3561    */
3562   @Override
3563   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3564   {
3565     viewport.setConservationSelected(conservationMenuItem.isSelected());
3566
3567     viewport.setAbovePIDThreshold(false);
3568     abovePIDThreshold.setSelected(false);
3569
3570     changeColour(viewport.getGlobalColourScheme());
3571
3572     modifyConservation_actionPerformed(null);
3573   }
3574
3575   /**
3576    * DOCUMENT ME!
3577    *
3578    * @param e
3579    *          DOCUMENT ME!
3580    */
3581   @Override
3582   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3583   {
3584     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3585
3586     conservationMenuItem.setSelected(false);
3587     viewport.setConservationSelected(false);
3588
3589     changeColour(viewport.getGlobalColourScheme());
3590
3591     modifyPID_actionPerformed(null);
3592   }
3593
3594   /**
3595    * DOCUMENT ME!
3596    *
3597    * @param e
3598    *          DOCUMENT ME!
3599    */
3600   @Override
3601   public void userDefinedColour_actionPerformed(ActionEvent e)
3602   {
3603     if (e.getActionCommand().equals(
3604             MessageManager.getString("action.user_defined")))
3605     {
3606       new UserDefinedColours(alignPanel, null);
3607     }
3608     else
3609     {
3610       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3611               .getUserColourSchemes().get(e.getActionCommand());
3612
3613       changeColour(udc);
3614     }
3615   }
3616
3617   public void updateUserColourMenu()
3618   {
3619
3620     Component[] menuItems = colourMenu.getMenuComponents();
3621     int iSize = menuItems.length;
3622     for (int i = 0; i < iSize; i++)
3623     {
3624       if (menuItems[i].getName() != null
3625               && menuItems[i].getName().equals("USER_DEFINED"))
3626       {
3627         colourMenu.remove(menuItems[i]);
3628         iSize--;
3629       }
3630     }
3631     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3632     {
3633       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3634               .getUserColourSchemes().keys();
3635
3636       while (userColours.hasMoreElements())
3637       {
3638         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3639                 userColours.nextElement().toString());
3640         radioItem.setName("USER_DEFINED");
3641         radioItem.addMouseListener(new MouseAdapter()
3642         {
3643           @Override
3644           public void mousePressed(MouseEvent evt)
3645           {
3646             if (evt.isPopupTrigger())
3647             {
3648               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3649
3650               int option = JOptionPane.showInternalConfirmDialog(
3651                       jalview.gui.Desktop.desktop,
3652                       MessageManager
3653                               .getString("label.remove_from_default_list"),
3654                       MessageManager
3655                               .getString("label.remove_user_defined_colour"),
3656                       JOptionPane.YES_NO_OPTION);
3657               if (option == JOptionPane.YES_OPTION)
3658               {
3659                 jalview.gui.UserDefinedColours
3660                         .removeColourFromDefaults(radioItem.getText());
3661                 colourMenu.remove(radioItem);
3662               }
3663               else
3664               {
3665                 radioItem.addActionListener(new ActionListener()
3666                 {
3667                   @Override
3668                   public void actionPerformed(ActionEvent evt)
3669                   {
3670                     userDefinedColour_actionPerformed(evt);
3671                   }
3672                 });
3673               }
3674             }
3675           }
3676         });
3677         radioItem.addActionListener(new ActionListener()
3678         {
3679           @Override
3680           public void actionPerformed(ActionEvent evt)
3681           {
3682             userDefinedColour_actionPerformed(evt);
3683           }
3684         });
3685
3686         colourMenu.insert(radioItem, 15);
3687         colours.add(radioItem);
3688       }
3689     }
3690   }
3691
3692   /**
3693    * DOCUMENT ME!
3694    *
3695    * @param e
3696    *          DOCUMENT ME!
3697    */
3698   @Override
3699   public void PIDColour_actionPerformed(ActionEvent e)
3700   {
3701     changeColour(new PIDColourScheme());
3702   }
3703
3704   /**
3705    * DOCUMENT ME!
3706    *
3707    * @param e
3708    *          DOCUMENT ME!
3709    */
3710   @Override
3711   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3712   {
3713     changeColour(new Blosum62ColourScheme());
3714   }
3715
3716   /**
3717    * DOCUMENT ME!
3718    *
3719    * @param e
3720    *          DOCUMENT ME!
3721    */
3722   @Override
3723   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3724   {
3725     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3726     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3727             .getAlignment().getSequenceAt(0), null);
3728     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3729             viewport.getAlignment()));
3730     alignPanel.paintAlignment(true);
3731   }
3732
3733   /**
3734    * DOCUMENT ME!
3735    *
3736    * @param e
3737    *          DOCUMENT ME!
3738    */
3739   @Override
3740   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3741   {
3742     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3743     AlignmentSorter.sortByID(viewport.getAlignment());
3744     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3745             viewport.getAlignment()));
3746     alignPanel.paintAlignment(true);
3747   }
3748
3749   /**
3750    * DOCUMENT ME!
3751    *
3752    * @param e
3753    *          DOCUMENT ME!
3754    */
3755   @Override
3756   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3757   {
3758     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3759     AlignmentSorter.sortByLength(viewport.getAlignment());
3760     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3761             viewport.getAlignment()));
3762     alignPanel.paintAlignment(true);
3763   }
3764
3765   /**
3766    * DOCUMENT ME!
3767    *
3768    * @param e
3769    *          DOCUMENT ME!
3770    */
3771   @Override
3772   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3773   {
3774     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3775     AlignmentSorter.sortByGroup(viewport.getAlignment());
3776     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3777             viewport.getAlignment()));
3778
3779     alignPanel.paintAlignment(true);
3780   }
3781
3782   /**
3783    * DOCUMENT ME!
3784    *
3785    * @param e
3786    *          DOCUMENT ME!
3787    */
3788   @Override
3789   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3790   {
3791     new RedundancyPanel(alignPanel, this);
3792   }
3793
3794   /**
3795    * DOCUMENT ME!
3796    *
3797    * @param e
3798    *          DOCUMENT ME!
3799    */
3800   @Override
3801   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3802   {
3803     if ((viewport.getSelectionGroup() == null)
3804             || (viewport.getSelectionGroup().getSize() < 2))
3805     {
3806       JOptionPane.showInternalMessageDialog(this, MessageManager
3807               .getString("label.you_must_select_least_two_sequences"),
3808               MessageManager.getString("label.invalid_selection"),
3809               JOptionPane.WARNING_MESSAGE);
3810     }
3811     else
3812     {
3813       JInternalFrame frame = new JInternalFrame();
3814       frame.setContentPane(new PairwiseAlignPanel(viewport));
3815       Desktop.addInternalFrame(frame,
3816               MessageManager.getString("action.pairwise_alignment"), 600,
3817               500);
3818     }
3819   }
3820
3821   /**
3822    * DOCUMENT ME!
3823    *
3824    * @param e
3825    *          DOCUMENT ME!
3826    */
3827   @Override
3828   public void PCAMenuItem_actionPerformed(ActionEvent e)
3829   {
3830     if (((viewport.getSelectionGroup() != null)
3831             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3832             .getSelectionGroup().getSize() > 0))
3833             || (viewport.getAlignment().getHeight() < 4))
3834     {
3835       JOptionPane
3836               .showInternalMessageDialog(
3837                       this,
3838                       MessageManager
3839                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3840                       MessageManager
3841                               .getString("label.sequence_selection_insufficient"),
3842                       JOptionPane.WARNING_MESSAGE);
3843
3844       return;
3845     }
3846
3847     new PCAPanel(alignPanel);
3848   }
3849
3850   @Override
3851   public void autoCalculate_actionPerformed(ActionEvent e)
3852   {
3853     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3854     if (viewport.autoCalculateConsensus)
3855     {
3856       viewport.firePropertyChange("alignment", null, viewport
3857               .getAlignment().getSequences());
3858     }
3859   }
3860
3861   @Override
3862   public void sortByTreeOption_actionPerformed(ActionEvent e)
3863   {
3864     viewport.sortByTree = sortByTree.isSelected();
3865   }
3866
3867   @Override
3868   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3869   {
3870     viewport.followSelection = listenToViewSelections.isSelected();
3871   }
3872
3873   /**
3874    * DOCUMENT ME!
3875    *
3876    * @param e
3877    *          DOCUMENT ME!
3878    */
3879   @Override
3880   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3881   {
3882     newTreePanel("AV", "PID", "Average distance tree using PID");
3883   }
3884
3885   /**
3886    * DOCUMENT ME!
3887    *
3888    * @param e
3889    *          DOCUMENT ME!
3890    */
3891   @Override
3892   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3893   {
3894     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3895   }
3896
3897   /**
3898    * DOCUMENT ME!
3899    *
3900    * @param e
3901    *          DOCUMENT ME!
3902    */
3903   @Override
3904   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3905   {
3906     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3907   }
3908
3909   /**
3910    * DOCUMENT ME!
3911    *
3912    * @param e
3913    *          DOCUMENT ME!
3914    */
3915   @Override
3916   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3917   {
3918     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3919   }
3920
3921   /**
3922    * DOCUMENT ME!
3923    *
3924    * @param type
3925    *          DOCUMENT ME!
3926    * @param pwType
3927    *          DOCUMENT ME!
3928    * @param title
3929    *          DOCUMENT ME!
