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.FileLoader;
  67 import jalview.io.FormatAdapter;
  68 import jalview.io.HtmlSvgOutput;
  69 import jalview.io.IdentifyFile;
  70 import jalview.io.JalviewFileChooser;
  71 import jalview.io.JalviewFileView;
  72 import jalview.io.JnetAnnotationMaker;
  73 import jalview.io.NewickFile;
  74 import jalview.io.TCoffeeScoreFile;
  75 import jalview.jbgui.GAlignFrame;
  76 import jalview.schemes.Blosum62ColourScheme;
  77 import jalview.schemes.BuriedColourScheme;
  78 import jalview.schemes.ClustalxColourScheme;
  79 import jalview.schemes.ColourSchemeI;
  80 import jalview.schemes.ColourSchemeProperty;
  81 import jalview.schemes.HelixColourScheme;
  82 import jalview.schemes.HydrophobicColourScheme;
  83 import jalview.schemes.NucleotideColourScheme;
  84 import jalview.schemes.PIDColourScheme;
  85 import jalview.schemes.PurinePyrimidineColourScheme;
  86 import jalview.schemes.RNAHelicesColourChooser;
  87 import jalview.schemes.ResidueProperties;
  88 import jalview.schemes.StrandColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.schemes.TaylorColourScheme;
  91 import jalview.schemes.TurnColourScheme;
  92 import jalview.schemes.UserColourScheme;
  93 import jalview.schemes.ZappoColourScheme;
  94 import jalview.structure.StructureSelectionManager;
  95 import jalview.util.MessageManager;
  96 import jalview.viewmodel.AlignmentViewport;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Rectangle;
 105 import java.awt.Toolkit;
 106 import java.awt.datatransfer.Clipboard;
 107 import java.awt.datatransfer.DataFlavor;
 108 import java.awt.datatransfer.StringSelection;
 109 import java.awt.datatransfer.Transferable;
 110 import java.awt.dnd.DnDConstants;
 111 import java.awt.dnd.DropTargetDragEvent;
 112 import java.awt.dnd.DropTargetDropEvent;
 113 import java.awt.dnd.DropTargetEvent;
 114 import java.awt.dnd.DropTargetListener;
 115 import java.awt.event.ActionEvent;
 116 import java.awt.event.ActionListener;
 117 import java.awt.event.ItemEvent;
 118 import java.awt.event.ItemListener;
 119 import java.awt.event.KeyAdapter;
 120 import java.awt.event.KeyEvent;
 121 import java.awt.event.MouseAdapter;
 122 import java.awt.event.MouseEvent;
 123 import java.awt.print.PageFormat;
 124 import java.awt.print.PrinterJob;
 125 import java.beans.PropertyChangeEvent;
 126 import java.io.File;
 127 import java.net.URL;
 128 import java.util.ArrayList;
 129 import java.util.Arrays;
 130 import java.util.Deque;
 131 import java.util.Enumeration;
 132 import java.util.Hashtable;
 133 import java.util.List;
 134 import java.util.Set;
 135 import java.util.Vector;
 136
 137 import javax.swing.JCheckBoxMenuItem;
 138 import javax.swing.JEditorPane;
 139 import javax.swing.JInternalFrame;
 140 import javax.swing.JLayeredPane;
 141 import javax.swing.JMenu;
 142 import javax.swing.JMenuItem;
 143 import javax.swing.JOptionPane;
 144 import javax.swing.JRadioButtonMenuItem;
 145 import javax.swing.JScrollPane;
 146 import javax.swing.SwingUtilities;
 147
 148 /**
 149  * DOCUMENT ME!
 150  *
 151  * @author $author$
 152  * @version $Revision$
 153  */
 154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 155         IProgressIndicator, AlignViewControllerGuiI
 156 {
 157
 158   public static final int DEFAULT_WIDTH = 700;
 159
 160   public static final int DEFAULT_HEIGHT = 500;
 161
 162   /*
 163    * The currently displayed panel (selected tabbed view if more than one)
 164    */
 165   public AlignmentPanel alignPanel;
 166
 167   AlignViewport viewport;
 168
 169   public AlignViewControllerI avc;
 170
 171   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 172
 173   /**
 174    * Last format used to load or save alignments in this window
 175    */
 176   String currentFileFormat = null;
 177
 178   /**
 179    * Current filename for this alignment
 180    */
 181   String fileName = null;
 182
 183   /**
 184    * Creates a new AlignFrame object with specific width and height.
 185    *
 186    * @param al
 187    * @param width
 188    * @param height
 189    */
 190   public AlignFrame(AlignmentI al, int width, int height)
 191   {
 192     this(al, null, width, height);
 193   }
 194
 195   /**
 196    * Creates a new AlignFrame object with specific width, height and
 197    * sequenceSetId
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    * @param sequenceSetId
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height,
 205           String sequenceSetId)
 206   {
 207     this(al, null, width, height, sequenceSetId);
 208   }
 209
 210   /**
 211    * Creates a new AlignFrame object with specific width, height and
 212    * sequenceSetId
 213    *
 214    * @param al
 215    * @param width
 216    * @param height
 217    * @param sequenceSetId
 218    * @param viewId
 219    */
 220   public AlignFrame(AlignmentI al, int width, int height,
 221           String sequenceSetId, String viewId)
 222   {
 223     this(al, null, width, height, sequenceSetId, viewId);
 224   }
 225
 226   /**
 227    * new alignment window with hidden columns
 228    *
 229    * @param al
 230    *          AlignmentI
 231    * @param hiddenColumns
 232    *          ColumnSelection or null
 233    * @param width
 234    *          Width of alignment frame
 235    * @param height
 236    *          height of frame.
 237    */
 238   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 239           int width, int height)
 240   {
 241     this(al, hiddenColumns, width, height, null);
 242   }
 243
 244   /**
 245    * Create alignment frame for al with hiddenColumns, a specific width and
 246    * height, and specific sequenceId
 247    *
 248    * @param al
 249    * @param hiddenColumns
 250    * @param width
 251    * @param height
 252    * @param sequenceSetId
 253    *          (may be null)
 254    */
 255   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 256           int width, int height, String sequenceSetId)
 257   {
 258     this(al, hiddenColumns, width, height, sequenceSetId, null);
 259   }
 260
 261   /**
 262    * Create alignment frame for al with hiddenColumns, a specific width and
 263    * height, and specific sequenceId
 264    *
 265    * @param al
 266    * @param hiddenColumns
 267    * @param width
 268    * @param height
 269    * @param sequenceSetId
 270    *          (may be null)
 271    * @param viewId
 272    *          (may be null)
 273    */
 274   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 275           int width, int height, String sequenceSetId, String viewId)
 276   {
 277     setSize(width, height);
 278
 279     if (al.getDataset() == null)
 280     {
 281       al.setDataset(null);
 282     }
 283
 284     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 285
 286     alignPanel = new AlignmentPanel(this, viewport);
 287
 288     addAlignmentPanel(alignPanel, true);
 289     init();
 290   }
 291
 292   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 293           ColumnSelection hiddenColumns, int width, int height)
 294   {
 295     setSize(width, height);
 296
 297     if (al.getDataset() == null)
 298     {
 299       al.setDataset(null);
 300     }
 301
 302     viewport = new AlignViewport(al, hiddenColumns);
 303
 304     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 305     {
 306       viewport.hideSequence(hiddenSeqs);
 307     }
 308     alignPanel = new AlignmentPanel(this, viewport);
 309     addAlignmentPanel(alignPanel, true);
 310     init();
 311   }
 312
 313   /**
 314    * Make a new AlignFrame from existing alignmentPanels
 315    *
 316    * @param ap
 317    *          AlignmentPanel
 318    * @param av
 319    *          AlignViewport
 320    */
 321   public AlignFrame(AlignmentPanel ap)
 322   {
 323     viewport = ap.av;
 324     alignPanel = ap;
 325     addAlignmentPanel(ap, false);
 326     init();
 327   }
 328
 329   /**
 330    * initalise the alignframe from the underlying viewport data and the
 331    * configurations
 332    */
 333   void init()
 334   {
 335     if (!Jalview.isHeadlessMode())
 336     {
 337       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 338     }
 339
 340     avc = new jalview.controller.AlignViewController(this, viewport,
 341             alignPanel);
 342     if (viewport.getAlignmentConservationAnnotation() == null)
 343     {
 344       BLOSUM62Colour.setEnabled(false);
 345       conservationMenuItem.setEnabled(false);
 346       modifyConservation.setEnabled(false);
 347       // PIDColour.setEnabled(false);
 348       // abovePIDThreshold.setEnabled(false);
 349       // modifyPID.setEnabled(false);
 350     }
 351
 352     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 353             "No sort");
 354
 355     if (sortby.equals("Id"))
 356     {
 357       sortIDMenuItem_actionPerformed(null);
 358     }
 359     else if (sortby.equals("Pairwise Identity"))
 360     {
 361       sortPairwiseMenuItem_actionPerformed(null);
 362     }
 363
 364     if (Desktop.desktop != null)
 365     {
 366       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 367       addServiceListeners();
 368       setGUINucleotide(viewport.getAlignment().isNucleotide());
 369     }
 370
 371     this.alignPanel.av
 372             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 373
 374     setMenusFromViewport(viewport);
 375     buildSortByAnnotationScoresMenu();
 376     buildTreeMenu();
 377
 378     if (viewport.getWrapAlignment())
 379     {
 380       wrapMenuItem_actionPerformed(null);
 381     }
 382
 383     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 384     {
 385       this.overviewMenuItem_actionPerformed(null);
 386     }
 387
 388     addKeyListener();
 389
 390     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 391     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 392     final String menuLabel = MessageManager
 393             .getString("label.copy_format_from");
 394     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 395             new ViewSetProvider()
 396             {
 397
 398               @Override
 399               public AlignmentPanel[] getAllAlignmentPanels()
 400               {
 401                 origview.clear();
 402                 origview.add(alignPanel);
 403                 // make an array of all alignment panels except for this one
 404                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 405                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 406                 aps.remove(AlignFrame.this.alignPanel);
 407                 return aps.toArray(new AlignmentPanel[aps.size()]);
 408               }
 409             }, selviews, new ItemListener()
 410             {
 411
 412               @Override
 413               public void itemStateChanged(ItemEvent e)
 414               {
 415                 if (origview.size() > 0)
 416                 {
 417                   final AlignmentPanel ap = origview.get(0);
 418
 419                   /*
 420                    * Copy the ViewStyle of the selected panel to 'this one'.
 421                    * Don't change value of 'scaleProteinAsCdna' unless copying
 422                    * from a SplitFrame.
 423                    */
 424                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 425                           .getViewStyle();
 426                   boolean fromSplitFrame = selviews.get(0)
 427                           .getAlignViewport().getCodingComplement() != null;
 428                   if (!fromSplitFrame)
 429                   {
 430                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 431                             .getViewStyle().isScaleProteinAsCdna());
 432                   }
 433                   ap.getAlignViewport().setViewStyle(vs);
 434
 435                   /*
 436                    * Also rescale ViewStyle of SplitFrame complement if there is
 437                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 438                    * the whole ViewStyle (allow cDNA protein to have different
 439                    * fonts)
 440                    */
 441                   AlignViewportI complement = ap.getAlignViewport()
 442                           .getCodingComplement();
 443                   if (complement != null && vs.isScaleProteinAsCdna())
 444                   {
 445                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 446                     ((SplitFrame) af.getSplitViewContainer())
 447                             .adjustLayout();
 448                     af.setMenusForViewport();
 449                   }
 450
 451                   ap.updateLayout();
 452                   ap.setSelected(true);
 453                   ap.alignFrame.setMenusForViewport();
 454
 455                 }
 456               }
 457             });
 458     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 459             .indexOf("devel") > -1
 460             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 461                     .indexOf("test") > -1)
 462     {
 463       formatMenu.add(vsel);
 464     }
 465
 466   }
 467
 468   /**
 469    * Change the filename and format for the alignment, and enable the 'reload'
 470    * button functionality.
 471    *
 472    * @param file
 473    *          valid filename
 474    * @param format
 475    *          format of file
 476    */
 477   public void setFileName(String file, String format)
 478   {
 479     fileName = file;
 480     setFileFormat(format);
 481     reload.setEnabled(true);
 482   }
 483
 484   /**
 485    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 486    * events
 487    */
 488   void addKeyListener()
 489   {
 490     addKeyListener(new KeyAdapter()
 491     {
 492       @Override
 493       public void keyPressed(KeyEvent evt)
 494       {
 495         if (viewport.cursorMode
 496                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 497                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 498                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 499                 && Character.isDigit(evt.getKeyChar()))
 500         {
 501           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 502         }
 503
 504         switch (evt.getKeyCode())
 505         {
 506
 507         case 27: // escape key
 508           deselectAllSequenceMenuItem_actionPerformed(null);
 509
 510           break;
 511
 512         case KeyEvent.VK_DOWN:
 513           if (evt.isAltDown() || !viewport.cursorMode)
 514           {
 515             moveSelectedSequences(false);
 516           }
 517           if (viewport.cursorMode)
 518           {
 519             alignPanel.getSeqPanel().moveCursor(0, 1);
 520           }
 521           break;
 522
 523         case KeyEvent.VK_UP:
 524           if (evt.isAltDown() || !viewport.cursorMode)
 525           {
 526             moveSelectedSequences(true);
 527           }
 528           if (viewport.cursorMode)
 529           {
 530             alignPanel.getSeqPanel().moveCursor(0, -1);
 531           }
 532
 533           break;
 534
 535         case KeyEvent.VK_LEFT:
 536           if (evt.isAltDown() || !viewport.cursorMode)
 537           {
 538             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 539           }
 540           else
 541           {
 542             alignPanel.getSeqPanel().moveCursor(-1, 0);
 543           }
 544
 545           break;
 546
 547         case KeyEvent.VK_RIGHT:
 548           if (evt.isAltDown() || !viewport.cursorMode)
 549           {
 550             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 551           }
 552           else
 553           {
 554             alignPanel.getSeqPanel().moveCursor(1, 0);
 555           }
 556           break;
 557
 558         case KeyEvent.VK_SPACE:
 559           if (viewport.cursorMode)
 560           {
 561             alignPanel.getSeqPanel().insertGapAtCursor(
 562                     evt.isControlDown() || evt.isShiftDown()
 563                             || evt.isAltDown());
 564           }
 565           break;
 566
 567         // case KeyEvent.VK_A:
 568         // if (viewport.cursorMode)
 569         // {
 570         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 571         // //System.out.println("A");
 572         // }
 573         // break;
 574         /*
 575          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 576          * System.out.println("closing bracket"); } break;
 577          */
 578         case KeyEvent.VK_DELETE:
 579         case KeyEvent.VK_BACK_SPACE:
 580           if (!viewport.cursorMode)
 581           {
 582             cut_actionPerformed(null);
 583           }
 584           else
 585           {
 586             alignPanel.getSeqPanel().deleteGapAtCursor(
 587                     evt.isControlDown() || evt.isShiftDown()
 588                             || evt.isAltDown());
 589           }
 590
 591           break;
 592
 593         case KeyEvent.VK_S:
 594           if (viewport.cursorMode)
 595           {
 596             alignPanel.getSeqPanel().setCursorRow();
 597           }
 598           break;
 599         case KeyEvent.VK_C:
 600           if (viewport.cursorMode && !evt.isControlDown())
 601           {
 602             alignPanel.getSeqPanel().setCursorColumn();
 603           }
 604           break;
 605         case KeyEvent.VK_P:
 606           if (viewport.cursorMode)
 607           {
 608             alignPanel.getSeqPanel().setCursorPosition();
 609           }
 610           break;
 611
 612         case KeyEvent.VK_ENTER:
 613         case KeyEvent.VK_COMMA:
 614           if (viewport.cursorMode)
 615           {
 616             alignPanel.getSeqPanel().setCursorRowAndColumn();
 617           }
 618           break;
 619
 620         case KeyEvent.VK_Q:
 621           if (viewport.cursorMode)
 622           {
 623             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 624           }
 625           break;
 626         case KeyEvent.VK_M:
 627           if (viewport.cursorMode)
 628           {
 629             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 630           }
 631           break;
 632
 633         case KeyEvent.VK_F2:
 634           viewport.cursorMode = !viewport.cursorMode;
 635           statusBar.setText(MessageManager.formatMessage(
 636                   "label.keyboard_editing_mode",
 637                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 641             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 642           }
 643           alignPanel.getSeqPanel().seqCanvas.repaint();
 644           break;
 645
 646         case KeyEvent.VK_F1:
 647           try
 648           {
 649             Help.showHelpWindow();
 650           } catch (Exception ex)
 651           {
 652             ex.printStackTrace();
 653           }
 654           break;
 655         case KeyEvent.VK_H:
 656         {
 657           boolean toggleSeqs = !evt.isControlDown();
 658           boolean toggleCols = !evt.isShiftDown();
 659           toggleHiddenRegions(toggleSeqs, toggleCols);
 660           break;
 661         }
 662         case KeyEvent.VK_PAGE_UP:
 663           if (viewport.getWrapAlignment())
 664           {
 665             alignPanel.scrollUp(true);
 666           }
 667           else
 668           {
 669             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 670                     - viewport.endSeq + viewport.startSeq);
 671           }
 672           break;
 673         case KeyEvent.VK_PAGE_DOWN:
 674           if (viewport.getWrapAlignment())
 675           {
 676             alignPanel.scrollUp(false);
 677           }
 678           else
 679           {
 680             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 681                     + viewport.endSeq - viewport.startSeq);
 682           }
 683           break;
 684         }
 685       }
 686
 687       @Override
 688       public void keyReleased(KeyEvent evt)
 689       {
 690         switch (evt.getKeyCode())
 691         {
 692         case KeyEvent.VK_LEFT:
 693           if (evt.isAltDown() || !viewport.cursorMode)
 694           {
 695             viewport.firePropertyChange("alignment", null, viewport
 696                     .getAlignment().getSequences());
 697           }
 698           break;
 699
 700         case KeyEvent.VK_RIGHT:
 701           if (evt.isAltDown() || !viewport.cursorMode)
 702           {
 703             viewport.firePropertyChange("alignment", null, viewport
 704                     .getAlignment().getSequences());
 705           }
 706           break;
 707         }
 708       }
 709     });
 710   }
 711
 712   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 713   {
 714     ap.alignFrame = this;
 715     avc = new jalview.controller.AlignViewController(this, viewport,
 716             alignPanel);
 717
 718     alignPanels.add(ap);
 719
 720     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 721
 722     int aSize = alignPanels.size();
 723
 724     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 725
 726     if (aSize == 1 && ap.av.viewName == null)
 727     {
 728       this.getContentPane().add(ap, BorderLayout.CENTER);
 729     }
 730     else
 731     {
 732       if (aSize == 2)
 733       {
 734         setInitialTabVisible();
 735       }
 736
 737       expandViews.setEnabled(true);
 738       gatherViews.setEnabled(true);
 739       tabbedPane.addTab(ap.av.viewName, ap);
 740
 741       ap.setVisible(false);
 742     }
 743
 744     if (newPanel)
 745     {
 746       if (ap.av.isPadGaps())
 747       {
 748         ap.av.getAlignment().padGaps();
 749       }
 750       ap.av.updateConservation(ap);
 751       ap.av.updateConsensus(ap);
 752       ap.av.updateStrucConsensus(ap);
 753     }
 754   }
 755
 756   public void setInitialTabVisible()
 757   {
 758     expandViews.setEnabled(true);
 759     gatherViews.setEnabled(true);
 760     tabbedPane.setVisible(true);
 761     AlignmentPanel first = alignPanels.get(0);
 762     tabbedPane.addTab(first.av.viewName, first);
 763     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 764   }
 765
 766   public AlignViewport getViewport()
 767   {
 768     return viewport;
 769   }
 770
 771   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 772   private void addServiceListeners()
 773   {
 774     final java.beans.PropertyChangeListener thisListener;
 775     Desktop.instance.addJalviewPropertyChangeListener("services",
 776             thisListener = new java.beans.PropertyChangeListener()
 777             {
 778               @Override
 779               public void propertyChange(PropertyChangeEvent evt)
 780               {
 781                 // // System.out.println("Discoverer property change.");
 782                 // if (evt.getPropertyName().equals("services"))
 783                 {
 784                   SwingUtilities.invokeLater(new Runnable()
 785                   {
 786
 787                     @Override
 788                     public void run()
 789                     {
 790                       System.err
 791                               .println("Rebuild WS Menu for service change");
 792                       BuildWebServiceMenu();
 793                     }
 794
 795                   });
 796                 }
 797               }
 798             });
 799     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 800     {
 801       @Override
 802       public void internalFrameClosed(
 803               javax.swing.event.InternalFrameEvent evt)
 804       {
 805         // System.out.println("deregistering discoverer listener");
 806         Desktop.instance.removeJalviewPropertyChangeListener("services",
 807                 thisListener);
 808         closeMenuItem_actionPerformed(true);
 809       };
 810     });
 811     // Finally, build the menu once to get current service state
 812     new Thread(new Runnable()
 813     {
 814       @Override
 815       public void run()
 816       {
 817         BuildWebServiceMenu();
 818       }
 819     }).start();
 820   }
 821
 822   /**
 823    * Configure menu items that vary according to whether the alignment is
 824    * nucleotide or protein
 825    *
 826    * @param nucleotide
 827    */
 828   public void setGUINucleotide(boolean nucleotide)
 829   {
 830     showTranslation.setVisible(nucleotide);
 831     conservationMenuItem.setEnabled(!nucleotide);
 832     modifyConservation.setEnabled(!nucleotide);
 833     showGroupConservation.setEnabled(!nucleotide);
 834     rnahelicesColour.setEnabled(nucleotide);
 835     purinePyrimidineColour.setEnabled(nucleotide);
 836     showComplementMenuItem.setText(MessageManager
 837             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 838     setColourSelected(jalview.bin.Cache.getDefault(
 839             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 840                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 841   }
 842
 843   /**
 844    * set up menus for the current viewport. This may be called after any
 845    * operation that affects the data in the current view (selection changed,
 846    * etc) to update the menus to reflect the new state.
