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, this);
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.isEmpty())
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", true, seqs,
2576                 column, viewport.getAlignment());
2577         viewport.setStartRes(0);
2578       }
2579       else
2580       {
2581         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2582                 column, viewport.getAlignment());
2583       }
2584
2585       statusBar.setText(MessageManager.formatMessage(
2586               "label.removed_columns",
2587               new String[] { Integer.valueOf(trimRegion.getSize())
2588                       .toString() }));
2589
2590       addHistoryItem(trimRegion);
2591
2592       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2593       {
2594         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2595                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2596         {
2597           viewport.getAlignment().deleteGroup(sg);
2598         }
2599       }
2600
2601       viewport.firePropertyChange("alignment", null, viewport
2602               .getAlignment().getSequences());
2603     }
2604   }
2605
2606   /**
2607    * DOCUMENT ME!
2608    *
2609    * @param e
2610    *          DOCUMENT ME!
2611    */
2612   @Override
2613   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2614   {
2615     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2616
2617     SequenceI[] seqs;
2618     if (viewport.getSelectionGroup() != null)
2619     {
2620       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2621               viewport.getHiddenRepSequences());
2622       start = viewport.getSelectionGroup().getStartRes();
2623       end = viewport.getSelectionGroup().getEndRes();
2624     }
2625     else
2626     {
2627       seqs = viewport.getAlignment().getSequencesArray();
2628     }
2629
2630     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2631             "Remove Gapped Columns", seqs, start, end,
2632             viewport.getAlignment());
2633
2634     addHistoryItem(removeGapCols);
2635
2636     statusBar.setText(MessageManager.formatMessage(
2637             "label.removed_empty_columns",
2638             new Object[] { Integer.valueOf(removeGapCols.getSize())
2639                     .toString() }));
2640
2641     // This is to maintain viewport position on first residue
2642     // of first sequence
2643     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644     int startRes = seq.findPosition(viewport.startRes);
2645     // ShiftList shifts;
2646     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2647     // edit.alColumnChanges=shifts.getInverse();
2648     // if (viewport.hasHiddenColumns)
2649     // viewport.getColumnSelection().compensateForEdits(shifts);
2650     viewport.setStartRes(seq.findIndex(startRes) - 1);
2651     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2652             .getSequences());
2653
2654   }
2655
2656   /**
2657    * DOCUMENT ME!
2658    *
2659    * @param e
2660    *          DOCUMENT ME!
2661    */
2662   @Override
2663   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2664   {
2665     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2666
2667     SequenceI[] seqs;
2668     if (viewport.getSelectionGroup() != null)
2669     {
2670       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2671               viewport.getHiddenRepSequences());
2672       start = viewport.getSelectionGroup().getStartRes();
2673       end = viewport.getSelectionGroup().getEndRes();
2674     }
2675     else
2676     {
2677       seqs = viewport.getAlignment().getSequencesArray();
2678     }
2679
2680     // This is to maintain viewport position on first residue
2681     // of first sequence
2682     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2683     int startRes = seq.findPosition(viewport.startRes);
2684
2685     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2686             viewport.getAlignment()));
2687
2688     viewport.setStartRes(seq.findIndex(startRes) - 1);
2689
2690     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2691             .getSequences());
2692
2693   }
2694
2695   /**
2696    * DOCUMENT ME!
2697    *
2698    * @param e
2699    *          DOCUMENT ME!
2700    */
2701   @Override
2702   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2703   {
2704     viewport.setPadGaps(padGapsMenuitem.isSelected());
2705     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2706             .getSequences());
2707   }
2708
2709   /**
2710    * DOCUMENT ME!
2711    *
2712    * @param e
2713    *          DOCUMENT ME!
2714    */
2715   @Override
2716   public void findMenuItem_actionPerformed(ActionEvent e)
2717   {
2718     new Finder();
2719   }
2720
2721   /**
2722    * Create a new view of the current alignment.
2723    */
2724   @Override
2725   public void newView_actionPerformed(ActionEvent e)
2726   {
2727     newView(null, true);
2728   }
2729
2730   /**
2731    * Creates and shows a new view of the current alignment.
2732    *
2733    * @param viewTitle
2734    *          title of newly created view; if null, one will be generated
2735    * @param copyAnnotation
2736    *          if true then duplicate all annnotation, groups and settings
2737    * @return new alignment panel, already displayed.
2738    */
2739   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2740   {
2741     /*
2742      * Create a new AlignmentPanel (with its own, new Viewport)
2743      */
2744     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2745             true);
2746     if (!copyAnnotation)
2747     {
2748       /*
2749        * remove all groups and annotation except for the automatic stuff
2750        */
2751       newap.av.getAlignment().deleteAllGroups();
2752       newap.av.getAlignment().deleteAllAnnotations(false);
2753     }
2754
2755     newap.av.setGatherViewsHere(false);
2756
2757     if (viewport.viewName == null)
2758     {
2759       viewport.viewName = MessageManager
2760               .getString("label.view_name_original");
2761     }
2762
2763     /*
2764      * Views share the same edits undo and redo stacks
2765      */
2766     newap.av.setHistoryList(viewport.getHistoryList());
2767     newap.av.setRedoList(viewport.getRedoList());
2768
2769     /*
2770      * Views share the same mappings; need to deregister any new mappings
2771      * created by copyAlignPanel, and register the new reference to the shared
2772      * mappings
2773      */
2774     newap.av.replaceMappings(viewport.getAlignment());
2775
2776     newap.av.viewName = getNewViewName(viewTitle);
2777
2778     addAlignmentPanel(newap, true);
2779     newap.alignmentChanged();
2780
2781     if (alignPanels.size() == 2)
2782     {
2783       viewport.setGatherViewsHere(true);
2784     }
2785     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2786     return newap;
2787   }
2788
2789   /**
2790    * Make a new name for the view, ensuring it is unique within the current
2791    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2792    * these now use viewId. Unique view names are still desirable for usability.)
2793    *
2794    * @param viewTitle
2795    * @return
2796    */
2797   protected String getNewViewName(String viewTitle)
2798   {
2799     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2800     boolean addFirstIndex = false;
2801     if (viewTitle == null || viewTitle.trim().length() == 0)
2802     {
2803       viewTitle = MessageManager.getString("action.view");
2804       addFirstIndex = true;
2805     }
2806     else
2807     {
2808       index = 1;// we count from 1 if given a specific name
2809     }
2810     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2811
2812     List<Component> comps = PaintRefresher.components.get(viewport
2813             .getSequenceSetId());
2814
2815     List<String> existingNames = getExistingViewNames(comps);
2816
2817     while (existingNames.contains(newViewName))
2818     {
2819       newViewName = viewTitle + " " + (++index);
2820     }
2821     return newViewName;
2822   }
2823
2824   /**
2825    * Returns a list of distinct view names found in the given list of
2826    * components. View names are held on the viewport of an AlignmentPanel.
2827    *
2828    * @param comps
2829    * @return
2830    */
2831   protected List<String> getExistingViewNames(List<Component> comps)
2832   {
2833     List<String> existingNames = new ArrayList<String>();
2834     for (Component comp : comps)
2835     {
2836       if (comp instanceof AlignmentPanel)
2837       {
2838         AlignmentPanel ap = (AlignmentPanel) comp;
2839         if (!existingNames.contains(ap.av.viewName))
2840         {
2841           existingNames.add(ap.av.viewName);
2842         }
2843       }
2844     }
2845     return existingNames;
2846   }
2847
2848   /**
2849    * Explode tabbed views into separate windows.
2850    */
2851   @Override
2852   public void expandViews_actionPerformed(ActionEvent e)
2853   {
2854     Desktop.instance.explodeViews(this);
2855   }
2856
2857   /**
2858    * Gather views in separate windows back into a tabbed presentation.