3930    */
3931   void newTreePanel(String type, String pwType, String title)
3932   {
3933     TreePanel tp;
3934
3935     if (viewport.getSelectionGroup() != null
3936             && viewport.getSelectionGroup().getSize() > 0)
3937     {
3938       if (viewport.getSelectionGroup().getSize() < 3)
3939       {
3940         JOptionPane
3941                 .showMessageDialog(
3942                         Desktop.desktop,
3943                         MessageManager
3944                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3945                         MessageManager
3946                                 .getString("label.not_enough_sequences"),
3947                         JOptionPane.WARNING_MESSAGE);
3948         return;
3949       }
3950
3951       SequenceGroup sg = viewport.getSelectionGroup();
3952
3953       /* Decide if the selection is a column region */
3954       for (SequenceI _s : sg.getSequences())
3955       {
3956         if (_s.getLength() < sg.getEndRes())
3957         {
3958           JOptionPane
3959                   .showMessageDialog(
3960                           Desktop.desktop,
3961                           MessageManager
3962                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3963                           MessageManager
3964                                   .getString("label.sequences_selection_not_aligned"),
3965                           JOptionPane.WARNING_MESSAGE);
3966
3967           return;
3968         }
3969       }
3970
3971       title = title + " on region";
3972       tp = new TreePanel(alignPanel, type, pwType);
3973     }
3974     else
3975     {
3976       // are the visible sequences aligned?
3977       if (!viewport.getAlignment().isAligned(false))
3978       {
3979         JOptionPane
3980                 .showMessageDialog(
3981                         Desktop.desktop,
3982                         MessageManager
3983                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3984                         MessageManager
3985                                 .getString("label.sequences_not_aligned"),
3986                         JOptionPane.WARNING_MESSAGE);
3987
3988         return;
3989       }
3990
3991       if (viewport.getAlignment().getHeight() < 2)
3992       {
3993         return;
3994       }
3995
3996       tp = new TreePanel(alignPanel, type, pwType);
3997     }
3998
3999     title += " from ";
4000
4001     if (viewport.viewName != null)
4002     {
4003       title += viewport.viewName + " of ";
4004     }
4005
4006     title += this.title;
4007
4008     Desktop.addInternalFrame(tp, title, 600, 500);
4009   }
4010
4011   /**
4012    * DOCUMENT ME!
4013    *
4014    * @param title
4015    *          DOCUMENT ME!
4016    * @param order
4017    *          DOCUMENT ME!
4018    */
4019   public void addSortByOrderMenuItem(String title,
4020           final AlignmentOrder order)
4021   {
4022     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4023             "action.by_title_param", new Object[] { title }));
4024     sort.add(item);
4025     item.addActionListener(new java.awt.event.ActionListener()
4026     {
4027       @Override
4028       public void actionPerformed(ActionEvent e)
4029       {
4030         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4031
4032         // TODO: JBPNote - have to map order entries to curent SequenceI
4033         // pointers
4034         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4035
4036         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4037                 .getAlignment()));
4038
4039         alignPanel.paintAlignment(true);
4040       }
4041     });
4042   }
4043
4044   /**
4045    * Add a new sort by annotation score menu item
4046    *
4047    * @param sort
4048    *          the menu to add the option to
4049    * @param scoreLabel
4050    *          the label used to retrieve scores for each sequence on the
4051    *          alignment
4052    */
4053   public void addSortByAnnotScoreMenuItem(JMenu sort,
4054           final String scoreLabel)
4055   {
4056     final JMenuItem item = new JMenuItem(scoreLabel);
4057     sort.add(item);
4058     item.addActionListener(new java.awt.event.ActionListener()
4059     {
4060       @Override
4061       public void actionPerformed(ActionEvent e)
4062       {
4063         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4064         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4065                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4066         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4067                 viewport.getAlignment()));
4068         alignPanel.paintAlignment(true);
4069       }
4070     });
4071   }
4072
4073   /**
4074    * last hash for alignment's annotation array - used to minimise cost of
4075    * rebuild.
4076    */
4077   protected int _annotationScoreVectorHash;
4078
4079   /**
4080    * search the alignment and rebuild the sort by annotation score submenu the
4081    * last alignment annotation vector hash is stored to minimize cost of
4082    * rebuilding in subsequence calls.
4083    *
4084    */
4085   @Override
4086   public void buildSortByAnnotationScoresMenu()
4087   {
4088     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4089     {
4090       return;
4091     }
4092
4093     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4094     {
4095       sortByAnnotScore.removeAll();
4096       // almost certainly a quicker way to do this - but we keep it simple
4097       Hashtable scoreSorts = new Hashtable();
4098       AlignmentAnnotation aann[];
4099       for (SequenceI sqa : viewport.getAlignment().getSequences())
4100       {
4101         aann = sqa.getAnnotation();
4102         for (int i = 0; aann != null && i < aann.length; i++)
4103         {
4104           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4105           {
4106             scoreSorts.put(aann[i].label, aann[i].label);
4107           }
4108         }
4109       }
4110       Enumeration labels = scoreSorts.keys();
4111       while (labels.hasMoreElements())
4112       {
4113         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4114                 (String) labels.nextElement());
4115       }
4116       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4117       scoreSorts.clear();
4118
4119       _annotationScoreVectorHash = viewport.getAlignment()
4120               .getAlignmentAnnotation().hashCode();
4121     }
4122   }
4123
4124   /**
4125    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4126    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4127    * call. Listeners are added to remove the menu item when the treePanel is
4128    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4129    * modified.
4130    *
4131    * @param treePanel
4132    *          Displayed tree window.
4133    * @param title
4134    *          SortBy menu item title.
4135    */
4136   @Override
4137   public void buildTreeMenu()
4138   {
4139     calculateTree.removeAll();
4140     // build the calculate menu
4141
4142     for (final String type : new String[] { "NJ", "AV" })
4143     {
4144       String treecalcnm = MessageManager.getString("label.tree_calc_"
4145               + type.toLowerCase());
4146       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4147       {
4148         JMenuItem tm = new JMenuItem();
4149         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4150         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4151                 || sm.isProtein() == !viewport.getAlignment()
4152                         .isNucleotide())
4153         {
4154           String smn = MessageManager.getStringOrReturn(
4155                   "label.score_model_", sm.getName());
4156           final String title = MessageManager.formatMessage(
4157                   "label.treecalc_title", treecalcnm, smn);
4158           tm.setText(title);//
4159           tm.addActionListener(new java.awt.event.ActionListener()
4160           {
4161             @Override
4162             public void actionPerformed(ActionEvent e)
4163             {
4164               newTreePanel(type, pwtype, title);
4165             }
4166           });
4167           calculateTree.add(tm);
4168         }
4169
4170       }
4171     }
4172     sortByTreeMenu.removeAll();
4173
4174     List<Component> comps = PaintRefresher.components.get(viewport
4175             .getSequenceSetId());
4176     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4177     for (Component comp : comps)
4178     {
4179       if (comp instanceof TreePanel)
4180       {
4181         treePanels.add((TreePanel) comp);
4182       }
4183     }
4184
4185     if (treePanels.size() < 1)
4186     {
4187       sortByTreeMenu.setVisible(false);
4188       return;
4189     }
4190
4191     sortByTreeMenu.setVisible(true);
4192
4193     for (final TreePanel tp : treePanels)
4194     {
4195       final JMenuItem item = new JMenuItem(tp.getTitle());
4196       item.addActionListener(new java.awt.event.ActionListener()
4197       {
4198         @Override
4199         public void actionPerformed(ActionEvent e)
4200         {
4201           tp.sortByTree_actionPerformed();
4202           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4203
4204         }
4205       });
4206
4207       sortByTreeMenu.add(item);
4208     }
4209   }
4210
4211   public boolean sortBy(AlignmentOrder alorder, String undoname)
4212   {
4213     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4214     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4215     if (undoname != null)
4216     {
4217       addHistoryItem(new OrderCommand(undoname, oldOrder,
4218               viewport.getAlignment()));
4219     }
4220     alignPanel.paintAlignment(true);
4221     return true;
4222   }
4223
4224   /**
4225    * Work out whether the whole set of sequences or just the selected set will
4226    * be submitted for multiple alignment.
4227    *
4228    */
4229   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4230   {
4231     // Now, check we have enough sequences
4232     AlignmentView msa = null;
4233
4234     if ((viewport.getSelectionGroup() != null)
4235             && (viewport.getSelectionGroup().getSize() > 1))
4236     {
4237       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4238       // some common interface!
4239       /*
4240        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4241        * SequenceI[sz = seqs.getSize(false)];
4242        *
4243        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4244        * seqs.getSequenceAt(i); }
4245        */
4246       msa = viewport.getAlignmentView(true);
4247     }
4248     else if (viewport.getSelectionGroup() != null
4249             && viewport.getSelectionGroup().getSize() == 1)
4250     {
4251       int option = JOptionPane.showConfirmDialog(this,
4252               MessageManager.getString("warn.oneseq_msainput_selection"),
4253               MessageManager.getString("label.invalid_selection"),
4254               JOptionPane.OK_CANCEL_OPTION);
4255       if (option == JOptionPane.OK_OPTION)
4256       {
4257         msa = viewport.getAlignmentView(false);
4258       }
4259     }
4260     else
4261     {
4262       msa = viewport.getAlignmentView(false);
4263     }
4264     return msa;
4265   }
4266
4267   /**
4268    * Decides what is submitted to a secondary structure prediction service: the
4269    * first sequence in the alignment, or in the current selection, or, if the
4270    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4271    * region or the whole alignment. (where the first sequence in the set is the
4272    * one that the prediction will be for).