 847    */
 848   @Override
 849   public void setMenusForViewport()
 850   {
 851     setMenusFromViewport(viewport);
 852   }
 853
 854   /**
 855    * Need to call this method when tabs are selected for multiple views, or when
 856    * loading from Jalview2XML.java
 857    *
 858    * @param av
 859    *          AlignViewport
 860    */
 861   void setMenusFromViewport(AlignViewport av)
 862   {
 863     padGapsMenuitem.setSelected(av.isPadGaps());
 864     colourTextMenuItem.setSelected(av.isShowColourText());
 865     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 866     conservationMenuItem.setSelected(av.getConservationSelected());
 867     seqLimits.setSelected(av.getShowJVSuffix());
 868     idRightAlign.setSelected(av.isRightAlignIds());
 869     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 870     renderGapsMenuItem.setSelected(av.isRenderGaps());
 871     wrapMenuItem.setSelected(av.getWrapAlignment());
 872     scaleAbove.setVisible(av.getWrapAlignment());
 873     scaleLeft.setVisible(av.getWrapAlignment());
 874     scaleRight.setVisible(av.getWrapAlignment());
 875     annotationPanelMenuItem.setState(av.isShowAnnotation());
 876     /*
 877      * Show/hide annotations only enabled if annotation panel is shown
 878      */
 879     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 880     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 881     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 882     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 883     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 884     viewTextMenuItem.setSelected(av.getShowText());
 885     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 886     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 887     showGroupConservation.setSelected(av.isShowGroupConservation());
 888     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 889     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 890     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 891
 892     setColourSelected(ColourSchemeProperty.getColourName(av
 893             .getGlobalColourScheme()));
 894
 895     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 896     hiddenMarkers.setState(av.getShowHiddenMarkers());
 897     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 898     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 899     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 900     autoCalculate.setSelected(av.autoCalculateConsensus);
 901     sortByTree.setSelected(av.sortByTree);
 902     listenToViewSelections.setSelected(av.followSelection);
 903     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 904     rnahelicesColour
 905             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 906     setShowProductsEnabled();
 907     updateEditMenuBar();
 908   }
 909
 910   private IProgressIndicator progressBar;
 911
 912   /*
 913    * (non-Javadoc)
 914    *
 915    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 916    */
 917   @Override
 918   public void setProgressBar(String message, long id)
 919   {
 920     progressBar.setProgressBar(message, id);
 921   }
 922
 923   @Override
 924   public void registerHandler(final long id,
 925           final IProgressIndicatorHandler handler)
 926   {
 927     progressBar.registerHandler(id, handler);
 928   }
 929
 930   /**
 931    *
 932    * @return true if any progress bars are still active
 933    */
 934   @Override
 935   public boolean operationInProgress()
 936   {
 937     return progressBar.operationInProgress();
 938   }
 939
 940   @Override
 941   public void setStatus(String text)
 942   {
 943     statusBar.setText(text);
 944   }
 945
 946   /*
 947    * Added so Castor Mapping file can obtain Jalview Version
 948    */
 949   public String getVersion()
 950   {
 951     return jalview.bin.Cache.getProperty("VERSION");
 952   }
 953
 954   public FeatureRenderer getFeatureRenderer()
 955   {
 956     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 957   }
 958
 959   @Override
 960   public void fetchSequence_actionPerformed(ActionEvent e)
 961   {
 962     new SequenceFetcher(this);
 963   }
 964
 965   @Override
 966   public void addFromFile_actionPerformed(ActionEvent e)
 967   {
 968     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 969   }
 970
 971   @Override
 972   public void reload_actionPerformed(ActionEvent e)
 973   {
 974     if (fileName != null)
 975     {
 976       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 977       // originating file's format
 978       // TODO: work out how to recover feature settings for correct view(s) when
 979       // file is reloaded.
 980       if (currentFileFormat.equals("Jalview"))
 981       {
 982         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 983         for (int i = 0; i < frames.length; i++)
 984         {
 985           if (frames[i] instanceof AlignFrame && frames[i] != this
 986                   && ((AlignFrame) frames[i]).fileName != null
 987                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 988           {
 989             try
 990             {
 991               frames[i].setSelected(true);
 992               Desktop.instance.closeAssociatedWindows();
 993             } catch (java.beans.PropertyVetoException ex)
 994             {
 995             }
 996           }
 997
 998         }
 999         Desktop.instance.closeAssociatedWindows();
1000
1001         FileLoader loader = new FileLoader();
1002         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1003         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1004       }
1005       else
1006       {
1007         Rectangle bounds = this.getBounds();
1008
1009         FileLoader loader = new FileLoader();
1010         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1011         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1012                 protocol, currentFileFormat);
1013
1014         newframe.setBounds(bounds);
1015         if (featureSettings != null && featureSettings.isShowing())
1016         {
1017           final Rectangle fspos = featureSettings.frame.getBounds();
1018           // TODO: need a 'show feature settings' function that takes bounds -
1019           // need to refactor Desktop.addFrame
1020           newframe.featureSettings_actionPerformed(null);
1021           final FeatureSettings nfs = newframe.featureSettings;
1022           SwingUtilities.invokeLater(new Runnable()
1023           {
1024             @Override
1025             public void run()
1026             {
1027               nfs.frame.setBounds(fspos);
1028             }
1029           });
1030           this.featureSettings.close();
1031           this.featureSettings = null;
1032         }
1033         this.closeMenuItem_actionPerformed(true);
1034       }
1035     }
1036   }
1037
1038   @Override
1039   public void addFromText_actionPerformed(ActionEvent e)
1040   {
1041     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1042             .getAlignPanel());
1043   }
1044
1045   @Override
1046   public void addFromURL_actionPerformed(ActionEvent e)
1047   {
1048     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1049   }
1050
1051   @Override
1052   public void save_actionPerformed(ActionEvent e)
1053   {
1054     if (fileName == null
1055             || (currentFileFormat == null || !jalview.io.FormatAdapter
1056                     .isValidIOFormat(currentFileFormat, true))
1057             || fileName.startsWith("http"))
1058     {
1059       saveAs_actionPerformed(null);
1060     }
1061     else
1062     {
1063       saveAlignment(fileName, currentFileFormat);
1064     }
1065   }
1066
1067   /**
1068    * DOCUMENT ME!
1069    *
1070    * @param e
1071    *          DOCUMENT ME!
1072    */
1073   @Override
1074   public void saveAs_actionPerformed(ActionEvent e)
1075   {
1076     JalviewFileChooser chooser = new JalviewFileChooser(
1077             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1078             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1079             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1080             currentFileFormat, false);
1081
1082     chooser.setFileView(new JalviewFileView());
1083     chooser.setDialogTitle(MessageManager
1084             .getString("label.save_alignment_to_file"));
1085     chooser.setToolTipText(MessageManager.getString("action.save"));
1086
1087     int value = chooser.showSaveDialog(this);
1088
1089     if (value == JalviewFileChooser.APPROVE_OPTION)
1090     {
1091       currentFileFormat = chooser.getSelectedFormat();
1092       while (currentFileFormat == null)
1093       {
1094         JOptionPane
1095                 .showInternalMessageDialog(
1096                         Desktop.desktop,
1097                         MessageManager
1098                                 .getString("label.select_file_format_before_saving"),
1099                         MessageManager
1100                                 .getString("label.file_format_not_specified"),
1101                         JOptionPane.WARNING_MESSAGE);
1102         currentFileFormat = chooser.getSelectedFormat();
1103         value = chooser.showSaveDialog(this);
1104         if (value != JalviewFileChooser.APPROVE_OPTION)
1105         {
1106           return;
1107         }
1108       }
1109
1110       fileName = chooser.getSelectedFile().getPath();
1111
1112       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1113               currentFileFormat);
1114
1115       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1116       if (currentFileFormat.indexOf(" ") > -1)
1117       {
1118         currentFileFormat = currentFileFormat.substring(0,
1119                 currentFileFormat.indexOf(" "));
1120       }
1121       saveAlignment(fileName, currentFileFormat);
1122     }
1123   }
1124
1125   public boolean saveAlignment(String file, String format)
1126   {
1127     boolean success = true;
1128
1129     if (format.equalsIgnoreCase("Jalview"))
1130     {
1131       String shortName = title;
1132
1133       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1134       {
1135         shortName = shortName.substring(shortName
1136                 .lastIndexOf(java.io.File.separatorChar) + 1);
1137       }
1138
1139       success = new Jalview2XML().saveAlignment(this, file, shortName);
1140
1141       statusBar.setText(MessageManager.formatMessage(
1142               "label.successfully_saved_to_file_in_format", new Object[] {
1143                   fileName, format }));
1144
1145     }
1146     else
1147     {
1148       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1149       {
1150         warningMessage("Cannot save file " + fileName + " using format "
1151                 + format, "Alignment output format not supported");
1152         if (!Jalview.isHeadlessMode())
1153         {
1154           saveAs_actionPerformed(null);
1155         }
1156         return false;
1157       }
1158
1159       AlignmentExportData exportData = getAlignmentForExport(format,
1160               viewport, null);
1161       if (exportData.getSettings().isCancelled())
1162       {
1163         return false;
1164       }
1165       FormatAdapter f = new FormatAdapter(alignPanel,
1166               exportData.getSettings());
1167       String output = f.formatSequences(
1168               format,
1169               exportData.getAlignment(), // class cast exceptions will
1170               // occur in the distant future
1171               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1172               f.getCacheSuffixDefault(format),
1173               viewport.getColumnSelection());
1174
1175       if (output == null)
1176       {
1177         success = false;
1178       }
1179       else
1180       {
1181         try
1182         {
1183           java.io.PrintWriter out = new java.io.PrintWriter(
1184                   new java.io.FileWriter(file));
1185
1186           out.print(output);
1187           out.close();
1188           this.setTitle(file);
1189           statusBar.setText(MessageManager.formatMessage(
1190                   "label.successfully_saved_to_file_in_format",
1191                   new Object[] { fileName, format }));
1192         } catch (Exception ex)
1193         {
1194           success = false;
1195           ex.printStackTrace();
1196         }
1197       }
1198     }
1199
1200     if (!success)
1201     {
1202       JOptionPane.showInternalMessageDialog(this, MessageManager
1203               .formatMessage("label.couldnt_save_file",
1204                       new Object[] { fileName }), MessageManager
1205               .getString("label.error_saving_file"),
1206               JOptionPane.WARNING_MESSAGE);
1207     }
1208
1209     return success;
1210   }
1211
1212   private void warningMessage(String warning, String title)
1213   {
1214     if (new jalview.util.Platform().isHeadless())
1215     {
1216       System.err.println("Warning: " + title + "\nWarning: " + warning);
1217
1218     }
1219     else
1220     {
1221       JOptionPane.showInternalMessageDialog(this, warning, title,
1222               JOptionPane.WARNING_MESSAGE);
1223     }
1224     return;
1225   }
1226
1227   /**
1228    * DOCUMENT ME!
1229    *
1230    * @param e
1231    *          DOCUMENT ME!
1232    */
1233   @Override
1234   protected void outputText_actionPerformed(ActionEvent e)
1235   {
1236
1237     AlignmentExportData exportData = getAlignmentForExport(
1238             e.getActionCommand(), viewport, null);
1239     if (exportData.getSettings().isCancelled())
1240     {
1241       return;
1242     }
1243     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1244     cap.setForInput(null);
1245     try
1246     {
1247       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1248               .formatSequences(e.getActionCommand(),
1249                       exportData.getAlignment(),
1250                       exportData.getOmitHidden(),
1251                       exportData.getStartEndPostions(),
1252                       viewport.getColumnSelection()));
1253       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1254               "label.alignment_output_command",
1255               new Object[] { e.getActionCommand() }), 600, 500);
1256     } catch (OutOfMemoryError oom)
1257     {
1258       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1259       cap.dispose();
1260     }
1261
1262   }
1263
1264   public static AlignmentExportData getAlignmentForExport(
1265           String exportFormat, AlignViewportI viewport,
1266           AlignExportSettingI exportSettings)
1267   {
1268     AlignmentI alignmentToExport = null;
1269     AlignExportSettingI settings = exportSettings;
1270     String[] omitHidden = null;
1271     int[] alignmentStartEnd = new int[2];
1272
1273     HiddenSequences hiddenSeqs = viewport.getAlignment()
1274             .getHiddenSequences();
1275
1276     alignmentToExport = viewport.getAlignment();
1277     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1278
1279     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1280     if (settings == null)
1281     {
1282       settings = new AlignExportSettings(hasHiddenSeqs,
1283               viewport.hasHiddenColumns(), exportFormat);
1284     }
1285     // settings.isExportAnnotations();
1286
1287     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1288     {
1289       omitHidden = viewport.getViewAsString(false);
1290     }
1291
1292     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1293     {
1294       alignmentToExport = hiddenSeqs.getFullAlignment();
1295     }
1296     else
1297     {
1298       alignmentToExport = viewport.getAlignment();
1299       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1300               .getColumnSelection().getHiddenColumns());
1301     }
1302     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1303             omitHidden, alignmentStartEnd, settings);
1304     return ed;
1305   }
1306
1307   public static int[] getStartEnd(int[] aligmentStartEnd,
1308           List<int[]> hiddenCols)
1309   {
1310     int startPos = aligmentStartEnd[0];
1311     int endPos = aligmentStartEnd[1];
1312
1313     int[] lowestRange = new int[] { -1, -1 };
1314     int[] higestRange = new int[] { -1, -1 };
1315
1316     for (int[] hiddenCol : hiddenCols)
1317     {
1318       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1319       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1320     }
1321
1322     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1323     {
1324       startPos = aligmentStartEnd[0];
1325     }
1326     else
1327     {
1328       startPos = lowestRange[1] + 1;
1329     }
1330
1331     if (higestRange[0] == -1 && higestRange[1] == -1)
1332     {
1333       endPos = aligmentStartEnd[1];
1334     }
1335     else
1336     {
1337       endPos = higestRange[0] - 1;
1338     }
1339
1340     // System.out.println("Export range : " + startPos + " - " + endPos);
1341     return new int[] { startPos, endPos };
1342   }
1343
1344   public static void main(String[] args)
1345   {
1346     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1347     hiddenCols.add(new int[] { 0, 0 });
1348     hiddenCols.add(new int[] { 6, 9 });
1349     hiddenCols.add(new int[] { 11, 12 });
1350     hiddenCols.add(new int[] { 33, 33 });
1351     hiddenCols.add(new int[] { 50, 50 });
1352
1353     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1354     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1355   }
1356
1357   /**
1358    * DOCUMENT ME!
1359    *
1360    * @param e
1361    *          DOCUMENT ME!
1362    */
1363   @Override
1364   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1365   {
1366     new HtmlSvgOutput(null, alignPanel);
1367   }
1368
1369   @Override
1370   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1371   {
1372     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1373     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1374   }
1375
1376   public void createImageMap(File file, String image)
1377   {
1378     alignPanel.makePNGImageMap(file, image);
1379   }
1380
1381   /**
1382    * DOCUMENT ME!
1383    *
1384    * @param e
1385    *          DOCUMENT ME!
1386    */
1387   @Override
1388   public void createPNG(File f)
1389   {
1390     alignPanel.makePNG(f);
1391   }
1392
1393   /**
1394    * DOCUMENT ME!
1395    *
1396    * @param e
1397    *          DOCUMENT ME!
1398    */
1399   @Override
1400   public void createEPS(File f)
1401   {
1402     alignPanel.makeEPS(f);
1403   }
1404
1405   @Override
1406   public void createSVG(File f)
1407   {
1408     alignPanel.makeSVG(f);
1409   }
1410
1411   @Override
1412   public void pageSetup_actionPerformed(ActionEvent e)
1413   {
1414     PrinterJob printJob = PrinterJob.getPrinterJob();
1415     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1416   }
1417
1418   /**
1419    * DOCUMENT ME!
1420    *
1421    * @param e
1422    *          DOCUMENT ME!
1423    */
1424   @Override
1425   public void printMenuItem_actionPerformed(ActionEvent e)
1426   {
1427     // Putting in a thread avoids Swing painting problems
1428     PrintThread thread = new PrintThread(alignPanel);
1429     thread.start();
1430   }
1431
1432   @Override
1433   public void exportFeatures_actionPerformed(ActionEvent e)
1434   {
1435     new AnnotationExporter().exportFeatures(alignPanel);
1436   }
1437
1438   @Override
1439   public void exportAnnotations_actionPerformed(ActionEvent e)
1440   {
1441     new AnnotationExporter().exportAnnotations(alignPanel);
1442   }
1443
1444   @Override
1445   public void associatedData_actionPerformed(ActionEvent e)
1446   {
1447     // Pick the tree file
1448     JalviewFileChooser chooser = new JalviewFileChooser(
1449             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1450     chooser.setFileView(new JalviewFileView());
1451     chooser.setDialogTitle(MessageManager
1452             .getString("label.load_jalview_annotations"));
1453     chooser.setToolTipText(MessageManager
1454             .getString("label.load_jalview_annotations"));
1455
1456     int value = chooser.showOpenDialog(null);
1457
1458     if (value == JalviewFileChooser.APPROVE_OPTION)
1459     {
1460       String choice = chooser.getSelectedFile().getPath();
1461       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1462       loadJalviewDataFile(choice, null, null, null);
1463     }
1464
1465   }
1466
1467   /**
1468    * Close the current view or all views in the alignment frame. If the frame
1469    * only contains one view then the alignment will be removed from memory.
1470    *
1471    * @param closeAllTabs
1472    */
1473   @Override
1474   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1475   {
1476     if (alignPanels != null && alignPanels.size() < 2)
1477     {
1478       closeAllTabs = true;
1479     }
1480
1481     try
1482     {
1483       if (alignPanels != null)
1484       {
1485         if (closeAllTabs)
1486         {
1487           if (this.isClosed())
1488           {
1489             // really close all the windows - otherwise wait till
1490             // setClosed(true) is called
1491             for (int i = 0; i < alignPanels.size(); i++)
1492             {
1493               AlignmentPanel ap = alignPanels.get(i);
1494               ap.closePanel();
1495             }
1496           }
1497         }
1498         else
1499         {
1500           closeView(alignPanel);
1501         }
1502       }
1503
1504       if (closeAllTabs)
1505       {
1506         /*
1507          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1508          * be called recursively, with the frame now in 'closed' state
1509          */
1510         this.setClosed(true);
1511       }
1512     } catch (Exception ex)
1513     {
1514       ex.printStackTrace();
1515     }
1516   }
1517
1518   /**
1519    * Close the specified panel and close up tabs appropriately.
1520    *
1521    * @param panelToClose
1522    */
1523   public void closeView(AlignmentPanel panelToClose)
1524   {
1525     int index = tabbedPane.getSelectedIndex();
1526     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1527     alignPanels.remove(panelToClose);
1528     panelToClose.closePanel();
1529     panelToClose = null;
1530
1531     tabbedPane.removeTabAt(closedindex);
1532     tabbedPane.validate();
1533
1534     if (index > closedindex || index == tabbedPane.getTabCount())
1535     {
1536       // modify currently selected tab index if necessary.
1537       index--;
1538     }
1539
1540     this.tabSelectionChanged(index);
1541   }
1542
1543   /**
1544    * DOCUMENT ME!
