src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  63 import jalview.io.AlignmentProperties;
  64 import jalview.io.AnnotationFile;
  65 import jalview.io.BioJsHTMLOutput;
  66 import jalview.io.DataSourceType;
  67 import jalview.io.FileFormat;
  68 import jalview.io.FileFormatI;
  69 import jalview.io.FileLoader;
  70 import jalview.io.FormatAdapter;
  71 import jalview.io.HtmlSvgOutput;
  72 import jalview.io.IdentifyFile;
  73 import jalview.io.JPredFile;
  74 import jalview.io.JalviewFileChooser;
  75 import jalview.io.JalviewFileView;
  76 import jalview.io.JnetAnnotationMaker;
  77 import jalview.io.NewickFile;
  78 import jalview.io.TCoffeeScoreFile;
  79 import jalview.jbgui.GAlignFrame;
  80 import jalview.schemes.Blosum62ColourScheme;
  81 import jalview.schemes.BuriedColourScheme;
  82 import jalview.schemes.ClustalxColourScheme;
  83 import jalview.schemes.ColourSchemeI;
  84 import jalview.schemes.ColourSchemeProperty;
  85 import jalview.schemes.HelixColourScheme;
  86 import jalview.schemes.HydrophobicColourScheme;
  87 import jalview.schemes.NucleotideColourScheme;
  88 import jalview.schemes.PIDColourScheme;
  89 import jalview.schemes.PurinePyrimidineColourScheme;
  90 import jalview.schemes.RNAHelicesColourChooser;
  91 import jalview.schemes.ResidueProperties;
  92 import jalview.schemes.StrandColourScheme;
  93 import jalview.schemes.TCoffeeColourScheme;
  94 import jalview.schemes.TaylorColourScheme;
  95 import jalview.schemes.TurnColourScheme;
  96 import jalview.schemes.UserColourScheme;
  97 import jalview.schemes.ZappoColourScheme;
  98 import jalview.util.MessageManager;
  99 import jalview.viewmodel.AlignmentViewport;
 100 import jalview.ws.DBRefFetcher;
 101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 102 import jalview.ws.jws1.Discoverer;
 103 import jalview.ws.jws2.Jws2Discoverer;
 104 import jalview.ws.jws2.jabaws2.Jws2Instance;
 105 import jalview.ws.seqfetcher.DbSourceProxy;
 106
 107 import java.awt.BorderLayout;
 108 import java.awt.Component;
 109 import java.awt.Rectangle;
 110 import java.awt.Toolkit;
 111 import java.awt.datatransfer.Clipboard;
 112 import java.awt.datatransfer.DataFlavor;
 113 import java.awt.datatransfer.StringSelection;
 114 import java.awt.datatransfer.Transferable;
 115 import java.awt.dnd.DnDConstants;
 116 import java.awt.dnd.DropTargetDragEvent;
 117 import java.awt.dnd.DropTargetDropEvent;
 118 import java.awt.dnd.DropTargetEvent;
 119 import java.awt.dnd.DropTargetListener;
 120 import java.awt.event.ActionEvent;
 121 import java.awt.event.ActionListener;
 122 import java.awt.event.FocusAdapter;
 123 import java.awt.event.FocusEvent;
 124 import java.awt.event.ItemEvent;
 125 import java.awt.event.ItemListener;
 126 import java.awt.event.KeyAdapter;
 127 import java.awt.event.KeyEvent;
 128 import java.awt.event.MouseEvent;
 129 import java.awt.print.PageFormat;
 130 import java.awt.print.PrinterJob;
 131 import java.beans.PropertyChangeEvent;
 132 import java.io.File;
 133 import java.net.URL;
 134 import java.util.ArrayList;
 135 import java.util.Arrays;
 136 import java.util.Deque;
 137 import java.util.Enumeration;
 138 import java.util.Hashtable;
 139 import java.util.List;
 140 import java.util.Vector;
 141
 142 import javax.swing.JCheckBoxMenuItem;
 143 import javax.swing.JEditorPane;
 144 import javax.swing.JInternalFrame;
 145 import javax.swing.JLayeredPane;
 146 import javax.swing.JMenu;
 147 import javax.swing.JMenuItem;
 148 import javax.swing.JScrollPane;
 149 import javax.swing.SwingUtilities;
 150
 151 /**
 152  * DOCUMENT ME!
 153  *
 154  * @author $author$
 155  * @version $Revision$
 156  */
 157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 158         IProgressIndicator, AlignViewControllerGuiI
 159 {
 160
 161   public static final int DEFAULT_WIDTH = 700;
 162
 163   public static final int DEFAULT_HEIGHT = 500;
 164
 165   /*
 166    * The currently displayed panel (selected tabbed view if more than one)
 167    */
 168   public AlignmentPanel alignPanel;
 169
 170   AlignViewport viewport;
 171
 172   public AlignViewControllerI avc;
 173
 174   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 175
 176   /**
 177    * Last format used to load or save alignments in this window
 178    */
 179   FileFormatI currentFileFormat = null;
 180
 181   /**
 182    * Current filename for this alignment
 183    */
 184   String fileName = null;
 185
 186   /**
 187    * Creates a new AlignFrame object with specific width and height.
 188    *
 189    * @param al
 190    * @param width
 191    * @param height
 192    */
 193   public AlignFrame(AlignmentI al, int width, int height)
 194   {
 195     this(al, null, width, height);
 196   }
 197
 198   /**
 199    * Creates a new AlignFrame object with specific width, height and
 200    * sequenceSetId
 201    *
 202    * @param al
 203    * @param width
 204    * @param height
 205    * @param sequenceSetId
 206    */
 207   public AlignFrame(AlignmentI al, int width, int height,
 208           String sequenceSetId)
 209   {
 210     this(al, null, width, height, sequenceSetId);
 211   }
 212
 213   /**
 214    * Creates a new AlignFrame object with specific width, height and
 215    * sequenceSetId
 216    *
 217    * @param al
 218    * @param width
 219    * @param height
 220    * @param sequenceSetId
 221    * @param viewId
 222    */
 223   public AlignFrame(AlignmentI al, int width, int height,
 224           String sequenceSetId, String viewId)
 225   {
 226     this(al, null, width, height, sequenceSetId, viewId);
 227   }
 228
 229   /**
 230    * new alignment window with hidden columns
 231    *
 232    * @param al
 233    *          AlignmentI
 234    * @param hiddenColumns
 235    *          ColumnSelection or null
 236    * @param width
 237    *          Width of alignment frame
 238    * @param height
 239    *          height of frame.
 240    */
 241   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 242           int width, int height)
 243   {
 244     this(al, hiddenColumns, width, height, null);
 245   }
 246
 247   /**
 248    * Create alignment frame for al with hiddenColumns, a specific width and
 249    * height, and specific sequenceId
 250    *
 251    * @param al
 252    * @param hiddenColumns
 253    * @param width
 254    * @param height
 255    * @param sequenceSetId
 256    *          (may be null)
 257    */
 258   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 259           int width, int height, String sequenceSetId)
 260   {
 261     this(al, hiddenColumns, width, height, sequenceSetId, null);
 262   }
 263
 264   /**
 265    * Create alignment frame for al with hiddenColumns, a specific width and
 266    * height, and specific sequenceId
 267    *
 268    * @param al
 269    * @param hiddenColumns
 270    * @param width
 271    * @param height
 272    * @param sequenceSetId
 273    *          (may be null)
 274    * @param viewId
 275    *          (may be null)
 276    */
 277   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 278           int width, int height, String sequenceSetId, String viewId)
 279   {
 280     setSize(width, height);
 281
 282     if (al.getDataset() == null)
 283     {
 284       al.setDataset(null);
 285     }
 286
 287     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 288
 289     alignPanel = new AlignmentPanel(this, viewport);
 290
 291     addAlignmentPanel(alignPanel, true);
 292     init();
 293   }
 294
 295   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 296           ColumnSelection hiddenColumns, int width, int height)
 297   {
 298     setSize(width, height);
 299
 300     if (al.getDataset() == null)
 301     {
 302       al.setDataset(null);
 303     }
 304
 305     viewport = new AlignViewport(al, hiddenColumns);
 306
 307     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 308     {
 309       viewport.hideSequence(hiddenSeqs);
 310     }
 311     alignPanel = new AlignmentPanel(this, viewport);
 312     addAlignmentPanel(alignPanel, true);
 313     init();
 314   }
 315
 316   /**
 317    * Make a new AlignFrame from existing alignmentPanels
 318    *
 319    * @param ap
 320    *          AlignmentPanel
 321    * @param av
 322    *          AlignViewport
 323    */
 324   public AlignFrame(AlignmentPanel ap)
 325   {
 326     viewport = ap.av;
 327     alignPanel = ap;
 328     addAlignmentPanel(ap, false);
 329     init();
 330   }
 331
 332   /**
 333    * initalise the alignframe from the underlying viewport data and the
 334    * configurations
 335    */
 336   void init()
 337   {
 338     if (!Jalview.isHeadlessMode())
 339     {
 340       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 341     }
 342
 343     avc = new jalview.controller.AlignViewController(this, viewport,
 344             alignPanel);
 345     if (viewport.getAlignmentConservationAnnotation() == null)
 346     {
 347       BLOSUM62Colour.setEnabled(false);
 348       conservationMenuItem.setEnabled(false);
 349       modifyConservation.setEnabled(false);
 350       // PIDColour.setEnabled(false);
 351       // abovePIDThreshold.setEnabled(false);
 352       // modifyPID.setEnabled(false);
 353     }
 354
 355     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 356             "No sort");
 357
 358     if (sortby.equals("Id"))
 359     {
 360       sortIDMenuItem_actionPerformed(null);
 361     }
 362     else if (sortby.equals("Pairwise Identity"))
 363     {
 364       sortPairwiseMenuItem_actionPerformed(null);
 365     }
 366
 367     if (Desktop.desktop != null)
 368     {
 369       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 370       addServiceListeners();
 371       setGUINucleotide(viewport.getAlignment().isNucleotide());
 372     }
 373
 374     this.alignPanel.av
 375             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 376
 377     setMenusFromViewport(viewport);
 378     buildSortByAnnotationScoresMenu();
 379     buildTreeMenu();
 380
 381     if (viewport.getWrapAlignment())
 382     {
 383       wrapMenuItem_actionPerformed(null);
 384     }
 385
 386     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 387     {
 388       this.overviewMenuItem_actionPerformed(null);
 389     }
 390
 391     addKeyListener();
 392
 393     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 394     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 395     final String menuLabel = MessageManager
 396             .getString("label.copy_format_from");
 397     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 398             new ViewSetProvider()
 399             {
 400
 401               @Override
 402               public AlignmentPanel[] getAllAlignmentPanels()
 403               {
 404                 origview.clear();
 405                 origview.add(alignPanel);
 406                 // make an array of all alignment panels except for this one
 407                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 408                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 409                 aps.remove(AlignFrame.this.alignPanel);
 410                 return aps.toArray(new AlignmentPanel[aps.size()]);
 411               }
 412             }, selviews, new ItemListener()
 413             {
 414
 415               @Override
 416               public void itemStateChanged(ItemEvent e)
 417               {
 418                 if (origview.size() > 0)
 419                 {
 420                   final AlignmentPanel ap = origview.get(0);
 421
 422                   /*
 423                    * Copy the ViewStyle of the selected panel to 'this one'.
 424                    * Don't change value of 'scaleProteinAsCdna' unless copying
 425                    * from a SplitFrame.
 426                    */
 427                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 428                           .getViewStyle();
 429                   boolean fromSplitFrame = selviews.get(0)
 430                           .getAlignViewport().getCodingComplement() != null;
 431                   if (!fromSplitFrame)
 432                   {
 433                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 434                             .getViewStyle().isScaleProteinAsCdna());
 435                   }
 436                   ap.getAlignViewport().setViewStyle(vs);
 437
 438                   /*
 439                    * Also rescale ViewStyle of SplitFrame complement if there is
 440                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 441                    * the whole ViewStyle (allow cDNA protein to have different
 442                    * fonts)
 443                    */
 444                   AlignViewportI complement = ap.getAlignViewport()
 445                           .getCodingComplement();
 446                   if (complement != null && vs.isScaleProteinAsCdna())
 447                   {
 448                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 449                     ((SplitFrame) af.getSplitViewContainer())
 450                             .adjustLayout();
 451                     af.setMenusForViewport();
 452                   }
 453
 454                   ap.updateLayout();
 455                   ap.setSelected(true);
 456                   ap.alignFrame.setMenusForViewport();
 457
 458                 }
 459               }
 460             });
 461     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 462             .indexOf("devel") > -1
 463             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 464                     .indexOf("test") > -1)
 465     {
 466       formatMenu.add(vsel);
 467     }
 468     addFocusListener(new FocusAdapter()
 469     {
 470       @Override
 471       public void focusGained(FocusEvent e)
 472       {
 473         Jalview.setCurrentAlignFrame(AlignFrame.this);
 474       }
 475     });
 476
 477   }
 478
 479   /**
 480    * Change the filename and format for the alignment, and enable the 'reload'
 481    * button functionality.
 482    *
 483    * @param file
 484    *          valid filename
 485    * @param format
 486    *          format of file
 487    */
 488   public void setFileName(String file, FileFormatI format)
 489   {
 490     fileName = file;
 491     setFileFormat(format);
 492     reload.setEnabled(true);
 493   }
 494
 495   /**
 496    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 497    * events
 498    */
 499   void addKeyListener()
 500   {
 501     addKeyListener(new KeyAdapter()
 502     {
 503       @Override
 504       public void keyPressed(KeyEvent evt)
 505       {
 506         if (viewport.cursorMode
 507                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 508                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 509                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 510                 && Character.isDigit(evt.getKeyChar()))
 511         {
 512           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 513         }
 514
 515         switch (evt.getKeyCode())
 516         {
 517
 518         case 27: // escape key
 519           deselectAllSequenceMenuItem_actionPerformed(null);
 520
 521           break;
 522
 523         case KeyEvent.VK_DOWN:
 524           if (evt.isAltDown() || !viewport.cursorMode)
 525           {
 526             moveSelectedSequences(false);
 527           }
 528           if (viewport.cursorMode)
 529           {
 530             alignPanel.getSeqPanel().moveCursor(0, 1);
 531           }
 532           break;
 533
 534         case KeyEvent.VK_UP:
 535           if (evt.isAltDown() || !viewport.cursorMode)
 536           {
 537             moveSelectedSequences(true);
 538           }
 539           if (viewport.cursorMode)
 540           {
 541             alignPanel.getSeqPanel().moveCursor(0, -1);
 542           }
 543
 544           break;
 545
 546         case KeyEvent.VK_LEFT:
 547           if (evt.isAltDown() || !viewport.cursorMode)
 548           {
 549             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 550           }
 551           else
 552           {
 553             alignPanel.getSeqPanel().moveCursor(-1, 0);
 554           }
 555
 556           break;
 557
 558         case KeyEvent.VK_RIGHT:
 559           if (evt.isAltDown() || !viewport.cursorMode)
 560           {
 561             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 562           }
 563           else
 564           {
 565             alignPanel.getSeqPanel().moveCursor(1, 0);
 566           }
 567           break;
 568
 569         case KeyEvent.VK_SPACE:
 570           if (viewport.cursorMode)
 571           {
 572             alignPanel.getSeqPanel().insertGapAtCursor(
 573                     evt.isControlDown() || evt.isShiftDown()
 574                             || evt.isAltDown());
 575           }
 576           break;
 577
 578         // case KeyEvent.VK_A:
 579         // if (viewport.cursorMode)
 580         // {
 581         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 582         // //System.out.println("A");
 583         // }
 584         // break;
 585         /*
 586          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 587          * System.out.println("closing bracket"); } break;
 588          */
 589         case KeyEvent.VK_DELETE:
 590         case KeyEvent.VK_BACK_SPACE:
 591           if (!viewport.cursorMode)
 592           {
 593             cut_actionPerformed(null);
 594           }
 595           else
 596           {
 597             alignPanel.getSeqPanel().deleteGapAtCursor(
 598                     evt.isControlDown() || evt.isShiftDown()
 599                             || evt.isAltDown());
 600           }
 601
 602           break;
 603
 604         case KeyEvent.VK_S:
 605           if (viewport.cursorMode)
 606           {
 607             alignPanel.getSeqPanel().setCursorRow();
 608           }
 609           break;
 610         case KeyEvent.VK_C:
 611           if (viewport.cursorMode && !evt.isControlDown())
 612           {
 613             alignPanel.getSeqPanel().setCursorColumn();
 614           }
 615           break;
 616         case KeyEvent.VK_P:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorPosition();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_ENTER:
 624         case KeyEvent.VK_COMMA:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setCursorRowAndColumn();
 628           }
 629           break;
 630
 631         case KeyEvent.VK_Q:
 632           if (viewport.cursorMode)
 633           {
 634             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 635           }
 636           break;
 637         case KeyEvent.VK_M:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 641           }
 642           break;
 643
 644         case KeyEvent.VK_F2:
 645           viewport.cursorMode = !viewport.cursorMode;
 646           statusBar.setText(MessageManager.formatMessage(
 647                   "label.keyboard_editing_mode",
 648                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 649           if (viewport.cursorMode)
 650           {
 651             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 652             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 653           }
 654           alignPanel.getSeqPanel().seqCanvas.repaint();
 655           break;
 656
 657         case KeyEvent.VK_F1:
 658           try
 659           {
 660             Help.showHelpWindow();
 661           } catch (Exception ex)
 662           {
 663             ex.printStackTrace();
 664           }
 665           break;
 666         case KeyEvent.VK_H:
 667         {
 668           boolean toggleSeqs = !evt.isControlDown();
 669           boolean toggleCols = !evt.isShiftDown();
 670           toggleHiddenRegions(toggleSeqs, toggleCols);
 671           break;
 672         }
 673         case KeyEvent.VK_B:
 674         {
 675           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 676           boolean modifyExisting = true; // always modify, don't clear
 677                                          // evt.isShiftDown();
 678           boolean invertHighlighted = evt.isAltDown();
 679           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 680                   toggleSel);
 681           break;
 682         }
 683         case KeyEvent.VK_PAGE_UP:
 684           if (viewport.getWrapAlignment())
 685           {
 686             alignPanel.scrollUp(true);
 687           }
 688           else
 689           {
 690             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 691                     - viewport.endSeq + viewport.startSeq);
 692           }
 693           break;
 694         case KeyEvent.VK_PAGE_DOWN:
 695           if (viewport.getWrapAlignment())
 696           {
 697             alignPanel.scrollUp(false);
 698           }
 699           else
 700           {
 701             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 702                     + viewport.endSeq - viewport.startSeq);
 703           }
 704           break;
 705         }
 706       }
 707
 708       @Override
 709       public void keyReleased(KeyEvent evt)
 710       {
 711         switch (evt.getKeyCode())
 712         {
 713         case KeyEvent.VK_LEFT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null, viewport
 717                     .getAlignment().getSequences());
 718           }
 719           break;
 720
 721         case KeyEvent.VK_RIGHT:
 722           if (evt.isAltDown() || !viewport.cursorMode)
 723           {
 724             viewport.firePropertyChange("alignment", null, viewport
 725                     .getAlignment().getSequences());
 726           }
 727           break;
 728         }
 729       }
 730     });
 731   }
 732
 733   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 734   {
 735     ap.alignFrame = this;
 736     avc = new jalview.controller.AlignViewController(this, viewport,
 737             alignPanel);
 738
 739     alignPanels.add(ap);
 740
 741     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 742
 743     int aSize = alignPanels.size();
 744
 745     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 746
 747     if (aSize == 1 && ap.av.viewName == null)
 748     {
 749       this.getContentPane().add(ap, BorderLayout.CENTER);
 750     }
 751     else
 752     {
 753       if (aSize == 2)
 754       {
 755         setInitialTabVisible();
 756       }
 757
 758       expandViews.setEnabled(true);
 759       gatherViews.setEnabled(true);
 760       tabbedPane.addTab(ap.av.viewName, ap);
 761
 762       ap.setVisible(false);
 763     }
 764
 765     if (newPanel)
 766     {
 767       if (ap.av.isPadGaps())
 768       {
 769         ap.av.getAlignment().padGaps();
 770       }
 771       ap.av.updateConservation(ap);
 772       ap.av.updateConsensus(ap);
 773       ap.av.updateStrucConsensus(ap);
 774     }
 775   }
 776
 777   public void setInitialTabVisible()
 778   {
 779     expandViews.setEnabled(true);
 780     gatherViews.setEnabled(true);
 781     tabbedPane.setVisible(true);
 782     AlignmentPanel first = alignPanels.get(0);
 783     tabbedPane.addTab(first.av.viewName, first);
 784     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 785   }
 786
 787   public AlignViewport getViewport()
 788   {
 789     return viewport;
 790   }
 791
 792   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 793   private void addServiceListeners()
 794   {
 795     final java.beans.PropertyChangeListener thisListener;
 796     Desktop.instance.addJalviewPropertyChangeListener("services",
 797             thisListener = new java.beans.PropertyChangeListener()
 798             {
 799               @Override
 800               public void propertyChange(PropertyChangeEvent evt)
 801               {
 802                 // // System.out.println("Discoverer property change.");
 803                 // if (evt.getPropertyName().equals("services"))
 804                 {
 805                   SwingUtilities.invokeLater(new Runnable()
 806                   {
 807
 808                     @Override
 809                     public void run()
 810                     {
 811                       System.err
 812                               .println("Rebuild WS Menu for service change");
 813                       BuildWebServiceMenu();
 814                     }
 815
 816                   });
 817                 }
 818               }
 819             });
 820     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 821     {
 822       @Override
 823       public void internalFrameClosed(
 824               javax.swing.event.InternalFrameEvent evt)
 825       {
 826         // System.out.println("deregistering discoverer listener");
 827         Desktop.instance.removeJalviewPropertyChangeListener("services",
 828                 thisListener);
 829         closeMenuItem_actionPerformed(true);
 830       };
 831     });
 832     // Finally, build the menu once to get current service state
 833     new Thread(new Runnable()
 834     {
 835       @Override
 836       public void run()
 837       {
 838         BuildWebServiceMenu();
 839       }
 840     }).start();
 841   }
 842
 843   /**
 844    * Configure menu items that vary according to whether the alignment is
 845    * nucleotide or protein
 846    *
 847    * @param nucleotide
 848    */
 849   public void setGUINucleotide(boolean nucleotide)
 850   {
 851     showTranslation.setVisible(nucleotide);
 852     showReverse.setVisible(nucleotide);
 853     showReverseComplement.setVisible(nucleotide);
 854     conservationMenuItem.setEnabled(!nucleotide);
 855     modifyConservation.setEnabled(!nucleotide);
 856     showGroupConservation.setEnabled(!nucleotide);
 857     clustalColour.setEnabled(!nucleotide);
 858     zappoColour.setEnabled(!nucleotide);
 859     taylorColour.setEnabled(!nucleotide);
 860     hydrophobicityColour.setEnabled(!nucleotide);
 861     helixColour.setEnabled(!nucleotide);
 862     strandColour.setEnabled(!nucleotide);
 863     turnColour.setEnabled(!nucleotide);
 864     buriedColour.setEnabled(!nucleotide);
 865     rnahelicesColour.setEnabled(nucleotide);
 866     nucleotideColour.setEnabled(nucleotide);
 867     purinePyrimidineColour.setEnabled(nucleotide);
 868     RNAInteractionColour.setEnabled(nucleotide);
 869     showComplementMenuItem.setText(nucleotide ? MessageManager
 870             .getString("label.protein") : MessageManager
 871             .getString("label.nucleotide"));
 872     String selectedColourScheme = Cache.getDefault(
 873             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 874                     : Preferences.DEFAULT_COLOUR_PROT, "None");
 875     setColourSelected(selectedColourScheme);
 876   }
 877
 878   /**
 879    * set up menus for the current viewport. This may be called after any
 880    * operation that affects the data in the current view (selection changed,
 881    * etc) to update the menus to reflect the new state.