4273    */
4274   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4275   {
4276     AlignmentView seqs = null;
4277
4278     if ((viewport.getSelectionGroup() != null)
4279             && (viewport.getSelectionGroup().getSize() > 0))
4280     {
4281       seqs = viewport.getAlignmentView(true);
4282     }
4283     else
4284     {
4285       seqs = viewport.getAlignmentView(false);
4286     }
4287     // limit sequences - JBPNote in future - could spawn multiple prediction
4288     // jobs
4289     // TODO: viewport.getAlignment().isAligned is a global state - the local
4290     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4291     if (!viewport.getAlignment().isAligned(false))
4292     {
4293       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4294       // TODO: if seqs.getSequences().length>1 then should really have warned
4295       // user!
4296
4297     }
4298     return seqs;
4299   }
4300
4301   /**
4302    * DOCUMENT ME!
4303    *
4304    * @param e
4305    *          DOCUMENT ME!
4306    */
4307   @Override
4308   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4309   {
4310     // Pick the tree file
4311     JalviewFileChooser chooser = new JalviewFileChooser(
4312             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4313     chooser.setFileView(new JalviewFileView());
4314     chooser.setDialogTitle(MessageManager
4315             .getString("label.select_newick_like_tree_file"));
4316     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4317
4318     int value = chooser.showOpenDialog(null);
4319
4320     if (value == JalviewFileChooser.APPROVE_OPTION)
4321     {
4322       String choice = chooser.getSelectedFile().getPath();
4323       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4324       jalview.io.NewickFile fin = null;
4325       try
4326       {
4327         fin = new NewickFile(choice, DataSourceType.FILE);
4328         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4329       } catch (Exception ex)
4330       {
4331         JOptionPane
4332                 .showMessageDialog(
4333                         Desktop.desktop,
4334                         ex.getMessage(),
4335                         MessageManager
4336                                 .getString("label.problem_reading_tree_file"),
4337                         JOptionPane.WARNING_MESSAGE);
4338         ex.printStackTrace();
4339       }
4340       if (fin != null && fin.hasWarningMessage())
4341       {
4342         JOptionPane.showMessageDialog(Desktop.desktop, fin
4343                 .getWarningMessage(), MessageManager
4344                 .getString("label.possible_problem_with_tree_file"),
4345                 JOptionPane.WARNING_MESSAGE);
4346       }
4347     }
4348   }
4349
4350   @Override
4351   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4352   {
4353     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4354   }
4355
4356   public TreePanel ShowNewickTree(NewickFile nf, String title)
4357   {
4358     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4359   }
4360
4361   public TreePanel ShowNewickTree(NewickFile nf, String title,
4362           AlignmentView input)
4363   {
4364     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4365   }
4366
4367   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4368           int h, int x, int y)
4369   {
4370     return ShowNewickTree(nf, title, null, w, h, x, y);
4371   }
4372
4373   /**
4374    * Add a treeviewer for the tree extracted from a newick file object to the
4375    * current alignment view
4376    *
4377    * @param nf
4378    *          the tree
4379    * @param title
4380    *          tree viewer title
4381    * @param input
4382    *          Associated alignment input data (or null)
4383    * @param w
4384    *          width
4385    * @param h
4386    *          height
4387    * @param x
4388    *          position
4389    * @param y
4390    *          position
4391    * @return TreePanel handle
4392    */
4393   public TreePanel ShowNewickTree(NewickFile nf, String title,
4394           AlignmentView input, int w, int h, int x, int y)
4395   {
4396     TreePanel tp = null;
4397
4398     try
4399     {
4400       nf.parse();
4401
4402       if (nf.getTree() != null)
4403       {
4404         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4405
4406         tp.setSize(w, h);
4407
4408         if (x > 0 && y > 0)
4409         {
4410           tp.setLocation(x, y);
4411         }
4412
4413         Desktop.addInternalFrame(tp, title, w, h);
4414       }
4415     } catch (Exception ex)
4416     {
4417       ex.printStackTrace();
4418     }
4419
4420     return tp;
4421   }
4422
4423   private boolean buildingMenu = false;
4424
4425   /**
4426    * Generates menu items and listener event actions for web service clients
4427    *
4428    */
4429   public void BuildWebServiceMenu()
4430   {
4431     while (buildingMenu)
4432     {
4433       try
4434       {
4435         System.err.println("Waiting for building menu to finish.");
4436         Thread.sleep(10);
4437       } catch (Exception e)
4438       {
4439       }
4440     }
4441     final AlignFrame me = this;
4442     buildingMenu = true;
4443     new Thread(new Runnable()
4444     {
4445       @Override
4446       public void run()
4447       {
4448         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4449         try
4450         {
4451           // System.err.println("Building ws menu again "
4452           // + Thread.currentThread());
4453           // TODO: add support for context dependent disabling of services based
4454           // on
4455           // alignment and current selection
4456           // TODO: add additional serviceHandle parameter to specify abstract
4457           // handler
4458           // class independently of AbstractName
4459           // TODO: add in rediscovery GUI function to restart discoverer
4460           // TODO: group services by location as well as function and/or
4461           // introduce
4462           // object broker mechanism.
4463           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4464           final IProgressIndicator af = me;
4465           final JMenu msawsmenu = new JMenu("Alignment");
4466           final JMenu secstrmenu = new JMenu(
4467                   "Secondary Structure Prediction");
4468           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4469           final JMenu analymenu = new JMenu("Analysis");
4470           final JMenu dismenu = new JMenu("Protein Disorder");
4471           // final JMenu msawsmenu = new
4472           // JMenu(MessageManager.getString("label.alignment"));
4473           // final JMenu secstrmenu = new
4474           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4475           // final JMenu seqsrchmenu = new
4476           // JMenu(MessageManager.getString("label.sequence_database_search"));
4477           // final JMenu analymenu = new
4478           // JMenu(MessageManager.getString("label.analysis"));
4479           // final JMenu dismenu = new
4480           // JMenu(MessageManager.getString("label.protein_disorder"));
4481           // JAL-940 - only show secondary structure prediction services from
4482           // the legacy server
4483           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4484               // &&
4485           Discoverer.services != null && (Discoverer.services.size() > 0))
4486           {
4487             // TODO: refactor to allow list of AbstractName/Handler bindings to
4488             // be
4489             // stored or retrieved from elsewhere
4490             // No MSAWS used any more:
4491             // Vector msaws = null; // (Vector)
4492             // Discoverer.services.get("MsaWS");
4493             Vector secstrpr = (Vector) Discoverer.services
4494                     .get("SecStrPred");
4495             if (secstrpr != null)
4496             {
4497               // Add any secondary structure prediction services
4498               for (int i = 0, j = secstrpr.size(); i < j; i++)
4499               {
4500                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4501                         .get(i);
4502                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4503                         .getServiceClient(sh);
4504                 int p = secstrmenu.getItemCount();
4505                 impl.attachWSMenuEntry(secstrmenu, me);
4506                 int q = secstrmenu.getItemCount();
4507                 for (int litm = p; litm < q; litm++)
4508                 {
4509                   legacyItems.add(secstrmenu.getItem(litm));
4510                 }
4511               }
4512             }
4513           }
4514
4515           // Add all submenus in the order they should appear on the web
4516           // services menu
4517           wsmenu.add(msawsmenu);
4518           wsmenu.add(secstrmenu);
4519           wsmenu.add(dismenu);
4520           wsmenu.add(analymenu);
4521           // No search services yet
4522           // wsmenu.add(seqsrchmenu);
4523
4524           javax.swing.SwingUtilities.invokeLater(new Runnable()
4525           {
4526             @Override
4527             public void run()
4528             {
4529               try
4530               {
4531                 webService.removeAll();
4532                 // first, add discovered services onto the webservices menu
4533                 if (wsmenu.size() > 0)
4534                 {
4535                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4536                   {
4537                     webService.add(wsmenu.get(i));
4538                   }
4539                 }
4540                 else
4541                 {
4542                   webService.add(me.webServiceNoServices);
4543                 }
4544                 // TODO: move into separate menu builder class.
4545                 boolean new_sspred = false;
4546                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4547                 {
4548                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4549                   if (jws2servs != null)
4550                   {
4551                     if (jws2servs.hasServices())
4552                     {
4553                       jws2servs.attachWSMenuEntry(webService, me);
4554                       for (Jws2Instance sv : jws2servs.getServices())
4555                       {
4556                         if (sv.description.toLowerCase().contains("jpred"))
4557                         {
4558                           for (JMenuItem jmi : legacyItems)
4559                           {
4560                             jmi.setVisible(false);
4561                           }
4562                         }
4563                       }
4564
4565                     }
4566                     if (jws2servs.isRunning())
4567                     {
4568                       JMenuItem tm = new JMenuItem(
4569                               "Still discovering JABA Services");
4570                       tm.setEnabled(false);
4571                       webService.add(tm);
4572                     }
4573                   }
4574                 }
4575                 build_urlServiceMenu(me.webService);
4576                 build_fetchdbmenu(webService);
4577                 for (JMenu item : wsmenu)
4578                 {
4579                   if (item.getItemCount() == 0)
4580                   {
4581                     item.setEnabled(false);
4582                   }
4583                   else
4584                   {
4585                     item.setEnabled(true);
4586                   }
4587                 }
4588               } catch (Exception e)
4589               {
4590                 Cache.log
4591                         .debug("Exception during web service menu building process.",
4592                                 e);
4593               }
4594             }
4595           });
4596         } catch (Exception e)
4597         {
4598         }
4599         buildingMenu = false;
4600       }
4601     }).start();
4602
4603   }
4604
4605   /**
4606    * construct any groupURL type service menu entries.