2859    */
2860   @Override
2861   public void gatherViews_actionPerformed(ActionEvent e)
2862   {
2863     Desktop.instance.gatherViews(this);
2864   }
2865
2866   /**
2867    * DOCUMENT ME!
2868    *
2869    * @param e
2870    *          DOCUMENT ME!
2871    */
2872   @Override
2873   public void font_actionPerformed(ActionEvent e)
2874   {
2875     new FontChooser(alignPanel);
2876   }
2877
2878   /**
2879    * DOCUMENT ME!
2880    *
2881    * @param e
2882    *          DOCUMENT ME!
2883    */
2884   @Override
2885   protected void seqLimit_actionPerformed(ActionEvent e)
2886   {
2887     viewport.setShowJVSuffix(seqLimits.isSelected());
2888
2889     alignPanel.getIdPanel().getIdCanvas()
2890             .setPreferredSize(alignPanel.calculateIdWidth());
2891     alignPanel.paintAlignment(true);
2892   }
2893
2894   @Override
2895   public void idRightAlign_actionPerformed(ActionEvent e)
2896   {
2897     viewport.setRightAlignIds(idRightAlign.isSelected());
2898     alignPanel.paintAlignment(true);
2899   }
2900
2901   @Override
2902   public void centreColumnLabels_actionPerformed(ActionEvent e)
2903   {
2904     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2905     alignPanel.paintAlignment(true);
2906   }
2907
2908   /*
2909    * (non-Javadoc)
2910    *
2911    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2912    */
2913   @Override
2914   protected void followHighlight_actionPerformed()
2915   {
2916     /*
2917      * Set the 'follow' flag on the Viewport (and scroll to position if now
2918      * true).
2919      */
2920     final boolean state = this.followHighlightMenuItem.getState();
2921     viewport.setFollowHighlight(state);
2922     if (state)
2923     {
2924       alignPanel.scrollToPosition(
2925               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2926     }
2927   }
2928
2929   /**
2930    * DOCUMENT ME!
2931    *
2932    * @param e
2933    *          DOCUMENT ME!
2934    */
2935   @Override
2936   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2937   {
2938     viewport.setColourText(colourTextMenuItem.isSelected());
2939     alignPanel.paintAlignment(true);
2940   }
2941
2942   /**
2943    * DOCUMENT ME!
2944    *
2945    * @param e
2946    *          DOCUMENT ME!
2947    */
2948   @Override
2949   public void wrapMenuItem_actionPerformed(ActionEvent e)
2950   {
2951     scaleAbove.setVisible(wrapMenuItem.isSelected());
2952     scaleLeft.setVisible(wrapMenuItem.isSelected());
2953     scaleRight.setVisible(wrapMenuItem.isSelected());
2954     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2955     alignPanel.updateLayout();
2956   }
2957
2958   @Override
2959   public void showAllSeqs_actionPerformed(ActionEvent e)
2960   {
2961     viewport.showAllHiddenSeqs();
2962   }
2963
2964   @Override
2965   public void showAllColumns_actionPerformed(ActionEvent e)
2966   {
2967     viewport.showAllHiddenColumns();
2968     repaint();
2969     viewport.sendSelection();
2970   }
2971
2972   @Override
2973   public void hideSelSequences_actionPerformed(ActionEvent e)
2974   {
2975     viewport.hideAllSelectedSeqs();
2976     // alignPanel.paintAlignment(true);
2977   }
2978
2979   /**
2980    * called by key handler and the hide all/show all menu items
2981    *
2982    * @param toggleSeqs
2983    * @param toggleCols
2984    */
2985   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2986   {
2987
2988     boolean hide = false;
2989     SequenceGroup sg = viewport.getSelectionGroup();
2990     if (!toggleSeqs && !toggleCols)
2991     {
2992       // Hide everything by the current selection - this is a hack - we do the
2993       // invert and then hide
2994       // first check that there will be visible columns after the invert.
2995       if ((viewport.getColumnSelection() != null
2996               && viewport.getColumnSelection().getSelected() != null && viewport
2997               .getColumnSelection().getSelected().size() > 0)
2998               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2999                       .getEndRes()))
3000       {
3001         // now invert the sequence set, if required - empty selection implies
3002         // that no hiding is required.
3003         if (sg != null)
3004         {
3005           invertSequenceMenuItem_actionPerformed(null);
3006           sg = viewport.getSelectionGroup();
3007           toggleSeqs = true;
3008
3009         }
3010         viewport.expandColSelection(sg, true);
3011         // finally invert the column selection and get the new sequence
3012         // selection.
3013         invertColSel_actionPerformed(null);
3014         toggleCols = true;
3015       }
3016     }
3017
3018     if (toggleSeqs)
3019     {
3020       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3021       {
3022         hideSelSequences_actionPerformed(null);
3023         hide = true;
3024       }
3025       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3026               .size() > 0))
3027       {
3028         showAllSeqs_actionPerformed(null);
3029       }
3030     }
3031
3032     if (toggleCols)
3033     {
3034       if (viewport.getColumnSelection().getSelected().size() > 0)
3035       {
3036         hideSelColumns_actionPerformed(null);
3037         if (!toggleSeqs)
3038         {
3039           viewport.setSelectionGroup(sg);
3040         }
3041       }
3042       else if (!hide)
3043       {
3044         showAllColumns_actionPerformed(null);
3045       }
3046     }
3047   }
3048
3049   /*
3050    * (non-Javadoc)
3051    *
3052    * @see
3053    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3054    * event.ActionEvent)
3055    */
3056   @Override
3057   public void hideAllButSelection_actionPerformed(ActionEvent e)
3058   {
3059     toggleHiddenRegions(false, false);
3060     viewport.sendSelection();
3061   }
3062
3063   /*
3064    * (non-Javadoc)
3065    *
3066    * @see
3067    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3068    * .ActionEvent)
3069    */
3070   @Override
3071   public void hideAllSelection_actionPerformed(ActionEvent e)
3072   {
3073     SequenceGroup sg = viewport.getSelectionGroup();
3074     viewport.expandColSelection(sg, false);
3075     viewport.hideAllSelectedSeqs();
3076     viewport.hideSelectedColumns();
3077     alignPanel.paintAlignment(true);
3078     viewport.sendSelection();
3079   }
3080
3081   /*
3082    * (non-Javadoc)
3083    *
3084    * @see
3085    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3086    * ActionEvent)
3087    */
3088   @Override
3089   public void showAllhidden_actionPerformed(ActionEvent e)
3090   {
3091     viewport.showAllHiddenColumns();
3092     viewport.showAllHiddenSeqs();
3093     alignPanel.paintAlignment(true);
3094     viewport.sendSelection();
3095   }
3096
3097   @Override
3098   public void hideSelColumns_actionPerformed(ActionEvent e)
3099   {
3100     viewport.hideSelectedColumns();
3101     alignPanel.paintAlignment(true);
3102     viewport.sendSelection();
3103   }
3104
3105   @Override
3106   public void hiddenMarkers_actionPerformed(ActionEvent e)
3107   {
3108     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3109     repaint();
3110   }
3111
3112   /**
3113    * DOCUMENT ME!
3114    *
3115    * @param e
3116    *          DOCUMENT ME!
3117    */
3118   @Override
3119   protected void scaleAbove_actionPerformed(ActionEvent e)
3120   {
3121     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3122     alignPanel.paintAlignment(true);
3123   }
3124
3125   /**
3126    * DOCUMENT ME!
3127    *
3128    * @param e
3129    *          DOCUMENT ME!