 882    */
 883   @Override
 884   public void setMenusForViewport()
 885   {
 886     setMenusFromViewport(viewport);
 887   }
 888
 889   /**
 890    * Need to call this method when tabs are selected for multiple views, or when
 891    * loading from Jalview2XML.java
 892    *
 893    * @param av
 894    *          AlignViewport
 895    */
 896   void setMenusFromViewport(AlignViewport av)
 897   {
 898     padGapsMenuitem.setSelected(av.isPadGaps());
 899     colourTextMenuItem.setSelected(av.isShowColourText());
 900     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 901     conservationMenuItem.setSelected(av.getConservationSelected());
 902     seqLimits.setSelected(av.getShowJVSuffix());
 903     idRightAlign.setSelected(av.isRightAlignIds());
 904     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 905     renderGapsMenuItem.setSelected(av.isRenderGaps());
 906     wrapMenuItem.setSelected(av.getWrapAlignment());
 907     scaleAbove.setVisible(av.getWrapAlignment());
 908     scaleLeft.setVisible(av.getWrapAlignment());
 909     scaleRight.setVisible(av.getWrapAlignment());
 910     annotationPanelMenuItem.setState(av.isShowAnnotation());
 911     /*
 912      * Show/hide annotations only enabled if annotation panel is shown
 913      */
 914     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 915     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 916     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 917     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 918     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 919     viewTextMenuItem.setSelected(av.getShowText());
 920     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 921     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 922     showGroupConservation.setSelected(av.isShowGroupConservation());
 923     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 924     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 925     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 926
 927     setColourSelected(ColourSchemeProperty.getColourName(av
 928             .getGlobalColourScheme()));
 929
 930     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 931     hiddenMarkers.setState(av.getShowHiddenMarkers());
 932     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 933     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 934     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 935     autoCalculate.setSelected(av.autoCalculateConsensus);
 936     sortByTree.setSelected(av.sortByTree);
 937     listenToViewSelections.setSelected(av.followSelection);
 938     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 939     rnahelicesColour
 940             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 941
 942     showProducts.setEnabled(canShowProducts());
 943     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 944
 945     updateEditMenuBar();
 946   }
 947
 948   /**
 949    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 950    *
 951    * @param b
 952    */
 953   public void setGroovyEnabled(boolean b)
 954   {
 955     runGroovy.setEnabled(b);
 956   }
 957
 958   private IProgressIndicator progressBar;
 959
 960   /*
 961    * (non-Javadoc)
 962    *
 963    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 964    */
 965   @Override
 966   public void setProgressBar(String message, long id)
 967   {
 968     progressBar.setProgressBar(message, id);
 969   }
 970
 971   @Override
 972   public void registerHandler(final long id,
 973           final IProgressIndicatorHandler handler)
 974   {
 975     progressBar.registerHandler(id, handler);
 976   }
 977
 978   /**
 979    *
 980    * @return true if any progress bars are still active
 981    */
 982   @Override
 983   public boolean operationInProgress()
 984   {
 985     return progressBar.operationInProgress();
 986   }
 987
 988   @Override
 989   public void setStatus(String text)
 990   {
 991     statusBar.setText(text);
 992   }
 993
 994   /*
 995    * Added so Castor Mapping file can obtain Jalview Version
 996    */
 997   public String getVersion()
 998   {
 999     return jalview.bin.Cache.getProperty("VERSION");
1000   }
1001
1002   public FeatureRenderer getFeatureRenderer()
1003   {
1004     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1005   }
1006
1007   @Override
1008   public void fetchSequence_actionPerformed(ActionEvent e)
1009   {
1010     new jalview.gui.SequenceFetcher(this);
1011   }
1012
1013   @Override
1014   public void addFromFile_actionPerformed(ActionEvent e)
1015   {
1016     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1017   }
1018
1019   @Override
1020   public void reload_actionPerformed(ActionEvent e)
1021   {
1022     if (fileName != null)
1023     {
1024       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1025       // originating file's format
1026       // TODO: work out how to recover feature settings for correct view(s) when
1027       // file is reloaded.
1028       if (FileFormat.Jalview.equals(currentFileFormat))
1029       {
1030         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1031         for (int i = 0; i < frames.length; i++)
1032         {
1033           if (frames[i] instanceof AlignFrame && frames[i] != this
1034                   && ((AlignFrame) frames[i]).fileName != null
1035                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1036           {
1037             try
1038             {
1039               frames[i].setSelected(true);
1040               Desktop.instance.closeAssociatedWindows();
1041             } catch (java.beans.PropertyVetoException ex)
1042             {
1043             }
1044           }
1045
1046         }
1047         Desktop.instance.closeAssociatedWindows();
1048
1049         FileLoader loader = new FileLoader();
1050         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1051                 : DataSourceType.FILE;
1052         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1053       }
1054       else
1055       {
1056         Rectangle bounds = this.getBounds();
1057
1058         FileLoader loader = new FileLoader();
1059         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1060                 : DataSourceType.FILE;
1061         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1062                 protocol, currentFileFormat);
1063
1064         newframe.setBounds(bounds);
1065         if (featureSettings != null && featureSettings.isShowing())
1066         {
1067           final Rectangle fspos = featureSettings.frame.getBounds();
1068           // TODO: need a 'show feature settings' function that takes bounds -
1069           // need to refactor Desktop.addFrame
1070           newframe.featureSettings_actionPerformed(null);
1071           final FeatureSettings nfs = newframe.featureSettings;
1072           SwingUtilities.invokeLater(new Runnable()
1073           {
1074             @Override
1075             public void run()
1076             {
1077               nfs.frame.setBounds(fspos);
1078             }
1079           });
1080           this.featureSettings.close();
1081           this.featureSettings = null;
1082         }
1083         this.closeMenuItem_actionPerformed(true);
1084       }
1085     }
1086   }
1087
1088   @Override
1089   public void addFromText_actionPerformed(ActionEvent e)
1090   {
1091     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1092             .getAlignPanel());
1093   }
1094
1095   @Override
1096   public void addFromURL_actionPerformed(ActionEvent e)
1097   {
1098     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1099   }
1100
1101   @Override
1102   public void save_actionPerformed(ActionEvent e)
1103   {
1104     if (fileName == null || (currentFileFormat == null)
1105             || fileName.startsWith("http"))
1106     {
1107       saveAs_actionPerformed(null);
1108     }
1109     else
1110     {
1111       saveAlignment(fileName, currentFileFormat);
1112     }
1113   }
1114
1115   /**
1116    * DOCUMENT ME!
1117    *
1118    * @param e
1119    *          DOCUMENT ME!
1120    */
1121   @Override
1122   public void saveAs_actionPerformed(ActionEvent e)
1123   {
1124     String format = currentFileFormat == null ? null : currentFileFormat
1125             .toString();
1126     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1127             Cache.getProperty("LAST_DIRECTORY"), format);
1128
1129     chooser.setFileView(new JalviewFileView());
1130     chooser.setDialogTitle(MessageManager
1131             .getString("label.save_alignment_to_file"));
1132     chooser.setToolTipText(MessageManager.getString("action.save"));
1133
1134     int value = chooser.showSaveDialog(this);
1135
1136     if (value == JalviewFileChooser.APPROVE_OPTION)
1137     {
1138       currentFileFormat = chooser.getSelectedFormat();
1139       while (currentFileFormat == null)
1140       {
1141         JvOptionPane
1142                 .showInternalMessageDialog(
1143                         Desktop.desktop,
1144                         MessageManager
1145                                 .getString("label.select_file_format_before_saving"),
1146                         MessageManager
1147                                 .getString("label.file_format_not_specified"),
1148                         JvOptionPane.WARNING_MESSAGE);
1149         currentFileFormat = chooser.getSelectedFormat();
1150         value = chooser.showSaveDialog(this);
1151         if (value != JalviewFileChooser.APPROVE_OPTION)
1152         {
1153           return;
1154         }
1155       }
1156
1157       fileName = chooser.getSelectedFile().getPath();
1158
1159       Cache.setProperty("DEFAULT_FILE_FORMAT",
1160               currentFileFormat.toString());
1161
1162       Cache.setProperty("LAST_DIRECTORY", fileName);
1163       saveAlignment(fileName, currentFileFormat);
1164     }
1165   }
1166
1167   public boolean saveAlignment(String file, FileFormatI format)
1168   {
1169     boolean success = true;
1170
1171     if (FileFormat.Jalview.equals(format))
1172     {
1173       String shortName = title;
1174
1175       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1176       {
1177         shortName = shortName.substring(shortName
1178                 .lastIndexOf(java.io.File.separatorChar) + 1);
1179       }
1180
1181       success = new Jalview2XML().saveAlignment(this, file, shortName);
1182
1183       statusBar.setText(MessageManager.formatMessage(
1184               "label.successfully_saved_to_file_in_format", new Object[] {
1185                   fileName, format }));
1186
1187     }
1188     else
1189     {
1190       // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1191       // {
1192       // warningMessage("Cannot save file " + fileName + " using format "
1193       // + format, "Alignment output format not supported");
1194       // if (!Jalview.isHeadlessMode())
1195       // {
1196       // saveAs_actionPerformed(null);
1197       // }
1198       // return false;
1199       // }
1200
1201       AlignmentExportData exportData = getAlignmentForExport(format,
1202               viewport, null);
1203       if (exportData.getSettings().isCancelled())
1204       {
1205         return false;
1206       }
1207       FormatAdapter f = new FormatAdapter(alignPanel,
1208               exportData.getSettings());
1209       String output = f.formatSequences(
1210               format,
1211               exportData.getAlignment(), // class cast exceptions will
1212               // occur in the distant future
1213               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1214               f.getCacheSuffixDefault(format),
1215               viewport.getColumnSelection());
1216
1217       if (output == null)
1218       {
1219         success = false;
1220       }
1221       else
1222       {
1223         try
1224         {
1225           java.io.PrintWriter out = new java.io.PrintWriter(
1226                   new java.io.FileWriter(file));
1227
1228           out.print(output);
1229           out.close();
1230           this.setTitle(file);
1231           statusBar.setText(MessageManager.formatMessage(
1232                   "label.successfully_saved_to_file_in_format",
1233                   new Object[] { fileName, format }));
1234         } catch (Exception ex)
1235         {
1236           success = false;
1237           ex.printStackTrace();
1238         }
1239       }
1240     }
1241
1242     if (!success)
1243     {
1244       JvOptionPane.showInternalMessageDialog(this, MessageManager
1245               .formatMessage("label.couldnt_save_file",
1246                       new Object[] { fileName }), MessageManager
1247               .getString("label.error_saving_file"),
1248               JvOptionPane.WARNING_MESSAGE);
1249     }
1250
1251     return success;
1252   }
1253
1254   private void warningMessage(String warning, String title)
1255   {
1256     if (new jalview.util.Platform().isHeadless())
1257     {
1258       System.err.println("Warning: " + title + "\nWarning: " + warning);
1259
1260     }
1261     else
1262     {
1263       JvOptionPane.showInternalMessageDialog(this, warning, title,
1264               JvOptionPane.WARNING_MESSAGE);
1265     }
1266     return;
1267   }
1268
1269   /**
1270    * DOCUMENT ME!
1271    *
1272    * @param e
1273    *          DOCUMENT ME!
1274    */
1275   @Override
1276   protected void outputText_actionPerformed(ActionEvent e)
1277   {
1278
1279     FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1280     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1281             viewport, null);
1282     if (exportData.getSettings().isCancelled())
1283     {
1284       return;
1285     }
1286     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1287     cap.setForInput(null);
1288     try
1289     {
1290       FileFormatI format = fileFormat;
1291       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1292               .formatSequences(format,
1293                       exportData.getAlignment(),
1294                       exportData.getOmitHidden(),
1295                       exportData.getStartEndPostions(),
1296                       viewport.getColumnSelection()));
1297       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1298               "label.alignment_output_command",
1299               new Object[] { e.getActionCommand() }), 600, 500);
1300     } catch (OutOfMemoryError oom)
1301     {
1302       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1303       cap.dispose();
1304     }
1305
1306   }
1307
1308   public static AlignmentExportData getAlignmentForExport(
1309           FileFormatI format, AlignViewportI viewport,
1310           AlignExportSettingI exportSettings)
1311   {
1312     AlignmentI alignmentToExport = null;
1313     AlignExportSettingI settings = exportSettings;
1314     String[] omitHidden = null;
1315
1316     HiddenSequences hiddenSeqs = viewport.getAlignment()
1317             .getHiddenSequences();
1318
1319     alignmentToExport = viewport.getAlignment();
1320
1321     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1322     if (settings == null)
1323     {
1324       settings = new AlignExportSettings(hasHiddenSeqs,
1325               viewport.hasHiddenColumns(), format);
1326     }
1327     // settings.isExportAnnotations();
1328
1329     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1330     {
1331       omitHidden = viewport.getViewAsString(false,
1332               settings.isExportHiddenSequences());
1333     }
1334
1335     int[] alignmentStartEnd = new int[2];
1336     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1337     {
1338       alignmentToExport = hiddenSeqs.getFullAlignment();
1339     }
1340     else
1341     {
1342       alignmentToExport = viewport.getAlignment();
1343     }
1344     alignmentStartEnd = alignmentToExport
1345             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1346                     .getHiddenColumns());
1347     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1348             omitHidden, alignmentStartEnd, settings);
1349     return ed;
1350   }
1351
1352   /**
1353    * DOCUMENT ME!
1354    *
1355    * @param e
1356    *          DOCUMENT ME!
1357    */
1358   @Override
1359   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1360   {
1361     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1362     htmlSVG.exportHTML(null);
1363   }
1364
1365   @Override
1366   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1367   {
1368     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1369     bjs.exportHTML(null);
1370   }
1371
1372   public void createImageMap(File file, String image)
1373   {
1374     alignPanel.makePNGImageMap(file, image);
1375   }
1376
1377   /**
1378    * DOCUMENT ME!
1379    *
1380    * @param e
1381    *          DOCUMENT ME!
1382    */
1383   @Override
1384   public void createPNG(File f)
1385   {
1386     alignPanel.makePNG(f);
1387   }
1388
1389   /**
1390    * DOCUMENT ME!
1391    *
1392    * @param e
1393    *          DOCUMENT ME!
1394    */
1395   @Override
1396   public void createEPS(File f)
1397   {
1398     alignPanel.makeEPS(f);
1399   }
1400
1401   @Override
1402   public void createSVG(File f)
1403   {
1404     alignPanel.makeSVG(f);
1405   }
1406
1407   @Override
1408   public void pageSetup_actionPerformed(ActionEvent e)
1409   {
1410     PrinterJob printJob = PrinterJob.getPrinterJob();
1411     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1412   }
1413
1414   /**
1415    * DOCUMENT ME!
1416    *
1417    * @param e
1418    *          DOCUMENT ME!
1419    */
1420   @Override
1421   public void printMenuItem_actionPerformed(ActionEvent e)
1422   {
1423     // Putting in a thread avoids Swing painting problems
1424     PrintThread thread = new PrintThread(alignPanel);
1425     thread.start();
1426   }
1427
1428   @Override
1429   public void exportFeatures_actionPerformed(ActionEvent e)
1430   {
1431     new AnnotationExporter().exportFeatures(alignPanel);
1432   }
1433
1434   @Override
1435   public void exportAnnotations_actionPerformed(ActionEvent e)
1436   {
1437     new AnnotationExporter().exportAnnotations(alignPanel);
1438   }
1439
1440   @Override
1441   public void associatedData_actionPerformed(ActionEvent e)
1442   {
1443     // Pick the tree file
1444     JalviewFileChooser chooser = new JalviewFileChooser(
1445             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1446     chooser.setFileView(new JalviewFileView());
1447     chooser.setDialogTitle(MessageManager
1448             .getString("label.load_jalview_annotations"));
1449     chooser.setToolTipText(MessageManager
1450             .getString("label.load_jalview_annotations"));
1451
1452     int value = chooser.showOpenDialog(null);
1453
1454     if (value == JalviewFileChooser.APPROVE_OPTION)
1455     {
1456       String choice = chooser.getSelectedFile().getPath();
1457       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1458       loadJalviewDataFile(choice, null, null, null);
1459     }
1460
1461   }
1462
1463   /**
1464    * Close the current view or all views in the alignment frame. If the frame
1465    * only contains one view then the alignment will be removed from memory.