4607    *
4608    * @param webService
4609    */
4610   private void build_urlServiceMenu(JMenu webService)
4611   {
4612     // TODO: remove this code when 2.7 is released
4613     // DEBUG - alignmentView
4614     /*
4615      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4616      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4617      *
4618      * @Override public void actionPerformed(ActionEvent e) {
4619      * jalview.datamodel.AlignmentView
4620      * .testSelectionViews(af.viewport.getAlignment(),
4621      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4622      *
4623      * }); webService.add(testAlView);
4624      */
4625     // TODO: refactor to RestClient discoverer and merge menu entries for
4626     // rest-style services with other types of analysis/calculation service
4627     // SHmmr test client - still being implemented.
4628     // DEBUG - alignmentView
4629
4630     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4631             .getRestClients())
4632     {
4633       client.attachWSMenuEntry(
4634               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4635               this);
4636     }
4637   }
4638
4639   /**
4640    * Searches selected sequences for xRef products and builds the Show
4641    * Cross-References menu (formerly called Show Products)
4642    *
4643    * @return true if Show Cross-references menu should be enabled.
4644    */
4645   public boolean canShowProducts()
4646   {
4647     SequenceI[] selection = viewport.getSequenceSelection();
4648     AlignmentI dataset = viewport.getAlignment().getDataset();
4649     boolean showp = false;
4650     try
4651     {
4652       showProducts.removeAll();
4653       final boolean dna = viewport.getAlignment().isNucleotide();
4654       String[] ptypes = (selection == null || selection.length == 0) ? null
4655               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4656
4657       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4658       {
4659         showp = true;
4660         final AlignFrame af = this;
4661         final String source = ptypes[t];
4662         JMenuItem xtype = new JMenuItem(ptypes[t]);
4663         xtype.addActionListener(new ActionListener()
4664         {
4665
4666           @Override
4667           public void actionPerformed(ActionEvent e)
4668           {
4669             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4670           }
4671
4672         });
4673         showProducts.add(xtype);
4674       }
4675       showProducts.setVisible(showp);
4676       showProducts.setEnabled(showp);
4677     } catch (Exception e)
4678     {
4679       jalview.bin.Cache.log
4680               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4681                       e);
4682       return false;
4683     }
4684     return showp;
4685   }
4686
4687   /**
4688    * Finds and displays cross-references for the selected sequences (protein
4689    * products for nucleotide sequences, dna coding sequences for peptides).
4690    *
4691    * @param sel
4692    *          the sequences to show cross-references for
4693    * @param dna
4694    *          true if from a nucleotide alignment (so showing proteins)
4695    * @param source
4696    *          the database to show cross-references for
4697    */
4698   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4699           final String source)
4700   {
4701     Runnable foo = new Runnable()
4702     {
4703
4704       @Override
4705       public void run()
4706       {
4707         final long sttime = System.currentTimeMillis();
4708         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4709                 "status.searching_for_sequences_from",
4710                 new Object[] { source }), sttime);
4711         try
4712         {
4713           AlignmentI alignment = AlignFrame.this.getViewport()
4714                   .getAlignment();
4715           AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4716                   alignment);
4717           if (xrefs != null)
4718           {
4719             /*
4720              * get display scheme (if any) to apply to features
4721              */
4722             FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4723                     .getFeatureColourScheme(source);
4724
4725             AlignmentI al = makeCrossReferencesAlignment(
4726                     alignment.getDataset(), xrefs);
4727
4728             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4729                     DEFAULT_HEIGHT);
4730             if (Cache.getDefault("HIDE_INTRONS", true))
4731             {
4732               newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4733             }
4734             String newtitle = String.format("%s %s %s",
4735                     MessageManager.getString(dna ? "label.proteins"
4736                             : "label.nucleotides"), MessageManager
4737                             .getString("label.for"), getTitle());
4738             newFrame.setTitle(newtitle);
4739
4740             if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4741             {
4742               /*
4743                * split frame display is turned off in preferences file
4744                */
4745               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4746                       DEFAULT_HEIGHT);
4747               return; // via finally clause
4748             }
4749
4750             /*
4751              * Make a copy of this alignment (sharing the same dataset
4752              * sequences). If we are DNA, drop introns and update mappings
4753              */
4754             AlignmentI copyAlignment = null;
4755             final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4756                     .getSequenceSelection();
4757             List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4758             boolean copyAlignmentIsAligned = false;
4759             if (dna)
4760             {
4761               copyAlignment = AlignmentUtils.makeCdsAlignment(
4762                       sequenceSelection, cf, alignment);
4763               if (copyAlignment.getHeight() == 0)
4764               {
4765                 System.err.println("Failed to make CDS alignment");
4766               }
4767               al.getCodonFrames().clear();
4768               al.addCodonFrames(copyAlignment.getCodonFrames());
4769               al.addCodonFrames(cf);
4770
4771               /*
4772                * pending getting Embl transcripts to 'align',
4773                * we are only doing this for Ensembl
4774                */
4775               // TODO proper criteria for 'can align as cdna'
4776               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4777                       || AlignmentUtils.looksLikeEnsembl(alignment))
4778               {
4779                 copyAlignment.alignAs(alignment);
4780                 copyAlignmentIsAligned = true;
4781               }
4782             }
4783             else
4784             {
4785               copyAlignment = AlignmentUtils.makeCopyAlignment(
4786                       sequenceSelection, xrefs.getSequencesArray());
4787               copyAlignment.addCodonFrames(cf);
4788               al.addCodonFrames(copyAlignment.getCodonFrames());
4789               al.addCodonFrames(cf);
4790             }
4791             copyAlignment.setGapCharacter(AlignFrame.this.viewport
4792                     .getGapCharacter());
4793
4794             StructureSelectionManager ssm = StructureSelectionManager
4795                     .getStructureSelectionManager(Desktop.instance);
4796             ssm.registerMappings(cf);
4797
4798             if (copyAlignment.getHeight() <= 0)
4799             {
4800               System.err.println("No Sequences generated for xRef type "
4801                       + source);
4802               return;
4803             }
4804             /*
4805              * align protein to dna
4806              */
4807             if (dna && copyAlignmentIsAligned)
4808             {
4809               al.alignAs(copyAlignment);
4810             }
4811             else
4812             {
4813               /*
4814                * align cdna to protein - currently only if
4815                * fetching and aligning Ensembl transcripts!
4816                */
4817               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4818               {
4819                 copyAlignment.alignAs(al);
4820               }
4821             }
4822
4823             AlignFrame copyThis = new AlignFrame(copyAlignment,
4824                     AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4825             copyThis.setTitle(AlignFrame.this.getTitle());
4826
4827             boolean showSequenceFeatures = viewport
4828                     .isShowSequenceFeatures();
4829             newFrame.setShowSeqFeatures(showSequenceFeatures);
4830             copyThis.setShowSeqFeatures(showSequenceFeatures);
4831             FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4832                     .getFeatureRenderer();
4833
4834             /*
4835              * copy feature rendering settings to split frame
4836              */
4837             newFrame.alignPanel.getSeqPanel().seqCanvas
4838                     .getFeatureRenderer()
4839                     .transferSettings(myFeatureStyling);
4840             copyThis.alignPanel.getSeqPanel().seqCanvas
4841                     .getFeatureRenderer()
4842                     .transferSettings(myFeatureStyling);
4843
4844             /*
4845              * apply 'database source' feature configuration
4846              * if any was found
4847              */
4848             // TODO is this the feature colouring for the original
4849             // alignment or the fetched xrefs? either could be Ensembl
4850             newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4851             copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4852
4853             SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4854                     dna ? newFrame : copyThis);
4855             newFrame.setVisible(true);
4856             copyThis.setVisible(true);
4857             String linkedTitle = MessageManager
4858                     .getString("label.linked_view_title");
4859             Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4860             sf.adjustDivider();
4861           }
4862         } catch (Exception e)
4863         {
4864           Cache.log.error("Exception when finding crossreferences", e);
4865         } catch (OutOfMemoryError e)
4866         {
4867           new OOMWarning("whilst fetching crossreferences", e);
4868         } catch (Throwable e)
4869         {
4870           Cache.log.error("Error when finding crossreferences", e);
4871         } finally
4872         {
4873           AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4874                   "status.finished_searching_for_sequences_from",
4875                   new Object[] { source }), sttime);
4876         }
4877       }
4878
4879       /**
4880        * Makes an alignment containing the given sequences. If this is of the
4881        * same type as the given dataset (nucleotide/protein), then the new
4882        * alignment shares the same dataset, and its dataset sequences are added
4883        * to it. Otherwise a new dataset sequence is created for the
4884        * cross-references.