3130    */
3131   @Override
3132   protected void scaleLeft_actionPerformed(ActionEvent e)
3133   {
3134     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3135     alignPanel.paintAlignment(true);
3136   }
3137
3138   /**
3139    * DOCUMENT ME!
3140    *
3141    * @param e
3142    *          DOCUMENT ME!
3143    */
3144   @Override
3145   protected void scaleRight_actionPerformed(ActionEvent e)
3146   {
3147     viewport.setScaleRightWrapped(scaleRight.isSelected());
3148     alignPanel.paintAlignment(true);
3149   }
3150
3151   /**
3152    * DOCUMENT ME!
3153    *
3154    * @param e
3155    *          DOCUMENT ME!
3156    */
3157   @Override
3158   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3159   {
3160     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3161     alignPanel.paintAlignment(true);
3162   }
3163
3164   /**
3165    * DOCUMENT ME!
3166    *
3167    * @param e
3168    *          DOCUMENT ME!
3169    */
3170   @Override
3171   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3172   {
3173     viewport.setShowText(viewTextMenuItem.isSelected());
3174     alignPanel.paintAlignment(true);
3175   }
3176
3177   /**
3178    * DOCUMENT ME!
3179    *
3180    * @param e
3181    *          DOCUMENT ME!
3182    */
3183   @Override
3184   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3185   {
3186     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3187     alignPanel.paintAlignment(true);
3188   }
3189
3190   public FeatureSettings featureSettings;
3191
3192   @Override
3193   public FeatureSettingsControllerI getFeatureSettingsUI()
3194   {
3195     return featureSettings;
3196   }
3197
3198   @Override
3199   public void featureSettings_actionPerformed(ActionEvent e)
3200   {
3201     if (featureSettings != null)
3202     {
3203       featureSettings.close();
3204       featureSettings = null;
3205     }
3206     if (!showSeqFeatures.isSelected())
3207     {
3208       // make sure features are actually displayed
3209       showSeqFeatures.setSelected(true);
3210       showSeqFeatures_actionPerformed(null);
3211     }
3212     featureSettings = new FeatureSettings(this);
3213   }
3214
3215   /**
3216    * Set or clear 'Show Sequence Features'
3217    *
3218    * @param evt
3219    *          DOCUMENT ME!
3220    */
3221   @Override
3222   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3223   {
3224     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3225     alignPanel.paintAlignment(true);
3226     if (alignPanel.getOverviewPanel() != null)
3227     {
3228       alignPanel.getOverviewPanel().updateOverviewImage();
3229     }
3230   }
3231
3232   /**
3233    * Set or clear 'Show Sequence Features'
3234    *
3235    * @param evt
3236    *          DOCUMENT ME!
3237    */
3238   @Override
3239   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3240   {
3241     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3242             .isSelected());
3243     if (viewport.isShowSequenceFeaturesHeight())
3244     {
3245       // ensure we're actually displaying features
3246       viewport.setShowSequenceFeatures(true);
3247       showSeqFeatures.setSelected(true);
3248     }
3249     alignPanel.paintAlignment(true);
3250     if (alignPanel.getOverviewPanel() != null)
3251     {
3252       alignPanel.getOverviewPanel().updateOverviewImage();
3253     }
3254   }
3255
3256   /**
3257    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3258    * the annotations panel as a whole.
3259    *
3260    * The options to show/hide all annotations should be enabled when the panel
3261    * is shown, and disabled when the panel is hidden.
3262    *
3263    * @param e
3264    */
3265   @Override
3266   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3267   {
3268     final boolean setVisible = annotationPanelMenuItem.isSelected();
3269     viewport.setShowAnnotation(setVisible);
3270     this.showAllSeqAnnotations.setEnabled(setVisible);
3271     this.hideAllSeqAnnotations.setEnabled(setVisible);
3272     this.showAllAlAnnotations.setEnabled(setVisible);
3273     this.hideAllAlAnnotations.setEnabled(setVisible);
3274     alignPanel.updateLayout();
3275   }
3276
3277   @Override
3278   public void alignmentProperties()
3279   {
3280     JEditorPane editPane = new JEditorPane("text/html", "");
3281     editPane.setEditable(false);
3282     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3283             .formatAsHtml();
3284     editPane.setText(MessageManager.formatMessage("label.html_content",
3285             new Object[] { contents.toString() }));
3286     JInternalFrame frame = new JInternalFrame();
3287     frame.getContentPane().add(new JScrollPane(editPane));
3288
3289     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3290             "label.alignment_properties", new Object[] { getTitle() }),
3291             500, 400);
3292   }
3293
3294   /**
3295    * DOCUMENT ME!
3296    *
3297    * @param e
3298    *          DOCUMENT ME!
3299    */
3300   @Override
3301   public void overviewMenuItem_actionPerformed(ActionEvent e)
3302   {
3303     if (alignPanel.overviewPanel != null)
3304     {
3305       return;
3306     }
3307
3308     JInternalFrame frame = new JInternalFrame();
3309     OverviewPanel overview = new OverviewPanel(alignPanel);
3310     frame.setContentPane(overview);
3311     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3312             "label.overview_params", new Object[] { this.getTitle() }),
3313             frame.getWidth(), frame.getHeight());
3314     frame.pack();
3315     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3316     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3317     {
3318       @Override
3319       public void internalFrameClosed(
3320               javax.swing.event.InternalFrameEvent evt)
3321       {
3322         alignPanel.setOverviewPanel(null);
3323       };
3324     });
3325
3326     alignPanel.setOverviewPanel(overview);
3327   }
3328
3329   @Override
3330   public void textColour_actionPerformed(ActionEvent e)
3331   {
3332     new TextColourChooser().chooseColour(alignPanel, null);
3333   }
3334
3335   /**
3336    * DOCUMENT ME!
3337    *
3338    * @param e
3339    *          DOCUMENT ME!
3340    */
3341   @Override
3342   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3343   {
3344     changeColour(null);
3345   }
3346
3347   /**
3348    * DOCUMENT ME!
3349    *
3350    * @param e
3351    *          DOCUMENT ME!
3352    */
3353   @Override
3354   public void clustalColour_actionPerformed(ActionEvent e)
3355   {
3356     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3357             viewport.getHiddenRepSequences()));
3358   }
3359
3360   /**
3361    * DOCUMENT ME!
3362    *
3363    * @param e
3364    *          DOCUMENT ME!
3365    */
3366   @Override
3367   public void zappoColour_actionPerformed(ActionEvent e)
3368   {
3369     changeColour(new ZappoColourScheme());
3370   }
3371
3372   /**
3373    * DOCUMENT ME!
3374    *
3375    * @param e
3376    *          DOCUMENT ME!
3377    */
3378   @Override
3379   public void taylorColour_actionPerformed(ActionEvent e)
3380   {
3381     changeColour(new TaylorColourScheme());
3382   }
3383
3384   /**
3385    * DOCUMENT ME!
3386    *
3387    * @param e
3388    *          DOCUMENT ME!
3389    */
3390   @Override
3391   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3392   {
3393     changeColour(new HydrophobicColourScheme());
3394   }
3395
3396   /**
3397    * DOCUMENT ME!
3398    *
3399    * @param e
3400    *          DOCUMENT ME!
3401    */
3402   @Override
3403   public void helixColour_actionPerformed(ActionEvent e)
3404   {
3405     changeColour(new HelixColourScheme());
3406   }
3407
3408   /**
3409    * DOCUMENT ME!
3410    *
3411    * @param e
3412    *          DOCUMENT ME!
3413    */
3414   @Override
3415   public void strandColour_actionPerformed(ActionEvent e)
3416   {
3417     changeColour(new StrandColourScheme());
3418   }
3419
3420   /**
3421    * DOCUMENT ME!
3422    *
3423    * @param e
3424    *          DOCUMENT ME!