1466    *
1467    * @param closeAllTabs
1468    */
1469   @Override
1470   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1471   {
1472     if (alignPanels != null && alignPanels.size() < 2)
1473     {
1474       closeAllTabs = true;
1475     }
1476
1477     try
1478     {
1479       if (alignPanels != null)
1480       {
1481         if (closeAllTabs)
1482         {
1483           if (this.isClosed())
1484           {
1485             // really close all the windows - otherwise wait till
1486             // setClosed(true) is called
1487             for (int i = 0; i < alignPanels.size(); i++)
1488             {
1489               AlignmentPanel ap = alignPanels.get(i);
1490               ap.closePanel();
1491             }
1492           }
1493         }
1494         else
1495         {
1496           closeView(alignPanel);
1497         }
1498       }
1499
1500       if (closeAllTabs)
1501       {
1502         /*
1503          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1504          * be called recursively, with the frame now in 'closed' state
1505          */
1506         this.setClosed(true);
1507       }
1508     } catch (Exception ex)
1509     {
1510       ex.printStackTrace();
1511     }
1512   }
1513
1514   /**
1515    * Close the specified panel and close up tabs appropriately.
1516    *
1517    * @param panelToClose
1518    */
1519   public void closeView(AlignmentPanel panelToClose)
1520   {
1521     int index = tabbedPane.getSelectedIndex();
1522     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1523     alignPanels.remove(panelToClose);
1524     panelToClose.closePanel();
1525     panelToClose = null;
1526
1527     tabbedPane.removeTabAt(closedindex);
1528     tabbedPane.validate();
1529
1530     if (index > closedindex || index == tabbedPane.getTabCount())
1531     {
1532       // modify currently selected tab index if necessary.
1533       index--;
1534     }
1535
1536     this.tabSelectionChanged(index);
1537   }
1538
1539   /**
1540    * DOCUMENT ME!
1541    */
1542   void updateEditMenuBar()
1543   {
1544
1545     if (viewport.getHistoryList().size() > 0)
1546     {
1547       undoMenuItem.setEnabled(true);
1548       CommandI command = viewport.getHistoryList().peek();
1549       undoMenuItem.setText(MessageManager.formatMessage(
1550               "label.undo_command",
1551               new Object[] { command.getDescription() }));
1552     }
1553     else
1554     {
1555       undoMenuItem.setEnabled(false);
1556       undoMenuItem.setText(MessageManager.getString("action.undo"));
1557     }
1558
1559     if (viewport.getRedoList().size() > 0)
1560     {
1561       redoMenuItem.setEnabled(true);
1562
1563       CommandI command = viewport.getRedoList().peek();
1564       redoMenuItem.setText(MessageManager.formatMessage(
1565               "label.redo_command",
1566               new Object[] { command.getDescription() }));
1567     }
1568     else
1569     {
1570       redoMenuItem.setEnabled(false);
1571       redoMenuItem.setText(MessageManager.getString("action.redo"));
1572     }
1573   }
1574
1575   @Override
1576   public void addHistoryItem(CommandI command)
1577   {
1578     if (command.getSize() > 0)
1579     {
1580       viewport.addToHistoryList(command);
1581       viewport.clearRedoList();
1582       updateEditMenuBar();
1583       viewport.updateHiddenColumns();
1584       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1585       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1586       // viewport.getColumnSelection()
1587       // .getHiddenColumns().size() > 0);
1588     }
1589   }
1590
1591   /**
1592    *
1593    * @return alignment objects for all views
1594    */
1595   AlignmentI[] getViewAlignments()
1596   {
1597     if (alignPanels != null)
1598     {
1599       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1600       int i = 0;
1601       for (AlignmentPanel ap : alignPanels)
1602       {
1603         als[i++] = ap.av.getAlignment();
1604       }
1605       return als;
1606     }
1607     if (viewport != null)
1608     {
1609       return new AlignmentI[] { viewport.getAlignment() };
1610     }
1611     return null;
1612   }
1613
1614   /**
1615    * DOCUMENT ME!
1616    *
1617    * @param e
1618    *          DOCUMENT ME!
1619    */
1620   @Override
1621   protected void undoMenuItem_actionPerformed(ActionEvent e)
1622   {
1623     if (viewport.getHistoryList().isEmpty())
1624     {
1625       return;
1626     }
1627     CommandI command = viewport.getHistoryList().pop();
1628     viewport.addToRedoList(command);
1629     command.undoCommand(getViewAlignments());
1630
1631     AlignmentViewport originalSource = getOriginatingSource(command);
1632     updateEditMenuBar();
1633
1634     if (originalSource != null)
1635     {
1636       if (originalSource != viewport)
1637       {
1638         Cache.log
1639                 .warn("Implementation worry: mismatch of viewport origin for undo");
1640       }
1641       originalSource.updateHiddenColumns();
1642       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1643       // null
1644       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1645       // viewport.getColumnSelection()
1646       // .getHiddenColumns().size() > 0);
1647       originalSource.firePropertyChange("alignment", null, originalSource
1648               .getAlignment().getSequences());
1649     }
1650   }
1651
1652   /**
1653    * DOCUMENT ME!
1654    *
1655    * @param e
1656    *          DOCUMENT ME!
1657    */
1658   @Override
1659   protected void redoMenuItem_actionPerformed(ActionEvent e)
1660   {
1661     if (viewport.getRedoList().size() < 1)
1662     {
1663       return;
1664     }
1665
1666     CommandI command = viewport.getRedoList().pop();
1667     viewport.addToHistoryList(command);
1668     command.doCommand(getViewAlignments());
1669
1670     AlignmentViewport originalSource = getOriginatingSource(command);
1671     updateEditMenuBar();
1672
1673     if (originalSource != null)
1674     {
1675
1676       if (originalSource != viewport)
1677       {
1678         Cache.log
1679                 .warn("Implementation worry: mismatch of viewport origin for redo");
1680       }
1681       originalSource.updateHiddenColumns();
1682       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1683       // null
1684       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1685       // viewport.getColumnSelection()
1686       // .getHiddenColumns().size() > 0);
1687       originalSource.firePropertyChange("alignment", null, originalSource
1688               .getAlignment().getSequences());
1689     }
1690   }
1691
1692   AlignmentViewport getOriginatingSource(CommandI command)
1693   {
1694     AlignmentViewport originalSource = null;
1695     // For sequence removal and addition, we need to fire
1696     // the property change event FROM the viewport where the
1697     // original alignment was altered
1698     AlignmentI al = null;
1699     if (command instanceof EditCommand)
1700     {
1701       EditCommand editCommand = (EditCommand) command;
1702       al = editCommand.getAlignment();
1703       List<Component> comps = PaintRefresher.components.get(viewport
1704               .getSequenceSetId());
1705
1706       for (Component comp : comps)
1707       {
1708         if (comp instanceof AlignmentPanel)
1709         {
1710           if (al == ((AlignmentPanel) comp).av.getAlignment())
1711           {
1712             originalSource = ((AlignmentPanel) comp).av;
1713             break;
1714           }
1715         }
1716       }
1717     }
1718
1719     if (originalSource == null)
1720     {
1721       // The original view is closed, we must validate
1722       // the current view against the closed view first
1723       if (al != null)
1724       {
1725         PaintRefresher.validateSequences(al, viewport.getAlignment());
1726       }
1727
1728       originalSource = viewport;
1729     }
1730
1731     return originalSource;
1732   }
1733
1734   /**
1735    * DOCUMENT ME!
1736    *
1737    * @param up
1738    *          DOCUMENT ME!
1739    */
1740   public void moveSelectedSequences(boolean up)
1741   {
1742     SequenceGroup sg = viewport.getSelectionGroup();
1743
1744     if (sg == null)
1745     {
1746       return;
1747     }
1748     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1749             viewport.getHiddenRepSequences(), up);
1750     alignPanel.paintAlignment(true);
1751   }
1752
1753   synchronized void slideSequences(boolean right, int size)
1754   {
1755     List<SequenceI> sg = new ArrayList<SequenceI>();
1756     if (viewport.cursorMode)
1757     {
1758       sg.add(viewport.getAlignment().getSequenceAt(
1759               alignPanel.getSeqPanel().seqCanvas.cursorY));
1760     }
1761     else if (viewport.getSelectionGroup() != null
1762             && viewport.getSelectionGroup().getSize() != viewport
1763                     .getAlignment().getHeight())
1764     {
1765       sg = viewport.getSelectionGroup().getSequences(
1766               viewport.getHiddenRepSequences());
1767     }
1768
1769     if (sg.size() < 1)
1770     {
1771       return;
1772     }
1773
1774     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1775
1776     for (SequenceI seq : viewport.getAlignment().getSequences())
1777     {
1778       if (!sg.contains(seq))
1779       {
1780         invertGroup.add(seq);
1781       }
1782     }
1783
1784     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1785
1786     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1787     for (int i = 0; i < invertGroup.size(); i++)
1788     {
1789       seqs2[i] = invertGroup.get(i);
1790     }
1791
1792     SlideSequencesCommand ssc;
1793     if (right)
1794     {
1795       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1796               size, viewport.getGapCharacter());
1797     }
1798     else
1799     {
1800       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1801               size, viewport.getGapCharacter());
1802     }
1803
1804     int groupAdjustment = 0;
1805     if (ssc.getGapsInsertedBegin() && right)
1806     {
1807       if (viewport.cursorMode)
1808       {
1809         alignPanel.getSeqPanel().moveCursor(size, 0);
1810       }
1811       else
1812       {
1813         groupAdjustment = size;
1814       }
1815     }
1816     else if (!ssc.getGapsInsertedBegin() && !right)
1817     {
1818       if (viewport.cursorMode)
1819       {
1820         alignPanel.getSeqPanel().moveCursor(-size, 0);
1821       }
1822       else
1823       {
1824         groupAdjustment = -size;
1825       }
1826     }
1827
1828     if (groupAdjustment != 0)
1829     {
1830       viewport.getSelectionGroup().setStartRes(
1831               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1832       viewport.getSelectionGroup().setEndRes(
1833               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1834     }
1835
1836     /*
1837      * just extend the last slide command if compatible; but not if in
1838      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1839      */
1840     boolean appendHistoryItem = false;
1841     Deque<CommandI> historyList = viewport.getHistoryList();
1842     boolean inSplitFrame = getSplitViewContainer() != null;
1843     if (!inSplitFrame && historyList != null && historyList.size() > 0
1844             && historyList.peek() instanceof SlideSequencesCommand)
1845     {
1846       appendHistoryItem = ssc
1847               .appendSlideCommand((SlideSequencesCommand) historyList
1848                       .peek());
1849     }
1850
1851     if (!appendHistoryItem)
1852     {
1853       addHistoryItem(ssc);
1854     }
1855
1856     repaint();
1857   }
1858
1859   /**
1860    * DOCUMENT ME!
1861    *
1862    * @param e
1863    *          DOCUMENT ME!
1864    */
1865   @Override
1866   protected void copy_actionPerformed(ActionEvent e)
1867   {
1868     System.gc();
1869     if (viewport.getSelectionGroup() == null)
1870     {
1871       return;
1872     }
1873     // TODO: preserve the ordering of displayed alignment annotation in any
1874     // internal paste (particularly sequence associated annotation)
1875     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1876     String[] omitHidden = null;
1877
1878     if (viewport.hasHiddenColumns())
1879     {
1880       omitHidden = viewport.getViewAsString(true);
1881     }
1882
1883     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1884             seqs,
1885             omitHidden, null);
1886
1887     StringSelection ss = new StringSelection(output);
1888
1889     try
1890     {
1891       jalview.gui.Desktop.internalCopy = true;
1892       // Its really worth setting the clipboard contents
1893       // to empty before setting the large StringSelection!!
1894       Toolkit.getDefaultToolkit().getSystemClipboard()
1895               .setContents(new StringSelection(""), null);
1896
1897       Toolkit.getDefaultToolkit().getSystemClipboard()
1898               .setContents(ss, Desktop.instance);
1899     } catch (OutOfMemoryError er)
1900     {
1901       new OOMWarning("copying region", er);
1902       return;
1903     }
1904
1905     ArrayList<int[]> hiddenColumns = null;
1906     if (viewport.hasHiddenColumns())
1907     {
1908       hiddenColumns = new ArrayList<int[]>();
1909       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1910               .getSelectionGroup().getEndRes();
1911       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1912       {
1913         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1914         {
1915           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1916               region[1] - hiddenOffset });
1917         }
1918       }
1919     }
1920
1921     Desktop.jalviewClipboard = new Object[] { seqs,
1922         viewport.getAlignment().getDataset(), hiddenColumns };
1923     statusBar.setText(MessageManager.formatMessage(
1924             "label.copied_sequences_to_clipboard", new Object[] { Integer
1925                     .valueOf(seqs.length).toString() }));
1926   }
1927
1928   /**
1929    * DOCUMENT ME!
1930    *
1931    * @param e
1932    *          DOCUMENT ME!
1933    */
1934   @Override
1935   protected void pasteNew_actionPerformed(ActionEvent e)
1936   {
1937     paste(true);
1938   }
1939
1940   /**
1941    * DOCUMENT ME!
1942    *
1943    * @param e
1944    *          DOCUMENT ME!
1945    */
1946   @Override
1947   protected void pasteThis_actionPerformed(ActionEvent e)
1948   {
1949     paste(false);
1950   }
1951
1952   /**
1953    * Paste contents of Jalview clipboard
1954    *
1955    * @param newAlignment
1956    *          true to paste to a new alignment, otherwise add to this.
1957    */
1958   void paste(boolean newAlignment)
1959   {
1960     boolean externalPaste = true;
1961     try
1962     {
1963       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1964       Transferable contents = c.getContents(this);
1965
1966       if (contents == null)
1967       {
1968         return;
1969       }
1970
1971       String str;
1972       FileFormatI format;
1973       try
1974       {
1975         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1976         if (str.length() < 1)
1977         {
1978           return;
1979         }
1980
1981         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1982
1983       } catch (OutOfMemoryError er)
1984       {
1985         new OOMWarning("Out of memory pasting sequences!!", er);
1986         return;
1987       }
1988
1989       SequenceI[] sequences;
1990       boolean annotationAdded = false;
1991       AlignmentI alignment = null;
1992
1993       if (Desktop.jalviewClipboard != null)
1994       {
1995         // The clipboard was filled from within Jalview, we must use the
1996         // sequences
1997         // And dataset from the copied alignment
1998         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1999         // be doubly sure that we create *new* sequence objects.
2000         sequences = new SequenceI[newseq.length];
2001         for (int i = 0; i < newseq.length; i++)
2002         {
2003           sequences[i] = new Sequence(newseq[i]);
2004         }
2005         alignment = new Alignment(sequences);
2006         externalPaste = false;
2007       }
2008       else
2009       {
2010         // parse the clipboard as an alignment.
2011         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2012                 format);
2013         sequences = alignment.getSequencesArray();
2014       }
2015
2016       int alwidth = 0;
2017       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2018       int fgroup = -1;
2019
2020       if (newAlignment)
2021       {
2022
2023         if (Desktop.jalviewClipboard != null)
2024         {
2025           // dataset is inherited
2026           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2027         }
2028         else
2029         {
2030           // new dataset is constructed
2031           alignment.setDataset(null);
2032         }
2033         alwidth = alignment.getWidth() + 1;
2034       }
2035       else
2036       {
2037         AlignmentI pastedal = alignment; // preserve pasted alignment object
2038         // Add pasted sequences and dataset into existing alignment.
2039         alignment = viewport.getAlignment();
2040         alwidth = alignment.getWidth() + 1;
2041         // decide if we need to import sequences from an existing dataset
2042         boolean importDs = Desktop.jalviewClipboard != null
2043                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2044         // importDs==true instructs us to copy over new dataset sequences from
2045         // an existing alignment
2046         Vector newDs = (importDs) ? new Vector() : null; // used to create
2047         // minimum dataset set
2048
2049         for (int i = 0; i < sequences.length; i++)
2050         {
2051           if (importDs)
2052           {
2053             newDs.addElement(null);
2054           }
2055           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2056           // paste
2057           if (importDs && ds != null)
2058           {
2059             if (!newDs.contains(ds))
2060             {
2061               newDs.setElementAt(ds, i);
2062               ds = new Sequence(ds);
2063               // update with new dataset sequence
2064               sequences[i].setDatasetSequence(ds);
2065             }
2066             else
2067             {
2068               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2069             }
2070           }
2071           else
2072           {
2073             // copy and derive new dataset sequence
2074             sequences[i] = sequences[i].deriveSequence();
2075             alignment.getDataset().addSequence(
2076                     sequences[i].getDatasetSequence());
2077             // TODO: avoid creation of duplicate dataset sequences with a
2078             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2079           }
2080           alignment.addSequence(sequences[i]); // merges dataset
2081         }
2082         if (newDs != null)
2083         {
2084           newDs.clear(); // tidy up
2085         }
2086         if (alignment.getAlignmentAnnotation() != null)
2087         {
2088           for (AlignmentAnnotation alan : alignment
2089                   .getAlignmentAnnotation())
2090           {
2091             if (alan.graphGroup > fgroup)
2092             {
2093               fgroup = alan.graphGroup;
2094             }
2095           }
2096         }
2097         if (pastedal.getAlignmentAnnotation() != null)
2098         {
2099           // Add any annotation attached to alignment.
2100           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2101           for (int i = 0; i < alann.length; i++)
2102           {
2103             annotationAdded = true;
2104             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2105             {
2106               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2107               if (newann.graphGroup > -1)
2108               {
2109                 if (newGraphGroups.size() <= newann.graphGroup
2110                         || newGraphGroups.get(newann.graphGroup) == null)
2111                 {
2112                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2113                   {
2114                     newGraphGroups.add(q, null);
2115                   }
2116                   newGraphGroups.set(newann.graphGroup, new Integer(
2117                           ++fgroup));
2118                 }
2119                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2120                         .intValue();
2121               }
2122
2123               newann.padAnnotation(alwidth);
2124               alignment.addAnnotation(newann);
2125             }
2126           }
2127         }
2128       }
2129       if (!newAlignment)
2130       {
2131         // /////
2132         // ADD HISTORY ITEM
2133         //
2134         addHistoryItem(new EditCommand(
2135                 MessageManager.getString("label.add_sequences"),
2136                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2137       }
2138       // Add any annotations attached to sequences
2139       for (int i = 0; i < sequences.length; i++)
2140       {
2141         if (sequences[i].getAnnotation() != null)
2142         {
2143           AlignmentAnnotation newann;
2144           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2145           {
2146             annotationAdded = true;
2147             newann = sequences[i].getAnnotation()[a];
2148             newann.adjustForAlignment();
2149             newann.padAnnotation(alwidth);
2150             if (newann.graphGroup > -1)
2151             {
2152               if (newann.graphGroup > -1)
2153               {
2154                 if (newGraphGroups.size() <= newann.graphGroup
2155                         || newGraphGroups.get(newann.graphGroup) == null)
2156                 {
2157                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2158                   {
2159                     newGraphGroups.add(q, null);
2160                   }
2161                   newGraphGroups.set(newann.graphGroup, new Integer(
2162                           ++fgroup));
2163                 }
2164                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2165                         .intValue();
2166               }
2167             }
2168             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2169             // was
2170             // duplicated
2171             // earlier
2172             alignment
2173                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2174           }
2175         }
2176       }
2177       if (!newAlignment)
2178       {
2179
2180         // propagate alignment changed.
2181         viewport.setEndSeq(alignment.getHeight());
2182         if (annotationAdded)
2183         {
2184           // Duplicate sequence annotation in all views.