4885        *
4886        * @param dataset
4887        * @param seqs
4888        * @return
4889        */
4890       protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4891               AlignmentI seqs)
4892       {
4893         boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4894
4895         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4896         for (int s = 0; s < sprods.length; s++)
4897         {
4898           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4899           if (sameType)
4900           {
4901             if (dataset.getSequences() == null
4902                     || !dataset.getSequences().contains(
4903                             sprods[s].getDatasetSequence()))
4904             {
4905               dataset.addSequence(sprods[s].getDatasetSequence());
4906             }
4907           }
4908           sprods[s].updatePDBIds();
4909         }
4910         Alignment al = new Alignment(sprods);
4911         if (sameType)
4912         {
4913           al.setDataset((Alignment) dataset);
4914         }
4915         else
4916         {
4917           al.createDatasetAlignment();
4918         }
4919         return al;
4920       }
4921
4922     };
4923     Thread frunner = new Thread(foo);
4924     frunner.start();
4925   }
4926
4927   /**
4928    * Construct and display a new frame containing the translation of this
4929    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4930    */
4931   @Override
4932   public void showTranslation_actionPerformed(ActionEvent e)
4933   {
4934     AlignmentI al = null;
4935     try
4936     {
4937       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4938
4939       al = dna.translateCdna();
4940     } catch (Exception ex)
4941     {
4942       jalview.bin.Cache.log.error(
4943               "Exception during translation. Please report this !", ex);
4944       final String msg = MessageManager
4945               .getString("label.error_when_translating_sequences_submit_bug_report");
4946       final String errorTitle = MessageManager
4947               .getString("label.implementation_error")
4948               + MessageManager.getString("label.translation_failed");
4949       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4950               JOptionPane.ERROR_MESSAGE);
4951       return;
4952     }
4953     if (al == null || al.getHeight() == 0)
4954     {
4955       final String msg = MessageManager
4956               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4957       final String errorTitle = MessageManager
4958               .getString("label.translation_failed");
4959       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4960               JOptionPane.WARNING_MESSAGE);
4961     }
4962     else
4963     {
4964       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4965       af.setFileFormat(this.currentFileFormat);
4966       final String newTitle = MessageManager.formatMessage(
4967               "label.translation_of_params",
4968               new Object[] { this.getTitle() });
4969       af.setTitle(newTitle);
4970       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4971       {
4972         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4973         viewport.openSplitFrame(af, new Alignment(seqs));
4974       }
4975       else
4976       {
4977         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4978                 DEFAULT_HEIGHT);
4979       }
4980     }
4981   }
4982
4983   /**
4984    * Set the file format
4985    *
4986    * @param format
4987    */
4988   public void setFileFormat(FileFormatI format)
4989   {
4990     this.currentFileFormat = format;
4991   }
4992
4993   /**
4994    * Try to load a features file onto the alignment.
4995    *
4996    * @param file
4997    *          contents or path to retrieve file
4998    * @param sourceType
4999    *          access mode of file (see jalview.io.AlignFile)
5000    * @return true if features file was parsed correctly.
5001    */
5002   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
5003   {
5004     return avc.parseFeaturesFile(file, sourceType,
5005             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5006
5007   }
5008
5009   @Override
5010   public void refreshFeatureUI(boolean enableIfNecessary)
5011   {
5012     // note - currently this is only still here rather than in the controller
5013     // because of the featureSettings hard reference that is yet to be
5014     // abstracted
5015     if (enableIfNecessary)
5016     {
5017       viewport.setShowSequenceFeatures(true);
5018       showSeqFeatures.setSelected(true);
5019     }
5020
5021   }
5022
5023   @Override
5024   public void dragEnter(DropTargetDragEvent evt)
5025   {
5026   }
5027
5028   @Override
5029   public void dragExit(DropTargetEvent evt)
5030   {
5031   }
5032
5033   @Override
5034   public void dragOver(DropTargetDragEvent evt)
5035   {
5036   }
5037
5038   @Override
5039   public void dropActionChanged(DropTargetDragEvent evt)
5040   {
5041   }
5042
5043   @Override
5044   public void drop(DropTargetDropEvent evt)
5045   {
5046     Transferable t = evt.getTransferable();
5047     List<String> files = new ArrayList<String>();
5048     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
5049
5050     try
5051     {
5052       Desktop.transferFromDropTarget(files, protocols, evt, t);
5053     } catch (Exception e)
5054     {
5055       e.printStackTrace();
5056     }
5057     if (files != null)
5058     {
5059       try
5060       {
5061         // check to see if any of these files have names matching sequences in
5062         // the alignment
5063         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5064                 .getAlignment().getSequencesArray());
5065         /**
5066          * Object[] { String,SequenceI}
5067          */
5068         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5069         ArrayList<String> filesnotmatched = new ArrayList<String>();
5070         for (int i = 0; i < files.size(); i++)
5071         {
5072           String file = files.get(i).toString();
5073           String pdbfn = "";
5074           DataSourceType protocol = FormatAdapter.checkProtocol(file);
5075           if (protocol == DataSourceType.FILE)
5076           {
5077             File fl = new File(file);
5078             pdbfn = fl.getName();
5079           }
5080           else if (protocol == DataSourceType.URL)
5081           {
5082             URL url = new URL(file);
5083             pdbfn = url.getFile();
5084           }
5085           if (pdbfn.length() > 0)
5086           {
5087             // attempt to find a match in the alignment
5088             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5089             int l = 0, c = pdbfn.indexOf(".");
5090             while (mtch == null && c != -1)
5091             {
5092               do
5093               {
5094                 l = c;
5095               } while ((c = pdbfn.indexOf(".", l)) > l);
5096               if (l > -1)
5097               {
5098                 pdbfn = pdbfn.substring(0, l);
5099               }
5100               mtch = idm.findAllIdMatches(pdbfn);
5101             }
5102             if (mtch != null)
5103             {
5104               FileFormatI type = null;
5105               try
5106               {
5107                 type = new IdentifyFile().identify(file, protocol);
5108               } catch (Exception ex)
5109               {
5110                 type = null;
5111               }
5112               if (type != null)
5113               {
5114                 if (type == FileFormat.PDB)
5115                 {
5116                   filesmatched.add(new Object[] { file, protocol, mtch });
5117                   continue;
5118                 }
5119               }
5120             }
5121             // File wasn't named like one of the sequences or wasn't a PDB file.
5122             filesnotmatched.add(file);
5123           }
5124         }
5125         int assocfiles = 0;
5126         if (filesmatched.size() > 0)
5127         {
5128           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5129                   || JOptionPane
5130                           .showConfirmDialog(
5131                                   this,
5132                                   MessageManager
5133                                           .formatMessage(
5134                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5135                                                   new Object[] { Integer
5136                                                           .valueOf(
5137                                                                   filesmatched
5138                                                                           .size())
5139                                                           .toString() }),
5140                                   MessageManager
5141                                           .getString("label.automatically_associate_pdb_files_by_name"),
5142                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5143
5144           {
5145             for (Object[] fm : filesmatched)
5146             {
5147               // try and associate
5148               // TODO: may want to set a standard ID naming formalism for
5149               // associating PDB files which have no IDs.
5150               for (SequenceI toassoc : (SequenceI[]) fm[2])
5151               {
5152                 PDBEntry pe = new AssociatePdbFileWithSeq()
5153                         .associatePdbWithSeq((String) fm[0],
5154                                 (DataSourceType) fm[1], toassoc, false,
5155                                 Desktop.instance);
5156                 if (pe != null)
5157                 {
5158                   System.err.println("Associated file : "
5159                           + ((String) fm[0]) + " with "
5160                           + toassoc.getDisplayId(true));
5161                   assocfiles++;
5162                 }
5163               }
5164               alignPanel.paintAlignment(true);
5165             }
5166           }
5167         }
5168         if (filesnotmatched.size() > 0)
5169         {
5170           if (assocfiles > 0
5171                   && (Cache.getDefault(
5172                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5173                           .showConfirmDialog(
5174                                   this,
5175                                   "<html>"
5176                                           + MessageManager
5177                                                   .formatMessage(
5178                                                           "label.ignore_unmatched_dropped_files_info",
5179                                                           new Object[] { Integer
5180                                                                   .valueOf(
5181                                                                           filesnotmatched
5182                                                                                   .size())
5183                                                                   .toString() })
5184                                           + "</html>",
5185                                   MessageManager
5186                                           .getString("label.ignore_unmatched_dropped_files"),
5187                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5188           {
5189             return;
5190           }
5191           for (String fn : filesnotmatched)
5192           {
5193             loadJalviewDataFile(fn, null, null, null);
5194           }
5195
5196         }
5197       } catch (Exception ex)
5198       {
5199         ex.printStackTrace();
5200       }
5201     }
5202   }
5203
5204   /**
5205    * Attempt to load a "dropped" file or URL string: First by testing whether
5206    * it's an Annotation file, then a JNet file, and finally a features file. If
5207    * all are false then the user may have dropped an alignment file onto this
5208    * AlignFrame.
5209    *
5210    * @param file
5211    *          either a filename or a URL string.