3425    */
3426   @Override
3427   public void turnColour_actionPerformed(ActionEvent e)
3428   {
3429     changeColour(new TurnColourScheme());
3430   }
3431
3432   /**
3433    * DOCUMENT ME!
3434    *
3435    * @param e
3436    *          DOCUMENT ME!
3437    */
3438   @Override
3439   public void buriedColour_actionPerformed(ActionEvent e)
3440   {
3441     changeColour(new BuriedColourScheme());
3442   }
3443
3444   /**
3445    * DOCUMENT ME!
3446    *
3447    * @param e
3448    *          DOCUMENT ME!
3449    */
3450   @Override
3451   public void nucleotideColour_actionPerformed(ActionEvent e)
3452   {
3453     changeColour(new NucleotideColourScheme());
3454   }
3455
3456   @Override
3457   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3458   {
3459     changeColour(new PurinePyrimidineColourScheme());
3460   }
3461
3462   /*
3463    * public void covariationColour_actionPerformed(ActionEvent e) {
3464    * changeColour(new
3465    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3466    * ()[0])); }
3467    */
3468   @Override
3469   public void annotationColour_actionPerformed(ActionEvent e)
3470   {
3471     new AnnotationColourChooser(viewport, alignPanel);
3472   }
3473
3474   @Override
3475   public void annotationColumn_actionPerformed(ActionEvent e)
3476   {
3477     new AnnotationColumnChooser(viewport, alignPanel);
3478   }
3479
3480   @Override
3481   public void rnahelicesColour_actionPerformed(ActionEvent e)
3482   {
3483     new RNAHelicesColourChooser(viewport, alignPanel);
3484   }
3485
3486   /**
3487    * DOCUMENT ME!
3488    *
3489    * @param e
3490    *          DOCUMENT ME!
3491    */
3492   @Override
3493   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3494   {
3495     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3496   }
3497
3498   /**
3499    * DOCUMENT ME!
3500    *
3501    * @param cs
3502    *          DOCUMENT ME!
3503    */
3504   @Override
3505   public void changeColour(ColourSchemeI cs)
3506   {
3507     // TODO: pull up to controller method
3508
3509     if (cs != null)
3510     {
3511       // Make sure viewport is up to date w.r.t. any sliders
3512       if (viewport.getAbovePIDThreshold())
3513       {
3514         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3515                 "Background");
3516         viewport.setThreshold(threshold);
3517       }
3518
3519       if (viewport.getConservationSelected())
3520       {
3521         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3522                 cs, "Background"));
3523       }
3524       if (cs instanceof TCoffeeColourScheme)
3525       {
3526         tcoffeeColour.setEnabled(true);
3527         tcoffeeColour.setSelected(true);
3528       }
3529     }
3530
3531     viewport.setGlobalColourScheme(cs);
3532
3533     alignPanel.paintAlignment(true);
3534   }
3535
3536   /**
3537    * DOCUMENT ME!
3538    *
3539    * @param e
3540    *          DOCUMENT ME!
3541    */
3542   @Override
3543   protected void modifyPID_actionPerformed(ActionEvent e)
3544   {
3545     if (viewport.getAbovePIDThreshold()
3546             && viewport.getGlobalColourScheme() != null)
3547     {
3548       SliderPanel.setPIDSliderSource(alignPanel,
3549               viewport.getGlobalColourScheme(), "Background");
3550       SliderPanel.showPIDSlider();
3551     }
3552   }
3553
3554   /**
3555    * DOCUMENT ME!
3556    *
3557    * @param e
3558    *          DOCUMENT ME!
3559    */
3560   @Override
3561   protected void modifyConservation_actionPerformed(ActionEvent e)
3562   {
3563     if (viewport.getConservationSelected()
3564             && viewport.getGlobalColourScheme() != null)
3565     {
3566       SliderPanel.setConservationSlider(alignPanel,
3567               viewport.getGlobalColourScheme(), "Background");
3568       SliderPanel.showConservationSlider();
3569     }
3570   }
3571
3572   /**
3573    * DOCUMENT ME!
3574    *
3575    * @param e
3576    *          DOCUMENT ME!
3577    */
3578   @Override
3579   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3580   {
3581     viewport.setConservationSelected(conservationMenuItem.isSelected());
3582
3583     viewport.setAbovePIDThreshold(false);
3584     abovePIDThreshold.setSelected(false);
3585
3586     changeColour(viewport.getGlobalColourScheme());
3587
3588     modifyConservation_actionPerformed(null);
3589   }
3590
3591   /**
3592    * DOCUMENT ME!
3593    *
3594    * @param e
3595    *          DOCUMENT ME!
3596    */
3597   @Override
3598   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3599   {
3600     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3601
3602     conservationMenuItem.setSelected(false);
3603     viewport.setConservationSelected(false);
3604
3605     changeColour(viewport.getGlobalColourScheme());
3606
3607     modifyPID_actionPerformed(null);
3608   }
3609
3610   /**
3611    * DOCUMENT ME!
3612    *
3613    * @param e
3614    *          DOCUMENT ME!
3615    */
3616   @Override
3617   public void userDefinedColour_actionPerformed(ActionEvent e)
3618   {
3619     if (e.getActionCommand().equals(
3620             MessageManager.getString("action.user_defined")))
3621     {
3622       new UserDefinedColours(alignPanel, null);
3623     }
3624     else
3625     {
3626       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3627               .getUserColourSchemes().get(e.getActionCommand());
3628
3629       changeColour(udc);
3630     }
3631   }
3632
3633   public void updateUserColourMenu()
3634   {
3635
3636     Component[] menuItems = colourMenu.getMenuComponents();
3637     int iSize = menuItems.length;
3638     for (int i = 0; i < iSize; i++)
3639     {
3640       if (menuItems[i].getName() != null
3641               && menuItems[i].getName().equals("USER_DEFINED"))
3642       {
3643         colourMenu.remove(menuItems[i]);
3644         iSize--;
3645       }
3646     }
3647     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3648     {
3649       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3650               .getUserColourSchemes().keys();
3651
3652       while (userColours.hasMoreElements())
3653       {
3654         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3655                 userColours.nextElement().toString());
3656         radioItem.setName("USER_DEFINED");
3657         radioItem.addMouseListener(new MouseAdapter()
3658         {
3659           @Override
3660           public void mousePressed(MouseEvent evt)
3661           {
3662             if (evt.isControlDown()
3663                     || SwingUtilities.isRightMouseButton(evt))
3664             {
3665               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3666
3667               int option = JOptionPane.showInternalConfirmDialog(
3668                       jalview.gui.Desktop.desktop,
3669                       MessageManager
3670                               .getString("label.remove_from_default_list"),
3671                       MessageManager
3672                               .getString("label.remove_user_defined_colour"),
3673                       JOptionPane.YES_NO_OPTION);
3674               if (option == JOptionPane.YES_OPTION)
3675               {
3676                 jalview.gui.UserDefinedColours
3677                         .removeColourFromDefaults(radioItem.getText());
3678                 colourMenu.remove(radioItem);
3679               }
3680               else
3681               {
3682                 radioItem.addActionListener(new ActionListener()
3683                 {
3684                   @Override
3685                   public void actionPerformed(ActionEvent evt)
3686                   {
3687                     userDefinedColour_actionPerformed(evt);
3688                   }
3689                 });
3690               }
3691             }
3692           }
3693         });
3694         radioItem.addActionListener(new ActionListener()
3695         {
3696           @Override
3697           public void actionPerformed(ActionEvent evt)
3698           {
3699             userDefinedColour_actionPerformed(evt);
3700           }
3701         });
3702
3703         colourMenu.insert(radioItem, 15);
3704         colours.add(radioItem);
3705       }
3706     }
3707   }
3708
3709   /**
3710    * DOCUMENT ME!