2185           AlignmentI[] alview = this.getViewAlignments();
2186           for (int i = 0; i < sequences.length; i++)
2187           {
2188             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2189             if (sann == null)
2190             {
2191               continue;
2192             }
2193             for (int avnum = 0; avnum < alview.length; avnum++)
2194             {
2195               if (alview[avnum] != alignment)
2196               {
2197                 // duplicate in a view other than the one with input focus
2198                 int avwidth = alview[avnum].getWidth() + 1;
2199                 // this relies on sann being preserved after we
2200                 // modify the sequence's annotation array for each duplication
2201                 for (int a = 0; a < sann.length; a++)
2202                 {
2203                   AlignmentAnnotation newann = new AlignmentAnnotation(
2204                           sann[a]);
2205                   sequences[i].addAlignmentAnnotation(newann);
2206                   newann.padAnnotation(avwidth);
2207                   alview[avnum].addAnnotation(newann); // annotation was
2208                   // duplicated earlier
2209                   // TODO JAL-1145 graphGroups are not updated for sequence
2210                   // annotation added to several views. This may cause
2211                   // strangeness
2212                   alview[avnum].setAnnotationIndex(newann, a);
2213                 }
2214               }
2215             }
2216           }
2217           buildSortByAnnotationScoresMenu();
2218         }
2219         viewport.firePropertyChange("alignment", null,
2220                 alignment.getSequences());
2221         if (alignPanels != null)
2222         {
2223           for (AlignmentPanel ap : alignPanels)
2224           {
2225             ap.validateAnnotationDimensions(false);
2226           }
2227         }
2228         else
2229         {
2230           alignPanel.validateAnnotationDimensions(false);
2231         }
2232
2233       }
2234       else
2235       {
2236         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2237                 DEFAULT_HEIGHT);
2238         String newtitle = new String("Copied sequences");
2239
2240         if (Desktop.jalviewClipboard != null
2241                 && Desktop.jalviewClipboard[2] != null)
2242         {
2243           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2244           for (int[] region : hc)
2245           {
2246             af.viewport.hideColumns(region[0], region[1]);
2247           }
2248         }
2249
2250         // >>>This is a fix for the moment, until a better solution is
2251         // found!!<<<
2252         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2253                 .transferSettings(
2254                         alignPanel.getSeqPanel().seqCanvas
2255                                 .getFeatureRenderer());
2256
2257         // TODO: maintain provenance of an alignment, rather than just make the
2258         // title a concatenation of operations.
2259         if (!externalPaste)
2260         {
2261           if (title.startsWith("Copied sequences"))
2262           {
2263             newtitle = title;
2264           }
2265           else
2266           {
2267             newtitle = newtitle.concat("- from " + title);
2268           }
2269         }
2270         else
2271         {
2272           newtitle = new String("Pasted sequences");
2273         }
2274
2275         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2276                 DEFAULT_HEIGHT);
2277
2278       }
2279
2280     } catch (Exception ex)
2281     {
2282       ex.printStackTrace();
2283       System.out.println("Exception whilst pasting: " + ex);
2284       // could be anything being pasted in here
2285     }
2286
2287   }
2288
2289   @Override
2290   protected void expand_newalign(ActionEvent e)
2291   {
2292     try
2293     {
2294       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2295               .getAlignment(), -1);
2296       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2297               DEFAULT_HEIGHT);
2298       String newtitle = new String("Flanking alignment");
2299
2300       if (Desktop.jalviewClipboard != null
2301               && Desktop.jalviewClipboard[2] != null)
2302       {
2303         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2304         for (int region[] : hc)
2305         {
2306           af.viewport.hideColumns(region[0], region[1]);
2307         }
2308       }
2309
2310       // >>>This is a fix for the moment, until a better solution is
2311       // found!!<<<
2312       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2313               .transferSettings(
2314                       alignPanel.getSeqPanel().seqCanvas
2315                               .getFeatureRenderer());
2316
2317       // TODO: maintain provenance of an alignment, rather than just make the
2318       // title a concatenation of operations.
2319       {
2320         if (title.startsWith("Copied sequences"))
2321         {
2322           newtitle = title;
2323         }
2324         else
2325         {
2326           newtitle = newtitle.concat("- from " + title);
2327         }
2328       }
2329
2330       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2331
2332     } catch (Exception ex)
2333     {
2334       ex.printStackTrace();
2335       System.out.println("Exception whilst pasting: " + ex);
2336       // could be anything being pasted in here
2337     } catch (OutOfMemoryError oom)
2338     {
2339       new OOMWarning("Viewing flanking region of alignment", oom);
2340     }
2341   }
2342
2343   /**
2344    * DOCUMENT ME!
2345    *
2346    * @param e
2347    *          DOCUMENT ME!
2348    */
2349   @Override
2350   protected void cut_actionPerformed(ActionEvent e)
2351   {
2352     copy_actionPerformed(null);
2353     delete_actionPerformed(null);
2354   }
2355
2356   /**
2357    * DOCUMENT ME!
2358    *
2359    * @param e
2360    *          DOCUMENT ME!
2361    */
2362   @Override
2363   protected void delete_actionPerformed(ActionEvent evt)
2364   {
2365
2366     SequenceGroup sg = viewport.getSelectionGroup();
2367     if (sg == null)
2368     {
2369       return;
2370     }
2371
2372     /*
2373      * If the cut affects all sequences, warn, remove highlighted columns
2374      */
2375     if (sg.getSize() == viewport.getAlignment().getHeight())
2376     {
2377       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2378               .getAlignment().getWidth()) ? true : false;
2379       if (isEntireAlignWidth)
2380       {
2381         int confirm = JvOptionPane.showConfirmDialog(this,
2382                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2383                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2384                 JvOptionPane.OK_CANCEL_OPTION);
2385
2386         if (confirm == JvOptionPane.CANCEL_OPTION
2387                 || confirm == JvOptionPane.CLOSED_OPTION)
2388         {
2389           return;
2390         }
2391       }
2392       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2393               sg.getEndRes() + 1);
2394     }
2395     SequenceI[] cut = sg.getSequences()
2396             .toArray(new SequenceI[sg.getSize()]);
2397
2398     addHistoryItem(new EditCommand(
2399             MessageManager.getString("label.cut_sequences"), Action.CUT,
2400             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2401             viewport.getAlignment()));
2402
2403     viewport.setSelectionGroup(null);
2404     viewport.sendSelection();
2405     viewport.getAlignment().deleteGroup(sg);
2406
2407     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2408             .getSequences());
2409     if (viewport.getAlignment().getHeight() < 1)
2410     {
2411       try
2412       {
2413         this.setClosed(true);
2414       } catch (Exception ex)
2415       {
2416       }
2417     }
2418   }
2419
2420   /**
2421    * DOCUMENT ME!
2422    *
2423    * @param e
2424    *          DOCUMENT ME!
2425    */
2426   @Override
2427   protected void deleteGroups_actionPerformed(ActionEvent e)
2428   {
2429     if (avc.deleteGroups())
2430     {
2431       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2432       alignPanel.updateAnnotation();
2433       alignPanel.paintAlignment(true);
2434     }
2435   }
2436
2437   /**
2438    * DOCUMENT ME!
2439    *
2440    * @param e
2441    *          DOCUMENT ME!
2442    */
2443   @Override
2444   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2445   {
2446     SequenceGroup sg = new SequenceGroup();
2447
2448     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2449     {
2450       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2451     }
2452
2453     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2454     viewport.setSelectionGroup(sg);
2455     viewport.sendSelection();
2456     // JAL-2034 - should delegate to
2457     // alignPanel to decide if overview needs
2458     // updating.
2459     alignPanel.paintAlignment(false);
2460     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2461   }
2462
2463   /**
2464    * DOCUMENT ME!
2465    *
2466    * @param e
2467    *          DOCUMENT ME!
2468    */
2469   @Override
2470   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2471   {
2472     if (viewport.cursorMode)
2473     {
2474       alignPanel.getSeqPanel().keyboardNo1 = null;
2475       alignPanel.getSeqPanel().keyboardNo2 = null;
2476     }
2477     viewport.setSelectionGroup(null);
2478     viewport.getColumnSelection().clear();
2479     viewport.setSelectionGroup(null);
2480     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2481     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2482     // JAL-2034 - should delegate to
2483     // alignPanel to decide if overview needs
2484     // updating.
2485     alignPanel.paintAlignment(false);
2486     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2487     viewport.sendSelection();
2488   }
2489
2490   /**
2491    * DOCUMENT ME!
2492    *
2493    * @param e
2494    *          DOCUMENT ME!
2495    */
2496   @Override
2497   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2498   {
2499     SequenceGroup sg = viewport.getSelectionGroup();
2500
2501     if (sg == null)
2502     {
2503       selectAllSequenceMenuItem_actionPerformed(null);
2504
2505       return;
2506     }
2507
2508     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2509     {
2510       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2511     }
2512     // JAL-2034 - should delegate to
2513     // alignPanel to decide if overview needs
2514     // updating.
2515
2516     alignPanel.paintAlignment(true);
2517     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2518     viewport.sendSelection();
2519   }
2520
2521   @Override
2522   public void invertColSel_actionPerformed(ActionEvent e)
2523   {
2524     viewport.invertColumnSelection();
2525     alignPanel.paintAlignment(true);
2526     viewport.sendSelection();
2527   }
2528
2529   /**
2530    * DOCUMENT ME!
2531    *
2532    * @param e
2533    *          DOCUMENT ME!
2534    */
2535   @Override
2536   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2537   {
2538     trimAlignment(true);
2539   }
2540
2541   /**
2542    * DOCUMENT ME!
2543    *
2544    * @param e
2545    *          DOCUMENT ME!
2546    */
2547   @Override
2548   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2549   {
2550     trimAlignment(false);
2551   }
2552
2553   void trimAlignment(boolean trimLeft)
2554   {
2555     ColumnSelection colSel = viewport.getColumnSelection();
2556     int column;
2557
2558     if (!colSel.isEmpty())
2559     {
2560       if (trimLeft)
2561       {
2562         column = colSel.getMin();
2563       }
2564       else
2565       {
2566         column = colSel.getMax();
2567       }
2568
2569       SequenceI[] seqs;
2570       if (viewport.getSelectionGroup() != null)
2571       {
2572         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2573                 viewport.getHiddenRepSequences());
2574       }
2575       else
2576       {
2577         seqs = viewport.getAlignment().getSequencesArray();
2578       }
2579
2580       TrimRegionCommand trimRegion;
2581       if (trimLeft)
2582       {
2583         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2584                 column, viewport.getAlignment());
2585         viewport.setStartRes(0);
2586       }
2587       else
2588       {
2589         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2590                 column, viewport.getAlignment());
2591       }
2592
2593       statusBar.setText(MessageManager.formatMessage(
2594               "label.removed_columns",
2595               new String[] { Integer.valueOf(trimRegion.getSize())
2596                       .toString() }));
2597
2598       addHistoryItem(trimRegion);
2599
2600       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2601       {
2602         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2603                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2604         {
2605           viewport.getAlignment().deleteGroup(sg);
2606         }
2607       }
2608
2609       viewport.firePropertyChange("alignment", null, viewport
2610               .getAlignment().getSequences());
2611     }
2612   }
2613
2614   /**
2615    * DOCUMENT ME!
2616    *
2617    * @param e
2618    *          DOCUMENT ME!
2619    */
2620   @Override
2621   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2622   {
2623     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2624
2625     SequenceI[] seqs;
2626     if (viewport.getSelectionGroup() != null)
2627     {
2628       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2629               viewport.getHiddenRepSequences());
2630       start = viewport.getSelectionGroup().getStartRes();
2631       end = viewport.getSelectionGroup().getEndRes();
2632     }
2633     else
2634     {
2635       seqs = viewport.getAlignment().getSequencesArray();
2636     }
2637
2638     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2639             "Remove Gapped Columns", seqs, start, end,
2640             viewport.getAlignment());
2641
2642     addHistoryItem(removeGapCols);
2643
2644     statusBar.setText(MessageManager.formatMessage(
2645             "label.removed_empty_columns",
2646             new Object[] { Integer.valueOf(removeGapCols.getSize())
2647                     .toString() }));
2648
2649     // This is to maintain viewport position on first residue
2650     // of first sequence
2651     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2652     int startRes = seq.findPosition(viewport.startRes);
2653     // ShiftList shifts;
2654     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2655     // edit.alColumnChanges=shifts.getInverse();
2656     // if (viewport.hasHiddenColumns)
2657     // viewport.getColumnSelection().compensateForEdits(shifts);
2658     viewport.setStartRes(seq.findIndex(startRes) - 1);
2659     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2660             .getSequences());
2661
2662   }
2663
2664   /**
2665    * DOCUMENT ME!
2666    *
2667    * @param e
2668    *          DOCUMENT ME!
2669    */
2670   @Override
2671   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2672   {
2673     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2674
2675     SequenceI[] seqs;
2676     if (viewport.getSelectionGroup() != null)
2677     {
2678       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2679               viewport.getHiddenRepSequences());
2680       start = viewport.getSelectionGroup().getStartRes();
2681       end = viewport.getSelectionGroup().getEndRes();
2682     }
2683     else
2684     {
2685       seqs = viewport.getAlignment().getSequencesArray();
2686     }
2687
2688     // This is to maintain viewport position on first residue
2689     // of first sequence
2690     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2691     int startRes = seq.findPosition(viewport.startRes);
2692
2693     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2694             viewport.getAlignment()));
2695
2696     viewport.setStartRes(seq.findIndex(startRes) - 1);
2697
2698     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2699             .getSequences());
2700
2701   }
2702
2703   /**
2704    * DOCUMENT ME!
2705    *
2706    * @param e
2707    *          DOCUMENT ME!
2708    */
2709   @Override
2710   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2711   {
2712     viewport.setPadGaps(padGapsMenuitem.isSelected());
2713     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2714             .getSequences());
2715   }
2716
2717   /**
2718    * DOCUMENT ME!
2719    *
2720    * @param e
2721    *          DOCUMENT ME!
2722    */
2723   @Override
2724   public void findMenuItem_actionPerformed(ActionEvent e)
2725   {
2726     new Finder();
2727   }
2728
2729   /**
2730    * Create a new view of the current alignment.
2731    */
2732   @Override
2733   public void newView_actionPerformed(ActionEvent e)
2734   {
2735     newView(null, true);
2736   }
2737
2738   /**
2739    * Creates and shows a new view of the current alignment.
2740    *
2741    * @param viewTitle
2742    *          title of newly created view; if null, one will be generated
2743    * @param copyAnnotation
2744    *          if true then duplicate all annnotation, groups and settings
2745    * @return new alignment panel, already displayed.
2746    */
2747   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2748   {
2749     /*
2750      * Create a new AlignmentPanel (with its own, new Viewport)
2751      */
2752     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2753             true);
2754     if (!copyAnnotation)
2755     {
2756       /*
2757        * remove all groups and annotation except for the automatic stuff
2758        */
2759       newap.av.getAlignment().deleteAllGroups();
2760       newap.av.getAlignment().deleteAllAnnotations(false);
2761     }
2762
2763     newap.av.setGatherViewsHere(false);
2764
2765     if (viewport.viewName == null)
2766     {
2767       viewport.viewName = MessageManager
2768               .getString("label.view_name_original");
2769     }
2770
2771     /*
2772      * Views share the same edits undo and redo stacks
2773      */
2774     newap.av.setHistoryList(viewport.getHistoryList());
2775     newap.av.setRedoList(viewport.getRedoList());
2776
2777     /*
2778      * Views share the same mappings; need to deregister any new mappings
2779      * created by copyAlignPanel, and register the new reference to the shared
2780      * mappings
2781      */
2782     newap.av.replaceMappings(viewport.getAlignment());
2783
2784     newap.av.viewName = getNewViewName(viewTitle);
2785
2786     addAlignmentPanel(newap, true);
2787     newap.alignmentChanged();
2788
2789     if (alignPanels.size() == 2)
2790     {
2791       viewport.setGatherViewsHere(true);
2792     }
2793     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2794     return newap;
2795   }
2796
2797   /**
2798    * Make a new name for the view, ensuring it is unique within the current
2799    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2800    * these now use viewId. Unique view names are still desirable for usability.)
2801    *
2802    * @param viewTitle
2803    * @return
2804    */
2805   protected String getNewViewName(String viewTitle)
2806   {
2807     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2808     boolean addFirstIndex = false;
2809     if (viewTitle == null || viewTitle.trim().length() == 0)
2810     {
2811       viewTitle = MessageManager.getString("action.view");
2812       addFirstIndex = true;
2813     }
2814     else
2815     {
2816       index = 1;// we count from 1 if given a specific name
2817     }
2818     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2819
2820     List<Component> comps = PaintRefresher.components.get(viewport
2821             .getSequenceSetId());
2822
2823     List<String> existingNames = getExistingViewNames(comps);
2824
2825     while (existingNames.contains(newViewName))
2826     {
2827       newViewName = viewTitle + " " + (++index);
2828     }
2829     return newViewName;
2830   }
2831
2832   /**
2833    * Returns a list of distinct view names found in the given list of
2834    * components. View names are held on the viewport of an AlignmentPanel.
2835    *
2836    * @param comps
2837    * @return
2838    */
2839   protected List<String> getExistingViewNames(List<Component> comps)
2840   {
2841     List<String> existingNames = new ArrayList<String>();
2842     for (Component comp : comps)
2843     {
2844       if (comp instanceof AlignmentPanel)
2845       {
2846         AlignmentPanel ap = (AlignmentPanel) comp;
2847         if (!existingNames.contains(ap.av.viewName))
2848         {
2849           existingNames.add(ap.av.viewName);
2850         }
2851       }
2852     }
2853     return existingNames;
2854   }
2855
2856   /**
2857    * Explode tabbed views into separate windows.
2858    */
2859   @Override
2860   public void expandViews_actionPerformed(ActionEvent e)
2861   {
2862     Desktop.explodeViews(this);
2863   }
2864
2865   /**
2866    * Gather views in separate windows back into a tabbed presentation.
2867    */
2868   @Override
2869   public void gatherViews_actionPerformed(ActionEvent e)
2870   {
2871     Desktop.instance.gatherViews(this);
2872   }
2873
2874   /**
2875    * DOCUMENT ME!
2876    *
2877    * @param e
2878    *          DOCUMENT ME!
2879    */
2880   @Override
2881   public void font_actionPerformed(ActionEvent e)
2882   {
2883     new FontChooser(alignPanel);
2884   }
2885
2886   /**
2887    * DOCUMENT ME!
2888    *
2889    * @param e
2890    *          DOCUMENT ME!
2891    */
2892   @Override
2893   protected void seqLimit_actionPerformed(ActionEvent e)
2894   {
2895     viewport.setShowJVSuffix(seqLimits.isSelected());
2896
2897     alignPanel.getIdPanel().getIdCanvas()
2898             .setPreferredSize(alignPanel.calculateIdWidth());
2899     alignPanel.paintAlignment(true);
2900   }
2901
2902   @Override
2903   public void idRightAlign_actionPerformed(ActionEvent e)
2904   {
2905     viewport.setRightAlignIds(idRightAlign.isSelected());
2906     alignPanel.paintAlignment(true);
2907   }
2908
2909   @Override
2910   public void centreColumnLabels_actionPerformed(ActionEvent e)
2911   {
2912     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2913     alignPanel.paintAlignment(true);
2914   }
2915
2916   /*
2917    * (non-Javadoc)
2918    *
2919    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2920    */
2921   @Override
2922   protected void followHighlight_actionPerformed()
2923   {
2924     /*
2925      * Set the 'follow' flag on the Viewport (and scroll to position if now
2926      * true).
2927      */
2928     final boolean state = this.followHighlightMenuItem.getState();
2929     viewport.setFollowHighlight(state);
2930     if (state)
2931     {
2932       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2933     }
2934   }
2935
2936   /**
2937    * DOCUMENT ME!
2938    *
2939    * @param e
2940    *          DOCUMENT ME!
2941    */
2942   @Override
2943   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2944   {
2945     viewport.setColourText(colourTextMenuItem.isSelected());
2946     alignPanel.paintAlignment(true);
2947   }
2948
2949   /**
2950    * DOCUMENT ME!
2951    *
2952    * @param e
2953    *          DOCUMENT ME!