5212    */
5213   public void loadJalviewDataFile(String file, DataSourceType sourceType,
5214           FileFormatI format, SequenceI assocSeq)
5215   {
5216     try
5217     {
5218       if (sourceType == null)
5219       {
5220         sourceType = FormatAdapter.checkProtocol(file);
5221       }
5222       // if the file isn't identified, or not positively identified as some
5223       // other filetype (PFAM is default unidentified alignment file type) then
5224       // try to parse as annotation.
5225       boolean isAnnotation = (format == null || format == FileFormat.Pfam) ? new AnnotationFile()
5226               .annotateAlignmentView(viewport, file, sourceType) : false;
5227
5228       if (!isAnnotation)
5229       {
5230         // first see if its a T-COFFEE score file
5231         TCoffeeScoreFile tcf = null;
5232         try
5233         {
5234           tcf = new TCoffeeScoreFile(file, sourceType);
5235           if (tcf.isValid())
5236           {
5237             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5238             {
5239               tcoffeeColour.setEnabled(true);
5240               tcoffeeColour.setSelected(true);
5241               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5242               isAnnotation = true;
5243               statusBar
5244                       .setText(MessageManager
5245                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5246             }
5247             else
5248             {
5249               // some problem - if no warning its probable that the ID matching
5250               // process didn't work
5251               JOptionPane
5252                       .showMessageDialog(
5253                               Desktop.desktop,
5254                               tcf.getWarningMessage() == null ? MessageManager
5255                                       .getString("label.check_file_matches_sequence_ids_alignment")
5256                                       : tcf.getWarningMessage(),
5257                               MessageManager
5258                                       .getString("label.problem_reading_tcoffee_score_file"),
5259                               JOptionPane.WARNING_MESSAGE);
5260             }
5261           }
5262           else
5263           {
5264             tcf = null;
5265           }
5266         } catch (Exception x)
5267         {
5268           Cache.log
5269                   .debug("Exception when processing data source as T-COFFEE score file",
5270                           x);
5271           tcf = null;
5272         }
5273         if (tcf == null)
5274         {
5275           // try to see if its a JNet 'concise' style annotation file *before*
5276           // we
5277           // try to parse it as a features file
5278           if (format == null)
5279           {
5280             format = new IdentifyFile().identify(file, sourceType);
5281           }
5282           if (format == FileFormat.Jnet)
5283           {
5284             JPredFile predictions = new JPredFile(
5285                     file, sourceType);
5286             new JnetAnnotationMaker();
5287             JnetAnnotationMaker.add_annotation(predictions,
5288                     viewport.getAlignment(), 0, false);
5289             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5290             viewport.getAlignment().setSeqrep(repseq);
5291             ColumnSelection cs = new ColumnSelection();
5292             cs.hideInsertionsFor(repseq);
5293             viewport.setColumnSelection(cs);
5294             isAnnotation = true;
5295           }
5296           else if (IdentifyFile.FeaturesFile.equals(format))
5297           {
5298             if (parseFeaturesFile(file, sourceType))
5299             {
5300               alignPanel.paintAlignment(true);
5301             }
5302           }
5303           else
5304           {
5305             new FileLoader().LoadFile(viewport, file, sourceType, format);
5306           }
5307         }
5308       }
5309       if (isAnnotation)
5310       {
5311
5312         alignPanel.adjustAnnotationHeight();
5313         viewport.updateSequenceIdColours();
5314         buildSortByAnnotationScoresMenu();
5315         alignPanel.paintAlignment(true);
5316       }
5317     } catch (Exception ex)
5318     {
5319       ex.printStackTrace();
5320     } catch (OutOfMemoryError oom)
5321     {
5322       try
5323       {
5324         System.gc();
5325       } catch (Exception x)
5326       {
5327       }
5328       new OOMWarning(
5329               "loading data "
5330                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5331                               : "using " + sourceType + " from " + file)
5332                               : ".")
5333                       + (format != null ? "(parsing as '" + format
5334                               + "' file)" : ""), oom, Desktop.desktop);
5335     }
5336   }
5337
5338   /**
5339    * Method invoked by the ChangeListener on the tabbed pane, in other words
5340    * when a different tabbed pane is selected by the user or programmatically.
5341    */
5342   @Override
5343   public void tabSelectionChanged(int index)
5344   {
5345     if (index > -1)
5346     {
5347       alignPanel = alignPanels.get(index);
5348       viewport = alignPanel.av;
5349       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5350       setMenusFromViewport(viewport);
5351     }
5352
5353     /*
5354      * If there is a frame linked to this one in a SplitPane, switch it to the
5355      * same view tab index. No infinite recursion of calls should happen, since
5356      * tabSelectionChanged() should not get invoked on setting the selected
5357      * index to an unchanged value. Guard against setting an invalid index
5358      * before the new view peer tab has been created.
5359      */
5360     final AlignViewportI peer = viewport.getCodingComplement();
5361     if (peer != null)
5362     {
5363       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5364       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5365       {
5366         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5367       }
5368     }
5369   }
5370
5371   /**
5372    * On right mouse click on view tab, prompt for and set new view name.
5373    */
5374   @Override
5375   public void tabbedPane_mousePressed(MouseEvent e)
5376   {
5377     if (e.isPopupTrigger())
5378     {
5379       String msg = MessageManager.getString("label.enter_view_name");
5380       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5381               JOptionPane.QUESTION_MESSAGE);
5382
5383       if (reply != null)
5384       {
5385         viewport.viewName = reply;
5386         // TODO warn if reply is in getExistingViewNames()?
5387         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5388       }
5389     }
5390   }
5391
5392   public AlignViewport getCurrentView()
5393   {
5394     return viewport;
5395   }
5396
5397   /**
5398    * Open the dialog for regex description parsing.
5399    */
5400   @Override
5401   protected void extractScores_actionPerformed(ActionEvent e)
5402   {
5403     ParseProperties pp = new jalview.analysis.ParseProperties(
5404             viewport.getAlignment());
5405     // TODO: verify regex and introduce GUI dialog for version 2.5
5406     // if (pp.getScoresFromDescription("col", "score column ",
5407     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5408     // true)>0)
5409     if (pp.getScoresFromDescription("description column",
5410             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5411     {
5412       buildSortByAnnotationScoresMenu();
5413     }
5414   }
5415
5416   /*
5417    * (non-Javadoc)
5418    *
5419    * @see
5420    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5421    * )
5422    */
5423   @Override
5424   protected void showDbRefs_actionPerformed(ActionEvent e)
5425   {
5426     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5427   }
5428
5429   /*
5430    * (non-Javadoc)
5431    *
5432    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5433    * ActionEvent)
5434    */
5435   @Override
5436   protected void showNpFeats_actionPerformed(ActionEvent e)
5437   {
5438     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5439   }
5440
5441   /**
5442    * find the viewport amongst the tabs in this alignment frame and close that
5443    * tab
5444    *
5445    * @param av
5446    */
5447   public boolean closeView(AlignViewportI av)
5448   {
5449     if (viewport == av)
5450     {
5451       this.closeMenuItem_actionPerformed(false);
5452       return true;
5453     }
5454     Component[] comp = tabbedPane.getComponents();
5455     for (int i = 0; comp != null && i < comp.length; i++)
5456     {
5457       if (comp[i] instanceof AlignmentPanel)
5458       {
5459         if (((AlignmentPanel) comp[i]).av == av)
5460         {
5461           // close the view.
5462           closeView((AlignmentPanel) comp[i]);
5463           return true;
5464         }
5465       }
5466     }
5467     return false;
5468   }
5469
5470   protected void build_fetchdbmenu(JMenu webService)
5471   {
5472     // Temporary hack - DBRef Fetcher always top level ws entry.