1545    */
1546   void updateEditMenuBar()
1547   {
1548
1549     if (viewport.getHistoryList().size() > 0)
1550     {
1551       undoMenuItem.setEnabled(true);
1552       CommandI command = viewport.getHistoryList().peek();
1553       undoMenuItem.setText(MessageManager.formatMessage(
1554               "label.undo_command",
1555               new Object[] { command.getDescription() }));
1556     }
1557     else
1558     {
1559       undoMenuItem.setEnabled(false);
1560       undoMenuItem.setText(MessageManager.getString("action.undo"));
1561     }
1562
1563     if (viewport.getRedoList().size() > 0)
1564     {
1565       redoMenuItem.setEnabled(true);
1566
1567       CommandI command = viewport.getRedoList().peek();
1568       redoMenuItem.setText(MessageManager.formatMessage(
1569               "label.redo_command",
1570               new Object[] { command.getDescription() }));
1571     }
1572     else
1573     {
1574       redoMenuItem.setEnabled(false);
1575       redoMenuItem.setText(MessageManager.getString("action.redo"));
1576     }
1577   }
1578
1579   @Override
1580   public void addHistoryItem(CommandI command)
1581   {
1582     if (command.getSize() > 0)
1583     {
1584       viewport.addToHistoryList(command);
1585       viewport.clearRedoList();
1586       updateEditMenuBar();
1587       viewport.updateHiddenColumns();
1588       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1589       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1590       // viewport.getColumnSelection()
1591       // .getHiddenColumns().size() > 0);
1592     }
1593   }
1594
1595   /**
1596    *
1597    * @return alignment objects for all views
1598    */
1599   AlignmentI[] getViewAlignments()
1600   {
1601     if (alignPanels != null)
1602     {
1603       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1604       int i = 0;
1605       for (AlignmentPanel ap : alignPanels)
1606       {
1607         als[i++] = ap.av.getAlignment();
1608       }
1609       return als;
1610     }
1611     if (viewport != null)
1612     {
1613       return new AlignmentI[] { viewport.getAlignment() };
1614     }
1615     return null;
1616   }
1617
1618   /**
1619    * DOCUMENT ME!
1620    *
1621    * @param e
1622    *          DOCUMENT ME!
1623    */
1624   @Override
1625   protected void undoMenuItem_actionPerformed(ActionEvent e)
1626   {
1627     if (viewport.getHistoryList().isEmpty())
1628     {
1629       return;
1630     }
1631     CommandI command = viewport.getHistoryList().pop();
1632     viewport.addToRedoList(command);
1633     command.undoCommand(getViewAlignments());
1634
1635     AlignmentViewport originalSource = getOriginatingSource(command);
1636     updateEditMenuBar();
1637
1638     if (originalSource != null)
1639     {
1640       if (originalSource != viewport)
1641       {
1642         Cache.log
1643                 .warn("Implementation worry: mismatch of viewport origin for undo");
1644       }
1645       originalSource.updateHiddenColumns();
1646       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1647       // null
1648       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649       // viewport.getColumnSelection()
1650       // .getHiddenColumns().size() > 0);
1651       originalSource.firePropertyChange("alignment", null, originalSource
1652               .getAlignment().getSequences());
1653     }
1654   }
1655
1656   /**
1657    * DOCUMENT ME!
1658    *
1659    * @param e
1660    *          DOCUMENT ME!
1661    */
1662   @Override
1663   protected void redoMenuItem_actionPerformed(ActionEvent e)
1664   {
1665     if (viewport.getRedoList().size() < 1)
1666     {
1667       return;
1668     }
1669
1670     CommandI command = viewport.getRedoList().pop();
1671     viewport.addToHistoryList(command);
1672     command.doCommand(getViewAlignments());
1673
1674     AlignmentViewport originalSource = getOriginatingSource(command);
1675     updateEditMenuBar();
1676
1677     if (originalSource != null)
1678     {
1679
1680       if (originalSource != viewport)
1681       {
1682         Cache.log
1683                 .warn("Implementation worry: mismatch of viewport origin for redo");
1684       }
1685       originalSource.updateHiddenColumns();
1686       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1687       // null
1688       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1689       // viewport.getColumnSelection()
1690       // .getHiddenColumns().size() > 0);
1691       originalSource.firePropertyChange("alignment", null, originalSource
1692               .getAlignment().getSequences());
1693     }
1694   }
1695
1696   AlignmentViewport getOriginatingSource(CommandI command)
1697   {
1698     AlignmentViewport originalSource = null;
1699     // For sequence removal and addition, we need to fire
1700     // the property change event FROM the viewport where the
1701     // original alignment was altered
1702     AlignmentI al = null;
1703     if (command instanceof EditCommand)
1704     {
1705       EditCommand editCommand = (EditCommand) command;
1706       al = editCommand.getAlignment();
1707       List<Component> comps = PaintRefresher.components.get(viewport
1708               .getSequenceSetId());
1709
1710       for (Component comp : comps)
1711       {
1712         if (comp instanceof AlignmentPanel)
1713         {
1714           if (al == ((AlignmentPanel) comp).av.getAlignment())
1715           {
1716             originalSource = ((AlignmentPanel) comp).av;
1717             break;
1718           }
1719         }
1720       }
1721     }
1722
1723     if (originalSource == null)
1724     {
1725       // The original view is closed, we must validate
1726       // the current view against the closed view first
1727       if (al != null)
1728       {
1729         PaintRefresher.validateSequences(al, viewport.getAlignment());
1730       }
1731
1732       originalSource = viewport;
1733     }
1734
1735     return originalSource;
1736   }
1737
1738   /**
1739    * DOCUMENT ME!
1740    *
1741    * @param up
1742    *          DOCUMENT ME!
1743    */
1744   public void moveSelectedSequences(boolean up)
1745   {
1746     SequenceGroup sg = viewport.getSelectionGroup();
1747
1748     if (sg == null)
1749     {
1750       return;
1751     }
1752     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753             viewport.getHiddenRepSequences(), up);
1754     alignPanel.paintAlignment(true);
1755   }
1756
1757   synchronized void slideSequences(boolean right, int size)
1758   {
1759     List<SequenceI> sg = new ArrayList<SequenceI>();
1760     if (viewport.cursorMode)
1761     {
1762       sg.add(viewport.getAlignment().getSequenceAt(
1763               alignPanel.getSeqPanel().seqCanvas.cursorY));
1764     }
1765     else if (viewport.getSelectionGroup() != null
1766             && viewport.getSelectionGroup().getSize() != viewport
1767                     .getAlignment().getHeight())
1768     {
1769       sg = viewport.getSelectionGroup().getSequences(
1770               viewport.getHiddenRepSequences());
1771     }
1772
1773     if (sg.size() < 1)
1774     {
1775       return;
1776     }
1777
1778     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1779
1780     for (SequenceI seq : viewport.getAlignment().getSequences())
1781     {
1782       if (!sg.contains(seq))
1783       {
1784         invertGroup.add(seq);
1785       }
1786     }
1787
1788     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1789
1790     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1791     for (int i = 0; i < invertGroup.size(); i++)
1792     {
1793       seqs2[i] = invertGroup.get(i);
1794     }
1795
1796     SlideSequencesCommand ssc;
1797     if (right)
1798     {
1799       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1800               size, viewport.getGapCharacter());
1801     }
1802     else
1803     {
1804       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1805               size, viewport.getGapCharacter());
1806     }
1807
1808     int groupAdjustment = 0;
1809     if (ssc.getGapsInsertedBegin() && right)
1810     {
1811       if (viewport.cursorMode)
1812       {
1813         alignPanel.getSeqPanel().moveCursor(size, 0);
1814       }
1815       else
1816       {
1817         groupAdjustment = size;
1818       }
1819     }
1820     else if (!ssc.getGapsInsertedBegin() && !right)
1821     {
1822       if (viewport.cursorMode)
1823       {
1824         alignPanel.getSeqPanel().moveCursor(-size, 0);
1825       }
1826       else
1827       {
1828         groupAdjustment = -size;
1829       }
1830     }
1831
1832     if (groupAdjustment != 0)
1833     {
1834       viewport.getSelectionGroup().setStartRes(
1835               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1836       viewport.getSelectionGroup().setEndRes(
1837               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1838     }
1839
1840     /*
1841      * just extend the last slide command if compatible; but not if in
1842      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1843      */
1844     boolean appendHistoryItem = false;
1845     Deque<CommandI> historyList = viewport.getHistoryList();
1846     boolean inSplitFrame = getSplitViewContainer() != null;
1847     if (!inSplitFrame && historyList != null && historyList.size() > 0
1848             && historyList.peek() instanceof SlideSequencesCommand)
1849     {
1850       appendHistoryItem = ssc
1851               .appendSlideCommand((SlideSequencesCommand) historyList
1852                       .peek());
1853     }
1854
1855     if (!appendHistoryItem)
1856     {
1857       addHistoryItem(ssc);
1858     }
1859
1860     repaint();
1861   }
1862
1863   /**
1864    * DOCUMENT ME!
1865    *
1866    * @param e
1867    *          DOCUMENT ME!
1868    */
1869   @Override
1870   protected void copy_actionPerformed(ActionEvent e)
1871   {
1872     System.gc();
1873     if (viewport.getSelectionGroup() == null)
1874     {
1875       return;
1876     }
1877     // TODO: preserve the ordering of displayed alignment annotation in any
1878     // internal paste (particularly sequence associated annotation)
1879     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1880     String[] omitHidden = null;
1881
1882     if (viewport.hasHiddenColumns())
1883     {
1884       omitHidden = viewport.getViewAsString(true);
1885     }
1886
1887     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1888             omitHidden, null);
1889
1890     StringSelection ss = new StringSelection(output);
1891
1892     try
1893     {
1894       jalview.gui.Desktop.internalCopy = true;
1895       // Its really worth setting the clipboard contents
1896       // to empty before setting the large StringSelection!!
1897       Toolkit.getDefaultToolkit().getSystemClipboard()
1898               .setContents(new StringSelection(""), null);
1899
1900       Toolkit.getDefaultToolkit().getSystemClipboard()
1901               .setContents(ss, Desktop.instance);
1902     } catch (OutOfMemoryError er)
1903     {
1904       new OOMWarning("copying region", er);
1905       return;
1906     }
1907
1908     ArrayList<int[]> hiddenColumns = null;
1909     if (viewport.hasHiddenColumns())
1910     {
1911       hiddenColumns = new ArrayList<int[]>();
1912       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1913               .getSelectionGroup().getEndRes();
1914       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1915       {
1916         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1917         {
1918           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1919               region[1] - hiddenOffset });
1920         }
1921       }
1922     }
1923
1924     Desktop.jalviewClipboard = new Object[] { seqs,
1925         viewport.getAlignment().getDataset(), hiddenColumns };
1926     statusBar.setText(MessageManager.formatMessage(
1927             "label.copied_sequences_to_clipboard", new Object[] { Integer
1928                     .valueOf(seqs.length).toString() }));
1929   }
1930
1931   /**
1932    * DOCUMENT ME!
1933    *
1934    * @param e
1935    *          DOCUMENT ME!
1936    */
1937   @Override
1938   protected void pasteNew_actionPerformed(ActionEvent e)
1939   {
1940     paste(true);
1941   }
1942
1943   /**
1944    * DOCUMENT ME!
1945    *
1946    * @param e
1947    *          DOCUMENT ME!
1948    */
1949   @Override
1950   protected void pasteThis_actionPerformed(ActionEvent e)
1951   {
1952     paste(false);
1953   }
1954
1955   /**
1956    * Paste contents of Jalview clipboard
1957    *
1958    * @param newAlignment
1959    *          true to paste to a new alignment, otherwise add to this.
1960    */
1961   void paste(boolean newAlignment)
1962   {
1963     boolean externalPaste = true;
1964     try
1965     {
1966       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1967       Transferable contents = c.getContents(this);
1968
1969       if (contents == null)
1970       {
1971         return;
1972       }
1973
1974       String str, format;
1975       try
1976       {
1977         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1978         if (str.length() < 1)
1979         {
1980           return;
1981         }
1982
1983         format = new IdentifyFile().Identify(str, "Paste");
1984
1985       } catch (OutOfMemoryError er)
1986       {
1987         new OOMWarning("Out of memory pasting sequences!!", er);
1988         return;
1989       }
1990
1991       SequenceI[] sequences;
1992       boolean annotationAdded = false;
1993       AlignmentI alignment = null;
1994
1995       if (Desktop.jalviewClipboard != null)
1996       {
1997         // The clipboard was filled from within Jalview, we must use the
1998         // sequences
1999         // And dataset from the copied alignment
2000         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2001         // be doubly sure that we create *new* sequence objects.
2002         sequences = new SequenceI[newseq.length];
2003         for (int i = 0; i < newseq.length; i++)
2004         {
2005           sequences[i] = new Sequence(newseq[i]);
2006         }
2007         alignment = new Alignment(sequences);
2008         externalPaste = false;
2009       }
2010       else
2011       {
2012         // parse the clipboard as an alignment.
2013         alignment = new FormatAdapter().readFile(str, "Paste", format);
2014         sequences = alignment.getSequencesArray();
2015       }
2016
2017       int alwidth = 0;
2018       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2019       int fgroup = -1;
2020
2021       if (newAlignment)
2022       {
2023
2024         if (Desktop.jalviewClipboard != null)
2025         {
2026           // dataset is inherited
2027           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2028         }
2029         else
2030         {
2031           // new dataset is constructed
2032           alignment.setDataset(null);
2033         }
2034         alwidth = alignment.getWidth() + 1;
2035       }
2036       else
2037       {
2038         AlignmentI pastedal = alignment; // preserve pasted alignment object
2039         // Add pasted sequences and dataset into existing alignment.
2040         alignment = viewport.getAlignment();
2041         alwidth = alignment.getWidth() + 1;
2042         // decide if we need to import sequences from an existing dataset
2043         boolean importDs = Desktop.jalviewClipboard != null
2044                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2045         // importDs==true instructs us to copy over new dataset sequences from
2046         // an existing alignment
2047         Vector newDs = (importDs) ? new Vector() : null; // used to create
2048         // minimum dataset set
2049
2050         for (int i = 0; i < sequences.length; i++)
2051         {
2052           if (importDs)
2053           {
2054             newDs.addElement(null);
2055           }
2056           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2057           // paste
2058           if (importDs && ds != null)
2059           {
2060             if (!newDs.contains(ds))
2061             {
2062               newDs.setElementAt(ds, i);
2063               ds = new Sequence(ds);
2064               // update with new dataset sequence
2065               sequences[i].setDatasetSequence(ds);
2066             }
2067             else
2068             {
2069               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2070             }
2071           }
2072           else
2073           {
2074             // copy and derive new dataset sequence
2075             sequences[i] = sequences[i].deriveSequence();
2076             alignment.getDataset().addSequence(
2077                     sequences[i].getDatasetSequence());
2078             // TODO: avoid creation of duplicate dataset sequences with a
2079             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2080           }
2081           alignment.addSequence(sequences[i]); // merges dataset
2082         }
2083         if (newDs != null)
2084         {
2085           newDs.clear(); // tidy up
2086         }
2087         if (alignment.getAlignmentAnnotation() != null)
2088         {
2089           for (AlignmentAnnotation alan : alignment
2090                   .getAlignmentAnnotation())
2091           {
2092             if (alan.graphGroup > fgroup)
2093             {
2094               fgroup = alan.graphGroup;
2095             }
2096           }
2097         }
2098         if (pastedal.getAlignmentAnnotation() != null)
2099         {
2100           // Add any annotation attached to alignment.
2101           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2102           for (int i = 0; i < alann.length; i++)
2103           {
2104             annotationAdded = true;
2105             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2106             {
2107               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2108               if (newann.graphGroup > -1)
2109               {
2110                 if (newGraphGroups.size() <= newann.graphGroup
2111                         || newGraphGroups.get(newann.graphGroup) == null)
2112                 {
2113                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2114                   {
2115                     newGraphGroups.add(q, null);
2116                   }
2117                   newGraphGroups.set(newann.graphGroup, new Integer(
2118                           ++fgroup));
2119                 }
2120                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2121                         .intValue();
2122               }
2123
2124               newann.padAnnotation(alwidth);
2125               alignment.addAnnotation(newann);
2126             }
2127           }
2128         }
2129       }
2130       if (!newAlignment)
2131       {
2132         // /////
2133         // ADD HISTORY ITEM
2134         //
2135         addHistoryItem(new EditCommand(
2136                 MessageManager.getString("label.add_sequences"),
2137                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2138       }
2139       // Add any annotations attached to sequences
2140       for (int i = 0; i < sequences.length; i++)
2141       {
2142         if (sequences[i].getAnnotation() != null)
2143         {
2144           AlignmentAnnotation newann;
2145           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2146           {
2147             annotationAdded = true;
2148             newann = sequences[i].getAnnotation()[a];
2149             newann.adjustForAlignment();
2150             newann.padAnnotation(alwidth);
2151             if (newann.graphGroup > -1)
2152             {
2153               if (newann.graphGroup > -1)
2154               {
2155                 if (newGraphGroups.size() <= newann.graphGroup
2156                         || newGraphGroups.get(newann.graphGroup) == null)
2157                 {
2158                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2159                   {
2160                     newGraphGroups.add(q, null);
2161                   }
2162                   newGraphGroups.set(newann.graphGroup, new Integer(
2163                           ++fgroup));
2164                 }
2165                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2166                         .intValue();
2167               }
2168             }
2169             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2170             // was
2171             // duplicated
2172             // earlier
2173             alignment
2174                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2175           }
2176         }
2177       }
2178       if (!newAlignment)
2179       {
2180
2181         // propagate alignment changed.
2182         viewport.setEndSeq(alignment.getHeight());
2183         if (annotationAdded)
2184         {
2185           // Duplicate sequence annotation in all views.
2186           AlignmentI[] alview = this.getViewAlignments();
2187           for (int i = 0; i < sequences.length; i++)
2188           {
2189             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2190             if (sann == null)
2191             {
2192               continue;
2193             }
2194             for (int avnum = 0; avnum < alview.length; avnum++)
2195             {
2196               if (alview[avnum] != alignment)
2197               {
2198                 // duplicate in a view other than the one with input focus
2199                 int avwidth = alview[avnum].getWidth() + 1;
2200                 // this relies on sann being preserved after we
2201                 // modify the sequence's annotation array for each duplication
2202                 for (int a = 0; a < sann.length; a++)
2203                 {
2204                   AlignmentAnnotation newann = new AlignmentAnnotation(
2205                           sann[a]);
2206                   sequences[i].addAlignmentAnnotation(newann);
2207                   newann.padAnnotation(avwidth);
2208                   alview[avnum].addAnnotation(newann); // annotation was
2209                   // duplicated earlier
2210                   // TODO JAL-1145 graphGroups are not updated for sequence
2211                   // annotation added to several views. This may cause
2212                   // strangeness
2213                   alview[avnum].setAnnotationIndex(newann, a);
2214                 }
2215               }
2216             }
2217           }
2218           buildSortByAnnotationScoresMenu();
2219         }
2220         viewport.firePropertyChange("alignment", null,
2221                 alignment.getSequences());
2222         if (alignPanels != null)
2223         {
2224           for (AlignmentPanel ap : alignPanels)
2225           {
2226             ap.validateAnnotationDimensions(false);
2227           }
2228         }
2229         else
2230         {
2231           alignPanel.validateAnnotationDimensions(false);
2232         }
2233
2234       }
2235       else
2236       {
2237         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2238                 DEFAULT_HEIGHT);
2239         String newtitle = new String("Copied sequences");
2240
2241         if (Desktop.jalviewClipboard != null
2242                 && Desktop.jalviewClipboard[2] != null)
2243         {
2244           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2245           for (int[] region : hc)
2246           {
2247             af.viewport.hideColumns(region[0], region[1]);
2248           }
2249         }
2250
2251         // >>>This is a fix for the moment, until a better solution is
2252         // found!!<<<
2253         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2254                 .transferSettings(
2255                         alignPanel.getSeqPanel().seqCanvas
2256                                 .getFeatureRenderer());
2257
2258         // TODO: maintain provenance of an alignment, rather than just make the
2259         // title a concatenation of operations.
2260         if (!externalPaste)
2261         {
2262           if (title.startsWith("Copied sequences"))
2263           {
2264             newtitle = title;
2265           }
2266           else
2267           {
2268             newtitle = newtitle.concat("- from " + title);
2269           }
2270         }
2271         else
2272         {
2273           newtitle = new String("Pasted sequences");
2274         }
2275
2276         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2277                 DEFAULT_HEIGHT);
2278
2279       }
2280
2281     } catch (Exception ex)
2282     {
2283       ex.printStackTrace();
2284       System.out.println("Exception whilst pasting: " + ex);
2285       // could be anything being pasted in here
2286     }
2287
2288   }
2289
2290   @Override
2291   protected void expand_newalign(ActionEvent e)
2292   {
2293     try
2294     {
2295       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2296               .getAlignment(), -1);
2297       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2298               DEFAULT_HEIGHT);
2299       String newtitle = new String("Flanking alignment");
2300
2301       if (Desktop.jalviewClipboard != null
2302               && Desktop.jalviewClipboard[2] != null)
2303       {
2304         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2305         for (int region[] : hc)
2306         {
2307           af.viewport.hideColumns(region[0], region[1]);
2308         }
2309       }
2310
2311       // >>>This is a fix for the moment, until a better solution is
2312       // found!!<<<
2313       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2314               .transferSettings(
2315                       alignPanel.getSeqPanel().seqCanvas
2316                               .getFeatureRenderer());
2317
2318       // TODO: maintain provenance of an alignment, rather than just make the
2319       // title a concatenation of operations.