2954    */
2955   @Override
2956   public void wrapMenuItem_actionPerformed(ActionEvent e)
2957   {
2958     scaleAbove.setVisible(wrapMenuItem.isSelected());
2959     scaleLeft.setVisible(wrapMenuItem.isSelected());
2960     scaleRight.setVisible(wrapMenuItem.isSelected());
2961     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2962     alignPanel.updateLayout();
2963   }
2964
2965   @Override
2966   public void showAllSeqs_actionPerformed(ActionEvent e)
2967   {
2968     viewport.showAllHiddenSeqs();
2969   }
2970
2971   @Override
2972   public void showAllColumns_actionPerformed(ActionEvent e)
2973   {
2974     viewport.showAllHiddenColumns();
2975     repaint();
2976     viewport.sendSelection();
2977   }
2978
2979   @Override
2980   public void hideSelSequences_actionPerformed(ActionEvent e)
2981   {
2982     viewport.hideAllSelectedSeqs();
2983     // alignPanel.paintAlignment(true);
2984   }
2985
2986   /**
2987    * called by key handler and the hide all/show all menu items
2988    *
2989    * @param toggleSeqs
2990    * @param toggleCols
2991    */
2992   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2993   {
2994
2995     boolean hide = false;
2996     SequenceGroup sg = viewport.getSelectionGroup();
2997     if (!toggleSeqs && !toggleCols)
2998     {
2999       // Hide everything by the current selection - this is a hack - we do the
3000       // invert and then hide
3001       // first check that there will be visible columns after the invert.
3002       if (viewport.hasSelectedColumns()
3003               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3004                       .getEndRes()))
3005       {
3006         // now invert the sequence set, if required - empty selection implies
3007         // that no hiding is required.
3008         if (sg != null)
3009         {
3010           invertSequenceMenuItem_actionPerformed(null);
3011           sg = viewport.getSelectionGroup();
3012           toggleSeqs = true;
3013
3014         }
3015         viewport.expandColSelection(sg, true);
3016         // finally invert the column selection and get the new sequence
3017         // selection.
3018         invertColSel_actionPerformed(null);
3019         toggleCols = true;
3020       }
3021     }
3022
3023     if (toggleSeqs)
3024     {
3025       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3026       {
3027         hideSelSequences_actionPerformed(null);
3028         hide = true;
3029       }
3030       else if (!(toggleCols && viewport.hasSelectedColumns()))
3031       {
3032         showAllSeqs_actionPerformed(null);
3033       }
3034     }
3035
3036     if (toggleCols)
3037     {
3038       if (viewport.hasSelectedColumns())
3039       {
3040         hideSelColumns_actionPerformed(null);
3041         if (!toggleSeqs)
3042         {
3043           viewport.setSelectionGroup(sg);
3044         }
3045       }
3046       else if (!hide)
3047       {
3048         showAllColumns_actionPerformed(null);
3049       }
3050     }
3051   }
3052
3053   /*
3054    * (non-Javadoc)
3055    *
3056    * @see
3057    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3058    * event.ActionEvent)
3059    */
3060   @Override
3061   public void hideAllButSelection_actionPerformed(ActionEvent e)
3062   {
3063     toggleHiddenRegions(false, false);
3064     viewport.sendSelection();
3065   }
3066
3067   /*
3068    * (non-Javadoc)
3069    *
3070    * @see
3071    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3072    * .ActionEvent)
3073    */
3074   @Override
3075   public void hideAllSelection_actionPerformed(ActionEvent e)
3076   {
3077     SequenceGroup sg = viewport.getSelectionGroup();
3078     viewport.expandColSelection(sg, false);
3079     viewport.hideAllSelectedSeqs();
3080     viewport.hideSelectedColumns();
3081     alignPanel.paintAlignment(true);
3082     viewport.sendSelection();
3083   }
3084
3085   /*
3086    * (non-Javadoc)
3087    *
3088    * @see
3089    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3090    * ActionEvent)
3091    */
3092   @Override
3093   public void showAllhidden_actionPerformed(ActionEvent e)
3094   {
3095     viewport.showAllHiddenColumns();
3096     viewport.showAllHiddenSeqs();
3097     alignPanel.paintAlignment(true);
3098     viewport.sendSelection();
3099   }
3100
3101   @Override
3102   public void hideSelColumns_actionPerformed(ActionEvent e)
3103   {
3104     viewport.hideSelectedColumns();
3105     alignPanel.paintAlignment(true);
3106     viewport.sendSelection();
3107   }
3108
3109   @Override
3110   public void hiddenMarkers_actionPerformed(ActionEvent e)
3111   {
3112     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3113     repaint();
3114   }
3115
3116   /**
3117    * DOCUMENT ME!
3118    *
3119    * @param e
3120    *          DOCUMENT ME!
3121    */
3122   @Override
3123   protected void scaleAbove_actionPerformed(ActionEvent e)
3124   {
3125     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3126     alignPanel.paintAlignment(true);
3127   }
3128
3129   /**
3130    * DOCUMENT ME!
3131    *
3132    * @param e
3133    *          DOCUMENT ME!
3134    */
3135   @Override
3136   protected void scaleLeft_actionPerformed(ActionEvent e)
3137   {
3138     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3139     alignPanel.paintAlignment(true);
3140   }
3141
3142   /**
3143    * DOCUMENT ME!
3144    *
3145    * @param e
3146    *          DOCUMENT ME!
3147    */
3148   @Override
3149   protected void scaleRight_actionPerformed(ActionEvent e)
3150   {
3151     viewport.setScaleRightWrapped(scaleRight.isSelected());
3152     alignPanel.paintAlignment(true);
3153   }
3154
3155   /**
3156    * DOCUMENT ME!
3157    *
3158    * @param e
3159    *          DOCUMENT ME!
3160    */
3161   @Override
3162   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3163   {
3164     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3165     alignPanel.paintAlignment(true);
3166   }
3167
3168   /**
3169    * DOCUMENT ME!
3170    *
3171    * @param e
3172    *          DOCUMENT ME!
3173    */
3174   @Override
3175   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3176   {
3177     viewport.setShowText(viewTextMenuItem.isSelected());
3178     alignPanel.paintAlignment(true);
3179   }
3180
3181   /**
3182    * DOCUMENT ME!
3183    *
3184    * @param e
3185    *          DOCUMENT ME!
3186    */
3187   @Override
3188   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3189   {
3190     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3191     alignPanel.paintAlignment(true);
3192   }
3193
3194   public FeatureSettings featureSettings;
3195
3196   @Override
3197   public FeatureSettingsControllerI getFeatureSettingsUI()
3198   {
3199     return featureSettings;
3200   }
3201
3202   @Override
3203   public void featureSettings_actionPerformed(ActionEvent e)
3204   {
3205     if (featureSettings != null)
3206     {
3207       featureSettings.close();
3208       featureSettings = null;
3209     }
3210     if (!showSeqFeatures.isSelected())
3211     {
3212       // make sure features are actually displayed
3213       showSeqFeatures.setSelected(true);
3214       showSeqFeatures_actionPerformed(null);
3215     }
3216     featureSettings = new FeatureSettings(this);
3217   }
3218
3219   /**
3220    * Set or clear 'Show Sequence Features'
3221    *
3222    * @param evt
3223    *          DOCUMENT ME!
3224    */
3225   @Override
3226   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3227   {
3228     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3229     alignPanel.paintAlignment(true);
3230     if (alignPanel.getOverviewPanel() != null)
3231     {
3232       alignPanel.getOverviewPanel().updateOverviewImage();
3233     }
3234   }
3235
3236   /**
3237    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3238    * the annotations panel as a whole.
3239    *
3240    * The options to show/hide all annotations should be enabled when the panel
3241    * is shown, and disabled when the panel is hidden.
3242    *
3243    * @param e
3244    */
3245   @Override
3246   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3247   {
3248     final boolean setVisible = annotationPanelMenuItem.isSelected();
3249     viewport.setShowAnnotation(setVisible);
3250     this.showAllSeqAnnotations.setEnabled(setVisible);
3251     this.hideAllSeqAnnotations.setEnabled(setVisible);
3252     this.showAllAlAnnotations.setEnabled(setVisible);
3253     this.hideAllAlAnnotations.setEnabled(setVisible);
3254     alignPanel.updateLayout();
3255   }
3256
3257   @Override
3258   public void alignmentProperties()
3259   {
3260     JEditorPane editPane = new JEditorPane("text/html", "");
3261     editPane.setEditable(false);
3262     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3263             .formatAsHtml();
3264     editPane.setText(MessageManager.formatMessage("label.html_content",
3265             new Object[] { contents.toString() }));
3266     JInternalFrame frame = new JInternalFrame();
3267     frame.getContentPane().add(new JScrollPane(editPane));
3268
3269     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3270             "label.alignment_properties", new Object[] { getTitle() }),
3271             500, 400);
3272   }
3273
3274   /**
3275    * DOCUMENT ME!
3276    *
3277    * @param e
3278    *          DOCUMENT ME!
3279    */
3280   @Override
3281   public void overviewMenuItem_actionPerformed(ActionEvent e)
3282   {
3283     if (alignPanel.overviewPanel != null)
3284     {
3285       return;
3286     }
3287
3288     JInternalFrame frame = new JInternalFrame();
3289     OverviewPanel overview = new OverviewPanel(alignPanel);
3290     frame.setContentPane(overview);
3291     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3292             "label.overview_params", new Object[] { this.getTitle() }),
3293             frame.getWidth(), frame.getHeight());
3294     frame.pack();
3295     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3296     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3297     {
3298       @Override
3299       public void internalFrameClosed(
3300               javax.swing.event.InternalFrameEvent evt)
3301       {
3302         alignPanel.setOverviewPanel(null);
3303       };
3304     });
3305
3306     alignPanel.setOverviewPanel(overview);
3307   }
3308
3309   @Override
3310   public void textColour_actionPerformed()
3311   {
3312     new TextColourChooser().chooseColour(alignPanel, null);
3313   }
3314
3315   /**
3316    * DOCUMENT ME!
3317    *
3318    * @param e
3319    *          DOCUMENT ME!
3320    */
3321   @Override
3322   protected void noColourmenuItem_actionPerformed()
3323   {
3324     changeColour(null);
3325   }
3326
3327   /**
3328    * DOCUMENT ME!
3329    *
3330    * @param e
3331    *          DOCUMENT ME!
3332    */
3333   @Override
3334   public void clustalColour_actionPerformed()
3335   {
3336     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3337             viewport.getHiddenRepSequences()));
3338   }
3339
3340   /**
3341    * DOCUMENT ME!
3342    *
3343    * @param e
3344    *          DOCUMENT ME!
3345    */
3346   @Override
3347   public void zappoColour_actionPerformed()
3348   {
3349     changeColour(new ZappoColourScheme());
3350   }
3351
3352   /**
3353    * DOCUMENT ME!
3354    *
3355    * @param e
3356    *          DOCUMENT ME!
3357    */
3358   @Override
3359   public void taylorColour_actionPerformed()
3360   {
3361     changeColour(new TaylorColourScheme());
3362   }
3363
3364   /**
3365    * DOCUMENT ME!
3366    *
3367    * @param e
3368    *          DOCUMENT ME!
3369    */
3370   @Override
3371   public void hydrophobicityColour_actionPerformed()
3372   {
3373     changeColour(new HydrophobicColourScheme());
3374   }
3375
3376   /**
3377    * DOCUMENT ME!
3378    *
3379    * @param e
3380    *          DOCUMENT ME!
3381    */
3382   @Override
3383   public void helixColour_actionPerformed()
3384   {
3385     changeColour(new HelixColourScheme());
3386   }
3387
3388   /**
3389    * DOCUMENT ME!
3390    *
3391    * @param e
3392    *          DOCUMENT ME!
3393    */
3394   @Override
3395   public void strandColour_actionPerformed()
3396   {
3397     changeColour(new StrandColourScheme());
3398   }
3399
3400   /**
3401    * DOCUMENT ME!
3402    *
3403    * @param e
3404    *          DOCUMENT ME!
3405    */
3406   @Override
3407   public void turnColour_actionPerformed()
3408   {
3409     changeColour(new TurnColourScheme());
3410   }
3411
3412   /**
3413    * DOCUMENT ME!
3414    *
3415    * @param e
3416    *          DOCUMENT ME!
3417    */
3418   @Override
3419   public void buriedColour_actionPerformed()
3420   {
3421     changeColour(new BuriedColourScheme());
3422   }
3423
3424   /**
3425    * DOCUMENT ME!
3426    *
3427    * @param e
3428    *          DOCUMENT ME!
3429    */
3430   @Override
3431   public void nucleotideColour_actionPerformed()
3432   {
3433     changeColour(new NucleotideColourScheme());
3434   }
3435
3436   @Override
3437   public void purinePyrimidineColour_actionPerformed()
3438   {
3439     changeColour(new PurinePyrimidineColourScheme());
3440   }
3441
3442   /*
3443    * public void covariationColour_actionPerformed() {
3444    * changeColour(new
3445    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3446    * ()[0])); }
3447    */
3448   @Override
3449   public void annotationColour_actionPerformed()
3450   {
3451     new AnnotationColourChooser(viewport, alignPanel);
3452   }
3453
3454   @Override
3455   public void annotationColumn_actionPerformed(ActionEvent e)
3456   {
3457     new AnnotationColumnChooser(viewport, alignPanel);
3458   }
3459
3460   @Override
3461   public void rnahelicesColour_actionPerformed()
3462   {
3463     new RNAHelicesColourChooser(viewport, alignPanel);
3464   }
3465
3466   /**
3467    * DOCUMENT ME!
3468    *
3469    */
3470   @Override
3471   protected void applyToAllGroups_actionPerformed()
3472   {
3473     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3474   }
3475
3476   /**
3477    * DOCUMENT ME!
3478    *
3479    * @param cs
3480    *          DOCUMENT ME!
3481    */
3482   @Override
3483   public void changeColour(ColourSchemeI cs)
3484   {
3485     // TODO: pull up to controller method
3486
3487     if (cs != null)
3488     {
3489       // Make sure viewport is up to date w.r.t. any sliders
3490       if (viewport.getAbovePIDThreshold())
3491       {
3492         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3493                 "Background");
3494         viewport.setThreshold(threshold);
3495       }
3496
3497       if (viewport.getConservationSelected())
3498       {
3499         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3500                 cs, "Background"));
3501       }
3502       if (cs instanceof TCoffeeColourScheme)
3503       {
3504         tcoffeeColour.setEnabled(true);
3505         tcoffeeColour.setSelected(true);
3506       }
3507     }
3508
3509     viewport.setGlobalColourScheme(cs);
3510
3511     alignPanel.paintAlignment(true);
3512   }
3513
3514   /**
3515    * DOCUMENT ME!
3516    *
3517    * @param e
3518    *          DOCUMENT ME!
3519    */
3520   @Override
3521   protected void modifyPID_actionPerformed()
3522   {
3523     if (viewport.getAbovePIDThreshold()
3524             && viewport.getGlobalColourScheme() != null)
3525     {
3526       SliderPanel.setPIDSliderSource(alignPanel,
3527               viewport.getGlobalColourScheme(), "Background");
3528       SliderPanel.showPIDSlider();
3529     }
3530   }
3531
3532   /**
3533    * DOCUMENT ME!
3534    *
3535    * @param e
3536    *          DOCUMENT ME!
3537    */
3538   @Override
3539   protected void modifyConservation_actionPerformed()
3540   {
3541     if (viewport.getConservationSelected()
3542             && viewport.getGlobalColourScheme() != null)
3543     {
3544       SliderPanel.setConservationSlider(alignPanel,
3545               viewport.getGlobalColourScheme(), "Background");
3546       SliderPanel.showConservationSlider();
3547     }
3548   }
3549
3550   /**
3551    * DOCUMENT ME!
3552    *
3553    * @param e
3554    *          DOCUMENT ME!
3555    */
3556   @Override
3557   protected void conservationMenuItem_actionPerformed()
3558   {
3559     viewport.setConservationSelected(conservationMenuItem.isSelected());
3560
3561     viewport.setAbovePIDThreshold(false);
3562     abovePIDThreshold.setSelected(false);
3563
3564     changeColour(viewport.getGlobalColourScheme());
3565
3566     modifyConservation_actionPerformed();
3567   }
3568
3569   /**
3570    * DOCUMENT ME!
3571    *
3572    * @param e
3573    *          DOCUMENT ME!
3574    */
3575   @Override
3576   public void abovePIDThreshold_actionPerformed()
3577   {
3578     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3579
3580     conservationMenuItem.setSelected(false);
3581     viewport.setConservationSelected(false);
3582
3583     changeColour(viewport.getGlobalColourScheme());
3584
3585     modifyPID_actionPerformed();
3586   }
3587
3588   /**
3589    * DOCUMENT ME!
3590    *
3591    * @param e
3592    *          DOCUMENT ME!
3593    */
3594   @Override
3595   public void userDefinedColour_actionPerformed(ActionEvent e)
3596   {
3597     if (e.getActionCommand().equals(
3598             MessageManager.getString("action.user_defined")))
3599     {
3600       new UserDefinedColours(alignPanel, null);
3601     }
3602     else
3603     {
3604       UserColourScheme udc = UserDefinedColours
3605               .getUserColourSchemes().get(e.getActionCommand());
3606
3607       changeColour(udc);
3608     }
3609   }
3610
3611   /**
3612    * DOCUMENT ME!
3613    *
3614    * @param e
3615    *          DOCUMENT ME!
3616    */
3617   @Override
3618   public void PIDColour_actionPerformed()
3619   {
3620     changeColour(new PIDColourScheme());
3621   }
3622
3623   /**
3624    * DOCUMENT ME!
3625    *
3626    * @param e
3627    *          DOCUMENT ME!
3628    */
3629   @Override
3630   public void BLOSUM62Colour_actionPerformed()
3631   {
3632     changeColour(new Blosum62ColourScheme());
3633   }
3634
3635   /**
3636    * DOCUMENT ME!
3637    *
3638    * @param e
3639    *          DOCUMENT ME!
3640    */
3641   @Override
3642   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3643   {
3644     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3645     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3646             .getAlignment().getSequenceAt(0), null);
3647     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3648             viewport.getAlignment()));
3649     alignPanel.paintAlignment(true);
3650   }
3651
3652   /**
3653    * DOCUMENT ME!
3654    *
3655    * @param e
3656    *          DOCUMENT ME!
3657    */
3658   @Override
3659   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3660   {
3661     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3662     AlignmentSorter.sortByID(viewport.getAlignment());
3663     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3664             viewport.getAlignment()));
3665     alignPanel.paintAlignment(true);
3666   }
3667
3668   /**
3669    * DOCUMENT ME!
3670    *
3671    * @param e
3672    *          DOCUMENT ME!
3673    */
3674   @Override
3675   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3676   {
3677     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3678     AlignmentSorter.sortByLength(viewport.getAlignment());
3679     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3680             viewport.getAlignment()));
3681     alignPanel.paintAlignment(true);
3682   }
3683
3684   /**
3685    * DOCUMENT ME!
3686    *
3687    * @param e
3688    *          DOCUMENT ME!
3689    */
3690   @Override
3691   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3692   {
3693     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3694     AlignmentSorter.sortByGroup(viewport.getAlignment());
3695     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3696             viewport.getAlignment()));
3697
3698     alignPanel.paintAlignment(true);
3699   }
3700
3701   /**
3702    * DOCUMENT ME!
3703    *
3704    * @param e
3705    *          DOCUMENT ME!
3706    */
3707   @Override
3708   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3709   {
3710     new RedundancyPanel(alignPanel, this);
3711   }
3712
3713   /**
3714    * DOCUMENT ME!
3715    *
3716    * @param e
3717    *          DOCUMENT ME!
3718    */
3719   @Override
3720   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3721   {
3722     if ((viewport.getSelectionGroup() == null)
3723             || (viewport.getSelectionGroup().getSize() < 2))
3724     {
3725       JvOptionPane.showInternalMessageDialog(this, MessageManager
3726               .getString("label.you_must_select_least_two_sequences"),
3727               MessageManager.getString("label.invalid_selection"),
3728               JvOptionPane.WARNING_MESSAGE);
3729     }
3730     else
3731     {
3732       JInternalFrame frame = new JInternalFrame();
3733       frame.setContentPane(new PairwiseAlignPanel(viewport));
3734       Desktop.addInternalFrame(frame,
3735               MessageManager.getString("action.pairwise_alignment"), 600,
3736               500);
3737     }
3738   }
3739
3740   /**
3741    * DOCUMENT ME!