5473     // TODO We probably want to store a sequence database checklist in
5474     // preferences and have checkboxes.. rather than individual sources selected
5475     // here
5476     final JMenu rfetch = new JMenu(
5477             MessageManager.getString("action.fetch_db_references"));
5478     rfetch.setToolTipText(MessageManager
5479             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5480     webService.add(rfetch);
5481
5482     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5483             MessageManager.getString("option.trim_retrieved_seqs"));
5484     trimrs.setToolTipText(MessageManager
5485             .getString("label.trim_retrieved_sequences"));
5486     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5487     trimrs.addActionListener(new ActionListener()
5488     {
5489       @Override
5490       public void actionPerformed(ActionEvent e)
5491       {
5492         trimrs.setSelected(trimrs.isSelected());
5493         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5494                 Boolean.valueOf(trimrs.isSelected()).toString());
5495       };
5496     });
5497     rfetch.add(trimrs);
5498     JMenuItem fetchr = new JMenuItem(
5499             MessageManager.getString("label.standard_databases"));
5500     fetchr.setToolTipText(MessageManager
5501             .getString("label.fetch_embl_uniprot"));
5502     fetchr.addActionListener(new ActionListener()
5503     {
5504
5505       @Override
5506       public void actionPerformed(ActionEvent e)
5507       {
5508         new Thread(new Runnable()
5509         {
5510           @Override
5511           public void run()
5512           {
5513             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5514                     .getAlignment().isNucleotide();
5515             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5516                     .getSequenceSelection(), alignPanel.alignFrame, null,
5517                     alignPanel.alignFrame.featureSettings, isNucleotide);
5518             dbRefFetcher.addListener(new FetchFinishedListenerI()
5519             {
5520               @Override
5521               public void finished()
5522               {
5523                 AlignFrame.this.setMenusForViewport();
5524               }
5525             });
5526             dbRefFetcher.fetchDBRefs(false);
5527           }
5528         }).start();
5529
5530       }
5531
5532     });
5533     rfetch.add(fetchr);
5534     final AlignFrame me = this;
5535     new Thread(new Runnable()
5536     {
5537       @Override
5538       public void run()
5539       {
5540         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5541                 .getSequenceFetcherSingleton(me);
5542         javax.swing.SwingUtilities.invokeLater(new Runnable()
5543         {
5544           @Override
5545           public void run()
5546           {
5547             String[] dbclasses = sf.getOrderedSupportedSources();
5548             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5549             // jalview.util.QuickSort.sort(otherdb, otherdb);
5550             List<DbSourceProxy> otherdb;
5551             JMenu dfetch = new JMenu();
5552             JMenu ifetch = new JMenu();
5553             JMenuItem fetchr = null;
5554             int comp = 0, icomp = 0, mcomp = 15;
5555             String mname = null;
5556             int dbi = 0;
5557             for (String dbclass : dbclasses)
5558             {
5559               otherdb = sf.getSourceProxy(dbclass);
5560               // add a single entry for this class, or submenu allowing 'fetch
5561               // all' or pick one
5562               if (otherdb == null || otherdb.size() < 1)
5563               {
5564                 continue;
5565               }
5566               // List<DbSourceProxy> dbs=otherdb;
5567               // otherdb=new ArrayList<DbSourceProxy>();
5568               // for (DbSourceProxy db:dbs)
5569               // {
5570               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5571               // }
5572               if (mname == null)
5573               {
5574                 mname = "From " + dbclass;
5575               }
5576               if (otherdb.size() == 1)
5577               {
5578                 final DbSourceProxy[] dassource = otherdb
5579                         .toArray(new DbSourceProxy[0]);
5580                 DbSourceProxy src = otherdb.get(0);
5581                 fetchr = new JMenuItem(src.getDbSource());
5582                 fetchr.addActionListener(new ActionListener()
5583                 {
5584
5585                   @Override
5586                   public void actionPerformed(ActionEvent e)
5587                   {
5588                     new Thread(new Runnable()
5589                     {
5590
5591                       @Override
5592                       public void run()
5593                       {
5594                         boolean isNucleotide = alignPanel.alignFrame
5595                                 .getViewport().getAlignment()
5596                                 .isNucleotide();
5597                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5598                                 alignPanel.av.getSequenceSelection(),
5599                                 alignPanel.alignFrame, dassource,
5600                                 alignPanel.alignFrame.featureSettings,
5601                                 isNucleotide);
5602                         dbRefFetcher
5603                                 .addListener(new FetchFinishedListenerI()
5604                                 {
5605                                   @Override
5606                                   public void finished()
5607                                   {
5608                                     AlignFrame.this.setMenusForViewport();
5609                                   }
5610                                 });
5611                         dbRefFetcher.fetchDBRefs(false);
5612                       }
5613                     }).start();
5614                   }
5615
5616                 });
5617                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5618                         MessageManager.formatMessage(
5619                                 "label.fetch_retrieve_from",
5620                                 new Object[] { src.getDbName() })));
5621                 dfetch.add(fetchr);
5622                 comp++;
5623               }
5624               else
5625               {
5626                 final DbSourceProxy[] dassource = otherdb
5627                         .toArray(new DbSourceProxy[0]);
5628                 // fetch all entry
5629                 DbSourceProxy src = otherdb.get(0);
5630                 fetchr = new JMenuItem(MessageManager.formatMessage(
5631                         "label.fetch_all_param",
5632                         new Object[] { src.getDbSource() }));
5633                 fetchr.addActionListener(new ActionListener()
5634                 {
5635                   @Override
5636                   public void actionPerformed(ActionEvent e)
5637                   {
5638                     new Thread(new Runnable()
5639                     {
5640
5641                       @Override
5642                       public void run()
5643                       {
5644                         boolean isNucleotide = alignPanel.alignFrame
5645                                 .getViewport().getAlignment()
5646                                 .isNucleotide();
5647                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5648                                 alignPanel.av.getSequenceSelection(),
5649                                 alignPanel.alignFrame, dassource,
5650                                 alignPanel.alignFrame.featureSettings,
5651                                 isNucleotide);
5652                         dbRefFetcher
5653                                 .addListener(new FetchFinishedListenerI()
5654                                 {
5655                                   @Override
5656                                   public void finished()
5657                                   {
5658                                     AlignFrame.this.setMenusForViewport();
5659                                   }
5660                                 });
5661                         dbRefFetcher.fetchDBRefs(false);
5662                       }
5663                     }).start();
5664                   }
5665                 });
5666
5667                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5668                         MessageManager.formatMessage(
5669                                 "label.fetch_retrieve_from_all_sources",
5670                                 new Object[] {
5671                                     Integer.valueOf(otherdb.size())
5672                                             .toString(), src.getDbSource(),
5673                                     src.getDbName() })));
5674                 dfetch.add(fetchr);
5675                 comp++;
5676                 // and then build the rest of the individual menus
5677                 ifetch = new JMenu(MessageManager.formatMessage(
5678                         "label.source_from_db_source",
5679                         new Object[] { src.getDbSource() }));
5680                 icomp = 0;
5681                 String imname = null;
5682                 int i = 0;
5683                 for (DbSourceProxy sproxy : otherdb)
5684                 {
5685                   String dbname = sproxy.getDbName();
5686                   String sname = dbname.length() > 5 ? dbname.substring(0,
5687                           5) + "..." : dbname;
5688                   String msname = dbname.length() > 10 ? dbname.substring(
5689                           0, 10) + "..." : dbname;
5690                   if (imname == null)
5691                   {
5692                     imname = MessageManager.formatMessage(
5693                             "label.from_msname", new Object[] { sname });
5694                   }
5695                   fetchr = new JMenuItem(msname);
5696                   final DbSourceProxy[] dassrc = { sproxy };
5697                   fetchr.addActionListener(new ActionListener()
5698                   {
5699
5700                     @Override
5701                     public void actionPerformed(ActionEvent e)
5702                     {
5703                       new Thread(new Runnable()
5704                       {
5705
5706                         @Override
5707                         public void run()
5708                         {
5709                           boolean isNucleotide = alignPanel.alignFrame
5710                                   .getViewport().getAlignment()
5711                                   .isNucleotide();
5712                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5713                                   alignPanel.av.getSequenceSelection(),
5714                                   alignPanel.alignFrame, dassrc,
5715                                   alignPanel.alignFrame.featureSettings,
5716                                   isNucleotide);
5717                           dbRefFetcher
5718                                   .addListener(new FetchFinishedListenerI()
5719                                   {
5720                                     @Override
5721                                     public void finished()
5722                                     {
5723                                       AlignFrame.this.setMenusForViewport();
5724                                     }
5725                                   });
5726                           dbRefFetcher.fetchDBRefs(false);
5727                         }
5728                       }).start();
5729                     }
5730
5731                   });
5732                   fetchr.setToolTipText("<html>"
5733                           + MessageManager.formatMessage(
5734                                   "label.fetch_retrieve_from", new Object[]
5735                                   { dbname }));
5736                   ifetch.add(fetchr);
5737                   ++i;
5738                   if (++icomp >= mcomp || i == (otherdb.size()))
5739                   {
5740                     ifetch.setText(MessageManager.formatMessage(
5741                             "label.source_to_target", imname, sname));
5742                     dfetch.add(ifetch);
5743                     ifetch = new JMenu();
5744                     imname = null;
5745                     icomp = 0;
5746                     comp++;
5747                   }
5748                 }
5749               }
5750               ++dbi;
5751               if (comp >= mcomp || dbi >= (dbclasses.length))
5752               {
5753                 dfetch.setText(MessageManager.formatMessage(
5754                         "label.source_to_target", mname, dbclass));
5755                 rfetch.add(dfetch);
5756                 dfetch = new JMenu();
5757                 mname = null;
5758                 comp = 0;
5759               }
5760             }
5761           }
5762         });
5763       }
5764     }).start();
5765
5766   }
5767
5768   /**
5769    * Left justify the whole alignment.
5770    */
5771   @Override
5772   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5773   {
5774     AlignmentI al = viewport.getAlignment();
5775     al.justify(false);
5776     viewport.firePropertyChange("alignment", null, al);
5777   }
5778
5779   /**
5780    * Right justify the whole alignment.