3711    *
3712    * @param e
3713    *          DOCUMENT ME!
3714    */
3715   @Override
3716   public void PIDColour_actionPerformed(ActionEvent e)
3717   {
3718     changeColour(new PIDColourScheme());
3719   }
3720
3721   /**
3722    * DOCUMENT ME!
3723    *
3724    * @param e
3725    *          DOCUMENT ME!
3726    */
3727   @Override
3728   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3729   {
3730     changeColour(new Blosum62ColourScheme());
3731   }
3732
3733   /**
3734    * DOCUMENT ME!
3735    *
3736    * @param e
3737    *          DOCUMENT ME!
3738    */
3739   @Override
3740   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3741   {
3742     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3743     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3744             .getAlignment().getSequenceAt(0), null);
3745     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3746             viewport.getAlignment()));
3747     alignPanel.paintAlignment(true);
3748   }
3749
3750   /**
3751    * DOCUMENT ME!
3752    *
3753    * @param e
3754    *          DOCUMENT ME!
3755    */
3756   @Override
3757   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3758   {
3759     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3760     AlignmentSorter.sortByID(viewport.getAlignment());
3761     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3762             viewport.getAlignment()));
3763     alignPanel.paintAlignment(true);
3764   }
3765
3766   /**
3767    * DOCUMENT ME!
3768    *
3769    * @param e
3770    *          DOCUMENT ME!
3771    */
3772   @Override
3773   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3774   {
3775     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3776     AlignmentSorter.sortByLength(viewport.getAlignment());
3777     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3778             viewport.getAlignment()));
3779     alignPanel.paintAlignment(true);
3780   }
3781
3782   /**
3783    * DOCUMENT ME!
3784    *
3785    * @param e
3786    *          DOCUMENT ME!
3787    */
3788   @Override
3789   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3790   {
3791     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3792     AlignmentSorter.sortByGroup(viewport.getAlignment());
3793     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3794             viewport.getAlignment()));
3795
3796     alignPanel.paintAlignment(true);
3797   }
3798
3799   /**
3800    * DOCUMENT ME!
3801    *
3802    * @param e
3803    *          DOCUMENT ME!
3804    */
3805   @Override
3806   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3807   {
3808     new RedundancyPanel(alignPanel, this);
3809   }
3810
3811   /**
3812    * DOCUMENT ME!
3813    *
3814    * @param e
3815    *          DOCUMENT ME!
3816    */
3817   @Override
3818   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3819   {
3820     if ((viewport.getSelectionGroup() == null)
3821             || (viewport.getSelectionGroup().getSize() < 2))
3822     {
3823       JOptionPane.showInternalMessageDialog(this, MessageManager
3824               .getString("label.you_must_select_least_two_sequences"),
3825               MessageManager.getString("label.invalid_selection"),
3826               JOptionPane.WARNING_MESSAGE);
3827     }
3828     else
3829     {
3830       JInternalFrame frame = new JInternalFrame();
3831       frame.setContentPane(new PairwiseAlignPanel(viewport));
3832       Desktop.addInternalFrame(frame,
3833               MessageManager.getString("action.pairwise_alignment"), 600,
3834               500);
3835     }
3836   }
3837
3838   /**
3839    * DOCUMENT ME!
3840    *
3841    * @param e
3842    *          DOCUMENT ME!
3843    */
3844   @Override
3845   public void PCAMenuItem_actionPerformed(ActionEvent e)
3846   {
3847     if (((viewport.getSelectionGroup() != null)
3848             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3849             .getSelectionGroup().getSize() > 0))
3850             || (viewport.getAlignment().getHeight() < 4))
3851     {
3852       JOptionPane
3853               .showInternalMessageDialog(
3854                       this,
3855                       MessageManager
3856                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3857                       MessageManager
3858                               .getString("label.sequence_selection_insufficient"),
3859                       JOptionPane.WARNING_MESSAGE);
3860
3861       return;
3862     }
3863
3864     new PCAPanel(alignPanel);
3865   }
3866
3867   @Override
3868   public void autoCalculate_actionPerformed(ActionEvent e)
3869   {
3870     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3871     if (viewport.autoCalculateConsensus)
3872     {
3873       viewport.firePropertyChange("alignment", null, viewport
3874               .getAlignment().getSequences());
3875     }
3876   }
3877
3878   @Override
3879   public void sortByTreeOption_actionPerformed(ActionEvent e)
3880   {
3881     viewport.sortByTree = sortByTree.isSelected();
3882   }
3883
3884   @Override
3885   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3886   {
3887     viewport.followSelection = listenToViewSelections.isSelected();
3888   }
3889
3890   /**
3891    * DOCUMENT ME!
3892    *
3893    * @param e
3894    *          DOCUMENT ME!
3895    */
3896   @Override
3897   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3898   {
3899     newTreePanel("AV", "PID", "Average distance tree using PID");
3900   }
3901
3902   /**
3903    * DOCUMENT ME!
3904    *
3905    * @param e
3906    *          DOCUMENT ME!
3907    */
3908   @Override
3909   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3910   {
3911     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3912   }
3913
3914   /**
3915    * DOCUMENT ME!
3916    *
3917    * @param e
3918    *          DOCUMENT ME!
3919    */
3920   @Override
3921   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3922   {
3923     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3924   }
3925
3926   /**
3927    * DOCUMENT ME!
3928    *
3929    * @param e
3930    *          DOCUMENT ME!
3931    */
3932   @Override
3933   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3934   {
3935     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3936   }
3937
3938   /**
3939    * DOCUMENT ME!
3940    *
3941    * @param type
3942    *          DOCUMENT ME!
3943    * @param pwType
3944    *          DOCUMENT ME!
3945    * @param title
3946    *          DOCUMENT ME!
3947    */
3948   void newTreePanel(String type, String pwType, String title)
3949   {
3950     TreePanel tp;
3951
3952     if (viewport.getSelectionGroup() != null
3953             && viewport.getSelectionGroup().getSize() > 0)
3954     {
3955       if (viewport.getSelectionGroup().getSize() < 3)
3956       {
3957         JOptionPane
3958                 .showMessageDialog(
3959                         Desktop.desktop,
3960                         MessageManager
3961                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3962                         MessageManager
3963                                 .getString("label.not_enough_sequences"),
3964                         JOptionPane.WARNING_MESSAGE);
3965         return;
3966       }
3967
3968       SequenceGroup sg = viewport.getSelectionGroup();
3969
3970       /* Decide if the selection is a column region */
3971       for (SequenceI _s : sg.getSequences())
3972       {
3973         if (_s.getLength() < sg.getEndRes())
3974         {
3975           JOptionPane
3976                   .showMessageDialog(
3977                           Desktop.desktop,
3978                           MessageManager
3979                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3980                           MessageManager
3981                                   .getString("label.sequences_selection_not_aligned"),
3982                           JOptionPane.WARNING_MESSAGE);
3983
3984           return;
3985         }
3986       }
3987
3988       title = title + " on region";
3989       tp = new TreePanel(alignPanel, type, pwType);
3990     }
3991     else
3992     {
3993       // are the visible sequences aligned?
3994       if (!viewport.getAlignment().isAligned(false))
3995       {
3996         JOptionPane
3997                 .showMessageDialog(
3998                         Desktop.desktop,
3999                         MessageManager
4000                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4001                         MessageManager
4002                                 .getString("label.sequences_not_aligned"),
4003                         JOptionPane.WARNING_MESSAGE);
4004
4005         return;
4006       }
4007
4008       if (viewport.getAlignment().getHeight() < 2)
4009       {
4010         return;
4011       }
4012
4013       tp = new TreePanel(alignPanel, type, pwType);
4014     }
4015
4016     title += " from ";
4017
4018     if (viewport.viewName != null)
4019     {
4020       title += viewport.viewName + " of ";
4021     }
4022
4023     title += this.title;
4024
4025     Desktop.addInternalFrame(tp, title, 600, 500);
4026   }
4027
4028   /**
4029    * DOCUMENT ME!