3742    *
3743    * @param e
3744    *          DOCUMENT ME!
3745    */
3746   @Override
3747   public void PCAMenuItem_actionPerformed(ActionEvent e)
3748   {
3749     if (((viewport.getSelectionGroup() != null)
3750             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3751             .getSelectionGroup().getSize() > 0))
3752             || (viewport.getAlignment().getHeight() < 4))
3753     {
3754       JvOptionPane
3755               .showInternalMessageDialog(
3756                       this,
3757                       MessageManager
3758                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3759                       MessageManager
3760                               .getString("label.sequence_selection_insufficient"),
3761                       JvOptionPane.WARNING_MESSAGE);
3762
3763       return;
3764     }
3765
3766     new PCAPanel(alignPanel);
3767   }
3768
3769   @Override
3770   public void autoCalculate_actionPerformed(ActionEvent e)
3771   {
3772     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3773     if (viewport.autoCalculateConsensus)
3774     {
3775       viewport.firePropertyChange("alignment", null, viewport
3776               .getAlignment().getSequences());
3777     }
3778   }
3779
3780   @Override
3781   public void sortByTreeOption_actionPerformed(ActionEvent e)
3782   {
3783     viewport.sortByTree = sortByTree.isSelected();
3784   }
3785
3786   @Override
3787   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3788   {
3789     viewport.followSelection = listenToViewSelections.isSelected();
3790   }
3791
3792   /**
3793    * DOCUMENT ME!
3794    *
3795    * @param e
3796    *          DOCUMENT ME!
3797    */
3798   @Override
3799   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3800   {
3801     newTreePanel("AV", "PID", "Average distance tree using PID");
3802   }
3803
3804   /**
3805    * DOCUMENT ME!
3806    *
3807    * @param e
3808    *          DOCUMENT ME!
3809    */
3810   @Override
3811   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3812   {
3813     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3814   }
3815
3816   /**
3817    * DOCUMENT ME!
3818    *
3819    * @param e
3820    *          DOCUMENT ME!
3821    */
3822   @Override
3823   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3824   {
3825     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3826   }
3827
3828   /**
3829    * DOCUMENT ME!
3830    *
3831    * @param e
3832    *          DOCUMENT ME!
3833    */
3834   @Override
3835   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3836   {
3837     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3838   }
3839
3840   /**
3841    * DOCUMENT ME!
3842    *
3843    * @param type
3844    *          DOCUMENT ME!
3845    * @param pwType
3846    *          DOCUMENT ME!
3847    * @param title
3848    *          DOCUMENT ME!
3849    */
3850   void newTreePanel(String type, String pwType, String title)
3851   {
3852     TreePanel tp;
3853
3854     if (viewport.getSelectionGroup() != null
3855             && viewport.getSelectionGroup().getSize() > 0)
3856     {
3857       if (viewport.getSelectionGroup().getSize() < 3)
3858       {
3859         JvOptionPane
3860                 .showMessageDialog(
3861                         Desktop.desktop,
3862                         MessageManager
3863                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3864                         MessageManager
3865                                 .getString("label.not_enough_sequences"),
3866                         JvOptionPane.WARNING_MESSAGE);
3867         return;
3868       }
3869
3870       SequenceGroup sg = viewport.getSelectionGroup();
3871
3872       /* Decide if the selection is a column region */
3873       for (SequenceI _s : sg.getSequences())
3874       {
3875         if (_s.getLength() < sg.getEndRes())
3876         {
3877           JvOptionPane
3878                   .showMessageDialog(
3879                           Desktop.desktop,
3880                           MessageManager
3881                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3882                           MessageManager
3883                                   .getString("label.sequences_selection_not_aligned"),
3884                           JvOptionPane.WARNING_MESSAGE);
3885
3886           return;
3887         }
3888       }
3889
3890       title = title + " on region";
3891       tp = new TreePanel(alignPanel, type, pwType);
3892     }
3893     else
3894     {
3895       // are the visible sequences aligned?
3896       if (!viewport.getAlignment().isAligned(false))
3897       {
3898         JvOptionPane
3899                 .showMessageDialog(
3900                         Desktop.desktop,
3901                         MessageManager
3902                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3903                         MessageManager
3904                                 .getString("label.sequences_not_aligned"),
3905                         JvOptionPane.WARNING_MESSAGE);
3906
3907         return;
3908       }
3909
3910       if (viewport.getAlignment().getHeight() < 2)
3911       {
3912         return;
3913       }
3914
3915       tp = new TreePanel(alignPanel, type, pwType);
3916     }
3917
3918     title += " from ";
3919
3920     if (viewport.viewName != null)
3921     {
3922       title += viewport.viewName + " of ";
3923     }
3924
3925     title += this.title;
3926
3927     Desktop.addInternalFrame(tp, title, 600, 500);
3928   }
3929
3930   /**
3931    * DOCUMENT ME!
3932    *
3933    * @param title
3934    *          DOCUMENT ME!
3935    * @param order
3936    *          DOCUMENT ME!
3937    */
3938   public void addSortByOrderMenuItem(String title,
3939           final AlignmentOrder order)
3940   {
3941     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3942             "action.by_title_param", new Object[] { title }));
3943     sort.add(item);
3944     item.addActionListener(new java.awt.event.ActionListener()
3945     {
3946       @Override
3947       public void actionPerformed(ActionEvent e)
3948       {
3949         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3950
3951         // TODO: JBPNote - have to map order entries to curent SequenceI
3952         // pointers
3953         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3954
3955         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3956                 .getAlignment()));
3957
3958         alignPanel.paintAlignment(true);
3959       }
3960     });
3961   }
3962
3963   /**
3964    * Add a new sort by annotation score menu item
3965    *
3966    * @param sort
3967    *          the menu to add the option to
3968    * @param scoreLabel
3969    *          the label used to retrieve scores for each sequence on the
3970    *          alignment
3971    */
3972   public void addSortByAnnotScoreMenuItem(JMenu sort,
3973           final String scoreLabel)
3974   {
3975     final JMenuItem item = new JMenuItem(scoreLabel);
3976     sort.add(item);
3977     item.addActionListener(new java.awt.event.ActionListener()
3978     {
3979       @Override
3980       public void actionPerformed(ActionEvent e)
3981       {
3982         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3983         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3984                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3985         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3986                 viewport.getAlignment()));
3987         alignPanel.paintAlignment(true);
3988       }
3989     });
3990   }
3991
3992   /**
3993    * last hash for alignment's annotation array - used to minimise cost of
3994    * rebuild.
3995    */
3996   protected int _annotationScoreVectorHash;
3997
3998   /**
3999    * search the alignment and rebuild the sort by annotation score submenu the
4000    * last alignment annotation vector hash is stored to minimize cost of
4001    * rebuilding in subsequence calls.
4002    *
4003    */
4004   @Override
4005   public void buildSortByAnnotationScoresMenu()
4006   {
4007     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4008     {
4009       return;
4010     }
4011
4012     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4013     {
4014       sortByAnnotScore.removeAll();
4015       // almost certainly a quicker way to do this - but we keep it simple
4016       Hashtable scoreSorts = new Hashtable();
4017       AlignmentAnnotation aann[];
4018       for (SequenceI sqa : viewport.getAlignment().getSequences())
4019       {
4020         aann = sqa.getAnnotation();
4021         for (int i = 0; aann != null && i < aann.length; i++)
4022         {
4023           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4024           {
4025             scoreSorts.put(aann[i].label, aann[i].label);
4026           }
4027         }
4028       }
4029       Enumeration labels = scoreSorts.keys();
4030       while (labels.hasMoreElements())
4031       {
4032         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4033                 (String) labels.nextElement());
4034       }
4035       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4036       scoreSorts.clear();
4037
4038       _annotationScoreVectorHash = viewport.getAlignment()
4039               .getAlignmentAnnotation().hashCode();
4040     }
4041   }
4042
4043   /**
4044    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4045    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4046    * call. Listeners are added to remove the menu item when the treePanel is
4047    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4048    * modified.
4049    *
4050    * @param treePanel
4051    *          Displayed tree window.
4052    * @param title
4053    *          SortBy menu item title.
4054    */
4055   @Override
4056   public void buildTreeMenu()
4057   {
4058     calculateTree.removeAll();
4059     // build the calculate menu
4060
4061     for (final String type : new String[] { "NJ", "AV" })
4062     {
4063       String treecalcnm = MessageManager.getString("label.tree_calc_"
4064               + type.toLowerCase());
4065       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4066       {
4067         JMenuItem tm = new JMenuItem();
4068         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4069         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4070                 || sm.isProtein() == !viewport.getAlignment()
4071                         .isNucleotide())
4072         {
4073           String smn = MessageManager.getStringOrReturn(
4074                   "label.score_model_", sm.getName());
4075           final String title = MessageManager.formatMessage(
4076                   "label.treecalc_title", treecalcnm, smn);
4077           tm.setText(title);//
4078           tm.addActionListener(new java.awt.event.ActionListener()
4079           {
4080             @Override
4081             public void actionPerformed(ActionEvent e)
4082             {
4083               newTreePanel(type, pwtype, title);
4084             }
4085           });
4086           calculateTree.add(tm);
4087         }
4088
4089       }
4090     }
4091     sortByTreeMenu.removeAll();
4092
4093     List<Component> comps = PaintRefresher.components.get(viewport
4094             .getSequenceSetId());
4095     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4096     for (Component comp : comps)
4097     {
4098       if (comp instanceof TreePanel)
4099       {
4100         treePanels.add((TreePanel) comp);
4101       }
4102     }
4103
4104     if (treePanels.size() < 1)
4105     {
4106       sortByTreeMenu.setVisible(false);
4107       return;
4108     }
4109
4110     sortByTreeMenu.setVisible(true);
4111
4112     for (final TreePanel tp : treePanels)
4113     {
4114       final JMenuItem item = new JMenuItem(tp.getTitle());
4115       item.addActionListener(new java.awt.event.ActionListener()
4116       {
4117         @Override
4118         public void actionPerformed(ActionEvent e)
4119         {
4120           tp.sortByTree_actionPerformed();
4121           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4122
4123         }
4124       });
4125
4126       sortByTreeMenu.add(item);
4127     }
4128   }
4129
4130   public boolean sortBy(AlignmentOrder alorder, String undoname)
4131   {
4132     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4133     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4134     if (undoname != null)
4135     {
4136       addHistoryItem(new OrderCommand(undoname, oldOrder,
4137               viewport.getAlignment()));
4138     }
4139     alignPanel.paintAlignment(true);
4140     return true;
4141   }
4142
4143   /**
4144    * Work out whether the whole set of sequences or just the selected set will
4145    * be submitted for multiple alignment.
4146    *
4147    */
4148   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4149   {
4150     // Now, check we have enough sequences
4151     AlignmentView msa = null;
4152
4153     if ((viewport.getSelectionGroup() != null)
4154             && (viewport.getSelectionGroup().getSize() > 1))
4155     {
4156       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4157       // some common interface!
4158       /*
4159        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4160        * SequenceI[sz = seqs.getSize(false)];
4161        *
4162        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4163        * seqs.getSequenceAt(i); }
4164        */
4165       msa = viewport.getAlignmentView(true);
4166     }
4167     else if (viewport.getSelectionGroup() != null
4168             && viewport.getSelectionGroup().getSize() == 1)
4169     {
4170       int option = JvOptionPane.showConfirmDialog(this,
4171               MessageManager.getString("warn.oneseq_msainput_selection"),
4172               MessageManager.getString("label.invalid_selection"),
4173               JvOptionPane.OK_CANCEL_OPTION);
4174       if (option == JvOptionPane.OK_OPTION)
4175       {
4176         msa = viewport.getAlignmentView(false);
4177       }
4178     }
4179     else
4180     {
4181       msa = viewport.getAlignmentView(false);
4182     }
4183     return msa;
4184   }
4185
4186   /**
4187    * Decides what is submitted to a secondary structure prediction service: the
4188    * first sequence in the alignment, or in the current selection, or, if the
4189    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4190    * region or the whole alignment. (where the first sequence in the set is the
4191    * one that the prediction will be for).
4192    */
4193   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4194   {
4195     AlignmentView seqs = null;
4196
4197     if ((viewport.getSelectionGroup() != null)
4198             && (viewport.getSelectionGroup().getSize() > 0))
4199     {
4200       seqs = viewport.getAlignmentView(true);
4201     }
4202     else
4203     {
4204       seqs = viewport.getAlignmentView(false);
4205     }
4206     // limit sequences - JBPNote in future - could spawn multiple prediction
4207     // jobs
4208     // TODO: viewport.getAlignment().isAligned is a global state - the local
4209     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4210     if (!viewport.getAlignment().isAligned(false))
4211     {
4212       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4213       // TODO: if seqs.getSequences().length>1 then should really have warned
4214       // user!
4215
4216     }
4217     return seqs;
4218   }
4219
4220   /**
4221    * DOCUMENT ME!
4222    *
4223    * @param e
4224    *          DOCUMENT ME!
4225    */
4226   @Override
4227   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4228   {
4229     // Pick the tree file
4230     JalviewFileChooser chooser = new JalviewFileChooser(
4231             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4232     chooser.setFileView(new JalviewFileView());
4233     chooser.setDialogTitle(MessageManager
4234             .getString("label.select_newick_like_tree_file"));
4235     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4236
4237     int value = chooser.showOpenDialog(null);
4238
4239     if (value == JalviewFileChooser.APPROVE_OPTION)
4240     {
4241       String choice = chooser.getSelectedFile().getPath();
4242       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4243       jalview.io.NewickFile fin = null;
4244       try
4245       {
4246         fin = new NewickFile(choice, DataSourceType.FILE);
4247         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4248       } catch (Exception ex)
4249       {
4250         JvOptionPane
4251                 .showMessageDialog(
4252                         Desktop.desktop,
4253                         ex.getMessage(),
4254                         MessageManager
4255                                 .getString("label.problem_reading_tree_file"),
4256                         JvOptionPane.WARNING_MESSAGE);
4257         ex.printStackTrace();
4258       }
4259       if (fin != null && fin.hasWarningMessage())
4260       {
4261         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4262                 .getWarningMessage(), MessageManager
4263                 .getString("label.possible_problem_with_tree_file"),
4264                 JvOptionPane.WARNING_MESSAGE);
4265       }
4266     }
4267   }
4268
4269   @Override
4270   protected void tcoffeeColorScheme_actionPerformed()
4271   {
4272     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4273   }
4274
4275   public TreePanel ShowNewickTree(NewickFile nf, String title)
4276   {
4277     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4278   }
4279
4280   public TreePanel ShowNewickTree(NewickFile nf, String title,
4281           AlignmentView input)
4282   {
4283     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4284   }
4285
4286   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4287           int h, int x, int y)
4288   {
4289     return ShowNewickTree(nf, title, null, w, h, x, y);
4290   }
4291
4292   /**
4293    * Add a treeviewer for the tree extracted from a newick file object to the
4294    * current alignment view
4295    *
4296    * @param nf
4297    *          the tree
4298    * @param title
4299    *          tree viewer title
4300    * @param input
4301    *          Associated alignment input data (or null)
4302    * @param w
4303    *          width
4304    * @param h
4305    *          height
4306    * @param x
4307    *          position
4308    * @param y
4309    *          position
4310    * @return TreePanel handle
4311    */
4312   public TreePanel ShowNewickTree(NewickFile nf, String title,
4313           AlignmentView input, int w, int h, int x, int y)
4314   {
4315     TreePanel tp = null;
4316
4317     try
4318     {
4319       nf.parse();
4320
4321       if (nf.getTree() != null)
4322       {
4323         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4324
4325         tp.setSize(w, h);
4326
4327         if (x > 0 && y > 0)
4328         {
4329           tp.setLocation(x, y);
4330         }
4331
4332         Desktop.addInternalFrame(tp, title, w, h);
4333       }
4334     } catch (Exception ex)
4335     {
4336       ex.printStackTrace();
4337     }
4338
4339     return tp;
4340   }
4341
4342   private boolean buildingMenu = false;
4343
4344   /**
4345    * Generates menu items and listener event actions for web service clients
4346    *
4347    */
4348   public void BuildWebServiceMenu()
4349   {
4350     while (buildingMenu)
4351     {
4352       try
4353       {
4354         System.err.println("Waiting for building menu to finish.");
4355         Thread.sleep(10);
4356       } catch (Exception e)
4357       {
4358       }
4359     }
4360     final AlignFrame me = this;
4361     buildingMenu = true;
4362     new Thread(new Runnable()
4363     {
4364       @Override
4365       public void run()
4366       {
4367         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4368         try
4369         {
4370           // System.err.println("Building ws menu again "
4371           // + Thread.currentThread());
4372           // TODO: add support for context dependent disabling of services based
4373           // on
4374           // alignment and current selection
4375           // TODO: add additional serviceHandle parameter to specify abstract
4376           // handler
4377           // class independently of AbstractName
4378           // TODO: add in rediscovery GUI function to restart discoverer
4379           // TODO: group services by location as well as function and/or
4380           // introduce
4381           // object broker mechanism.
4382           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4383           final IProgressIndicator af = me;
4384
4385           /*
4386            * do not i18n these strings - they are hard-coded in class
4387            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4388            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4389            */
4390           final JMenu msawsmenu = new JMenu("Alignment");
4391           final JMenu secstrmenu = new JMenu(
4392                   "Secondary Structure Prediction");
4393           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4394           final JMenu analymenu = new JMenu("Analysis");
4395           final JMenu dismenu = new JMenu("Protein Disorder");
4396           // JAL-940 - only show secondary structure prediction services from
4397           // the legacy server
4398           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4399               // &&
4400           Discoverer.services != null && (Discoverer.services.size() > 0))
4401           {
4402             // TODO: refactor to allow list of AbstractName/Handler bindings to
4403             // be
4404             // stored or retrieved from elsewhere
4405             // No MSAWS used any more:
4406             // Vector msaws = null; // (Vector)
4407             // Discoverer.services.get("MsaWS");
4408             Vector secstrpr = (Vector) Discoverer.services
4409                     .get("SecStrPred");
4410             if (secstrpr != null)
4411             {
4412               // Add any secondary structure prediction services
4413               for (int i = 0, j = secstrpr.size(); i < j; i++)
4414               {
4415                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4416                         .get(i);
4417                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4418                         .getServiceClient(sh);
4419                 int p = secstrmenu.getItemCount();
4420                 impl.attachWSMenuEntry(secstrmenu, me);
4421                 int q = secstrmenu.getItemCount();
4422                 for (int litm = p; litm < q; litm++)
4423                 {
4424                   legacyItems.add(secstrmenu.getItem(litm));
4425                 }
4426               }
4427             }
4428           }
4429
4430           // Add all submenus in the order they should appear on the web
4431           // services menu
4432           wsmenu.add(msawsmenu);
4433           wsmenu.add(secstrmenu);
4434           wsmenu.add(dismenu);
4435           wsmenu.add(analymenu);
4436           // No search services yet
4437           // wsmenu.add(seqsrchmenu);
4438
4439           javax.swing.SwingUtilities.invokeLater(new Runnable()
4440           {
4441             @Override
4442             public void run()
4443             {
4444               try
4445               {
4446                 webService.removeAll();
4447                 // first, add discovered services onto the webservices menu
4448                 if (wsmenu.size() > 0)
4449                 {
4450                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4451                   {
4452                     webService.add(wsmenu.get(i));
4453                   }
4454                 }
4455                 else
4456                 {
4457                   webService.add(me.webServiceNoServices);
4458                 }
4459                 // TODO: move into separate menu builder class.