2320       {
2321         if (title.startsWith("Copied sequences"))
2322         {
2323           newtitle = title;
2324         }
2325         else
2326         {
2327           newtitle = newtitle.concat("- from " + title);
2328         }
2329       }
2330
2331       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2332
2333     } catch (Exception ex)
2334     {
2335       ex.printStackTrace();
2336       System.out.println("Exception whilst pasting: " + ex);
2337       // could be anything being pasted in here
2338     } catch (OutOfMemoryError oom)
2339     {
2340       new OOMWarning("Viewing flanking region of alignment", oom);
2341     }
2342   }
2343
2344   /**
2345    * DOCUMENT ME!
2346    *
2347    * @param e
2348    *          DOCUMENT ME!
2349    */
2350   @Override
2351   protected void cut_actionPerformed(ActionEvent e)
2352   {
2353     copy_actionPerformed(null);
2354     delete_actionPerformed(null);
2355   }
2356
2357   /**
2358    * DOCUMENT ME!
2359    *
2360    * @param e
2361    *          DOCUMENT ME!
2362    */
2363   @Override
2364   protected void delete_actionPerformed(ActionEvent evt)
2365   {
2366
2367     SequenceGroup sg = viewport.getSelectionGroup();
2368     if (sg == null)
2369     {
2370       return;
2371     }
2372
2373     /*
2374      * If the cut affects all sequences, warn, remove highlighted columns
2375      */
2376     if (sg.getSize() == viewport.getAlignment().getHeight())
2377     {
2378       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2379               .getAlignment().getWidth()) ? true : false;
2380       if (isEntireAlignWidth)
2381       {
2382         int confirm = JOptionPane.showConfirmDialog(this,
2383                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2384                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2385                 JOptionPane.OK_CANCEL_OPTION);
2386
2387         if (confirm == JOptionPane.CANCEL_OPTION
2388                 || confirm == JOptionPane.CLOSED_OPTION)
2389         {
2390           return;
2391         }
2392       }
2393       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2394               sg.getEndRes() + 1);
2395     }
2396     SequenceI[] cut = sg.getSequences()
2397             .toArray(new SequenceI[sg.getSize()]);
2398
2399     addHistoryItem(new EditCommand(
2400             MessageManager.getString("label.cut_sequences"), Action.CUT,
2401             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2402             viewport.getAlignment()));
2403
2404     viewport.setSelectionGroup(null);
2405     viewport.sendSelection();
2406     viewport.getAlignment().deleteGroup(sg);
2407
2408     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2409             .getSequences());
2410     if (viewport.getAlignment().getHeight() < 1)
2411     {
2412       try
2413       {
2414         this.setClosed(true);
2415       } catch (Exception ex)
2416       {
2417       }
2418     }
2419   }
2420
2421   /**
2422    * DOCUMENT ME!
2423    *
2424    * @param e
2425    *          DOCUMENT ME!
2426    */
2427   @Override
2428   protected void deleteGroups_actionPerformed(ActionEvent e)
2429   {
2430     if (avc.deleteGroups())
2431     {
2432       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2433       alignPanel.updateAnnotation();
2434       alignPanel.paintAlignment(true);
2435     }
2436   }
2437
2438   /**
2439    * DOCUMENT ME!
2440    *
2441    * @param e
2442    *          DOCUMENT ME!
2443    */
2444   @Override
2445   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2446   {
2447     SequenceGroup sg = new SequenceGroup();
2448
2449     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2450     {
2451       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2452     }
2453
2454     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2455     viewport.setSelectionGroup(sg);
2456     viewport.sendSelection();
2457     alignPanel.paintAlignment(true);
2458     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2459   }
2460
2461   /**
2462    * DOCUMENT ME!
2463    *
2464    * @param e
2465    *          DOCUMENT ME!
2466    */
2467   @Override
2468   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2469   {
2470     if (viewport.cursorMode)
2471     {
2472       alignPanel.getSeqPanel().keyboardNo1 = null;
2473       alignPanel.getSeqPanel().keyboardNo2 = null;
2474     }
2475     viewport.setSelectionGroup(null);
2476     viewport.getColumnSelection().clear();
2477     viewport.setSelectionGroup(null);
2478     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2479     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2480     alignPanel.paintAlignment(true);
2481     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482     viewport.sendSelection();
2483   }
2484
2485   /**
2486    * DOCUMENT ME!
2487    *
2488    * @param e
2489    *          DOCUMENT ME!
2490    */
2491   @Override
2492   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2493   {
2494     SequenceGroup sg = viewport.getSelectionGroup();
2495
2496     if (sg == null)
2497     {
2498       selectAllSequenceMenuItem_actionPerformed(null);
2499
2500       return;
2501     }
2502
2503     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2504     {
2505       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2506     }
2507
2508     alignPanel.paintAlignment(true);
2509     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2510     viewport.sendSelection();
2511   }
2512
2513   @Override
2514   public void invertColSel_actionPerformed(ActionEvent e)
2515   {
2516     viewport.invertColumnSelection();
2517     alignPanel.paintAlignment(true);
2518     viewport.sendSelection();
2519   }
2520
2521   /**
2522    * DOCUMENT ME!
2523    *
2524    * @param e
2525    *          DOCUMENT ME!
2526    */
2527   @Override
2528   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2529   {
2530     trimAlignment(true);
2531   }
2532
2533   /**
2534    * DOCUMENT ME!
2535    *
2536    * @param e
2537    *          DOCUMENT ME!
2538    */
2539   @Override
2540   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2541   {
2542     trimAlignment(false);
2543   }
2544
2545   void trimAlignment(boolean trimLeft)
2546   {
2547     ColumnSelection colSel = viewport.getColumnSelection();
2548     int column;
2549
2550     if (colSel.size() > 0)
2551     {
2552       if (trimLeft)
2553       {
2554         column = colSel.getMin();
2555       }
2556       else
2557       {
2558         column = colSel.getMax();
2559       }
2560
2561       SequenceI[] seqs;
2562       if (viewport.getSelectionGroup() != null)
2563       {
2564         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2565                 viewport.getHiddenRepSequences());
2566       }
2567       else
2568       {
2569         seqs = viewport.getAlignment().getSequencesArray();
2570       }
2571
2572       TrimRegionCommand trimRegion;
2573       if (trimLeft)
2574       {
2575         trimRegion = new TrimRegionCommand("Remove Left",
2576                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2577                 viewport.getAlignment(), viewport.getColumnSelection(),
2578                 viewport.getSelectionGroup());
2579         viewport.setStartRes(0);
2580       }
2581       else
2582       {
2583         trimRegion = new TrimRegionCommand("Remove Right",
2584                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2585                 viewport.getAlignment(), viewport.getColumnSelection(),
2586                 viewport.getSelectionGroup());
2587       }
2588
2589       statusBar.setText(MessageManager.formatMessage(
2590               "label.removed_columns",
2591               new String[] { Integer.valueOf(trimRegion.getSize())
2592                       .toString() }));
2593
2594       addHistoryItem(trimRegion);
2595
2596       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2597       {
2598         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2599                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2600         {
2601           viewport.getAlignment().deleteGroup(sg);
2602         }
2603       }
2604
2605       viewport.firePropertyChange("alignment", null, viewport
2606               .getAlignment().getSequences());
2607     }
2608   }
2609
2610   /**
2611    * DOCUMENT ME!
2612    *
2613    * @param e
2614    *          DOCUMENT ME!
2615    */
2616   @Override
2617   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2618   {
2619     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2620
2621     SequenceI[] seqs;
2622     if (viewport.getSelectionGroup() != null)
2623     {
2624       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2625               viewport.getHiddenRepSequences());
2626       start = viewport.getSelectionGroup().getStartRes();
2627       end = viewport.getSelectionGroup().getEndRes();
2628     }
2629     else
2630     {
2631       seqs = viewport.getAlignment().getSequencesArray();
2632     }
2633
2634     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2635             "Remove Gapped Columns", seqs, start, end,
2636             viewport.getAlignment());
2637
2638     addHistoryItem(removeGapCols);
2639
2640     statusBar.setText(MessageManager.formatMessage(
2641             "label.removed_empty_columns",
2642             new Object[] { Integer.valueOf(removeGapCols.getSize())
2643                     .toString() }));
2644
2645     // This is to maintain viewport position on first residue
2646     // of first sequence
2647     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2648     int startRes = seq.findPosition(viewport.startRes);
2649     // ShiftList shifts;
2650     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2651     // edit.alColumnChanges=shifts.getInverse();
2652     // if (viewport.hasHiddenColumns)
2653     // viewport.getColumnSelection().compensateForEdits(shifts);
2654     viewport.setStartRes(seq.findIndex(startRes) - 1);
2655     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2656             .getSequences());
2657
2658   }
2659
2660   /**
2661    * DOCUMENT ME!
2662    *
2663    * @param e
2664    *          DOCUMENT ME!
2665    */
2666   @Override
2667   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2668   {
2669     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2670
2671     SequenceI[] seqs;
2672     if (viewport.getSelectionGroup() != null)
2673     {
2674       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2675               viewport.getHiddenRepSequences());
2676       start = viewport.getSelectionGroup().getStartRes();
2677       end = viewport.getSelectionGroup().getEndRes();
2678     }
2679     else
2680     {
2681       seqs = viewport.getAlignment().getSequencesArray();
2682     }
2683
2684     // This is to maintain viewport position on first residue
2685     // of first sequence
2686     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2687     int startRes = seq.findPosition(viewport.startRes);
2688
2689     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2690             viewport.getAlignment()));
2691
2692     viewport.setStartRes(seq.findIndex(startRes) - 1);
2693
2694     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2695             .getSequences());
2696
2697   }
2698
2699   /**
2700    * DOCUMENT ME!
2701    *
2702    * @param e
2703    *          DOCUMENT ME!
2704    */
2705   @Override
2706   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2707   {
2708     viewport.setPadGaps(padGapsMenuitem.isSelected());
2709     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2710             .getSequences());
2711   }
2712
2713   /**
2714    * DOCUMENT ME!
2715    *
2716    * @param e
2717    *          DOCUMENT ME!
2718    */
2719   @Override
2720   public void findMenuItem_actionPerformed(ActionEvent e)
2721   {
2722     new Finder();
2723   }
2724
2725   /**
2726    * Create a new view of the current alignment.
2727    */
2728   @Override
2729   public void newView_actionPerformed(ActionEvent e)
2730   {
2731     newView(null, true);
2732   }
2733
2734   /**
2735    * Creates and shows a new view of the current alignment.
2736    *
2737    * @param viewTitle
2738    *          title of newly created view; if null, one will be generated
2739    * @param copyAnnotation
2740    *          if true then duplicate all annnotation, groups and settings
2741    * @return new alignment panel, already displayed.
2742    */
2743   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2744   {
2745     /*
2746      * Create a new AlignmentPanel (with its own, new Viewport)
2747      */
2748     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2749             true);
2750     if (!copyAnnotation)
2751     {
2752       /*
2753        * remove all groups and annotation except for the automatic stuff
2754        */
2755       newap.av.getAlignment().deleteAllGroups();
2756       newap.av.getAlignment().deleteAllAnnotations(false);
2757     }
2758
2759     newap.av.setGatherViewsHere(false);
2760
2761     if (viewport.viewName == null)
2762     {
2763       viewport.viewName = MessageManager
2764               .getString("label.view_name_original");
2765     }
2766
2767     /*
2768      * Views share the same edits undo and redo stacks
2769      */
2770     newap.av.setHistoryList(viewport.getHistoryList());
2771     newap.av.setRedoList(viewport.getRedoList());
2772
2773     /*
2774      * Views share the same mappings; need to deregister any new mappings
2775      * created by copyAlignPanel, and register the new reference to the shared
2776      * mappings
2777      */
2778     newap.av.replaceMappings(viewport.getAlignment());
2779
2780     newap.av.viewName = getNewViewName(viewTitle);
2781
2782     addAlignmentPanel(newap, true);
2783     newap.alignmentChanged();
2784
2785     if (alignPanels.size() == 2)
2786     {
2787       viewport.setGatherViewsHere(true);
2788     }
2789     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2790     return newap;
2791   }
2792
2793   /**
2794    * Make a new name for the view, ensuring it is unique within the current
2795    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2796    * these now use viewId. Unique view names are still desirable for usability.)
2797    *
2798    * @param viewTitle
2799    * @return
2800    */
2801   protected String getNewViewName(String viewTitle)
2802   {
2803     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2804     boolean addFirstIndex = false;
2805     if (viewTitle == null || viewTitle.trim().length() == 0)
2806     {
2807       viewTitle = MessageManager.getString("action.view");
2808       addFirstIndex = true;
2809     }
2810     else
2811     {
2812       index = 1;// we count from 1 if given a specific name
2813     }
2814     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2815
2816     List<Component> comps = PaintRefresher.components.get(viewport
2817             .getSequenceSetId());
2818
2819     List<String> existingNames = getExistingViewNames(comps);
2820
2821     while (existingNames.contains(newViewName))
2822     {
2823       newViewName = viewTitle + " " + (++index);
2824     }
2825     return newViewName;
2826   }
2827
2828   /**
2829    * Returns a list of distinct view names found in the given list of
2830    * components. View names are held on the viewport of an AlignmentPanel.
2831    *
2832    * @param comps
2833    * @return
2834    */
2835   protected List<String> getExistingViewNames(List<Component> comps)
2836   {
2837     List<String> existingNames = new ArrayList<String>();
2838     for (Component comp : comps)
2839     {
2840       if (comp instanceof AlignmentPanel)
2841       {
2842         AlignmentPanel ap = (AlignmentPanel) comp;
2843         if (!existingNames.contains(ap.av.viewName))
2844         {
2845           existingNames.add(ap.av.viewName);
2846         }
2847       }
2848     }
2849     return existingNames;
2850   }
2851
2852   /**
2853    * Explode tabbed views into separate windows.
2854    */
2855   @Override
2856   public void expandViews_actionPerformed(ActionEvent e)
2857   {
2858     Desktop.instance.explodeViews(this);
2859   }
2860
2861   /**
2862    * Gather views in separate windows back into a tabbed presentation.
2863    */
2864   @Override
2865   public void gatherViews_actionPerformed(ActionEvent e)
2866   {
2867     Desktop.instance.gatherViews(this);
2868   }
2869
2870   /**
2871    * DOCUMENT ME!
2872    *
2873    * @param e
2874    *          DOCUMENT ME!
2875    */
2876   @Override
2877   public void font_actionPerformed(ActionEvent e)
2878   {
2879     new FontChooser(alignPanel);
2880   }
2881
2882   /**
2883    * DOCUMENT ME!
2884    *
2885    * @param e
2886    *          DOCUMENT ME!
2887    */
2888   @Override
2889   protected void seqLimit_actionPerformed(ActionEvent e)
2890   {
2891     viewport.setShowJVSuffix(seqLimits.isSelected());
2892
2893     alignPanel.getIdPanel().getIdCanvas()
2894             .setPreferredSize(alignPanel.calculateIdWidth());
2895     alignPanel.paintAlignment(true);
2896   }
2897
2898   @Override
2899   public void idRightAlign_actionPerformed(ActionEvent e)
2900   {
2901     viewport.setRightAlignIds(idRightAlign.isSelected());
2902     alignPanel.paintAlignment(true);
2903   }
2904
2905   @Override
2906   public void centreColumnLabels_actionPerformed(ActionEvent e)
2907   {
2908     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2909     alignPanel.paintAlignment(true);
2910   }
2911
2912   /*
2913    * (non-Javadoc)
2914    *
2915    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2916    */
2917   @Override
2918   protected void followHighlight_actionPerformed()
2919   {
2920     /*
2921      * Set the 'follow' flag on the Viewport (and scroll to position if now
2922      * true).
2923      */
2924     final boolean state = this.followHighlightMenuItem.getState();
2925     viewport.setFollowHighlight(state);
2926     if (state)
2927     {
2928       alignPanel.scrollToPosition(
2929               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2930     }
2931   }
2932
2933   /**
2934    * DOCUMENT ME!
2935    *
2936    * @param e
2937    *          DOCUMENT ME!
2938    */
2939   @Override
2940   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2941   {
2942     viewport.setColourText(colourTextMenuItem.isSelected());
2943     alignPanel.paintAlignment(true);
2944   }
2945
2946   /**
2947    * DOCUMENT ME!
2948    *
2949    * @param e
2950    *          DOCUMENT ME!
2951    */
2952   @Override
2953   public void wrapMenuItem_actionPerformed(ActionEvent e)
2954   {
2955     scaleAbove.setVisible(wrapMenuItem.isSelected());
2956     scaleLeft.setVisible(wrapMenuItem.isSelected());
2957     scaleRight.setVisible(wrapMenuItem.isSelected());
2958     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2959     alignPanel.updateLayout();
2960   }
2961
2962   @Override
2963   public void showAllSeqs_actionPerformed(ActionEvent e)
2964   {
2965     viewport.showAllHiddenSeqs();
2966   }
2967
2968   @Override
2969   public void showAllColumns_actionPerformed(ActionEvent e)
2970   {
2971     viewport.showAllHiddenColumns();
2972     repaint();
2973   }
2974
2975   @Override
2976   public void hideSelSequences_actionPerformed(ActionEvent e)
2977   {
2978     viewport.hideAllSelectedSeqs();
2979     // alignPanel.paintAlignment(true);
2980   }
2981
2982   /**
2983    * called by key handler and the hide all/show all menu items
2984    *
2985    * @param toggleSeqs
2986    * @param toggleCols
2987    */
2988   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2989   {
2990
2991     boolean hide = false;
2992     SequenceGroup sg = viewport.getSelectionGroup();
2993     if (!toggleSeqs && !toggleCols)
2994     {
2995       // Hide everything by the current selection - this is a hack - we do the
2996       // invert and then hide
2997       // first check that there will be visible columns after the invert.
2998       if ((viewport.getColumnSelection() != null
2999               && viewport.getColumnSelection().getSelected() != null && viewport
3000               .getColumnSelection().getSelected().size() > 0)
3001               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3002                       .getEndRes()))
3003       {
3004         // now invert the sequence set, if required - empty selection implies
3005         // that no hiding is required.
3006         if (sg != null)
3007         {
3008           invertSequenceMenuItem_actionPerformed(null);
3009           sg = viewport.getSelectionGroup();
3010           toggleSeqs = true;
3011
3012         }
3013         viewport.expandColSelection(sg, true);
3014         // finally invert the column selection and get the new sequence
3015         // selection.
3016         invertColSel_actionPerformed(null);
3017         toggleCols = true;
3018       }
3019     }
3020
3021     if (toggleSeqs)
3022     {
3023       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3024       {
3025         hideSelSequences_actionPerformed(null);
3026         hide = true;
3027       }
3028       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3029               .size() > 0))
3030       {
3031         showAllSeqs_actionPerformed(null);
3032       }
3033     }
3034
3035     if (toggleCols)
3036     {
3037       if (viewport.getColumnSelection().getSelected().size() > 0)
3038       {
3039         hideSelColumns_actionPerformed(null);
3040         if (!toggleSeqs)
3041         {
3042           viewport.setSelectionGroup(sg);
3043         }
3044       }
3045       else if (!hide)
3046       {
3047         showAllColumns_actionPerformed(null);
3048       }
3049     }
3050   }
3051
3052   /*
3053    * (non-Javadoc)
3054    *
3055    * @see
3056    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3057    * event.ActionEvent)
3058    */
3059   @Override
3060   public void hideAllButSelection_actionPerformed(ActionEvent e)
3061   {
3062     toggleHiddenRegions(false, false);
3063   }
3064
3065   /*
3066    * (non-Javadoc)
3067    *
3068    * @see
3069    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3070    * .ActionEvent)
3071    */
3072   @Override
3073   public void hideAllSelection_actionPerformed(ActionEvent e)
3074   {
3075     SequenceGroup sg = viewport.getSelectionGroup();
3076     viewport.expandColSelection(sg, false);
3077     viewport.hideAllSelectedSeqs();
3078     viewport.hideSelectedColumns();
3079     alignPanel.paintAlignment(true);
3080   }
3081
3082   /*
3083    * (non-Javadoc)
3084    *
3085    * @see
3086    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3087    * ActionEvent)
3088    */
3089   @Override
3090   public void showAllhidden_actionPerformed(ActionEvent e)
3091   {
3092     viewport.showAllHiddenColumns();
3093     viewport.showAllHiddenSeqs();
3094     alignPanel.paintAlignment(true);
3095   }
3096
3097   @Override
3098   public void hideSelColumns_actionPerformed(ActionEvent e)
3099   {
3100     viewport.hideSelectedColumns();
3101     alignPanel.paintAlignment(true);
3102   }
3103
3104   @Override
3105   public void hiddenMarkers_actionPerformed(ActionEvent e)
3106   {
3107     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3108     repaint();
3109   }
3110
3111   /**
3112    * DOCUMENT ME!