4030    *
4031    * @param title
4032    *          DOCUMENT ME!
4033    * @param order
4034    *          DOCUMENT ME!
4035    */
4036   public void addSortByOrderMenuItem(String title,
4037           final AlignmentOrder order)
4038   {
4039     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4040             "action.by_title_param", new Object[] { title }));
4041     sort.add(item);
4042     item.addActionListener(new java.awt.event.ActionListener()
4043     {
4044       @Override
4045       public void actionPerformed(ActionEvent e)
4046       {
4047         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4048
4049         // TODO: JBPNote - have to map order entries to curent SequenceI
4050         // pointers
4051         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4052
4053         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4054                 .getAlignment()));
4055
4056         alignPanel.paintAlignment(true);
4057       }
4058     });
4059   }
4060
4061   /**
4062    * Add a new sort by annotation score menu item
4063    *
4064    * @param sort
4065    *          the menu to add the option to
4066    * @param scoreLabel
4067    *          the label used to retrieve scores for each sequence on the
4068    *          alignment
4069    */
4070   public void addSortByAnnotScoreMenuItem(JMenu sort,
4071           final String scoreLabel)
4072   {
4073     final JMenuItem item = new JMenuItem(scoreLabel);
4074     sort.add(item);
4075     item.addActionListener(new java.awt.event.ActionListener()
4076     {
4077       @Override
4078       public void actionPerformed(ActionEvent e)
4079       {
4080         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4081         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4082                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4083         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4084                 viewport.getAlignment()));
4085         alignPanel.paintAlignment(true);
4086       }
4087     });
4088   }
4089
4090   /**
4091    * last hash for alignment's annotation array - used to minimise cost of
4092    * rebuild.
4093    */
4094   protected int _annotationScoreVectorHash;
4095
4096   /**
4097    * search the alignment and rebuild the sort by annotation score submenu the
4098    * last alignment annotation vector hash is stored to minimize cost of
4099    * rebuilding in subsequence calls.
4100    *
4101    */
4102   @Override
4103   public void buildSortByAnnotationScoresMenu()
4104   {
4105     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4106     {
4107       return;
4108     }
4109
4110     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4111     {
4112       sortByAnnotScore.removeAll();
4113       // almost certainly a quicker way to do this - but we keep it simple
4114       Hashtable scoreSorts = new Hashtable();
4115       AlignmentAnnotation aann[];
4116       for (SequenceI sqa : viewport.getAlignment().getSequences())
4117       {
4118         aann = sqa.getAnnotation();
4119         for (int i = 0; aann != null && i < aann.length; i++)
4120         {
4121           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4122           {
4123             scoreSorts.put(aann[i].label, aann[i].label);
4124           }
4125         }
4126       }
4127       Enumeration labels = scoreSorts.keys();
4128       while (labels.hasMoreElements())
4129       {
4130         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4131                 (String) labels.nextElement());
4132       }
4133       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4134       scoreSorts.clear();
4135
4136       _annotationScoreVectorHash = viewport.getAlignment()
4137               .getAlignmentAnnotation().hashCode();
4138     }
4139   }
4140
4141   /**
4142    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4143    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4144    * call. Listeners are added to remove the menu item when the treePanel is
4145    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4146    * modified.
4147    *
4148    * @param treePanel
4149    *          Displayed tree window.
4150    * @param title
4151    *          SortBy menu item title.
4152    */
4153   @Override
4154   public void buildTreeMenu()
4155   {
4156     calculateTree.removeAll();
4157     // build the calculate menu
4158
4159     for (final String type : new String[] { "NJ", "AV" })
4160     {
4161       String treecalcnm = MessageManager.getString("label.tree_calc_"
4162               + type.toLowerCase());
4163       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4164       {
4165         JMenuItem tm = new JMenuItem();
4166         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4167         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4168         {
4169           String smn = MessageManager.getStringOrReturn(
4170                   "label.score_model_", sm.getName());
4171           final String title = MessageManager.formatMessage(
4172                   "label.treecalc_title", treecalcnm, smn);
4173           tm.setText(title);//
4174           tm.addActionListener(new java.awt.event.ActionListener()
4175           {
4176             @Override
4177             public void actionPerformed(ActionEvent e)
4178             {
4179               newTreePanel(type, pwtype, title);
4180             }
4181           });
4182           calculateTree.add(tm);
4183         }
4184
4185       }
4186     }
4187     sortByTreeMenu.removeAll();
4188
4189     List<Component> comps = PaintRefresher.components.get(viewport
4190             .getSequenceSetId());
4191     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4192     for (Component comp : comps)
4193     {
4194       if (comp instanceof TreePanel)
4195       {
4196         treePanels.add((TreePanel) comp);
4197       }
4198     }
4199
4200     if (treePanels.size() < 1)
4201     {
4202       sortByTreeMenu.setVisible(false);
4203       return;
4204     }
4205
4206     sortByTreeMenu.setVisible(true);
4207
4208     for (final TreePanel tp : treePanels)
4209     {
4210       final JMenuItem item = new JMenuItem(tp.getTitle());
4211       item.addActionListener(new java.awt.event.ActionListener()
4212       {
4213         @Override
4214         public void actionPerformed(ActionEvent e)
4215         {
4216           tp.sortByTree_actionPerformed();
4217           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4218
4219         }
4220       });
4221
4222       sortByTreeMenu.add(item);
4223     }
4224   }
4225
4226   public boolean sortBy(AlignmentOrder alorder, String undoname)
4227   {
4228     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4229     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4230     if (undoname != null)
4231     {
4232       addHistoryItem(new OrderCommand(undoname, oldOrder,
4233               viewport.getAlignment()));
4234     }
4235     alignPanel.paintAlignment(true);
4236     return true;
4237   }
4238
4239   /**
4240    * Work out whether the whole set of sequences or just the selected set will
4241    * be submitted for multiple alignment.
4242    *
4243    */
4244   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4245   {
4246     // Now, check we have enough sequences
4247     AlignmentView msa = null;
4248
4249     if ((viewport.getSelectionGroup() != null)
4250             && (viewport.getSelectionGroup().getSize() > 1))
4251     {
4252       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4253       // some common interface!
4254       /*
4255        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4256        * SequenceI[sz = seqs.getSize(false)];
4257        *
4258        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4259        * seqs.getSequenceAt(i); }
4260        */
4261       msa = viewport.getAlignmentView(true);
4262     }
4263     else if (viewport.getSelectionGroup() != null
4264             && viewport.getSelectionGroup().getSize() == 1)
4265     {
4266       int option = JOptionPane.showConfirmDialog(this,
4267               MessageManager.getString("warn.oneseq_msainput_selection"),
4268               MessageManager.getString("label.invalid_selection"),
4269               JOptionPane.OK_CANCEL_OPTION);
4270       if (option == JOptionPane.OK_OPTION)
4271       {
4272         msa = viewport.getAlignmentView(false);
4273       }
4274     }
4275     else
4276     {
4277       msa = viewport.getAlignmentView(false);
4278     }
4279     return msa;
4280   }
4281
4282   /**
4283    * Decides what is submitted to a secondary structure prediction service: the
4284    * first sequence in the alignment, or in the current selection, or, if the
4285    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4286    * region or the whole alignment. (where the first sequence in the set is the
4287    * one that the prediction will be for).