4460                 boolean new_sspred = false;
4461                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4462                 {
4463                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4464                   if (jws2servs != null)
4465                   {
4466                     if (jws2servs.hasServices())
4467                     {
4468                       jws2servs.attachWSMenuEntry(webService, me);
4469                       for (Jws2Instance sv : jws2servs.getServices())
4470                       {
4471                         if (sv.description.toLowerCase().contains("jpred"))
4472                         {
4473                           for (JMenuItem jmi : legacyItems)
4474                           {
4475                             jmi.setVisible(false);
4476                           }
4477                         }
4478                       }
4479
4480                     }
4481                     if (jws2servs.isRunning())
4482                     {
4483                       JMenuItem tm = new JMenuItem(
4484                               "Still discovering JABA Services");
4485                       tm.setEnabled(false);
4486                       webService.add(tm);
4487                     }
4488                   }
4489                 }
4490                 build_urlServiceMenu(me.webService);
4491                 build_fetchdbmenu(webService);
4492                 for (JMenu item : wsmenu)
4493                 {
4494                   if (item.getItemCount() == 0)
4495                   {
4496                     item.setEnabled(false);
4497                   }
4498                   else
4499                   {
4500                     item.setEnabled(true);
4501                   }
4502                 }
4503               } catch (Exception e)
4504               {
4505                 Cache.log
4506                         .debug("Exception during web service menu building process.",
4507                                 e);
4508               }
4509             }
4510           });
4511         } catch (Exception e)
4512         {
4513         }
4514         buildingMenu = false;
4515       }
4516     }).start();
4517
4518   }
4519
4520   /**
4521    * construct any groupURL type service menu entries.
4522    *
4523    * @param webService
4524    */
4525   private void build_urlServiceMenu(JMenu webService)
4526   {
4527     // TODO: remove this code when 2.7 is released
4528     // DEBUG - alignmentView
4529     /*
4530      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4531      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4532      *
4533      * @Override public void actionPerformed(ActionEvent e) {
4534      * jalview.datamodel.AlignmentView
4535      * .testSelectionViews(af.viewport.getAlignment(),
4536      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4537      *
4538      * }); webService.add(testAlView);
4539      */
4540     // TODO: refactor to RestClient discoverer and merge menu entries for
4541     // rest-style services with other types of analysis/calculation service
4542     // SHmmr test client - still being implemented.
4543     // DEBUG - alignmentView
4544
4545     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4546             .getRestClients())
4547     {
4548       client.attachWSMenuEntry(
4549               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4550               this);
4551     }
4552   }
4553
4554   /**
4555    * Searches the alignment sequences for xRefs and builds the Show
4556    * Cross-References menu (formerly called Show Products), with database
4557    * sources for which cross-references are found (protein sources for a
4558    * nucleotide alignment and vice versa)
4559    *
4560    * @return true if Show Cross-references menu should be enabled
4561    */
4562   public boolean canShowProducts()
4563   {
4564     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4565     AlignmentI dataset = viewport.getAlignment().getDataset();
4566
4567     showProducts.removeAll();
4568     final boolean dna = viewport.getAlignment().isNucleotide();
4569
4570     if (seqs == null || seqs.length == 0)
4571     {
4572       // nothing to see here.
4573       return false;
4574     }
4575
4576     boolean showp = false;
4577     try
4578     {
4579       List<String> ptypes = new CrossRef(seqs, dataset)
4580               .findXrefSourcesForSequences(dna);
4581
4582       for (final String source : ptypes)
4583       {
4584         showp = true;
4585         final AlignFrame af = this;
4586         JMenuItem xtype = new JMenuItem(source);
4587         xtype.addActionListener(new ActionListener()
4588         {
4589           @Override
4590           public void actionPerformed(ActionEvent e)
4591           {
4592             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4593           }
4594         });
4595         showProducts.add(xtype);
4596       }
4597       showProducts.setVisible(showp);
4598       showProducts.setEnabled(showp);
4599     } catch (Exception e)
4600     {
4601       Cache.log
4602               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4603                       e);
4604       return false;
4605     }
4606     return showp;
4607   }
4608
4609   /**
4610    * Finds and displays cross-references for the selected sequences (protein
4611    * products for nucleotide sequences, dna coding sequences for peptides).
4612    *
4613    * @param sel
4614    *          the sequences to show cross-references for
4615    * @param dna
4616    *          true if from a nucleotide alignment (so showing proteins)
4617    * @param source
4618    *          the database to show cross-references for
4619    */
4620   protected void showProductsFor(final SequenceI[] sel,
4621           final boolean _odna, final String source)
4622   {
4623     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4624             .start();
4625   }
4626
4627   /**
4628    * Construct and display a new frame containing the translation of this
4629    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4630    */
4631   @Override
4632   public void showTranslation_actionPerformed(ActionEvent e)
4633   {
4634     AlignmentI al = null;
4635     try
4636     {
4637       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4638
4639       al = dna.translateCdna();
4640     } catch (Exception ex)
4641     {
4642       jalview.bin.Cache.log.error(
4643               "Exception during translation. Please report this !", ex);
4644       final String msg = MessageManager
4645               .getString("label.error_when_translating_sequences_submit_bug_report");
4646       final String errorTitle = MessageManager
4647               .getString("label.implementation_error")
4648               + MessageManager.getString("label.translation_failed");
4649       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4650               JvOptionPane.ERROR_MESSAGE);
4651       return;
4652     }
4653     if (al == null || al.getHeight() == 0)
4654     {
4655       final String msg = MessageManager
4656               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4657       final String errorTitle = MessageManager
4658               .getString("label.translation_failed");
4659       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4660               JvOptionPane.WARNING_MESSAGE);
4661     }
4662     else
4663     {
4664       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4665       af.setFileFormat(this.currentFileFormat);
4666       final String newTitle = MessageManager.formatMessage(
4667               "label.translation_of_params",
4668               new Object[] { this.getTitle() });
4669       af.setTitle(newTitle);
4670       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4671       {
4672         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4673         viewport.openSplitFrame(af, new Alignment(seqs));
4674       }
4675       else
4676       {
4677         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4678                 DEFAULT_HEIGHT);
4679       }
4680     }
4681   }
4682
4683   /**
4684    * Set the file format
4685    *
4686    * @param format
4687    */
4688   public void setFileFormat(FileFormatI format)
4689   {
4690     this.currentFileFormat = format;
4691   }
4692
4693   /**
4694    * Try to load a features file onto the alignment.
4695    *
4696    * @param file
4697    *          contents or path to retrieve file
4698    * @param sourceType
4699    *          access mode of file (see jalview.io.AlignFile)
4700    * @return true if features file was parsed correctly.
4701    */
4702   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4703   {
4704     return avc.parseFeaturesFile(file, sourceType,
4705             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4706
4707   }
4708
4709   @Override
4710   public void refreshFeatureUI(boolean enableIfNecessary)
4711   {
4712     // note - currently this is only still here rather than in the controller
4713     // because of the featureSettings hard reference that is yet to be
4714     // abstracted
4715     if (enableIfNecessary)
4716     {
4717       viewport.setShowSequenceFeatures(true);
4718       showSeqFeatures.setSelected(true);
4719     }
4720
4721   }
4722
4723   @Override
4724   public void dragEnter(DropTargetDragEvent evt)
4725   {
4726   }
4727
4728   @Override
4729   public void dragExit(DropTargetEvent evt)
4730   {
4731   }
4732
4733   @Override
4734   public void dragOver(DropTargetDragEvent evt)
4735   {
4736   }
4737
4738   @Override
4739   public void dropActionChanged(DropTargetDragEvent evt)
4740   {
4741   }
4742
4743   @Override
4744   public void drop(DropTargetDropEvent evt)
4745   {
4746     // JAL-1552 - acceptDrop required before getTransferable call for
4747     // Java's Transferable for native dnd
4748     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4749     Transferable t = evt.getTransferable();
4750     List<String> files = new ArrayList<String>();
4751     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4752
4753     try
4754     {
4755       Desktop.transferFromDropTarget(files, protocols, evt, t);
4756     } catch (Exception e)
4757     {
4758       e.printStackTrace();
4759     }
4760     if (files != null)
4761     {
4762       try
4763       {
4764         // check to see if any of these files have names matching sequences in
4765         // the alignment
4766         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4767                 .getAlignment().getSequencesArray());
4768         /**
4769          * Object[] { String,SequenceI}
4770          */
4771         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4772         ArrayList<String> filesnotmatched = new ArrayList<String>();
4773         for (int i = 0; i < files.size(); i++)
4774         {
4775           String file = files.get(i).toString();
4776           String pdbfn = "";
4777           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4778           if (protocol == DataSourceType.FILE)
4779           {
4780             File fl = new File(file);
4781             pdbfn = fl.getName();
4782           }
4783           else if (protocol == DataSourceType.URL)
4784           {
4785             URL url = new URL(file);
4786             pdbfn = url.getFile();
4787           }
4788           if (pdbfn.length() > 0)
4789           {
4790             // attempt to find a match in the alignment
4791             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4792             int l = 0, c = pdbfn.indexOf(".");
4793             while (mtch == null && c != -1)
4794             {
4795               do
4796               {
4797                 l = c;
4798               } while ((c = pdbfn.indexOf(".", l)) > l);
4799               if (l > -1)
4800               {
4801                 pdbfn = pdbfn.substring(0, l);
4802               }
4803               mtch = idm.findAllIdMatches(pdbfn);
4804             }
4805             if (mtch != null)
4806             {
4807               FileFormatI type = null;
4808               try
4809               {
4810                 type = new IdentifyFile().identify(file, protocol);
4811               } catch (Exception ex)
4812               {
4813                 type = null;
4814               }
4815               if (type != null && type.isStructureFile())
4816               {
4817                 filesmatched.add(new Object[] { file, protocol, mtch });
4818                 continue;
4819               }
4820             }
4821             // File wasn't named like one of the sequences or wasn't a PDB file.
4822             filesnotmatched.add(file);
4823           }
4824         }
4825         int assocfiles = 0;
4826         if (filesmatched.size() > 0)
4827         {
4828           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4829                   || JvOptionPane
4830                           .showConfirmDialog(
4831                                   this,
4832                                   MessageManager
4833                                           .formatMessage(
4834                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4835                                                   new Object[] { Integer
4836                                                           .valueOf(
4837                                                                   filesmatched
4838                                                                           .size())
4839                                                           .toString() }),
4840                                   MessageManager
4841                                           .getString("label.automatically_associate_structure_files_by_name"),
4842                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4843
4844           {
4845             for (Object[] fm : filesmatched)
4846             {
4847               // try and associate
4848               // TODO: may want to set a standard ID naming formalism for
4849               // associating PDB files which have no IDs.
4850               for (SequenceI toassoc : (SequenceI[]) fm[2])
4851               {
4852                 PDBEntry pe = new AssociatePdbFileWithSeq()
4853                         .associatePdbWithSeq((String) fm[0],
4854                                 (DataSourceType) fm[1], toassoc, false,
4855                                 Desktop.instance);
4856                 if (pe != null)
4857                 {
4858                   System.err.println("Associated file : "
4859                           + ((String) fm[0]) + " with "
4860                           + toassoc.getDisplayId(true));
4861                   assocfiles++;
4862                 }
4863               }
4864               alignPanel.paintAlignment(true);
4865             }
4866           }
4867         }
4868         if (filesnotmatched.size() > 0)
4869         {
4870           if (assocfiles > 0
4871                   && (Cache.getDefault(
4872                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4873                           .showConfirmDialog(
4874                                   this,
4875                                   "<html>"
4876                                           + MessageManager
4877                                                   .formatMessage(
4878                                                           "label.ignore_unmatched_dropped_files_info",
4879                                                           new Object[] { Integer
4880                                                                   .valueOf(
4881                                                                           filesnotmatched
4882                                                                                   .size())
4883                                                                   .toString() })
4884                                           + "</html>",
4885                                   MessageManager
4886                                           .getString("label.ignore_unmatched_dropped_files"),
4887                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4888           {
4889             return;
4890           }
4891           for (String fn : filesnotmatched)
4892           {
4893             loadJalviewDataFile(fn, null, null, null);
4894           }
4895
4896         }
4897       } catch (Exception ex)
4898       {
4899         ex.printStackTrace();
4900       }
4901     }
4902   }
4903
4904   /**
4905    * Attempt to load a "dropped" file or URL string: First by testing whether
4906    * it's an Annotation file, then a JNet file, and finally a features file. If
4907    * all are false then the user may have dropped an alignment file onto this
4908    * AlignFrame.
4909    *
4910    * @param file
4911    *          either a filename or a URL string.
4912    */
4913   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4914           FileFormatI format, SequenceI assocSeq)
4915   {
4916     try
4917     {
4918       if (sourceType == null)
4919       {
4920         sourceType = FormatAdapter.checkProtocol(file);
4921       }
4922       // if the file isn't identified, or not positively identified as some
4923       // other filetype (PFAM is default unidentified alignment file type) then
4924       // try to parse as annotation.
4925       boolean isAnnotation = (format == null || FileFormat.Pfam
4926               .equals(format)) ? new AnnotationFile()
4927               .annotateAlignmentView(viewport, file, sourceType) : false;
4928
4929       if (!isAnnotation)
4930       {
4931         // first see if its a T-COFFEE score file
4932         TCoffeeScoreFile tcf = null;
4933         try
4934         {
4935           tcf = new TCoffeeScoreFile(file, sourceType);
4936           if (tcf.isValid())
4937           {
4938             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4939             {
4940               tcoffeeColour.setEnabled(true);
4941               tcoffeeColour.setSelected(true);
4942               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4943               isAnnotation = true;
4944               statusBar
4945                       .setText(MessageManager
4946                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4947             }
4948             else
4949             {
4950               // some problem - if no warning its probable that the ID matching
4951               // process didn't work
4952               JvOptionPane
4953                       .showMessageDialog(
4954                               Desktop.desktop,
4955                               tcf.getWarningMessage() == null ? MessageManager
4956                                       .getString("label.check_file_matches_sequence_ids_alignment")
4957                                       : tcf.getWarningMessage(),
4958                               MessageManager
4959                                       .getString("label.problem_reading_tcoffee_score_file"),
4960                               JvOptionPane.WARNING_MESSAGE);
4961             }
4962           }
4963           else
4964           {
4965             tcf = null;
4966           }
4967         } catch (Exception x)
4968         {
4969           Cache.log
4970                   .debug("Exception when processing data source as T-COFFEE score file",
4971                           x);
4972           tcf = null;
4973         }
4974         if (tcf == null)
4975         {
4976           // try to see if its a JNet 'concise' style annotation file *before*
4977           // we
4978           // try to parse it as a features file
4979           if (format == null)
4980           {
4981             format = new IdentifyFile().identify(file, sourceType);
4982           }
4983           if (FileFormat.Jnet.equals(format))
4984           {
4985             JPredFile predictions = new JPredFile(
4986                     file, sourceType);
4987             new JnetAnnotationMaker();
4988             JnetAnnotationMaker.add_annotation(predictions,
4989                     viewport.getAlignment(), 0, false);
4990             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4991             viewport.getAlignment().setSeqrep(repseq);
4992             ColumnSelection cs = new ColumnSelection();
4993             cs.hideInsertionsFor(repseq);
4994             viewport.setColumnSelection(cs);
4995             isAnnotation = true;
4996           }
4997           // else if (IdentifyFile.FeaturesFile.equals(format))
4998           else if (FileFormat.Features.equals(format))
4999           {
5000             if (parseFeaturesFile(file, sourceType))
5001             {
5002               alignPanel.paintAlignment(true);
5003             }
5004           }
5005           else
5006           {
5007             new FileLoader().LoadFile(viewport, file, sourceType, format);
5008           }
5009         }
5010       }
5011       if (isAnnotation)
5012       {
5013
5014         alignPanel.adjustAnnotationHeight();
5015         viewport.updateSequenceIdColours();
5016         buildSortByAnnotationScoresMenu();
5017         alignPanel.paintAlignment(true);
5018       }
5019     } catch (Exception ex)
5020     {
5021       ex.printStackTrace();
5022     } catch (OutOfMemoryError oom)
5023     {
5024       try
5025       {
5026         System.gc();
5027       } catch (Exception x)
5028       {
5029       }
5030       new OOMWarning(
5031               "loading data "
5032                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5033                               : "using " + sourceType + " from " + file)
5034                               : ".")
5035                       + (format != null ? "(parsing as '" + format
5036                               + "' file)" : ""), oom, Desktop.desktop);
5037     }
5038   }
5039
5040   /**
5041    * Method invoked by the ChangeListener on the tabbed pane, in other words
5042    * when a different tabbed pane is selected by the user or programmatically.
5043    */
5044   @Override
5045   public void tabSelectionChanged(int index)
5046   {
5047     if (index > -1)
5048     {
5049       alignPanel = alignPanels.get(index);
5050       viewport = alignPanel.av;
5051       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5052       setMenusFromViewport(viewport);
5053     }
5054
5055     /*
5056      * If there is a frame linked to this one in a SplitPane, switch it to the
5057      * same view tab index. No infinite recursion of calls should happen, since
5058      * tabSelectionChanged() should not get invoked on setting the selected
5059      * index to an unchanged value. Guard against setting an invalid index
5060      * before the new view peer tab has been created.
5061      */
5062     final AlignViewportI peer = viewport.getCodingComplement();
5063     if (peer != null)
5064     {
5065       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5066       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5067       {
5068         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5069       }
5070     }
5071   }
5072
5073   /**
5074    * On right mouse click on view tab, prompt for and set new view name.
5075    */
5076   @Override
5077   public void tabbedPane_mousePressed(MouseEvent e)
5078   {
5079     if (e.isPopupTrigger())
5080     {
5081       String msg = MessageManager.getString("label.enter_view_name");
5082       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5083               JvOptionPane.QUESTION_MESSAGE);
5084
5085       if (reply != null)
5086       {
5087         viewport.viewName = reply;
5088         // TODO warn if reply is in getExistingViewNames()?
5089         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5090       }
5091     }
5092   }
5093
5094   public AlignViewport getCurrentView()
5095   {
5096     return viewport;
5097   }
5098
5099   /**
5100    * Open the dialog for regex description parsing.
5101    */
5102   @Override
5103   protected void extractScores_actionPerformed(ActionEvent e)
5104   {
5105     ParseProperties pp = new jalview.analysis.ParseProperties(
5106             viewport.getAlignment());
5107     // TODO: verify regex and introduce GUI dialog for version 2.5
5108     // if (pp.getScoresFromDescription("col", "score column ",
5109     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5110     // true)>0)
5111     if (pp.getScoresFromDescription("description column",
5112             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5113     {
5114       buildSortByAnnotationScoresMenu();
5115     }
5116   }
5117
5118   /*
5119    * (non-Javadoc)
5120    *
5121    * @see
5122    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5123    * )
5124    */
5125   @Override
5126   protected void showDbRefs_actionPerformed(ActionEvent e)
5127   {
5128     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5129   }
5130
5131   /*
5132    * (non-Javadoc)
5133    *
5134    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5135    * ActionEvent)
5136    */
5137   @Override
5138   protected void showNpFeats_actionPerformed(ActionEvent e)
5139   {
5140     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5141   }
5142
5143   /**
5144    * find the viewport amongst the tabs in this alignment frame and close that
5145    * tab
5146    *
5147    * @param av
5148    */
5149   public boolean closeView(AlignViewportI av)
5150   {
5151     if (viewport == av)
5152     {
5153       this.closeMenuItem_actionPerformed(false);
5154       return true;
5155     }
5156     Component[] comp = tabbedPane.getComponents();
5157     for (int i = 0; comp != null && i < comp.length; i++)
5158     {
5159       if (comp[i] instanceof AlignmentPanel)
5160       {
5161         if (((AlignmentPanel) comp[i]).av == av)
5162         {
5163           // close the view.
5164           closeView((AlignmentPanel) comp[i]);
5165           return true;
5166         }
5167       }
5168     }
5169     return false;
5170   }
5171
5172   protected void build_fetchdbmenu(JMenu webService)
5173   {
5174     // Temporary hack - DBRef Fetcher always top level ws entry.