3113    *
3114    * @param e
3115    *          DOCUMENT ME!
3116    */
3117   @Override
3118   protected void scaleAbove_actionPerformed(ActionEvent e)
3119   {
3120     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3121     alignPanel.paintAlignment(true);
3122   }
3123
3124   /**
3125    * DOCUMENT ME!
3126    *
3127    * @param e
3128    *          DOCUMENT ME!
3129    */
3130   @Override
3131   protected void scaleLeft_actionPerformed(ActionEvent e)
3132   {
3133     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3134     alignPanel.paintAlignment(true);
3135   }
3136
3137   /**
3138    * DOCUMENT ME!
3139    *
3140    * @param e
3141    *          DOCUMENT ME!
3142    */
3143   @Override
3144   protected void scaleRight_actionPerformed(ActionEvent e)
3145   {
3146     viewport.setScaleRightWrapped(scaleRight.isSelected());
3147     alignPanel.paintAlignment(true);
3148   }
3149
3150   /**
3151    * DOCUMENT ME!
3152    *
3153    * @param e
3154    *          DOCUMENT ME!
3155    */
3156   @Override
3157   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3158   {
3159     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3160     alignPanel.paintAlignment(true);
3161   }
3162
3163   /**
3164    * DOCUMENT ME!
3165    *
3166    * @param e
3167    *          DOCUMENT ME!
3168    */
3169   @Override
3170   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3171   {
3172     viewport.setShowText(viewTextMenuItem.isSelected());
3173     alignPanel.paintAlignment(true);
3174   }
3175
3176   /**
3177    * DOCUMENT ME!
3178    *
3179    * @param e
3180    *          DOCUMENT ME!
3181    */
3182   @Override
3183   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3184   {
3185     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3186     alignPanel.paintAlignment(true);
3187   }
3188
3189   public FeatureSettings featureSettings;
3190
3191   @Override
3192   public FeatureSettingsControllerI getFeatureSettingsUI()
3193   {
3194     return featureSettings;
3195   }
3196
3197   @Override
3198   public void featureSettings_actionPerformed(ActionEvent e)
3199   {
3200     if (featureSettings != null)
3201     {
3202       featureSettings.close();
3203       featureSettings = null;
3204     }
3205     if (!showSeqFeatures.isSelected())
3206     {
3207       // make sure features are actually displayed
3208       showSeqFeatures.setSelected(true);
3209       showSeqFeatures_actionPerformed(null);
3210     }
3211     featureSettings = new FeatureSettings(this);
3212   }
3213
3214   /**
3215    * Set or clear 'Show Sequence Features'
3216    *
3217    * @param evt
3218    *          DOCUMENT ME!
3219    */
3220   @Override
3221   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3222   {
3223     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3224     alignPanel.paintAlignment(true);
3225     if (alignPanel.getOverviewPanel() != null)
3226     {
3227       alignPanel.getOverviewPanel().updateOverviewImage();
3228     }
3229   }
3230
3231   /**
3232    * Set or clear 'Show Sequence Features'
3233    *
3234    * @param evt
3235    *          DOCUMENT ME!
3236    */
3237   @Override
3238   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3239   {
3240     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3241             .isSelected());
3242     if (viewport.isShowSequenceFeaturesHeight())
3243     {
3244       // ensure we're actually displaying features
3245       viewport.setShowSequenceFeatures(true);
3246       showSeqFeatures.setSelected(true);
3247     }
3248     alignPanel.paintAlignment(true);
3249     if (alignPanel.getOverviewPanel() != null)
3250     {
3251       alignPanel.getOverviewPanel().updateOverviewImage();
3252     }
3253   }
3254
3255   /**
3256    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3257    * the annotations panel as a whole.
3258    *
3259    * The options to show/hide all annotations should be enabled when the panel
3260    * is shown, and disabled when the panel is hidden.
3261    *
3262    * @param e
3263    */
3264   @Override
3265   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3266   {
3267     final boolean setVisible = annotationPanelMenuItem.isSelected();
3268     viewport.setShowAnnotation(setVisible);
3269     this.showAllSeqAnnotations.setEnabled(setVisible);
3270     this.hideAllSeqAnnotations.setEnabled(setVisible);
3271     this.showAllAlAnnotations.setEnabled(setVisible);
3272     this.hideAllAlAnnotations.setEnabled(setVisible);
3273     alignPanel.updateLayout();
3274   }
3275
3276   @Override
3277   public void alignmentProperties()
3278   {
3279     JEditorPane editPane = new JEditorPane("text/html", "");
3280     editPane.setEditable(false);
3281     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3282             .formatAsHtml();
3283     editPane.setText(MessageManager.formatMessage("label.html_content",
3284             new Object[] { contents.toString() }));
3285     JInternalFrame frame = new JInternalFrame();
3286     frame.getContentPane().add(new JScrollPane(editPane));
3287
3288     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3289             "label.alignment_properties", new Object[] { getTitle() }),
3290             500, 400);
3291   }
3292
3293   /**
3294    * DOCUMENT ME!
3295    *
3296    * @param e
3297    *          DOCUMENT ME!
3298    */
3299   @Override
3300   public void overviewMenuItem_actionPerformed(ActionEvent e)
3301   {
3302     if (alignPanel.overviewPanel != null)
3303     {
3304       return;
3305     }
3306
3307     JInternalFrame frame = new JInternalFrame();
3308     OverviewPanel overview = new OverviewPanel(alignPanel);
3309     frame.setContentPane(overview);
3310     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3311             "label.overview_params", new Object[] { this.getTitle() }),
3312             frame.getWidth(), frame.getHeight());
3313     frame.pack();
3314     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3315     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3316     {
3317       @Override
3318       public void internalFrameClosed(
3319               javax.swing.event.InternalFrameEvent evt)
3320       {
3321         alignPanel.setOverviewPanel(null);
3322       };
3323     });
3324
3325     alignPanel.setOverviewPanel(overview);
3326   }
3327
3328   @Override
3329   public void textColour_actionPerformed(ActionEvent e)
3330   {
3331     new TextColourChooser().chooseColour(alignPanel, null);
3332   }
3333
3334   /**
3335    * DOCUMENT ME!
3336    *
3337    * @param e
3338    *          DOCUMENT ME!
3339    */
3340   @Override
3341   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3342   {
3343     changeColour(null);
3344   }
3345
3346   /**
3347    * DOCUMENT ME!
3348    *
3349    * @param e
3350    *          DOCUMENT ME!
3351    */
3352   @Override
3353   public void clustalColour_actionPerformed(ActionEvent e)
3354   {
3355     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3356             viewport.getHiddenRepSequences()));
3357   }
3358
3359   /**
3360    * DOCUMENT ME!
3361    *
3362    * @param e
3363    *          DOCUMENT ME!
3364    */
3365   @Override
3366   public void zappoColour_actionPerformed(ActionEvent e)
3367   {
3368     changeColour(new ZappoColourScheme());
3369   }
3370
3371   /**
3372    * DOCUMENT ME!
3373    *
3374    * @param e
3375    *          DOCUMENT ME!
3376    */
3377   @Override
3378   public void taylorColour_actionPerformed(ActionEvent e)
3379   {
3380     changeColour(new TaylorColourScheme());
3381   }
3382
3383   /**
3384    * DOCUMENT ME!
3385    *
3386    * @param e
3387    *          DOCUMENT ME!
3388    */
3389   @Override
3390   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3391   {
3392     changeColour(new HydrophobicColourScheme());
3393   }
3394
3395   /**
3396    * DOCUMENT ME!
3397    *
3398    * @param e
3399    *          DOCUMENT ME!
3400    */
3401   @Override
3402   public void helixColour_actionPerformed(ActionEvent e)
3403   {
3404     changeColour(new HelixColourScheme());
3405   }
3406
3407   /**
3408    * DOCUMENT ME!
3409    *
3410    * @param e
3411    *          DOCUMENT ME!
3412    */
3413   @Override
3414   public void strandColour_actionPerformed(ActionEvent e)
3415   {
3416     changeColour(new StrandColourScheme());
3417   }
3418
3419   /**
3420    * DOCUMENT ME!
3421    *
3422    * @param e
3423    *          DOCUMENT ME!
3424    */
3425   @Override
3426   public void turnColour_actionPerformed(ActionEvent e)
3427   {
3428     changeColour(new TurnColourScheme());
3429   }
3430
3431   /**
3432    * DOCUMENT ME!
3433    *
3434    * @param e
3435    *          DOCUMENT ME!
3436    */
3437   @Override
3438   public void buriedColour_actionPerformed(ActionEvent e)
3439   {
3440     changeColour(new BuriedColourScheme());
3441   }
3442
3443   /**
3444    * DOCUMENT ME!
3445    *
3446    * @param e
3447    *          DOCUMENT ME!
3448    */
3449   @Override
3450   public void nucleotideColour_actionPerformed(ActionEvent e)
3451   {
3452     changeColour(new NucleotideColourScheme());
3453   }
3454
3455   @Override
3456   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3457   {
3458     changeColour(new PurinePyrimidineColourScheme());
3459   }
3460
3461   /*
3462    * public void covariationColour_actionPerformed(ActionEvent e) {
3463    * changeColour(new
3464    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3465    * ()[0])); }
3466    */
3467   @Override
3468   public void annotationColour_actionPerformed(ActionEvent e)
3469   {
3470     new AnnotationColourChooser(viewport, alignPanel);
3471   }
3472
3473   @Override
3474   public void annotationColumn_actionPerformed(ActionEvent e)
3475   {
3476     new AnnotationColumnChooser(viewport, alignPanel);
3477   }
3478
3479   @Override
3480   public void rnahelicesColour_actionPerformed(ActionEvent e)
3481   {
3482     new RNAHelicesColourChooser(viewport, alignPanel);
3483   }
3484
3485   /**
3486    * DOCUMENT ME!
3487    *
3488    * @param e
3489    *          DOCUMENT ME!
3490    */
3491   @Override
3492   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3493   {
3494     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3495   }
3496
3497   /**
3498    * DOCUMENT ME!
3499    *
3500    * @param cs
3501    *          DOCUMENT ME!
3502    */
3503   @Override
3504   public void changeColour(ColourSchemeI cs)
3505   {
3506     // TODO: pull up to controller method
3507
3508     if (cs != null)
3509     {
3510       // Make sure viewport is up to date w.r.t. any sliders
3511       if (viewport.getAbovePIDThreshold())
3512       {
3513         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3514                 "Background");
3515         viewport.setThreshold(threshold);
3516       }
3517
3518       if (viewport.getConservationSelected())
3519       {
3520         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3521                 cs, "Background"));
3522       }
3523       if (cs instanceof TCoffeeColourScheme)
3524       {
3525         tcoffeeColour.setEnabled(true);
3526         tcoffeeColour.setSelected(true);
3527       }
3528     }
3529
3530     viewport.setGlobalColourScheme(cs);
3531
3532     alignPanel.paintAlignment(true);
3533   }
3534
3535   /**
3536    * DOCUMENT ME!
3537    *
3538    * @param e
3539    *          DOCUMENT ME!
3540    */
3541   @Override
3542   protected void modifyPID_actionPerformed(ActionEvent e)
3543   {
3544     if (viewport.getAbovePIDThreshold()
3545             && viewport.getGlobalColourScheme() != null)
3546     {
3547       SliderPanel.setPIDSliderSource(alignPanel,
3548               viewport.getGlobalColourScheme(), "Background");
3549       SliderPanel.showPIDSlider();
3550     }
3551   }
3552
3553   /**
3554    * DOCUMENT ME!
3555    *
3556    * @param e
3557    *          DOCUMENT ME!
3558    */
3559   @Override
3560   protected void modifyConservation_actionPerformed(ActionEvent e)
3561   {
3562     if (viewport.getConservationSelected()
3563             && viewport.getGlobalColourScheme() != null)
3564     {
3565       SliderPanel.setConservationSlider(alignPanel,
3566               viewport.getGlobalColourScheme(), "Background");
3567       SliderPanel.showConservationSlider();
3568     }
3569   }
3570
3571   /**
3572    * DOCUMENT ME!
3573    *
3574    * @param e
3575    *          DOCUMENT ME!
3576    */
3577   @Override
3578   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3579   {
3580     viewport.setConservationSelected(conservationMenuItem.isSelected());
3581
3582     viewport.setAbovePIDThreshold(false);
3583     abovePIDThreshold.setSelected(false);
3584
3585     changeColour(viewport.getGlobalColourScheme());
3586
3587     modifyConservation_actionPerformed(null);
3588   }
3589
3590   /**
3591    * DOCUMENT ME!
3592    *
3593    * @param e
3594    *          DOCUMENT ME!
3595    */
3596   @Override
3597   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3598   {
3599     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3600
3601     conservationMenuItem.setSelected(false);
3602     viewport.setConservationSelected(false);
3603
3604     changeColour(viewport.getGlobalColourScheme());
3605
3606     modifyPID_actionPerformed(null);
3607   }
3608
3609   /**
3610    * DOCUMENT ME!
3611    *
3612    * @param e
3613    *          DOCUMENT ME!
3614    */
3615   @Override
3616   public void userDefinedColour_actionPerformed(ActionEvent e)
3617   {
3618     if (e.getActionCommand().equals(
3619             MessageManager.getString("action.user_defined")))
3620     {
3621       new UserDefinedColours(alignPanel, null);
3622     }
3623     else
3624     {
3625       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3626               .getUserColourSchemes().get(e.getActionCommand());
3627
3628       changeColour(udc);
3629     }
3630   }
3631
3632   public void updateUserColourMenu()
3633   {
3634
3635     Component[] menuItems = colourMenu.getMenuComponents();
3636     int iSize = menuItems.length;
3637     for (int i = 0; i < iSize; i++)
3638     {
3639       if (menuItems[i].getName() != null
3640               && menuItems[i].getName().equals("USER_DEFINED"))
3641       {
3642         colourMenu.remove(menuItems[i]);
3643         iSize--;
3644       }
3645     }
3646     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3647     {
3648       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3649               .getUserColourSchemes().keys();
3650
3651       while (userColours.hasMoreElements())
3652       {
3653         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3654                 userColours.nextElement().toString());
3655         radioItem.setName("USER_DEFINED");
3656         radioItem.addMouseListener(new MouseAdapter()
3657         {
3658           @Override
3659           public void mousePressed(MouseEvent evt)
3660           {
3661             if (evt.isControlDown()
3662                     || SwingUtilities.isRightMouseButton(evt))
3663             {
3664               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3665
3666               int option = JOptionPane.showInternalConfirmDialog(
3667                       jalview.gui.Desktop.desktop,
3668                       MessageManager
3669                               .getString("label.remove_from_default_list"),
3670                       MessageManager
3671                               .getString("label.remove_user_defined_colour"),
3672                       JOptionPane.YES_NO_OPTION);
3673               if (option == JOptionPane.YES_OPTION)
3674               {
3675                 jalview.gui.UserDefinedColours
3676                         .removeColourFromDefaults(radioItem.getText());
3677                 colourMenu.remove(radioItem);
3678               }
3679               else
3680               {
3681                 radioItem.addActionListener(new ActionListener()
3682                 {
3683                   @Override
3684                   public void actionPerformed(ActionEvent evt)
3685                   {
3686                     userDefinedColour_actionPerformed(evt);
3687                   }
3688                 });
3689               }
3690             }
3691           }
3692         });
3693         radioItem.addActionListener(new ActionListener()
3694         {
3695           @Override
3696           public void actionPerformed(ActionEvent evt)
3697           {
3698             userDefinedColour_actionPerformed(evt);
3699           }
3700         });
3701
3702         colourMenu.insert(radioItem, 15);
3703         colours.add(radioItem);
3704       }
3705     }
3706   }
3707
3708   /**
3709    * DOCUMENT ME!
3710    *
3711    * @param e
3712    *          DOCUMENT ME!
3713    */
3714   @Override
3715   public void PIDColour_actionPerformed(ActionEvent e)
3716   {
3717     changeColour(new PIDColourScheme());
3718   }
3719
3720   /**
3721    * DOCUMENT ME!
3722    *
3723    * @param e
3724    *          DOCUMENT ME!
3725    */
3726   @Override
3727   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3728   {
3729     changeColour(new Blosum62ColourScheme());
3730   }
3731
3732   /**
3733    * DOCUMENT ME!
3734    *
3735    * @param e
3736    *          DOCUMENT ME!
3737    */
3738   @Override
3739   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3740   {
3741     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3742     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3743             .getAlignment().getSequenceAt(0), null);
3744     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3745             viewport.getAlignment()));
3746     alignPanel.paintAlignment(true);
3747   }
3748
3749   /**
3750    * DOCUMENT ME!
3751    *
3752    * @param e
3753    *          DOCUMENT ME!
3754    */
3755   @Override
3756   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3757   {
3758     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3759     AlignmentSorter.sortByID(viewport.getAlignment());
3760     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3761             viewport.getAlignment()));
3762     alignPanel.paintAlignment(true);
3763   }
3764
3765   /**
3766    * DOCUMENT ME!
3767    *
3768    * @param e
3769    *          DOCUMENT ME!
3770    */
3771   @Override
3772   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3773   {
3774     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3775     AlignmentSorter.sortByLength(viewport.getAlignment());
3776     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3777             viewport.getAlignment()));
3778     alignPanel.paintAlignment(true);
3779   }
3780
3781   /**
3782    * DOCUMENT ME!
3783    *
3784    * @param e
3785    *          DOCUMENT ME!
3786    */
3787   @Override
3788   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3789   {
3790     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3791     AlignmentSorter.sortByGroup(viewport.getAlignment());
3792     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3793             viewport.getAlignment()));
3794
3795     alignPanel.paintAlignment(true);
3796   }
3797
3798   /**
3799    * DOCUMENT ME!
3800    *
3801    * @param e
3802    *          DOCUMENT ME!
3803    */
3804   @Override
3805   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3806   {
3807     new RedundancyPanel(alignPanel, this);
3808   }
3809
3810   /**
3811    * DOCUMENT ME!
3812    *
3813    * @param e
3814    *          DOCUMENT ME!
3815    */
3816   @Override
3817   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3818   {
3819     if ((viewport.getSelectionGroup() == null)
3820             || (viewport.getSelectionGroup().getSize() < 2))
3821     {
3822       JOptionPane.showInternalMessageDialog(this, MessageManager
3823               .getString("label.you_must_select_least_two_sequences"),
3824               MessageManager.getString("label.invalid_selection"),
3825               JOptionPane.WARNING_MESSAGE);
3826     }
3827     else
3828     {
3829       JInternalFrame frame = new JInternalFrame();
3830       frame.setContentPane(new PairwiseAlignPanel(viewport));
3831       Desktop.addInternalFrame(frame,
3832               MessageManager.getString("action.pairwise_alignment"), 600,
3833               500);
3834     }
3835   }
3836
3837   /**
3838    * DOCUMENT ME!
3839    *
3840    * @param e
3841    *          DOCUMENT ME!
3842    */
3843   @Override
3844   public void PCAMenuItem_actionPerformed(ActionEvent e)
3845   {
3846     if (((viewport.getSelectionGroup() != null)
3847             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3848             .getSelectionGroup().getSize() > 0))
3849             || (viewport.getAlignment().getHeight() < 4))
3850     {
3851       JOptionPane
3852               .showInternalMessageDialog(
3853                       this,
3854                       MessageManager
3855                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3856                       MessageManager
3857                               .getString("label.sequence_selection_insufficient"),
3858                       JOptionPane.WARNING_MESSAGE);
3859
3860       return;
3861     }
3862
3863     new PCAPanel(alignPanel);
3864   }
3865
3866   @Override
3867   public void autoCalculate_actionPerformed(ActionEvent e)
3868   {
3869     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3870     if (viewport.autoCalculateConsensus)
3871     {
3872       viewport.firePropertyChange("alignment", null, viewport
3873               .getAlignment().getSequences());
3874     }
3875   }
3876
3877   @Override
3878   public void sortByTreeOption_actionPerformed(ActionEvent e)
3879   {
3880     viewport.sortByTree = sortByTree.isSelected();
3881   }
3882
3883   @Override
3884   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3885   {
3886     viewport.followSelection = listenToViewSelections.isSelected();
3887   }
3888
3889   /**
3890    * DOCUMENT ME!