5781    */
5782   @Override
5783   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5784   {
5785     AlignmentI al = viewport.getAlignment();
5786     al.justify(true);
5787     viewport.firePropertyChange("alignment", null, al);
5788   }
5789
5790   @Override
5791   public void setShowSeqFeatures(boolean b)
5792   {
5793     showSeqFeatures.setSelected(b);
5794     viewport.setShowSequenceFeatures(b);
5795   }
5796
5797   /*
5798    * (non-Javadoc)
5799    *
5800    * @see
5801    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5802    * awt.event.ActionEvent)
5803    */
5804   @Override
5805   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5806   {
5807     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5808     alignPanel.paintAlignment(true);
5809   }
5810
5811   /*
5812    * (non-Javadoc)
5813    *
5814    * @see
5815    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5816    * .ActionEvent)
5817    */
5818   @Override
5819   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5820   {
5821     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5822     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5823
5824   }
5825
5826   /*
5827    * (non-Javadoc)
5828    *
5829    * @see
5830    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5831    * .event.ActionEvent)
5832    */
5833   @Override
5834   protected void showGroupConservation_actionPerformed(ActionEvent e)
5835   {
5836     viewport.setShowGroupConservation(showGroupConservation.getState());
5837     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5838   }
5839
5840   /*
5841    * (non-Javadoc)
5842    *
5843    * @see
5844    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5845    * .event.ActionEvent)
5846    */
5847   @Override
5848   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5849   {
5850     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5851     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5852   }
5853
5854   /*
5855    * (non-Javadoc)
5856    *
5857    * @see
5858    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5859    * .event.ActionEvent)
5860    */
5861   @Override
5862   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5863   {
5864     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5865     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5866   }
5867
5868   @Override
5869   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5870   {
5871     showSequenceLogo.setState(true);
5872     viewport.setShowSequenceLogo(true);
5873     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5874     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5875   }
5876
5877   @Override
5878   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5879   {
5880     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5881   }
5882
5883   /*
5884    * (non-Javadoc)
5885    *
5886    * @see
5887    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5888    * .event.ActionEvent)
5889    */
5890   @Override
5891   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5892   {
5893     if (avc.makeGroupsFromSelection())
5894     {
5895       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5896       alignPanel.updateAnnotation();
5897       alignPanel.paintAlignment(true);
5898     }
5899   }
5900
5901   public void clearAlignmentSeqRep()
5902   {
5903     // TODO refactor alignmentseqrep to controller
5904     if (viewport.getAlignment().hasSeqrep())
5905     {
5906       viewport.getAlignment().setSeqrep(null);
5907       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5908       alignPanel.updateAnnotation();
5909       alignPanel.paintAlignment(true);
5910     }
5911   }
5912
5913   @Override
5914   protected void createGroup_actionPerformed(ActionEvent e)
5915   {
5916     if (avc.createGroup())
5917     {
5918       alignPanel.alignmentChanged();
5919     }
5920   }
5921
5922   @Override
5923   protected void unGroup_actionPerformed(ActionEvent e)
5924   {
5925     if (avc.unGroup())
5926     {
5927       alignPanel.alignmentChanged();
5928     }
5929   }
5930
5931   /**
5932    * make the given alignmentPanel the currently selected tab
5933    *
5934    * @param alignmentPanel
5935    */
5936   public void setDisplayedView(AlignmentPanel alignmentPanel)
5937   {
5938     if (!viewport.getSequenceSetId().equals(
5939             alignmentPanel.av.getSequenceSetId()))
5940     {
5941       throw new Error(
5942               MessageManager
5943                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5944     }
5945     if (tabbedPane != null
5946             && tabbedPane.getTabCount() > 0
5947             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5948                     .getSelectedIndex())
5949     {
5950       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5951     }
5952   }
5953
5954   /**
5955    * Action on selection of menu options to Show or Hide annotations.
5956    *
5957    * @param visible
5958    * @param forSequences
5959    *          update sequence-related annotations
5960    * @param forAlignment
5961    *          update non-sequence-related annotations
5962    */
5963   @Override
5964   protected void setAnnotationsVisibility(boolean visible,
5965           boolean forSequences, boolean forAlignment)
5966   {
5967     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5968             .getAlignmentAnnotation();
5969     if (anns == null)
5970     {
5971       return;
5972     }
5973     for (AlignmentAnnotation aa : anns)
5974     {
5975       /*
5976        * don't display non-positional annotations on an alignment
5977        */
5978       if (aa.annotations == null)
5979       {
5980         continue;
5981       }
5982       boolean apply = (aa.sequenceRef == null && forAlignment)
5983               || (aa.sequenceRef != null && forSequences);
5984       if (apply)
5985       {
5986         aa.visible = visible;
5987       }
5988     }
5989     alignPanel.validateAnnotationDimensions(true);
5990     alignPanel.alignmentChanged();
5991   }
5992
5993   /**
5994    * Store selected annotation sort order for the view and repaint.
5995    */
5996   @Override
5997   protected void sortAnnotations_actionPerformed()
5998   {
5999     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6000     this.alignPanel.av
6001             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6002     alignPanel.paintAlignment(true);
6003   }
6004
6005   /**
6006    *
6007    * @return alignment panels in this alignment frame
6008    */
6009   public List<? extends AlignmentViewPanel> getAlignPanels()
6010   {
6011     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6012   }
6013
6014   /**
6015    * Open a new alignment window, with the cDNA associated with this (protein)
6016    * alignment, aligned as is the protein.
6017    */
6018   protected void viewAsCdna_actionPerformed()
6019   {
6020     // TODO no longer a menu action - refactor as required
6021     final AlignmentI alignment = getViewport().getAlignment();
6022     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6023     if (mappings == null)
6024     {
6025       return;
6026     }
6027     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6028     for (SequenceI aaSeq : alignment.getSequences())
6029     {
6030       for (AlignedCodonFrame acf : mappings)
6031       {
6032         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6033         if (dnaSeq != null)
6034         {
6035           /*
6036            * There is a cDNA mapping for this protein sequence - add to new
6037            * alignment. It will share the same dataset sequence as other mapped
6038            * cDNA (no new mappings need to be created).
6039            */
6040           final Sequence newSeq = new Sequence(dnaSeq);
6041           newSeq.setDatasetSequence(dnaSeq);
6042           cdnaSeqs.add(newSeq);
6043         }
6044       }
6045     }
6046     if (cdnaSeqs.size() == 0)
6047     {
6048       // show a warning dialog no mapped cDNA
6049       return;
6050     }
6051     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6052             .size()]));
6053     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6054             AlignFrame.DEFAULT_HEIGHT);
6055     cdna.alignAs(alignment);
6056     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6057             + this.title;
6058     Desktop.addInternalFrame(alignFrame, newtitle,
6059             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6060   }
6061
6062   /**
6063    * Set visibility of dna/protein complement view (available when shown in a
6064    * split frame).
6065    *
6066    * @param show
6067    */
6068   @Override
6069   protected void showComplement_actionPerformed(boolean show)
6070   {
6071     SplitContainerI sf = getSplitViewContainer();
6072     if (sf != null)
6073     {
6074       sf.setComplementVisible(this, show);
6075     }
6076   }
6077
6078   /**
6079    * Generate the reverse (optionally complemented) of the selected sequences,
6080    * and add them to the alignment
6081    */
6082   @Override
6083   protected void showReverse_actionPerformed(boolean complement)
6084   {
6085     AlignmentI al = null;
6086     try
6087     {
6088       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6089       al = dna.reverseCdna(complement);
6090       viewport.addAlignment(al, "");
6091       addHistoryItem(new EditCommand(
6092               MessageManager.getString("label.add_sequences"),
6093               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
6094               viewport.getAlignment()));
6095     } catch (Exception ex)
6096     {
6097       System.err.println(ex.getMessage());
6098       return;
6099     }
6100   }
6101
6102   /**
6103    * Try to run a script in the Groovy console, having first ensured that this
6104    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6105    * be targeted at this alignment.
6106    */
6107   @Override
6108   protected void runGroovy_actionPerformed()
6109   {
6110     Jalview.setCurrentAlignFrame(this);
6111     groovy.ui.Console console = Desktop.getGroovyConsole();
6112     if (console != null)
6113     {
6114       try
6115       {
6116         console.runScript();
6117       } catch (Exception ex)
6118       {
6119         System.err.println((ex.toString()));
6120         JOptionPane
6121                 .showInternalMessageDialog(Desktop.desktop, MessageManager
6122                         .getString("label.couldnt_run_groovy_script"),
6123                         MessageManager
6124                                 .getString("label.groovy_support_failed"),
6125                         JOptionPane.ERROR_MESSAGE);
6126       }
6127     }
6128     else
6129     {
6130       System.err.println("Can't run Groovy script as console not found");
6131     }
6132   }
6133
6134   /**
6135    * Hides columns containing (or not containing) a specified feature, provided
6136    * that would not leave all columns hidden
6137    *
6138    * @param featureType
6139    * @param columnsContaining
6140    * @return
6141    */
6142   public boolean hideFeatureColumns(String featureType,
6143           boolean columnsContaining)
6144   {
6145     boolean notForHiding = avc.markColumnsContainingFeatures(
6146             columnsContaining, false, false, featureType);
6147     if (notForHiding)
6148     {
6149       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6150               false, featureType))
6151       {
6152         getViewport().hideSelectedColumns();
6153         return true;
6154       }
6155     }
6156     return false;
6157   }
6158 }
6159
6160 class PrintThread extends Thread
6161 {
6162   AlignmentPanel ap;
6163
6164   public PrintThread(AlignmentPanel ap)
6165   {
6166     this.ap = ap;
6167   }
6168
6169   static PageFormat pf;
6170
6171   @Override
6172   public void run()
6173   {
6174     PrinterJob printJob = PrinterJob.getPrinterJob();
6175
6176     if (pf != null)
6177     {
6178       printJob.setPrintable(ap, pf);
6179     }
6180     else
6181     {
6182       printJob.setPrintable(ap);
6183     }
6184
6185     if (printJob.printDialog())
6186     {
6187       try
6188       {
6189         printJob.print();
6190       } catch (Exception PrintException)
6191       {
6192         PrintException.printStackTrace();
6193       }
6194     }
6195   }
6196 }