5175     // TODO We probably want to store a sequence database checklist in
5176     // preferences and have checkboxes.. rather than individual sources selected
5177     // here
5178     final JMenu rfetch = new JMenu(
5179             MessageManager.getString("action.fetch_db_references"));
5180     rfetch.setToolTipText(MessageManager
5181             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5182     webService.add(rfetch);
5183
5184     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5185             MessageManager.getString("option.trim_retrieved_seqs"));
5186     trimrs.setToolTipText(MessageManager
5187             .getString("label.trim_retrieved_sequences"));
5188     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5189     trimrs.addActionListener(new ActionListener()
5190     {
5191       @Override
5192       public void actionPerformed(ActionEvent e)
5193       {
5194         trimrs.setSelected(trimrs.isSelected());
5195         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5196                 Boolean.valueOf(trimrs.isSelected()).toString());
5197       };
5198     });
5199     rfetch.add(trimrs);
5200     JMenuItem fetchr = new JMenuItem(
5201             MessageManager.getString("label.standard_databases"));
5202     fetchr.setToolTipText(MessageManager
5203             .getString("label.fetch_embl_uniprot"));
5204     fetchr.addActionListener(new ActionListener()
5205     {
5206
5207       @Override
5208       public void actionPerformed(ActionEvent e)
5209       {
5210         new Thread(new Runnable()
5211         {
5212           @Override
5213           public void run()
5214           {
5215             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5216                     .getAlignment().isNucleotide();
5217             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5218                     .getSequenceSelection(), alignPanel.alignFrame, null,
5219                     alignPanel.alignFrame.featureSettings, isNucleotide);
5220             dbRefFetcher.addListener(new FetchFinishedListenerI()
5221             {
5222               @Override
5223               public void finished()
5224               {
5225                 AlignFrame.this.setMenusForViewport();
5226               }
5227             });
5228             dbRefFetcher.fetchDBRefs(false);
5229           }
5230         }).start();
5231
5232       }
5233
5234     });
5235     rfetch.add(fetchr);
5236     final AlignFrame me = this;
5237     new Thread(new Runnable()
5238     {
5239       @Override
5240       public void run()
5241       {
5242         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5243                 .getSequenceFetcherSingleton(me);
5244         javax.swing.SwingUtilities.invokeLater(new Runnable()
5245         {
5246           @Override
5247           public void run()
5248           {
5249             String[] dbclasses = sf.getOrderedSupportedSources();
5250             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5251             // jalview.util.QuickSort.sort(otherdb, otherdb);
5252             List<DbSourceProxy> otherdb;
5253             JMenu dfetch = new JMenu();
5254             JMenu ifetch = new JMenu();
5255             JMenuItem fetchr = null;
5256             int comp = 0, icomp = 0, mcomp = 15;
5257             String mname = null;
5258             int dbi = 0;
5259             for (String dbclass : dbclasses)
5260             {
5261               otherdb = sf.getSourceProxy(dbclass);
5262               // add a single entry for this class, or submenu allowing 'fetch
5263               // all' or pick one
5264               if (otherdb == null || otherdb.size() < 1)
5265               {
5266                 continue;
5267               }
5268               // List<DbSourceProxy> dbs=otherdb;
5269               // otherdb=new ArrayList<DbSourceProxy>();
5270               // for (DbSourceProxy db:dbs)
5271               // {
5272               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5273               // }
5274               if (mname == null)
5275               {
5276                 mname = "From " + dbclass;
5277               }
5278               if (otherdb.size() == 1)
5279               {
5280                 final DbSourceProxy[] dassource = otherdb
5281                         .toArray(new DbSourceProxy[0]);
5282                 DbSourceProxy src = otherdb.get(0);
5283                 fetchr = new JMenuItem(src.getDbSource());
5284                 fetchr.addActionListener(new ActionListener()
5285                 {
5286
5287                   @Override
5288                   public void actionPerformed(ActionEvent e)
5289                   {
5290                     new Thread(new Runnable()
5291                     {
5292
5293                       @Override
5294                       public void run()
5295                       {
5296                         boolean isNucleotide = alignPanel.alignFrame
5297                                 .getViewport().getAlignment()
5298                                 .isNucleotide();
5299                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5300                                 alignPanel.av.getSequenceSelection(),
5301                                 alignPanel.alignFrame, dassource,
5302                                 alignPanel.alignFrame.featureSettings,
5303                                 isNucleotide);
5304                         dbRefFetcher
5305                                 .addListener(new FetchFinishedListenerI()
5306                                 {
5307                                   @Override
5308                                   public void finished()
5309                                   {
5310                                     AlignFrame.this.setMenusForViewport();
5311                                   }
5312                                 });
5313                         dbRefFetcher.fetchDBRefs(false);
5314                       }
5315                     }).start();
5316                   }
5317
5318                 });
5319                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5320                         MessageManager.formatMessage(
5321                                 "label.fetch_retrieve_from",
5322                                 new Object[] { src.getDbName() })));
5323                 dfetch.add(fetchr);
5324                 comp++;
5325               }
5326               else
5327               {
5328                 final DbSourceProxy[] dassource = otherdb
5329                         .toArray(new DbSourceProxy[0]);
5330                 // fetch all entry
5331                 DbSourceProxy src = otherdb.get(0);
5332                 fetchr = new JMenuItem(MessageManager.formatMessage(
5333                         "label.fetch_all_param",
5334                         new Object[] { src.getDbSource() }));
5335                 fetchr.addActionListener(new ActionListener()
5336                 {
5337                   @Override
5338                   public void actionPerformed(ActionEvent e)
5339                   {
5340                     new Thread(new Runnable()
5341                     {
5342
5343                       @Override
5344                       public void run()
5345                       {
5346                         boolean isNucleotide = alignPanel.alignFrame
5347                                 .getViewport().getAlignment()
5348                                 .isNucleotide();
5349                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5350                                 alignPanel.av.getSequenceSelection(),
5351                                 alignPanel.alignFrame, dassource,
5352                                 alignPanel.alignFrame.featureSettings,
5353                                 isNucleotide);
5354                         dbRefFetcher
5355                                 .addListener(new FetchFinishedListenerI()
5356                                 {
5357                                   @Override
5358                                   public void finished()
5359                                   {
5360                                     AlignFrame.this.setMenusForViewport();
5361                                   }
5362                                 });
5363                         dbRefFetcher.fetchDBRefs(false);
5364                       }
5365                     }).start();
5366                   }
5367                 });
5368
5369                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5370                         MessageManager.formatMessage(
5371                                 "label.fetch_retrieve_from_all_sources",
5372                                 new Object[] {
5373                                     Integer.valueOf(otherdb.size())
5374                                             .toString(), src.getDbSource(),
5375                                     src.getDbName() })));
5376                 dfetch.add(fetchr);
5377                 comp++;
5378                 // and then build the rest of the individual menus
5379                 ifetch = new JMenu(MessageManager.formatMessage(
5380                         "label.source_from_db_source",
5381                         new Object[] { src.getDbSource() }));
5382                 icomp = 0;
5383                 String imname = null;
5384                 int i = 0;
5385                 for (DbSourceProxy sproxy : otherdb)
5386                 {
5387                   String dbname = sproxy.getDbName();
5388                   String sname = dbname.length() > 5 ? dbname.substring(0,
5389                           5) + "..." : dbname;
5390                   String msname = dbname.length() > 10 ? dbname.substring(
5391                           0, 10) + "..." : dbname;
5392                   if (imname == null)
5393                   {
5394                     imname = MessageManager.formatMessage(
5395                             "label.from_msname", new Object[] { sname });
5396                   }
5397                   fetchr = new JMenuItem(msname);
5398                   final DbSourceProxy[] dassrc = { sproxy };
5399                   fetchr.addActionListener(new ActionListener()
5400                   {
5401
5402                     @Override
5403                     public void actionPerformed(ActionEvent e)
5404                     {
5405                       new Thread(new Runnable()
5406                       {
5407
5408                         @Override
5409                         public void run()
5410                         {
5411                           boolean isNucleotide = alignPanel.alignFrame
5412                                   .getViewport().getAlignment()
5413                                   .isNucleotide();
5414                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5415                                   alignPanel.av.getSequenceSelection(),
5416                                   alignPanel.alignFrame, dassrc,
5417                                   alignPanel.alignFrame.featureSettings,
5418                                   isNucleotide);
5419                           dbRefFetcher
5420                                   .addListener(new FetchFinishedListenerI()
5421                                   {
5422                                     @Override
5423                                     public void finished()
5424                                     {
5425                                       AlignFrame.this.setMenusForViewport();
5426                                     }
5427                                   });
5428                           dbRefFetcher.fetchDBRefs(false);
5429                         }
5430                       }).start();
5431                     }
5432
5433                   });
5434                   fetchr.setToolTipText("<html>"
5435                           + MessageManager.formatMessage(
5436                                   "label.fetch_retrieve_from", new Object[]
5437                                   { dbname }));
5438                   ifetch.add(fetchr);
5439                   ++i;
5440                   if (++icomp >= mcomp || i == (otherdb.size()))
5441                   {
5442                     ifetch.setText(MessageManager.formatMessage(
5443                             "label.source_to_target", imname, sname));
5444                     dfetch.add(ifetch);
5445                     ifetch = new JMenu();
5446                     imname = null;
5447                     icomp = 0;
5448                     comp++;
5449                   }
5450                 }
5451               }
5452               ++dbi;
5453               if (comp >= mcomp || dbi >= (dbclasses.length))
5454               {
5455                 dfetch.setText(MessageManager.formatMessage(
5456                         "label.source_to_target", mname, dbclass));
5457                 rfetch.add(dfetch);
5458                 dfetch = new JMenu();
5459                 mname = null;
5460                 comp = 0;
5461               }
5462             }
5463           }
5464         });
5465       }
5466     }).start();
5467
5468   }
5469
5470   /**
5471    * Left justify the whole alignment.
5472    */
5473   @Override
5474   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5475   {
5476     AlignmentI al = viewport.getAlignment();
5477     al.justify(false);
5478     viewport.firePropertyChange("alignment", null, al);
5479   }
5480
5481   /**
5482    * Right justify the whole alignment.
5483    */
5484   @Override
5485   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5486   {
5487     AlignmentI al = viewport.getAlignment();
5488     al.justify(true);
5489     viewport.firePropertyChange("alignment", null, al);
5490   }
5491
5492   @Override
5493   public void setShowSeqFeatures(boolean b)
5494   {
5495     showSeqFeatures.setSelected(b);
5496     viewport.setShowSequenceFeatures(b);
5497   }
5498
5499   /*
5500    * (non-Javadoc)
5501    *
5502    * @see
5503    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5504    * awt.event.ActionEvent)
5505    */
5506   @Override
5507   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5508   {
5509     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5510     alignPanel.paintAlignment(true);
5511   }
5512
5513   /*
5514    * (non-Javadoc)
5515    *
5516    * @see
5517    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5518    * .ActionEvent)
5519    */
5520   @Override
5521   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5522   {
5523     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5524     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5525
5526   }
5527
5528   /*
5529    * (non-Javadoc)
5530    *
5531    * @see
5532    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5533    * .event.ActionEvent)
5534    */
5535   @Override
5536   protected void showGroupConservation_actionPerformed(ActionEvent e)
5537   {
5538     viewport.setShowGroupConservation(showGroupConservation.getState());
5539     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5540   }
5541
5542   /*
5543    * (non-Javadoc)
5544    *
5545    * @see
5546    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5547    * .event.ActionEvent)
5548    */
5549   @Override
5550   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5551   {
5552     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5553     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5554   }
5555
5556   /*
5557    * (non-Javadoc)
5558    *
5559    * @see
5560    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5561    * .event.ActionEvent)
5562    */
5563   @Override
5564   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5565   {
5566     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5567     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5568   }
5569
5570   @Override
5571   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5572   {
5573     showSequenceLogo.setState(true);
5574     viewport.setShowSequenceLogo(true);
5575     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5576     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5577   }
5578
5579   @Override
5580   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5581   {
5582     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5583   }
5584
5585   /*
5586    * (non-Javadoc)
5587    *
5588    * @see
5589    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5590    * .event.ActionEvent)
5591    */
5592   @Override
5593   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5594   {
5595     if (avc.makeGroupsFromSelection())
5596     {
5597       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5598       alignPanel.updateAnnotation();
5599       alignPanel.paintAlignment(true);
5600     }
5601   }
5602
5603   public void clearAlignmentSeqRep()
5604   {
5605     // TODO refactor alignmentseqrep to controller
5606     if (viewport.getAlignment().hasSeqrep())
5607     {
5608       viewport.getAlignment().setSeqrep(null);
5609       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5610       alignPanel.updateAnnotation();
5611       alignPanel.paintAlignment(true);
5612     }
5613   }
5614
5615   @Override
5616   protected void createGroup_actionPerformed(ActionEvent e)
5617   {
5618     if (avc.createGroup())
5619     {
5620       alignPanel.alignmentChanged();
5621     }
5622   }
5623
5624   @Override
5625   protected void unGroup_actionPerformed(ActionEvent e)
5626   {
5627     if (avc.unGroup())
5628     {
5629       alignPanel.alignmentChanged();
5630     }
5631   }
5632
5633   /**
5634    * make the given alignmentPanel the currently selected tab
5635    *
5636    * @param alignmentPanel
5637    */
5638   public void setDisplayedView(AlignmentPanel alignmentPanel)
5639   {
5640     if (!viewport.getSequenceSetId().equals(
5641             alignmentPanel.av.getSequenceSetId()))
5642     {
5643       throw new Error(
5644               MessageManager
5645                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5646     }
5647     if (tabbedPane != null
5648             && tabbedPane.getTabCount() > 0
5649             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5650                     .getSelectedIndex())
5651     {
5652       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5653     }
5654   }
5655
5656   /**
5657    * Action on selection of menu options to Show or Hide annotations.
5658    *
5659    * @param visible
5660    * @param forSequences
5661    *          update sequence-related annotations
5662    * @param forAlignment
5663    *          update non-sequence-related annotations
5664    */
5665   @Override
5666   protected void setAnnotationsVisibility(boolean visible,
5667           boolean forSequences, boolean forAlignment)
5668   {
5669     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5670             .getAlignmentAnnotation();
5671     if (anns == null)
5672     {
5673       return;
5674     }
5675     for (AlignmentAnnotation aa : anns)
5676     {
5677       /*
5678        * don't display non-positional annotations on an alignment
5679        */
5680       if (aa.annotations == null)
5681       {
5682         continue;
5683       }
5684       boolean apply = (aa.sequenceRef == null && forAlignment)
5685               || (aa.sequenceRef != null && forSequences);
5686       if (apply)
5687       {
5688         aa.visible = visible;
5689       }
5690     }
5691     alignPanel.validateAnnotationDimensions(true);
5692     alignPanel.alignmentChanged();
5693   }
5694
5695   /**
5696    * Store selected annotation sort order for the view and repaint.
5697    */
5698   @Override
5699   protected void sortAnnotations_actionPerformed()
5700   {
5701     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5702     this.alignPanel.av
5703             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5704     alignPanel.paintAlignment(true);
5705   }
5706
5707   /**
5708    *
5709    * @return alignment panels in this alignment frame
5710    */
5711   public List<? extends AlignmentViewPanel> getAlignPanels()
5712   {
5713     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5714   }
5715
5716   /**
5717    * Open a new alignment window, with the cDNA associated with this (protein)
5718    * alignment, aligned as is the protein.
5719    */
5720   protected void viewAsCdna_actionPerformed()
5721   {
5722     // TODO no longer a menu action - refactor as required
5723     final AlignmentI alignment = getViewport().getAlignment();
5724     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5725     if (mappings == null)
5726     {
5727       return;
5728     }
5729     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5730     for (SequenceI aaSeq : alignment.getSequences())
5731     {
5732       for (AlignedCodonFrame acf : mappings)
5733       {
5734         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5735         if (dnaSeq != null)
5736         {
5737           /*
5738            * There is a cDNA mapping for this protein sequence - add to new
5739            * alignment. It will share the same dataset sequence as other mapped
5740            * cDNA (no new mappings need to be created).
5741            */
5742           final Sequence newSeq = new Sequence(dnaSeq);
5743           newSeq.setDatasetSequence(dnaSeq);
5744           cdnaSeqs.add(newSeq);
5745         }
5746       }
5747     }
5748     if (cdnaSeqs.size() == 0)
5749     {
5750       // show a warning dialog no mapped cDNA
5751       return;
5752     }
5753     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5754             .size()]));
5755     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5756             AlignFrame.DEFAULT_HEIGHT);
5757     cdna.alignAs(alignment);
5758     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5759             + this.title;
5760     Desktop.addInternalFrame(alignFrame, newtitle,
5761             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5762   }
5763
5764   /**
5765    * Set visibility of dna/protein complement view (available when shown in a
5766    * split frame).
5767    *
5768    * @param show
5769    */
5770   @Override
5771   protected void showComplement_actionPerformed(boolean show)
5772   {
5773     SplitContainerI sf = getSplitViewContainer();
5774     if (sf != null)
5775     {
5776       sf.setComplementVisible(this, show);
5777     }
5778   }
5779
5780   /**
5781    * Generate the reverse (optionally complemented) of the selected sequences,
5782    * and add them to the alignment
5783    */
5784   @Override
5785   protected void showReverse_actionPerformed(boolean complement)
5786   {
5787     AlignmentI al = null;
5788     try
5789     {
5790       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5791       al = dna.reverseCdna(complement);
5792       viewport.addAlignment(al, "");
5793       addHistoryItem(new EditCommand(
5794               MessageManager.getString("label.add_sequences"),
5795               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5796               viewport.getAlignment()));
5797     } catch (Exception ex)
5798     {
5799       System.err.println(ex.getMessage());
5800       return;
5801     }
5802   }
5803
5804   /**
5805    * Try to run a script in the Groovy console, having first ensured that this
5806    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5807    * be targeted at this alignment.
5808    */
5809   @Override
5810   protected void runGroovy_actionPerformed()
5811   {
5812     Jalview.setCurrentAlignFrame(this);
5813     groovy.ui.Console console = Desktop.getGroovyConsole();
5814     if (console != null)
5815     {
5816       try
5817       {
5818         console.runScript();
5819       } catch (Exception ex)
5820       {
5821         System.err.println((ex.toString()));
5822         JvOptionPane
5823                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5824                         .getString("label.couldnt_run_groovy_script"),
5825                         MessageManager
5826                                 .getString("label.groovy_support_failed"),
5827                         JvOptionPane.ERROR_MESSAGE);
5828       }
5829     }
5830     else
5831     {
5832       System.err.println("Can't run Groovy script as console not found");
5833     }
5834   }
5835
5836   /**
5837    * Hides columns containing (or not containing) a specified feature, provided
5838    * that would not leave all columns hidden
5839    *
5840    * @param featureType
5841    * @param columnsContaining
5842    * @return
5843    */
5844   public boolean hideFeatureColumns(String featureType,
5845           boolean columnsContaining)
5846   {
5847     boolean notForHiding = avc.markColumnsContainingFeatures(
5848             columnsContaining, false, false, featureType);
5849     if (notForHiding)
5850     {
5851       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5852               false, featureType))
5853       {
5854         getViewport().hideSelectedColumns();
5855         return true;
5856       }
5857     }
5858     return false;
5859   }
5860
5861   @Override
5862   protected void selectHighlightedColumns_actionPerformed(
5863           ActionEvent actionEvent)
5864   {
5865     // include key modifier check in case user selects from menu
5866     avc.markHighlightedColumns(
5867             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5868             true,
5869             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5870   }
5871 }
5872
5873 class PrintThread extends Thread
5874 {
5875   AlignmentPanel ap;
5876
5877   public PrintThread(AlignmentPanel ap)
5878   {
5879     this.ap = ap;
5880   }
5881
5882   static PageFormat pf;
5883
5884   @Override
5885   public void run()
5886   {
5887     PrinterJob printJob = PrinterJob.getPrinterJob();
5888
5889     if (pf != null)
5890     {
5891       printJob.setPrintable(ap, pf);
5892     }
5893     else
5894     {
5895       printJob.setPrintable(ap);
5896     }
5897
5898     if (printJob.printDialog())
5899     {
5900       try
5901       {
5902         printJob.print();
5903       } catch (Exception PrintException)
5904       {
5905         PrintException.printStackTrace();
5906       }
5907     }
5908   }
5909 }