4288    */
4289   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4290   {
4291     AlignmentView seqs = null;
4292
4293     if ((viewport.getSelectionGroup() != null)
4294             && (viewport.getSelectionGroup().getSize() > 0))
4295     {
4296       seqs = viewport.getAlignmentView(true);
4297     }
4298     else
4299     {
4300       seqs = viewport.getAlignmentView(false);
4301     }
4302     // limit sequences - JBPNote in future - could spawn multiple prediction
4303     // jobs
4304     // TODO: viewport.getAlignment().isAligned is a global state - the local
4305     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4306     if (!viewport.getAlignment().isAligned(false))
4307     {
4308       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4309       // TODO: if seqs.getSequences().length>1 then should really have warned
4310       // user!
4311
4312     }
4313     return seqs;
4314   }
4315
4316   /**
4317    * DOCUMENT ME!
4318    *
4319    * @param e
4320    *          DOCUMENT ME!
4321    */
4322   @Override
4323   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4324   {
4325     // Pick the tree file
4326     JalviewFileChooser chooser = new JalviewFileChooser(
4327             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4328     chooser.setFileView(new JalviewFileView());
4329     chooser.setDialogTitle(MessageManager
4330             .getString("label.select_newick_like_tree_file"));
4331     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4332
4333     int value = chooser.showOpenDialog(null);
4334
4335     if (value == JalviewFileChooser.APPROVE_OPTION)
4336     {
4337       String choice = chooser.getSelectedFile().getPath();
4338       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4339       jalview.io.NewickFile fin = null;
4340       try
4341       {
4342         fin = new jalview.io.NewickFile(choice, "File");
4343         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4344       } catch (Exception ex)
4345       {
4346         JOptionPane
4347                 .showMessageDialog(
4348                         Desktop.desktop,
4349                         ex.getMessage(),
4350                         MessageManager
4351                                 .getString("label.problem_reading_tree_file"),
4352                         JOptionPane.WARNING_MESSAGE);
4353         ex.printStackTrace();
4354       }
4355       if (fin != null && fin.hasWarningMessage())
4356       {
4357         JOptionPane.showMessageDialog(Desktop.desktop, fin
4358                 .getWarningMessage(), MessageManager
4359                 .getString("label.possible_problem_with_tree_file"),
4360                 JOptionPane.WARNING_MESSAGE);
4361       }
4362     }
4363   }
4364
4365   @Override
4366   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4367   {
4368     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4369   }
4370
4371   public TreePanel ShowNewickTree(NewickFile nf, String title)
4372   {
4373     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4374   }
4375
4376   public TreePanel ShowNewickTree(NewickFile nf, String title,
4377           AlignmentView input)
4378   {
4379     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4380   }
4381
4382   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4383           int h, int x, int y)
4384   {
4385     return ShowNewickTree(nf, title, null, w, h, x, y);
4386   }
4387
4388   /**
4389    * Add a treeviewer for the tree extracted from a newick file object to the
4390    * current alignment view
4391    *
4392    * @param nf
4393    *          the tree
4394    * @param title
4395    *          tree viewer title
4396    * @param input
4397    *          Associated alignment input data (or null)
4398    * @param w
4399    *          width
4400    * @param h
4401    *          height
4402    * @param x
4403    *          position
4404    * @param y
4405    *          position
4406    * @return TreePanel handle
4407    */
4408   public TreePanel ShowNewickTree(NewickFile nf, String title,
4409           AlignmentView input, int w, int h, int x, int y)
4410   {
4411     TreePanel tp = null;
4412
4413     try
4414     {
4415       nf.parse();
4416
4417       if (nf.getTree() != null)
4418       {
4419         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4420
4421         tp.setSize(w, h);
4422
4423         if (x > 0 && y > 0)
4424         {
4425           tp.setLocation(x, y);
4426         }
4427
4428         Desktop.addInternalFrame(tp, title, w, h);
4429       }
4430     } catch (Exception ex)
4431     {
4432       ex.printStackTrace();
4433     }
4434
4435     return tp;
4436   }
4437
4438   private boolean buildingMenu = false;
4439
4440   /**
4441    * Generates menu items and listener event actions for web service clients
4442    *
4443    */
4444   public void BuildWebServiceMenu()
4445   {
4446     while (buildingMenu)
4447     {
4448       try
4449       {
4450         System.err.println("Waiting for building menu to finish.");
4451         Thread.sleep(10);
4452       } catch (Exception e)
4453       {
4454       }
4455     }
4456     final AlignFrame me = this;
4457     buildingMenu = true;
4458     new Thread(new Runnable()
4459     {
4460       @Override
4461       public void run()
4462       {
4463         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4464         try
4465         {
4466           // System.err.println("Building ws menu again "
4467           // + Thread.currentThread());
4468           // TODO: add support for context dependent disabling of services based
4469           // on
4470           // alignment and current selection
4471           // TODO: add additional serviceHandle parameter to specify abstract
4472           // handler
4473           // class independently of AbstractName
4474           // TODO: add in rediscovery GUI function to restart discoverer
4475           // TODO: group services by location as well as function and/or
4476           // introduce
4477           // object broker mechanism.
4478           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4479           final IProgressIndicator af = me;
4480           final JMenu msawsmenu = new JMenu("Alignment");
4481           final JMenu secstrmenu = new JMenu(
4482                   "Secondary Structure Prediction");
4483           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4484           final JMenu analymenu = new JMenu("Analysis");
4485           final JMenu dismenu = new JMenu("Protein Disorder");
4486           // final JMenu msawsmenu = new
4487           // JMenu(MessageManager.getString("label.alignment"));
4488           // final JMenu secstrmenu = new
4489           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4490           // final JMenu seqsrchmenu = new
4491           // JMenu(MessageManager.getString("label.sequence_database_search"));
4492           // final JMenu analymenu = new
4493           // JMenu(MessageManager.getString("label.analysis"));
4494           // final JMenu dismenu = new
4495           // JMenu(MessageManager.getString("label.protein_disorder"));
4496           // JAL-940 - only show secondary structure prediction services from
4497           // the legacy server
4498           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4499               // &&
4500           Discoverer.services != null && (Discoverer.services.size() > 0))
4501           {
4502             // TODO: refactor to allow list of AbstractName/Handler bindings to
4503             // be
4504             // stored or retrieved from elsewhere
4505             // No MSAWS used any more:
4506             // Vector msaws = null; // (Vector)
4507             // Discoverer.services.get("MsaWS");
4508             Vector secstrpr = (Vector) Discoverer.services
4509                     .get("SecStrPred");
4510             if (secstrpr != null)
4511             {
4512               // Add any secondary structure prediction services
4513               for (int i = 0, j = secstrpr.size(); i < j; i++)
4514               {
4515                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4516                         .get(i);
4517                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4518                         .getServiceClient(sh);
4519                 int p = secstrmenu.getItemCount();
4520                 impl.attachWSMenuEntry(secstrmenu, me);
4521                 int q = secstrmenu.getItemCount();
4522                 for (int litm = p; litm < q; litm++)
4523                 {
4524                   legacyItems.add(secstrmenu.getItem(litm));
4525                 }
4526               }
4527             }
4528           }
4529
4530           // Add all submenus in the order they should appear on the web
4531           // services menu
4532           wsmenu.add(msawsmenu);
4533           wsmenu.add(secstrmenu);
4534           wsmenu.add(dismenu);
4535           wsmenu.add(analymenu);
4536           // No search services yet
4537           // wsmenu.add(seqsrchmenu);
4538
4539           javax.swing.SwingUtilities.invokeLater(new Runnable()
4540           {
4541             @Override
4542             public void run()
4543             {
4544               try
4545               {
4546                 webService.removeAll();
4547                 // first, add discovered services onto the webservices menu
4548                 if (wsmenu.size() > 0)
4549                 {
4550                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4551                   {
4552                     webService.add(wsmenu.get(i));
4553                   }
4554                 }
4555                 else
4556                 {
4557                   webService.add(me.webServiceNoServices);
4558                 }
4559                 // TODO: move into separate menu builder class.