3891    *
3892    * @param e
3893    *          DOCUMENT ME!
3894    */
3895   @Override
3896   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3897   {
3898     newTreePanel("AV", "PID", "Average distance tree using PID");
3899   }
3900
3901   /**
3902    * DOCUMENT ME!
3903    *
3904    * @param e
3905    *          DOCUMENT ME!
3906    */
3907   @Override
3908   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3909   {
3910     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3911   }
3912
3913   /**
3914    * DOCUMENT ME!
3915    *
3916    * @param e
3917    *          DOCUMENT ME!
3918    */
3919   @Override
3920   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3921   {
3922     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3923   }
3924
3925   /**
3926    * DOCUMENT ME!
3927    *
3928    * @param e
3929    *          DOCUMENT ME!
3930    */
3931   @Override
3932   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3933   {
3934     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3935   }
3936
3937   /**
3938    * DOCUMENT ME!
3939    *
3940    * @param type
3941    *          DOCUMENT ME!
3942    * @param pwType
3943    *          DOCUMENT ME!
3944    * @param title
3945    *          DOCUMENT ME!
3946    */
3947   void newTreePanel(String type, String pwType, String title)
3948   {
3949     TreePanel tp;
3950
3951     if (viewport.getSelectionGroup() != null
3952             && viewport.getSelectionGroup().getSize() > 0)
3953     {
3954       if (viewport.getSelectionGroup().getSize() < 3)
3955       {
3956         JOptionPane
3957                 .showMessageDialog(
3958                         Desktop.desktop,
3959                         MessageManager
3960                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3961                         MessageManager
3962                                 .getString("label.not_enough_sequences"),
3963                         JOptionPane.WARNING_MESSAGE);
3964         return;
3965       }
3966
3967       SequenceGroup sg = viewport.getSelectionGroup();
3968
3969       /* Decide if the selection is a column region */
3970       for (SequenceI _s : sg.getSequences())
3971       {
3972         if (_s.getLength() < sg.getEndRes())
3973         {
3974           JOptionPane
3975                   .showMessageDialog(
3976                           Desktop.desktop,
3977                           MessageManager
3978                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3979                           MessageManager
3980                                   .getString("label.sequences_selection_not_aligned"),
3981                           JOptionPane.WARNING_MESSAGE);
3982
3983           return;
3984         }
3985       }
3986
3987       title = title + " on region";
3988       tp = new TreePanel(alignPanel, type, pwType);
3989     }
3990     else
3991     {
3992       // are the visible sequences aligned?
3993       if (!viewport.getAlignment().isAligned(false))
3994       {
3995         JOptionPane
3996                 .showMessageDialog(
3997                         Desktop.desktop,
3998                         MessageManager
3999                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4000                         MessageManager
4001                                 .getString("label.sequences_not_aligned"),
4002                         JOptionPane.WARNING_MESSAGE);
4003
4004         return;
4005       }
4006
4007       if (viewport.getAlignment().getHeight() < 2)
4008       {
4009         return;
4010       }
4011
4012       tp = new TreePanel(alignPanel, type, pwType);
4013     }
4014
4015     title += " from ";
4016
4017     if (viewport.viewName != null)
4018     {
4019       title += viewport.viewName + " of ";
4020     }
4021
4022     title += this.title;
4023
4024     Desktop.addInternalFrame(tp, title, 600, 500);
4025   }
4026
4027   /**
4028    * DOCUMENT ME!
4029    *
4030    * @param title
4031    *          DOCUMENT ME!
4032    * @param order
4033    *          DOCUMENT ME!
4034    */
4035   public void addSortByOrderMenuItem(String title,
4036           final AlignmentOrder order)
4037   {
4038     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4039             "action.by_title_param", new Object[] { title }));
4040     sort.add(item);
4041     item.addActionListener(new java.awt.event.ActionListener()
4042     {
4043       @Override
4044       public void actionPerformed(ActionEvent e)
4045       {
4046         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4047
4048         // TODO: JBPNote - have to map order entries to curent SequenceI
4049         // pointers
4050         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4051
4052         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4053                 .getAlignment()));
4054
4055         alignPanel.paintAlignment(true);
4056       }
4057     });
4058   }
4059
4060   /**
4061    * Add a new sort by annotation score menu item
4062    *
4063    * @param sort
4064    *          the menu to add the option to
4065    * @param scoreLabel
4066    *          the label used to retrieve scores for each sequence on the
4067    *          alignment
4068    */
4069   public void addSortByAnnotScoreMenuItem(JMenu sort,
4070           final String scoreLabel)
4071   {
4072     final JMenuItem item = new JMenuItem(scoreLabel);
4073     sort.add(item);
4074     item.addActionListener(new java.awt.event.ActionListener()
4075     {
4076       @Override
4077       public void actionPerformed(ActionEvent e)
4078       {
4079         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4080         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4081                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4082         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4083                 viewport.getAlignment()));
4084         alignPanel.paintAlignment(true);
4085       }
4086     });
4087   }
4088
4089   /**
4090    * last hash for alignment's annotation array - used to minimise cost of
4091    * rebuild.
4092    */
4093   protected int _annotationScoreVectorHash;
4094
4095   /**
4096    * search the alignment and rebuild the sort by annotation score submenu the
4097    * last alignment annotation vector hash is stored to minimize cost of
4098    * rebuilding in subsequence calls.
4099    *
4100    */
4101   @Override
4102   public void buildSortByAnnotationScoresMenu()
4103   {
4104     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4105     {
4106       return;
4107     }
4108
4109     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4110     {
4111       sortByAnnotScore.removeAll();
4112       // almost certainly a quicker way to do this - but we keep it simple
4113       Hashtable scoreSorts = new Hashtable();
4114       AlignmentAnnotation aann[];
4115       for (SequenceI sqa : viewport.getAlignment().getSequences())
4116       {
4117         aann = sqa.getAnnotation();
4118         for (int i = 0; aann != null && i < aann.length; i++)
4119         {
4120           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4121           {
4122             scoreSorts.put(aann[i].label, aann[i].label);
4123           }
4124         }
4125       }
4126       Enumeration labels = scoreSorts.keys();
4127       while (labels.hasMoreElements())
4128       {
4129         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4130                 (String) labels.nextElement());
4131       }
4132       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4133       scoreSorts.clear();
4134
4135       _annotationScoreVectorHash = viewport.getAlignment()
4136               .getAlignmentAnnotation().hashCode();
4137     }
4138   }
4139
4140   /**
4141    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4142    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4143    * call. Listeners are added to remove the menu item when the treePanel is
4144    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4145    * modified.
4146    *
4147    * @param treePanel
4148    *          Displayed tree window.
4149    * @param title
4150    *          SortBy menu item title.
4151    */
4152   @Override
4153   public void buildTreeMenu()
4154   {
4155     calculateTree.removeAll();
4156     // build the calculate menu
4157
4158     for (final String type : new String[] { "NJ", "AV" })
4159     {
4160       String treecalcnm = MessageManager.getString("label.tree_calc_"
4161               + type.toLowerCase());
4162       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4163       {
4164         JMenuItem tm = new JMenuItem();
4165         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4166         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4167         {
4168           String smn = MessageManager.getStringOrReturn(
4169                   "label.score_model_", sm.getName());
4170           final String title = MessageManager.formatMessage(
4171                   "label.treecalc_title", treecalcnm, smn);
4172           tm.setText(title);//
4173           tm.addActionListener(new java.awt.event.ActionListener()
4174           {
4175             @Override
4176             public void actionPerformed(ActionEvent e)
4177             {
4178               newTreePanel(type, pwtype, title);
4179             }
4180           });
4181           calculateTree.add(tm);
4182         }
4183
4184       }
4185     }
4186     sortByTreeMenu.removeAll();
4187
4188     List<Component> comps = PaintRefresher.components.get(viewport
4189             .getSequenceSetId());
4190     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4191     for (Component comp : comps)
4192     {
4193       if (comp instanceof TreePanel)
4194       {
4195         treePanels.add((TreePanel) comp);
4196       }
4197     }
4198
4199     if (treePanels.size() < 1)
4200     {
4201       sortByTreeMenu.setVisible(false);
4202       return;
4203     }
4204
4205     sortByTreeMenu.setVisible(true);
4206
4207     for (final TreePanel tp : treePanels)
4208     {
4209       final JMenuItem item = new JMenuItem(tp.getTitle());
4210       item.addActionListener(new java.awt.event.ActionListener()
4211       {
4212         @Override
4213         public void actionPerformed(ActionEvent e)
4214         {
4215           tp.sortByTree_actionPerformed();
4216           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4217
4218         }
4219       });
4220
4221       sortByTreeMenu.add(item);
4222     }
4223   }
4224
4225   public boolean sortBy(AlignmentOrder alorder, String undoname)
4226   {
4227     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4228     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4229     if (undoname != null)
4230     {
4231       addHistoryItem(new OrderCommand(undoname, oldOrder,
4232               viewport.getAlignment()));
4233     }
4234     alignPanel.paintAlignment(true);
4235     return true;
4236   }
4237
4238   /**
4239    * Work out whether the whole set of sequences or just the selected set will
4240    * be submitted for multiple alignment.
4241    *
4242    */
4243   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4244   {
4245     // Now, check we have enough sequences
4246     AlignmentView msa = null;
4247
4248     if ((viewport.getSelectionGroup() != null)
4249             && (viewport.getSelectionGroup().getSize() > 1))
4250     {
4251       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4252       // some common interface!
4253       /*
4254        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4255        * SequenceI[sz = seqs.getSize(false)];
4256        *
4257        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4258        * seqs.getSequenceAt(i); }
4259        */
4260       msa = viewport.getAlignmentView(true);
4261     }
4262     else if (viewport.getSelectionGroup() != null
4263             && viewport.getSelectionGroup().getSize() == 1)
4264     {
4265       int option = JOptionPane.showConfirmDialog(this,
4266               MessageManager.getString("warn.oneseq_msainput_selection"),
4267               MessageManager.getString("label.invalid_selection"),
4268               JOptionPane.OK_CANCEL_OPTION);
4269       if (option == JOptionPane.OK_OPTION)
4270       {
4271         msa = viewport.getAlignmentView(false);
4272       }
4273     }
4274     else
4275     {
4276       msa = viewport.getAlignmentView(false);
4277     }
4278     return msa;
4279   }
4280
4281   /**
4282    * Decides what is submitted to a secondary structure prediction service: the
4283    * first sequence in the alignment, or in the current selection, or, if the
4284    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4285    * region or the whole alignment. (where the first sequence in the set is the
4286    * one that the prediction will be for).
4287    */
4288   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4289   {
4290     AlignmentView seqs = null;
4291
4292     if ((viewport.getSelectionGroup() != null)
4293             && (viewport.getSelectionGroup().getSize() > 0))
4294     {
4295       seqs = viewport.getAlignmentView(true);
4296     }
4297     else
4298     {
4299       seqs = viewport.getAlignmentView(false);
4300     }
4301     // limit sequences - JBPNote in future - could spawn multiple prediction
4302     // jobs
4303     // TODO: viewport.getAlignment().isAligned is a global state - the local
4304     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4305     if (!viewport.getAlignment().isAligned(false))
4306     {
4307       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4308       // TODO: if seqs.getSequences().length>1 then should really have warned
4309       // user!
4310
4311     }
4312     return seqs;
4313   }
4314
4315   /**
4316    * DOCUMENT ME!
4317    *
4318    * @param e
4319    *          DOCUMENT ME!
4320    */
4321   @Override
4322   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4323   {
4324     // Pick the tree file
4325     JalviewFileChooser chooser = new JalviewFileChooser(
4326             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4327     chooser.setFileView(new JalviewFileView());
4328     chooser.setDialogTitle(MessageManager
4329             .getString("label.select_newick_like_tree_file"));
4330     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4331
4332     int value = chooser.showOpenDialog(null);
4333
4334     if (value == JalviewFileChooser.APPROVE_OPTION)
4335     {
4336       String choice = chooser.getSelectedFile().getPath();
4337       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4338       jalview.io.NewickFile fin = null;
4339       try
4340       {
4341         fin = new jalview.io.NewickFile(choice, "File");
4342         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4343       } catch (Exception ex)
4344       {
4345         JOptionPane
4346                 .showMessageDialog(
4347                         Desktop.desktop,
4348                         ex.getMessage(),
4349                         MessageManager
4350                                 .getString("label.problem_reading_tree_file"),
4351                         JOptionPane.WARNING_MESSAGE);
4352         ex.printStackTrace();
4353       }
4354       if (fin != null && fin.hasWarningMessage())
4355       {
4356         JOptionPane.showMessageDialog(Desktop.desktop, fin
4357                 .getWarningMessage(), MessageManager
4358                 .getString("label.possible_problem_with_tree_file"),
4359                 JOptionPane.WARNING_MESSAGE);
4360       }
4361     }
4362   }
4363
4364   @Override
4365   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4366   {
4367     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4368   }
4369
4370   public TreePanel ShowNewickTree(NewickFile nf, String title)
4371   {
4372     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4373   }
4374
4375   public TreePanel ShowNewickTree(NewickFile nf, String title,
4376           AlignmentView input)
4377   {
4378     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4379   }
4380
4381   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4382           int h, int x, int y)
4383   {
4384     return ShowNewickTree(nf, title, null, w, h, x, y);
4385   }
4386
4387   /**
4388    * Add a treeviewer for the tree extracted from a newick file object to the
4389    * current alignment view
4390    *
4391    * @param nf
4392    *          the tree
4393    * @param title
4394    *          tree viewer title
4395    * @param input
4396    *          Associated alignment input data (or null)
4397    * @param w
4398    *          width
4399    * @param h
4400    *          height
4401    * @param x
4402    *          position
4403    * @param y
4404    *          position
4405    * @return TreePanel handle
4406    */
4407   public TreePanel ShowNewickTree(NewickFile nf, String title,
4408           AlignmentView input, int w, int h, int x, int y)
4409   {
4410     TreePanel tp = null;
4411
4412     try
4413     {
4414       nf.parse();
4415
4416       if (nf.getTree() != null)
4417       {
4418         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4419
4420         tp.setSize(w, h);
4421
4422         if (x > 0 && y > 0)
4423         {
4424           tp.setLocation(x, y);
4425         }
4426
4427         Desktop.addInternalFrame(tp, title, w, h);
4428       }
4429     } catch (Exception ex)
4430     {
4431       ex.printStackTrace();
4432     }
4433
4434     return tp;
4435   }
4436
4437   private boolean buildingMenu = false;
4438
4439   /**
4440    * Generates menu items and listener event actions for web service clients
4441    *
4442    */
4443   public void BuildWebServiceMenu()
4444   {
4445     while (buildingMenu)
4446     {
4447       try
4448       {
4449         System.err.println("Waiting for building menu to finish.");
4450         Thread.sleep(10);
4451       } catch (Exception e)
4452       {
4453       }
4454     }
4455     final AlignFrame me = this;
4456     buildingMenu = true;
4457     new Thread(new Runnable()
4458     {
4459       @Override
4460       public void run()
4461       {
4462         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4463         try
4464         {
4465           // System.err.println("Building ws menu again "
4466           // + Thread.currentThread());
4467           // TODO: add support for context dependent disabling of services based
4468           // on
4469           // alignment and current selection
4470           // TODO: add additional serviceHandle parameter to specify abstract
4471           // handler
4472           // class independently of AbstractName
4473           // TODO: add in rediscovery GUI function to restart discoverer
4474           // TODO: group services by location as well as function and/or
4475           // introduce
4476           // object broker mechanism.
4477           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4478           final IProgressIndicator af = me;
4479           final JMenu msawsmenu = new JMenu("Alignment");
4480           final JMenu secstrmenu = new JMenu(
4481                   "Secondary Structure Prediction");
4482           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4483           final JMenu analymenu = new JMenu("Analysis");
4484           final JMenu dismenu = new JMenu("Protein Disorder");
4485           // final JMenu msawsmenu = new
4486           // JMenu(MessageManager.getString("label.alignment"));
4487           // final JMenu secstrmenu = new
4488           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4489           // final JMenu seqsrchmenu = new
4490           // JMenu(MessageManager.getString("label.sequence_database_search"));
4491           // final JMenu analymenu = new
4492           // JMenu(MessageManager.getString("label.analysis"));
4493           // final JMenu dismenu = new
4494           // JMenu(MessageManager.getString("label.protein_disorder"));
4495           // JAL-940 - only show secondary structure prediction services from
4496           // the legacy server
4497           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4498               // &&
4499           Discoverer.services != null && (Discoverer.services.size() > 0))
4500           {
4501             // TODO: refactor to allow list of AbstractName/Handler bindings to
4502             // be
4503             // stored or retrieved from elsewhere
4504             // No MSAWS used any more:
4505             // Vector msaws = null; // (Vector)
4506             // Discoverer.services.get("MsaWS");
4507             Vector secstrpr = (Vector) Discoverer.services
4508                     .get("SecStrPred");
4509             if (secstrpr != null)
4510             {
4511               // Add any secondary structure prediction services
4512               for (int i = 0, j = secstrpr.size(); i < j; i++)
4513               {
4514                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4515                         .get(i);
4516                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4517                         .getServiceClient(sh);
4518                 int p = secstrmenu.getItemCount();
4519                 impl.attachWSMenuEntry(secstrmenu, me);
4520                 int q = secstrmenu.getItemCount();
4521                 for (int litm = p; litm < q; litm++)
4522                 {
4523                   legacyItems.add(secstrmenu.getItem(litm));
4524                 }
4525               }
4526             }
4527           }
4528
4529           // Add all submenus in the order they should appear on the web
4530           // services menu
4531           wsmenu.add(msawsmenu);
4532           wsmenu.add(secstrmenu);
4533           wsmenu.add(dismenu);
4534           wsmenu.add(analymenu);
4535           // No search services yet
4536           // wsmenu.add(seqsrchmenu);
4537
4538           javax.swing.SwingUtilities.invokeLater(new Runnable()
4539           {
4540             @Override
4541             public void run()
4542             {
4543               try
4544               {
4545                 webService.removeAll();
4546                 // first, add discovered services onto the webservices menu
4547                 if (wsmenu.size() > 0)
4548                 {
4549                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4550                   {
4551                     webService.add(wsmenu.get(i));
4552                   }
4553                 }
4554                 else
4555                 {
4556                   webService.add(me.webServiceNoServices);
4557                 }
4558                 // TODO: move into separate menu builder class.
4559                 boolean new_sspred = false;
4560                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4561                 {
4562                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4563                   if (jws2servs != null)
4564                   {
4565                     if (jws2servs.hasServices())
4566                     {
4567                       jws2servs.attachWSMenuEntry(webService, me);
4568                       for (Jws2Instance sv : jws2servs.getServices())
4569                       {
4570                         if (sv.description.toLowerCase().contains("jpred"))
4571                         {
4572                           for (JMenuItem jmi : legacyItems)
4573                           {
4574                             jmi.setVisible(false);
4575                           }
4576                         }
4577                       }
4578
4579                     }
4580                     if (jws2servs.isRunning())
4581                     {
4582                       JMenuItem tm = new JMenuItem(
4583                               "Still discovering JABA Services");
4584                       tm.setEnabled(false);
4585                       webService.add(tm);
4586                     }
4587                   }
4588                 }
4589                 build_urlServiceMenu(me.webService);
4590                 build_fetchdbmenu(webService);
4591                 for (JMenu item : wsmenu)
4592                 {
4593                   if (item.getItemCount() == 0)
4594                   {
4595                     item.setEnabled(false);
4596                   }
4597                   else
4598                   {
4599                     item.setEnabled(true);
4600                   }
4601                 }
4602               } catch (Exception e)
4603               {
4604                 Cache.log
4605                         .debug("Exception during web service menu building process.",
4606                                 e);
4607               }
4608             }
4609           });
4610         } catch (Exception e)
4611         {
4612         }
4613         buildingMenu = false;
4614       }
4615     }).start();
4616
4617   }
4618
4619   /**
4620    * construct any groupURL type service menu entries.
4621    *
4622    * @param webService
4623    */
4624   private void build_urlServiceMenu(JMenu webService)
4625   {
4626     // TODO: remove this code when 2.7 is released
4627     // DEBUG - alignmentView
4628     /*
4629      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4630      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4631      *
4632      * @Override public void actionPerformed(ActionEvent e) {
4633      * jalview.datamodel.AlignmentView
4634      * .testSelectionViews(af.viewport.getAlignment(),
4635      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4636      *
4637      * }); webService.add(testAlView);
4638      */
4639     // TODO: refactor to RestClient discoverer and merge menu entries for
4640     // rest-style services with other types of analysis/calculation service
4641     // SHmmr test client - still being implemented.
4642     // DEBUG - alignmentView
4643
4644     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4645             .getRestClients())
4646     {
4647       client.attachWSMenuEntry(
4648               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4649               this);
4650     }
4651   }
4652
4653   /*
4654    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4655    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4656    * getProperty("LAST_DIRECTORY"));
4657    *
4658    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4659    * to Vamsas file"); chooser.setToolTipText("Export");
4660    *
4661    * int value = chooser.showSaveDialog(this);
4662    *
4663    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4664    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4665    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4666    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4667    */
4668   /**
4669    * prototype of an automatically enabled/disabled analysis function
4670    *
4671    */
4672   protected void setShowProductsEnabled()
4673   {
4674     SequenceI[] selection = viewport.getSequenceSelection();
4675     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4676             viewport.getAlignment().getDataset()))
4677     {
4678       showProducts.setEnabled(true);
4679
4680     }
4681     else
4682     {
4683       showProducts.setEnabled(false);
4684     }
4685   }
4686
4687   /**
4688    * search selection for sequence xRef products and build the show products
4689    * menu.
4690    *
4691    * @param selection
4692    * @param dataset
4693    * @return true if showProducts menu should be enabled.
4694    */
4695   public boolean canShowProducts(SequenceI[] selection,
4696           boolean isRegionSelection, Alignment dataset)
4697   {
4698     boolean showp = false;
4699     try
4700     {
4701       showProducts.removeAll();
4702       final boolean dna = viewport.getAlignment().isNucleotide();
4703       final Alignment ds = dataset;
4704       String[] ptypes = (selection == null || selection.length == 0) ? null
4705               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4706       // Object[] prods =
4707       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4708       // selection, dataset, true);
4709       final SequenceI[] sel = selection;
4710       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4711       {
4712         showp = true;
4713         final boolean isRegSel = isRegionSelection;
4714         final AlignFrame af = this;
4715         final String source = ptypes[t];
4716         JMenuItem xtype = new JMenuItem(ptypes[t]);
4717         xtype.addActionListener(new ActionListener()
4718         {
4719
4720           @Override
4721           public void actionPerformed(ActionEvent e)
4722           {
4723             // TODO: new thread for this call with vis-delay
4724             af.showProductsFor(af.viewport.getSequenceSelection(),
4725                     isRegSel, dna, source);
4726           }
4727
4728         });
4729         showProducts.add(xtype);
4730       }
4731       showProducts.setVisible(showp);
4732       showProducts.setEnabled(showp);
4733     } catch (Exception e)
4734     {
4735       jalview.bin.Cache.log
4736               .warn("canTranslate threw an exception - please report to help@jalview.org",
4737                       e);
4738       return false;
4739     }
4740     return showp;
4741   }
4742
4743   protected void showProductsFor(final SequenceI[] sel,
4744           final boolean isRegSel, final boolean dna, final String source)
4745   {
4746     Runnable foo = new Runnable()
4747     {
4748
4749       @Override
4750       public void run()
4751       {
4752         final long sttime = System.currentTimeMillis();
4753         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4754                 "status.searching_for_sequences_from",
4755                 new Object[] { source }), sttime);
4756         try
4757         {
4758           // update our local dataset reference
4759           Alignment ds = AlignFrame.this.getViewport().getAlignment()
4760                   .getDataset();
4761           Alignment prods = CrossRef
4762                   .findXrefSequences(sel, dna, source, ds);
4763           if (prods != null)
4764           {
4765             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4766             for (int s = 0; s < sprods.length; s++)
4767             {
4768               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4769               if (ds.getSequences() == null
4770                       || !ds.getSequences().contains(
4771                               sprods[s].getDatasetSequence()))
4772               {
4773                 ds.addSequence(sprods[s].getDatasetSequence());
4774               }
4775               sprods[s].updatePDBIds();
4776             }
4777             Alignment al = new Alignment(sprods);
4778             al.setDataset(ds);
4779
4780             /*
4781              * Copy dna-to-protein mappings to new alignment
4782              */
4783             // TODO 1: no mappings are set up for EMBL product
4784             // TODO 2: if they were, should add them to protein alignment, not
4785             // dna
4786             Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4787             for (AlignedCodonFrame acf : cf)
4788             {
4789               al.addCodonFrame(acf);
4790             }
4791             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4792                     DEFAULT_HEIGHT);
4793             String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4794                     + " for " + ((isRegSel) ? "selected region of " : "")
4795                     + getTitle();
4796             naf.setTitle(newtitle);
4797
4798             // temporary flag until SplitFrame is released
4799             boolean asSplitFrame = Cache.getDefault(
4800                     Preferences.ENABLE_SPLIT_FRAME, true);
4801             if (asSplitFrame)
4802             {
4803               /*
4804                * Make a copy of this alignment (sharing the same dataset
4805                * sequences). If we are DNA, drop introns and update mappings
4806                */
4807               AlignmentI copyAlignment = null;
4808               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4809                       .getSequenceSelection();
4810               if (dna)
4811               {
4812                 copyAlignment = AlignmentUtils.makeExonAlignment(
4813                         sequenceSelection, cf);
4814                 al.getCodonFrames().clear();
4815                 al.getCodonFrames().addAll(cf);
4816                 final StructureSelectionManager ssm = StructureSelectionManager
4817                         .getStructureSelectionManager(Desktop.instance);
4818                 ssm.registerMappings(cf);
4819               }
4820               else
4821               {
4822                 copyAlignment = new Alignment(new Alignment(
4823                         sequenceSelection));
4824               }
4825               AlignFrame copyThis = new AlignFrame(copyAlignment,
4826                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4827               copyThis.setTitle(AlignFrame.this.getTitle());
4828               // SplitFrame with dna above, protein below
4829               SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4830                       dna ? naf : copyThis);
4831               naf.setVisible(true);
4832               copyThis.setVisible(true);
4833               String linkedTitle = MessageManager
4834                       .getString("label.linked_view_title");
4835               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4836             }
4837             else
4838             {
4839               Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4840                       DEFAULT_HEIGHT);
4841             }
4842           }
4843           else
4844           {
4845             System.err.println("No Sequences generated for xRef type "
4846                     + source);
4847           }
4848         } catch (Exception e)
4849         {
4850           jalview.bin.Cache.log.error(
4851                   "Exception when finding crossreferences", e);
4852         } catch (OutOfMemoryError e)
4853         {
4854           new OOMWarning("whilst fetching crossreferences", e);
4855         } catch (Error e)
4856         {
4857           jalview.bin.Cache.log.error("Error when finding crossreferences",
4858                   e);
4859         }
4860         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4861                 "status.finished_searching_for_sequences_from",
4862                 new Object[] { source }), sttime);
4863       }
4864
4865     };
4866     Thread frunner = new Thread(foo);
4867     frunner.start();
4868   }
4869
4870   public boolean canShowTranslationProducts(SequenceI[] selection,
4871           AlignmentI alignment)
4872   {
4873     // old way
4874     try
4875     {
4876       return (jalview.analysis.Dna.canTranslate(selection,
4877               viewport.getViewAsVisibleContigs(true)));
4878     } catch (Exception e)
4879     {
4880       jalview.bin.Cache.log
4881               .warn("canTranslate threw an exception - please report to help@jalview.org",
4882                       e);
4883       return false;
4884     }
4885   }
4886
4887   /**
4888    * Construct and display a new frame containing the translation of this
4889    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4890    */
4891   @Override
4892   public void showTranslation_actionPerformed(ActionEvent e)
4893   {
4894     AlignmentI al = null;
4895     try
4896     {
4897       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4898
4899       al = dna.translateCdna();
4900     } catch (Exception ex)
4901     {
4902       jalview.bin.Cache.log.error(
4903               "Exception during translation. Please report this !", ex);
4904       final String msg = MessageManager
4905               .getString("label.error_when_translating_sequences_submit_bug_report");
4906       final String errorTitle = MessageManager
4907               .getString("label.implementation_error")
4908               + MessageManager.getString("translation_failed");
4909       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4910               JOptionPane.ERROR_MESSAGE);
4911       return;
4912     }
4913     if (al == null || al.getHeight() == 0)
4914     {
4915       final String msg = MessageManager
4916               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4917       final String errorTitle = MessageManager
4918               .getString("label.translation_failed");
4919       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4920               JOptionPane.WARNING_MESSAGE);
4921     }
4922     else
4923     {
4924       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4925       af.setFileFormat(this.currentFileFormat);
4926       final String newTitle = MessageManager.formatMessage(
4927               "label.translation_of_params",
4928               new Object[] { this.getTitle() });
4929       af.setTitle(newTitle);
4930       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4931       {
4932         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4933         viewport.openSplitFrame(af, new Alignment(seqs));
4934       }
4935       else
4936       {
4937         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4938                 DEFAULT_HEIGHT);
4939       }
4940     }
4941   }
4942
4943   /**
4944    * Set the file format
4945    *
4946    * @param fileFormat
4947    */
4948   public void setFileFormat(String fileFormat)
4949   {
4950     this.currentFileFormat = fileFormat;
4951   }
4952
4953   /**
4954    * Try to load a features file onto the alignment.
4955    *
4956    * @param file
4957    *          contents or path to retrieve file
4958    * @param type
4959    *          access mode of file (see jalview.io.AlignFile)
4960    * @return true if features file was parsed correctly.
4961    */
4962   public boolean parseFeaturesFile(String file, String type)
4963   {
4964     return avc.parseFeaturesFile(file, type,
4965             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4966
4967   }
4968
4969   @Override
4970   public void refreshFeatureUI(boolean enableIfNecessary)
4971   {
4972     // note - currently this is only still here rather than in the controller
4973     // because of the featureSettings hard reference that is yet to be
4974     // abstracted
4975     if (enableIfNecessary)
4976     {
4977       viewport.setShowSequenceFeatures(true);
4978       showSeqFeatures.setSelected(true);
4979     }
4980
4981   }
4982
4983   @Override
4984   public void dragEnter(DropTargetDragEvent evt)
4985   {
4986   }
4987
4988   @Override
4989   public void dragExit(DropTargetEvent evt)
4990   {
4991   }
4992
4993   @Override
4994   public void dragOver(DropTargetDragEvent evt)
4995   {
4996   }
4997
4998   @Override
4999   public void dropActionChanged(DropTargetDragEvent evt)
5000   {
5001   }
5002
5003   @Override
5004   public void drop(DropTargetDropEvent evt)
5005   {
5006     Transferable t = evt.getTransferable();
5007     java.util.List files = null;
5008
5009     try
5010     {
5011       DataFlavor uriListFlavor = new DataFlavor(
5012               "text/uri-list;class=java.lang.String");
5013       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5014       {
5015         // Works on Windows and MacOSX
5016         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5017         files = (java.util.List) t
5018                 .getTransferData(DataFlavor.javaFileListFlavor);
5019       }
5020       else if (t.isDataFlavorSupported(uriListFlavor))
5021       {
5022         // This is used by Unix drag system
5023         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5024         String data = (String) t.getTransferData(uriListFlavor);
5025         files = new java.util.ArrayList(1);
5026         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5027                 data, "\r\n"); st.hasMoreTokens();)
5028         {
5029           String s = st.nextToken();
5030           if (s.startsWith("#"))
5031           {
5032             // the line is a comment (as per the RFC 2483)
5033             continue;
5034           }
5035
5036           java.net.URI uri = new java.net.URI(s);
5037           // check to see if we can handle this kind of URI
5038           if (uri.getScheme().toLowerCase().startsWith("http"))
5039           {
5040             files.add(uri.toString());
5041           }
5042           else
5043           {
5044             // otherwise preserve old behaviour: catch all for file objects
5045             java.io.File file = new java.io.File(uri);
5046             files.add(file.toString());
5047           }
5048         }
5049       }
5050     } catch (Exception e)
5051     {
5052       e.printStackTrace();
5053     }
5054     if (files != null)
5055     {
5056       try
5057       {
5058         // check to see if any of these files have names matching sequences in
5059         // the alignment
5060         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5061                 .getAlignment().getSequencesArray());
5062         /**
5063          * Object[] { String,SequenceI}
5064          */
5065         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5066         ArrayList<String> filesnotmatched = new ArrayList<String>();
5067         for (int i = 0; i < files.size(); i++)
5068         {
5069           String file = files.get(i).toString();
5070           String pdbfn = "";
5071           String protocol = FormatAdapter.checkProtocol(file);
5072           if (protocol == jalview.io.FormatAdapter.FILE)
5073           {
5074             File fl = new File(file);
5075             pdbfn = fl.getName();
5076           }
5077           else if (protocol == jalview.io.FormatAdapter.URL)
5078           {
5079             URL url = new URL(file);
5080             pdbfn = url.getFile();
5081           }
5082           if (pdbfn.length() > 0)
5083           {
5084             // attempt to find a match in the alignment
5085             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5086             int l = 0, c = pdbfn.indexOf(".");
5087             while (mtch == null && c != -1)
5088             {
5089               do
5090               {
5091                 l = c;
5092               } while ((c = pdbfn.indexOf(".", l)) > l);
5093               if (l > -1)
5094               {
5095                 pdbfn = pdbfn.substring(0, l);
5096               }
5097               mtch = idm.findAllIdMatches(pdbfn);
5098             }
5099             if (mtch != null)
5100             {
5101               String type = null;
5102               try
5103               {
5104                 type = new IdentifyFile().Identify(file, protocol);
5105               } catch (Exception ex)
5106               {
5107                 type = null;
5108               }
5109               if (type != null)
5110               {
5111                 if (type.equalsIgnoreCase("PDB"))
5112                 {
5113                   filesmatched.add(new Object[] { file, protocol, mtch });
5114                   continue;
5115                 }
5116               }
5117             }
5118             // File wasn't named like one of the sequences or wasn't a PDB file.
5119             filesnotmatched.add(file);
5120           }
5121         }
5122         int assocfiles = 0;
5123         if (filesmatched.size() > 0)
5124         {
5125           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5126                   || JOptionPane
5127                           .showConfirmDialog(
5128                                   this,
5129                                   MessageManager
5130                                           .formatMessage(
5131                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5132                                                   new Object[] { Integer
5133                                                           .valueOf(
5134                                                                   filesmatched
5135                                                                           .size())
5136                                                           .toString() }),
5137                                   MessageManager
5138                                           .getString("label.automatically_associate_pdb_files_by_name"),
5139                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5140
5141           {
5142             for (Object[] fm : filesmatched)
5143             {
5144               // try and associate
5145               // TODO: may want to set a standard ID naming formalism for
5146               // associating PDB files which have no IDs.
5147               for (SequenceI toassoc : (SequenceI[]) fm[2])
5148               {
5149                 PDBEntry pe = new AssociatePdbFileWithSeq()
5150                         .associatePdbWithSeq((String) fm[0],
5151                                 (String) fm[1], toassoc, false,
5152                                 Desktop.instance);
5153                 if (pe != null)
5154                 {
5155                   System.err.println("Associated file : "
5156                           + ((String) fm[0]) + " with "
5157                           + toassoc.getDisplayId(true));
5158                   assocfiles++;
5159                 }
5160               }
5161               alignPanel.paintAlignment(true);
5162             }
5163           }
5164         }
5165         if (filesnotmatched.size() > 0)
5166         {
5167           if (assocfiles > 0
5168                   && (Cache.getDefault(
5169                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5170                           .showConfirmDialog(
5171                                   this,
5172                                   "<html>"
5173                                           + MessageManager
5174                                                   .formatMessage(
5175                                                           "label.ignore_unmatched_dropped_files_info",
5176                                                           new Object[] { Integer
5177                                                                   .valueOf(
5178                                                                           filesnotmatched
5179                                                                                   .size())
5180                                                                   .toString() })
5181                                           + "</html>",
5182                                   MessageManager
5183                                           .getString("label.ignore_unmatched_dropped_files"),
5184                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5185           {
5186             return;
5187           }
5188           for (String fn : filesnotmatched)
5189           {
5190             loadJalviewDataFile(fn, null, null, null);
5191           }
5192
5193         }
5194       } catch (Exception ex)
5195       {
5196         ex.printStackTrace();
5197       }
5198     }
5199   }
5200
5201   /**
5202    * Attempt to load a "dropped" file or URL string: First by testing whether
5203    * it's and Annotation file, then a JNet file, and finally a features file. If
5204    * all are false then the user may have dropped an alignment file onto this
5205    * AlignFrame.
5206    *
5207    * @param file
5208    *          either a filename or a URL string.
5209    */
5210   public void loadJalviewDataFile(String file, String protocol,
5211           String format, SequenceI assocSeq)
5212   {
5213     try
5214     {
5215       if (protocol == null)
5216       {
5217         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5218       }
5219       // if the file isn't identified, or not positively identified as some
5220       // other filetype (PFAM is default unidentified alignment file type) then
5221       // try to parse as annotation.
5222       boolean isAnnotation = (format == null || format
5223               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5224               .annotateAlignmentView(viewport, file, protocol) : false;
5225
5226       if (!isAnnotation)
5227       {
5228         // first see if its a T-COFFEE score file
5229         TCoffeeScoreFile tcf = null;
5230         try
5231         {
5232           tcf = new TCoffeeScoreFile(file, protocol);
5233           if (tcf.isValid())
5234           {
5235             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5236             {
5237               tcoffeeColour.setEnabled(true);
5238               tcoffeeColour.setSelected(true);
5239               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5240               isAnnotation = true;
5241               statusBar
5242                       .setText(MessageManager
5243                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5244             }
5245             else
5246             {
5247               // some problem - if no warning its probable that the ID matching
5248               // process didn't work
5249               JOptionPane
5250                       .showMessageDialog(
5251                               Desktop.desktop,
5252                               tcf.getWarningMessage() == null ? MessageManager
5253                                       .getString("label.check_file_matches_sequence_ids_alignment")
5254                                       : tcf.getWarningMessage(),
5255                               MessageManager
5256                                       .getString("label.problem_reading_tcoffee_score_file"),
5257                               JOptionPane.WARNING_MESSAGE);
5258             }
5259           }
5260           else
5261           {
5262             tcf = null;
5263           }
5264         } catch (Exception x)
5265         {
5266           Cache.log
5267                   .debug("Exception when processing data source as T-COFFEE score file",
5268                           x);
5269           tcf = null;
5270         }
5271         if (tcf == null)
5272         {
5273           // try to see if its a JNet 'concise' style annotation file *before*
5274           // we
5275           // try to parse it as a features file
5276           if (format == null)
5277           {
5278             format = new IdentifyFile().Identify(file, protocol);
5279           }
5280           if (format.equalsIgnoreCase("JnetFile"))
5281           {
5282             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5283                     file, protocol);
5284             new JnetAnnotationMaker();
5285             JnetAnnotationMaker.add_annotation(predictions,
5286                     viewport.getAlignment(), 0, false);
5287             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5288             viewport.getAlignment().setSeqrep(repseq);
5289             ColumnSelection cs = new ColumnSelection();
5290             cs.hideInsertionsFor(repseq);
5291             viewport.setColumnSelection(cs);
5292             isAnnotation = true;
5293           }
5294           else
5295           {
5296             /*
5297              * if (format.equalsIgnoreCase("PDB")) {
5298              *
5299              * String pdbfn = ""; // try to match up filename with sequence id
5300              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5301              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5302              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5303              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5304              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5305              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5306              * // attempt to find a match in the alignment SequenceI mtch =
5307              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5308              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5309              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5310              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5311              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5312              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5313              * { System.err.println("Associated file : " + file + " with " +
5314              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5315              * TODO: maybe need to load as normal otherwise return; } }
5316              */
5317             // try to parse it as a features file
5318             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5319             // if it wasn't a features file then we just treat it as a general
5320             // alignment file to load into the current view.
5321             if (!isGroupsFile)
5322             {
5323               new FileLoader().LoadFile(viewport, file, protocol, format);
5324             }
5325             else
5326             {
5327               alignPanel.paintAlignment(true);
5328             }
5329           }
5330         }
5331       }
5332       if (isAnnotation)
5333       {
5334
5335         alignPanel.adjustAnnotationHeight();
5336         viewport.updateSequenceIdColours();
5337         buildSortByAnnotationScoresMenu();
5338         alignPanel.paintAlignment(true);
5339       }
5340     } catch (Exception ex)
5341     {
5342       ex.printStackTrace();
5343     } catch (OutOfMemoryError oom)
5344     {
5345       try
5346       {
5347         System.gc();
5348       } catch (Exception x)
5349       {
5350       }
5351       ;
5352       new OOMWarning(
5353               "loading data "
5354                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5355                               : "using " + protocol + " from " + file)
5356                               : ".")
5357                       + (format != null ? "(parsing as '" + format
5358                               + "' file)" : ""), oom, Desktop.desktop);
5359     }
5360   }
5361
5362   /**
5363    * Method invoked by the ChangeListener on the tabbed pane, in other words
5364    * when a different tabbed pane is selected by the user or programmatically.
5365    */
5366   @Override
5367   public void tabSelectionChanged(int index)
5368   {
5369     if (index > -1)
5370     {
5371       alignPanel = alignPanels.get(index);
5372       viewport = alignPanel.av;
5373       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5374       setMenusFromViewport(viewport);
5375     }
5376
5377     /*
5378      * If there is a frame linked to this one in a SplitPane, switch it to the
5379      * same view tab index. No infinite recursion of calls should happen, since
5380      * tabSelectionChanged() should not get invoked on setting the selected
5381      * index to an unchanged value. Guard against setting an invalid index
5382      * before the new view peer tab has been created.
5383      */
5384     final AlignViewportI peer = viewport.getCodingComplement();
5385     if (peer != null)
5386     {
5387       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5388       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5389       {
5390         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5391       }
5392     }
5393   }
5394
5395   /**
5396    * On right mouse click on view tab, prompt for and set new view name.
5397    */
5398   @Override
5399   public void tabbedPane_mousePressed(MouseEvent e)
5400   {
5401     if (SwingUtilities.isRightMouseButton(e))
5402     {
5403       String msg = MessageManager.getString("label.enter_view_name");
5404       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5405               JOptionPane.QUESTION_MESSAGE);
5406
5407       if (reply != null)
5408       {
5409         viewport.viewName = reply;
5410         // TODO warn if reply is in getExistingViewNames()?
5411         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5412       }
5413     }
5414   }
5415
5416   public AlignViewport getCurrentView()
5417   {
5418     return viewport;
5419   }
5420
5421   /**
5422    * Open the dialog for regex description parsing.
5423    */
5424   @Override
5425   protected void extractScores_actionPerformed(ActionEvent e)
5426   {
5427     ParseProperties pp = new jalview.analysis.ParseProperties(
5428             viewport.getAlignment());
5429     // TODO: verify regex and introduce GUI dialog for version 2.5
5430     // if (pp.getScoresFromDescription("col", "score column ",
5431     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5432     // true)>0)
5433     if (pp.getScoresFromDescription("description column",
5434             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5435     {
5436       buildSortByAnnotationScoresMenu();
5437     }
5438   }
5439
5440   /*
5441    * (non-Javadoc)
5442    *
5443    * @see
5444    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5445    * )
5446    */
5447   @Override
5448   protected void showDbRefs_actionPerformed(ActionEvent e)
5449   {
5450     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5451   }
5452
5453   /*
5454    * (non-Javadoc)
5455    *
5456    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5457    * ActionEvent)
5458    */
5459   @Override
5460   protected void showNpFeats_actionPerformed(ActionEvent e)
5461   {
5462     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5463   }
5464
5465   /**
5466    * find the viewport amongst the tabs in this alignment frame and close that
5467    * tab
5468    *
5469    * @param av
5470    */
5471   public boolean closeView(AlignViewportI av)
5472   {
5473     if (viewport == av)
5474     {
5475       this.closeMenuItem_actionPerformed(false);
5476       return true;
5477     }
5478     Component[] comp = tabbedPane.getComponents();
5479     for (int i = 0; comp != null && i < comp.length; i++)
5480     {
5481       if (comp[i] instanceof AlignmentPanel)
5482       {
5483         if (((AlignmentPanel) comp[i]).av == av)
5484         {
5485           // close the view.
5486           closeView((AlignmentPanel) comp[i]);
5487           return true;
5488         }
5489       }
5490     }
5491     return false;
5492   }
5493
5494   protected void build_fetchdbmenu(JMenu webService)
5495   {
5496     // Temporary hack - DBRef Fetcher always top level ws entry.
5497     // TODO We probably want to store a sequence database checklist in
5498     // preferences and have checkboxes.. rather than individual sources selected
5499     // here
5500     final JMenu rfetch = new JMenu(
5501             MessageManager.getString("action.fetch_db_references"));
5502     rfetch.setToolTipText(MessageManager
5503             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5504     webService.add(rfetch);
5505
5506     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5507             MessageManager.getString("option.trim_retrieved_seqs"));
5508     trimrs.setToolTipText(MessageManager
5509             .getString("label.trim_retrieved_sequences"));
5510     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5511     trimrs.addActionListener(new ActionListener()
5512     {
5513       @Override
5514       public void actionPerformed(ActionEvent e)
5515       {
5516         trimrs.setSelected(trimrs.isSelected());
5517         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5518                 Boolean.valueOf(trimrs.isSelected()).toString());
5519       };
5520     });
5521     rfetch.add(trimrs);
5522     JMenuItem fetchr = new JMenuItem(
5523             MessageManager.getString("label.standard_databases"));
5524     fetchr.setToolTipText(MessageManager
5525             .getString("label.fetch_embl_uniprot"));
5526     fetchr.addActionListener(new ActionListener()
5527     {
5528
5529       @Override
5530       public void actionPerformed(ActionEvent e)
5531       {
5532         new Thread(new Runnable()
5533         {
5534
5535           @Override
5536           public void run()
5537           {
5538             boolean isNuclueotide = alignPanel.alignFrame
5539                     .getViewport().getAlignment()
5540                     .isNucleotide();
5541             new jalview.ws.DBRefFetcher(alignPanel.av
5542                     .getSequenceSelection(),
5543                     alignPanel.alignFrame, null,
5544                     alignPanel.alignFrame.featureSettings,
5545                     isNuclueotide)
5546                     .fetchDBRefs(false);
5547           }
5548         }).start();
5549
5550       }
5551
5552     });
5553     rfetch.add(fetchr);
5554     final AlignFrame me = this;
5555     new Thread(new Runnable()
5556     {
5557       @Override
5558       public void run()
5559       {
5560         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5561                 .getSequenceFetcherSingleton(me);
5562         javax.swing.SwingUtilities.invokeLater(new Runnable()
5563         {
5564           @Override
5565           public void run()
5566           {
5567             String[] dbclasses = sf.getOrderedSupportedSources();
5568             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5569             // jalview.util.QuickSort.sort(otherdb, otherdb);
5570             List<DbSourceProxy> otherdb;
5571             JMenu dfetch = new JMenu();
5572             JMenu ifetch = new JMenu();
5573             JMenuItem fetchr = null;
5574             int comp = 0, icomp = 0, mcomp = 15;
5575             String mname = null;
5576             int dbi = 0;
5577             for (String dbclass : dbclasses)
5578             {
5579               otherdb = sf.getSourceProxy(dbclass);
5580               // add a single entry for this class, or submenu allowing 'fetch
5581               // all' or pick one
5582               if (otherdb == null || otherdb.size() < 1)
5583               {
5584                 continue;
5585               }
5586               // List<DbSourceProxy> dbs=otherdb;
5587               // otherdb=new ArrayList<DbSourceProxy>();
5588               // for (DbSourceProxy db:dbs)
5589               // {
5590               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5591               // }
5592               if (mname == null)
5593               {
5594                 mname = "From " + dbclass;
5595               }
5596               if (otherdb.size() == 1)
5597               {
5598                 final DbSourceProxy[] dassource = otherdb
5599                         .toArray(new DbSourceProxy[0]);
5600                 DbSourceProxy src = otherdb.get(0);
5601                 fetchr = new JMenuItem(src.getDbSource());
5602                 fetchr.addActionListener(new ActionListener()
5603                 {
5604
5605                   @Override
5606                   public void actionPerformed(ActionEvent e)
5607                   {
5608                     new Thread(new Runnable()
5609                     {
5610
5611                       @Override
5612                       public void run()
5613                       {
5614                         boolean isNuclueotide = alignPanel.alignFrame
5615                                 .getViewport().getAlignment()
5616                                 .isNucleotide();
5617                         new jalview.ws.DBRefFetcher(alignPanel.av
5618                                 .getSequenceSelection(),
5619                                 alignPanel.alignFrame, dassource,
5620                                 alignPanel.alignFrame.featureSettings,
5621                                 isNuclueotide)
5622                                 .fetchDBRefs(false);
5623                       }
5624                     }).start();
5625                   }
5626
5627                 });
5628                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5629                         MessageManager.formatMessage(
5630                                 "label.fetch_retrieve_from",
5631                                 new Object[] { src.getDbName() })));
5632                 dfetch.add(fetchr);
5633                 comp++;
5634               }
5635               else
5636               {
5637                 final DbSourceProxy[] dassource = otherdb
5638                         .toArray(new DbSourceProxy[0]);
5639                 // fetch all entry
5640                 DbSourceProxy src = otherdb.get(0);
5641                 fetchr = new JMenuItem(MessageManager.formatMessage(
5642                         "label.fetch_all_param",
5643                         new Object[] { src.getDbSource() }));
5644                 fetchr.addActionListener(new ActionListener()
5645                 {
5646                   @Override
5647                   public void actionPerformed(ActionEvent e)
5648                   {
5649                     new Thread(new Runnable()
5650                     {
5651
5652                       @Override
5653                       public void run()
5654                       {
5655                         boolean isNuclueotide = alignPanel.alignFrame
5656                                 .getViewport().getAlignment()
5657                                 .isNucleotide();
5658                         new jalview.ws.DBRefFetcher(alignPanel.av
5659                                 .getSequenceSelection(),
5660                                 alignPanel.alignFrame, dassource,
5661                                 alignPanel.alignFrame.featureSettings,
5662                                 isNuclueotide)
5663                                 .fetchDBRefs(false);
5664                       }
5665                     }).start();
5666                   }
5667                 });
5668
5669                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5670                         MessageManager.formatMessage(
5671                                 "label.fetch_retrieve_from_all_sources",
5672                                 new Object[] {
5673                                     Integer.valueOf(otherdb.size())
5674                                             .toString(), src.getDbSource(),
5675                                     src.getDbName() })));
5676                 dfetch.add(fetchr);
5677                 comp++;
5678                 // and then build the rest of the individual menus
5679                 ifetch = new JMenu(MessageManager.formatMessage(
5680                         "label.source_from_db_source",
5681                         new Object[] { src.getDbSource() }));
5682                 icomp = 0;
5683                 String imname = null;
5684                 int i = 0;
5685                 for (DbSourceProxy sproxy : otherdb)
5686                 {
5687                   String dbname = sproxy.getDbName();
5688                   String sname = dbname.length() > 5 ? dbname.substring(0,
5689                           5) + "..." : dbname;
5690                   String msname = dbname.length() > 10 ? dbname.substring(
5691                           0, 10) + "..." : dbname;
5692                   if (imname == null)
5693                   {
5694                     imname = MessageManager.formatMessage(
5695                             "label.from_msname", new Object[] { sname });
5696                   }
5697                   fetchr = new JMenuItem(msname);
5698                   final DbSourceProxy[] dassrc = { sproxy };
5699                   fetchr.addActionListener(new ActionListener()
5700                   {
5701
5702                     @Override
5703                     public void actionPerformed(ActionEvent e)
5704                     {
5705                       new Thread(new Runnable()
5706                       {
5707
5708                         @Override
5709                         public void run()
5710                         {
5711                           boolean isNuclueotide = alignPanel.alignFrame
5712                                   .getViewport().getAlignment()
5713                                   .isNucleotide();
5714                           new jalview.ws.DBRefFetcher(alignPanel.av
5715                                   .getSequenceSelection(),
5716                                   alignPanel.alignFrame, dassrc,
5717                                   alignPanel.alignFrame.featureSettings,
5718                                   isNuclueotide)
5719                                   .fetchDBRefs(false);
5720                         }
5721                       }).start();
5722                     }
5723
5724                   });
5725                   fetchr.setToolTipText("<html>"
5726                           + MessageManager.formatMessage(
5727                                   "label.fetch_retrieve_from", new Object[]
5728                                   { dbname }));
5729                   ifetch.add(fetchr);
5730                   ++i;
5731                   if (++icomp >= mcomp || i == (otherdb.size()))
5732                   {
5733                     ifetch.setText(MessageManager.formatMessage(
5734                             "label.source_to_target", imname, sname));
5735                     dfetch.add(ifetch);
5736                     ifetch = new JMenu();
5737                     imname = null;
5738                     icomp = 0;
5739                     comp++;
5740                   }
5741                 }
5742               }
5743               ++dbi;
5744               if (comp >= mcomp || dbi >= (dbclasses.length))
5745               {
5746                 dfetch.setText(MessageManager.formatMessage(
5747                         "label.source_to_target", mname, dbclass));
5748                 rfetch.add(dfetch);
5749                 dfetch = new JMenu();
5750                 mname = null;
5751                 comp = 0;
5752               }
5753             }
5754           }
5755         });
5756       }
5757     }).start();
5758
5759   }
5760
5761   /**
5762    * Left justify the whole alignment.
5763    */
5764   @Override
5765   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5766   {
5767     AlignmentI al = viewport.getAlignment();
5768     al.justify(false);
5769     viewport.firePropertyChange("alignment", null, al);
5770   }
5771
5772   /**
5773    * Right justify the whole alignment.
5774    */
5775   @Override
5776   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5777   {
5778     AlignmentI al = viewport.getAlignment();
5779     al.justify(true);
5780     viewport.firePropertyChange("alignment", null, al);
5781   }
5782
5783   @Override
5784   public void setShowSeqFeatures(boolean b)
5785   {
5786     showSeqFeatures.setSelected(b);
5787     viewport.setShowSequenceFeatures(b);
5788   }
5789
5790   /*
5791    * (non-Javadoc)
5792    *
5793    * @see
5794    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5795    * awt.event.ActionEvent)
5796    */
5797   @Override
5798   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5799   {
5800     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5801     alignPanel.paintAlignment(true);
5802   }
5803
5804   /*
5805    * (non-Javadoc)
5806    *
5807    * @see
5808    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5809    * .ActionEvent)
5810    */
5811   @Override
5812   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5813   {
5814     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5815     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5816
5817   }
5818
5819   /*
5820    * (non-Javadoc)
5821    *
5822    * @see
5823    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5824    * .event.ActionEvent)
5825    */
5826   @Override
5827   protected void showGroupConservation_actionPerformed(ActionEvent e)
5828   {
5829     viewport.setShowGroupConservation(showGroupConservation.getState());
5830     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5831   }
5832
5833   /*
5834    * (non-Javadoc)
5835    *
5836    * @see
5837    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5838    * .event.ActionEvent)
5839    */
5840   @Override
5841   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5842   {
5843     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5844     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5845   }
5846
5847   /*
5848    * (non-Javadoc)
5849    *
5850    * @see
5851    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5852    * .event.ActionEvent)
5853    */
5854   @Override
5855   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5856   {
5857     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5858     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5859   }
5860
5861   @Override
5862   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5863   {
5864     showSequenceLogo.setState(true);
5865     viewport.setShowSequenceLogo(true);
5866     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5867     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5868   }
5869
5870   @Override
5871   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5872   {
5873     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5874   }
5875
5876   /*
5877    * (non-Javadoc)
5878    *
5879    * @see
5880    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5881    * .event.ActionEvent)
5882    */
5883   @Override
5884   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5885   {
5886     if (avc.makeGroupsFromSelection())
5887     {
5888       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5889       alignPanel.updateAnnotation();
5890       alignPanel.paintAlignment(true);
5891     }
5892   }
5893
5894   public void clearAlignmentSeqRep()
5895   {
5896     // TODO refactor alignmentseqrep to controller
5897     if (viewport.getAlignment().hasSeqrep())
5898     {
5899       viewport.getAlignment().setSeqrep(null);
5900       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5901       alignPanel.updateAnnotation();
5902       alignPanel.paintAlignment(true);
5903     }
5904   }
5905
5906   @Override
5907   protected void createGroup_actionPerformed(ActionEvent e)
5908   {
5909     if (avc.createGroup())
5910     {
5911       alignPanel.alignmentChanged();
5912     }
5913   }
5914
5915   @Override
5916   protected void unGroup_actionPerformed(ActionEvent e)
5917   {
5918     if (avc.unGroup())
5919     {
5920       alignPanel.alignmentChanged();
5921     }
5922   }
5923
5924   /**
5925    * make the given alignmentPanel the currently selected tab
5926    *
5927    * @param alignmentPanel
5928    */
5929   public void setDisplayedView(AlignmentPanel alignmentPanel)
5930   {
5931     if (!viewport.getSequenceSetId().equals(
5932             alignmentPanel.av.getSequenceSetId()))
5933     {
5934       throw new Error(
5935               MessageManager
5936                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5937     }
5938     if (tabbedPane != null
5939             && tabbedPane.getTabCount() > 0
5940             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5941                     .getSelectedIndex())
5942     {
5943       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5944     }
5945   }
5946
5947   /**
5948    * Action on selection of menu options to Show or Hide annotations.
5949    *
5950    * @param visible
5951    * @param forSequences
5952    *          update sequence-related annotations
5953    * @param forAlignment
5954    *          update non-sequence-related annotations
5955    */
5956   @Override
5957   protected void setAnnotationsVisibility(boolean visible,
5958           boolean forSequences, boolean forAlignment)
5959   {
5960     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5961             .getAlignmentAnnotation())
5962     {
5963       /*
5964        * don't display non-positional annotations on an alignment
5965        */
5966       if (aa.annotations == null)
5967       {
5968         continue;
5969       }
5970       boolean apply = (aa.sequenceRef == null && forAlignment)
5971               || (aa.sequenceRef != null && forSequences);
5972       if (apply)
5973       {
5974         aa.visible = visible;
5975       }
5976     }
5977     alignPanel.validateAnnotationDimensions(true);
5978     alignPanel.alignmentChanged();
5979   }
5980
5981   /**
5982    * Store selected annotation sort order for the view and repaint.
5983    */
5984   @Override
5985   protected void sortAnnotations_actionPerformed()
5986   {
5987     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5988     this.alignPanel.av
5989             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5990     alignPanel.paintAlignment(true);
5991   }
5992
5993   /**
5994    *
5995    * @return alignment panels in this alignment frame
5996    */
5997   public List<? extends AlignmentViewPanel> getAlignPanels()
5998   {
5999     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6000   }
6001
6002   /**
6003    * Open a new alignment window, with the cDNA associated with this (protein)
6004    * alignment, aligned as is the protein.
6005    */
6006   protected void viewAsCdna_actionPerformed()
6007   {
6008     // TODO no longer a menu action - refactor as required
6009     final AlignmentI alignment = getViewport().getAlignment();
6010     Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6011     if (mappings == null)
6012     {
6013       return;
6014     }
6015     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6016     for (SequenceI aaSeq : alignment.getSequences())
6017     {
6018       for (AlignedCodonFrame acf : mappings)
6019       {
6020         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6021         if (dnaSeq != null)
6022         {
6023           /*
6024            * There is a cDNA mapping for this protein sequence - add to new
6025            * alignment. It will share the same dataset sequence as other mapped
6026            * cDNA (no new mappings need to be created).
6027            */
6028           final Sequence newSeq = new Sequence(dnaSeq);
6029           newSeq.setDatasetSequence(dnaSeq);
6030           cdnaSeqs.add(newSeq);
6031         }
6032       }
6033     }
6034     if (cdnaSeqs.size() == 0)
6035     {
6036       // show a warning dialog no mapped cDNA
6037       return;
6038     }
6039     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6040             .size()]));
6041     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6042             AlignFrame.DEFAULT_HEIGHT);
6043     cdna.alignAs(alignment);
6044     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6045             + this.title;
6046     Desktop.addInternalFrame(alignFrame, newtitle,
6047             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6048   }
6049
6050   /**
6051    * Set visibility of dna/protein complement view (available when shown in a
6052    * split frame).
6053    *
6054    * @param show
6055    */
6056   @Override
6057   protected void showComplement_actionPerformed(boolean show)
6058   {
6059     SplitContainerI sf = getSplitViewContainer();
6060     if (sf != null)
6061     {
6062       sf.setComplementVisible(this, show);
6063     }
6064   }
6065 }
6066
6067 class PrintThread extends Thread
6068 {
6069   AlignmentPanel ap;
6070
6071   public PrintThread(AlignmentPanel ap)
6072   {
6073     this.ap = ap;
6074   }
6075
6076   static PageFormat pf;
6077
6078   @Override
6079   public void run()
6080   {
6081     PrinterJob printJob = PrinterJob.getPrinterJob();
6082
6083     if (pf != null)
6084     {
6085       printJob.setPrintable(ap, pf);
6086     }
6087     else
6088     {
6089       printJob.setPrintable(ap);
6090     }
6091
6092     if (printJob.printDialog())
6093     {
6094       try
6095       {
6096         printJob.print();
6097       } catch (Exception PrintException)
6098       {
6099         PrintException.printStackTrace();
6100       }
6101     }
6102   }
6103 }