4560                 boolean new_sspred = false;
4561                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4562                 {
4563                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4564                   if (jws2servs != null)
4565                   {
4566                     if (jws2servs.hasServices())
4567                     {
4568                       jws2servs.attachWSMenuEntry(webService, me);
4569                       for (Jws2Instance sv : jws2servs.getServices())
4570                       {
4571                         if (sv.description.toLowerCase().contains("jpred"))
4572                         {
4573                           for (JMenuItem jmi : legacyItems)
4574                           {
4575                             jmi.setVisible(false);
4576                           }
4577                         }
4578                       }
4579
4580                     }
4581                     if (jws2servs.isRunning())
4582                     {
4583                       JMenuItem tm = new JMenuItem(
4584                               "Still discovering JABA Services");
4585                       tm.setEnabled(false);
4586                       webService.add(tm);
4587                     }
4588                   }
4589                 }
4590                 build_urlServiceMenu(me.webService);
4591                 build_fetchdbmenu(webService);
4592                 for (JMenu item : wsmenu)
4593                 {
4594                   if (item.getItemCount() == 0)
4595                   {
4596                     item.setEnabled(false);
4597                   }
4598                   else
4599                   {
4600                     item.setEnabled(true);
4601                   }
4602                 }
4603               } catch (Exception e)
4604               {
4605                 Cache.log
4606                         .debug("Exception during web service menu building process.",
4607                                 e);
4608               }
4609             }
4610           });
4611         } catch (Exception e)
4612         {
4613         }
4614         buildingMenu = false;
4615       }
4616     }).start();
4617
4618   }
4619
4620   /**
4621    * construct any groupURL type service menu entries.
4622    *
4623    * @param webService
4624    */
4625   private void build_urlServiceMenu(JMenu webService)
4626   {
4627     // TODO: remove this code when 2.7 is released
4628     // DEBUG - alignmentView
4629     /*
4630      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4631      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4632      *
4633      * @Override public void actionPerformed(ActionEvent e) {
4634      * jalview.datamodel.AlignmentView
4635      * .testSelectionViews(af.viewport.getAlignment(),
4636      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4637      *
4638      * }); webService.add(testAlView);
4639      */
4640     // TODO: refactor to RestClient discoverer and merge menu entries for
4641     // rest-style services with other types of analysis/calculation service
4642     // SHmmr test client - still being implemented.
4643     // DEBUG - alignmentView
4644
4645     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4646             .getRestClients())
4647     {
4648       client.attachWSMenuEntry(
4649               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4650               this);
4651     }
4652   }
4653
4654   /*
4655    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4656    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4657    * getProperty("LAST_DIRECTORY"));
4658    *
4659    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4660    * to Vamsas file"); chooser.setToolTipText("Export");
4661    *
4662    * int value = chooser.showSaveDialog(this);
4663    *
4664    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4665    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4666    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4667    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4668    */
4669   /**
4670    * prototype of an automatically enabled/disabled analysis function
4671    *
4672    */
4673   protected void setShowProductsEnabled()
4674   {
4675     SequenceI[] selection = viewport.getSequenceSelection();
4676     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4677             viewport.getAlignment().getDataset()))
4678     {
4679       showProducts.setEnabled(true);
4680
4681     }
4682     else
4683     {
4684       showProducts.setEnabled(false);
4685     }
4686   }
4687
4688   /**
4689    * search selection for sequence xRef products and build the show products
4690    * menu.
4691    *
4692    * @param selection
4693    * @param dataset
4694    * @return true if showProducts menu should be enabled.
4695    */
4696   public boolean canShowProducts(SequenceI[] selection,
4697           boolean isRegionSelection, Alignment dataset)
4698   {
4699     boolean showp = false;
4700     try
4701     {
4702       showProducts.removeAll();
4703       final boolean dna = viewport.getAlignment().isNucleotide();
4704       final Alignment ds = dataset;
4705       String[] ptypes = (selection == null || selection.length == 0) ? null
4706               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4707       // Object[] prods =
4708       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4709       // selection, dataset, true);
4710       final SequenceI[] sel = selection;
4711       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4712       {
4713         showp = true;
4714         final boolean isRegSel = isRegionSelection;
4715         final AlignFrame af = this;
4716         final String source = ptypes[t];
4717         JMenuItem xtype = new JMenuItem(ptypes[t]);
4718         xtype.addActionListener(new ActionListener()
4719         {
4720
4721           @Override
4722           public void actionPerformed(ActionEvent e)
4723           {
4724             // TODO: new thread for this call with vis-delay
4725             af.showProductsFor(af.viewport.getSequenceSelection(),
4726                     isRegSel, dna, source);
4727           }
4728
4729         });
4730         showProducts.add(xtype);
4731       }
4732       showProducts.setVisible(showp);
4733       showProducts.setEnabled(showp);
4734     } catch (Exception e)
4735     {
4736       jalview.bin.Cache.log
4737               .warn("canTranslate threw an exception - please report to help@jalview.org",
4738                       e);
4739       return false;
4740     }
4741     return showp;
4742   }
4743
4744   protected void showProductsFor(final SequenceI[] sel,
4745           final boolean isRegSel, final boolean dna, final String source)
4746   {
4747     Runnable foo = new Runnable()
4748     {
4749
4750       @Override
4751       public void run()
4752       {
4753         final long sttime = System.currentTimeMillis();
4754         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4755                 "status.searching_for_sequences_from",
4756                 new Object[] { source }), sttime);
4757         try
4758         {
4759           // update our local dataset reference
4760           Alignment ds = AlignFrame.this.getViewport().getAlignment()
4761                   .getDataset();
4762           Alignment prods = CrossRef
4763                   .findXrefSequences(sel, dna, source, ds);
4764           if (prods != null)
4765           {
4766             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4767             for (int s = 0; s < sprods.length; s++)
4768             {
4769               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4770               if (ds.getSequences() == null
4771                       || !ds.getSequences().contains(
4772                               sprods[s].getDatasetSequence()))
4773               {
4774                 ds.addSequence(sprods[s].getDatasetSequence());
4775               }
4776               sprods[s].updatePDBIds();
4777             }
4778             Alignment al = new Alignment(sprods);
4779             al.setDataset(ds);
4780
4781             /*
4782              * Copy dna-to-protein mappings to new alignment
4783              */
4784             // TODO 1: no mappings are set up for EMBL product
4785             // TODO 2: if they were, should add them to protein alignment, not
4786             // dna
4787             Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4788             for (AlignedCodonFrame acf : cf)
4789             {
4790               al.addCodonFrame(acf);
4791             }
4792             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4793                     DEFAULT_HEIGHT);
4794             String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4795                     + " for " + ((isRegSel) ? "selected region of " : "")
4796                     + getTitle();
4797             naf.setTitle(newtitle);
4798
4799             // temporary flag until SplitFrame is released
4800             boolean asSplitFrame = Cache.getDefault(
4801                     Preferences.ENABLE_SPLIT_FRAME, true);
4802             if (asSplitFrame)
4803             {
4804               /*
4805                * Make a copy of this alignment (sharing the same dataset
4806                * sequences). If we are DNA, drop introns and update mappings
4807                */
4808               AlignmentI copyAlignment = null;
4809               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4810                       .getSequenceSelection();
4811               if (dna)
4812               {
4813                 copyAlignment = AlignmentUtils.makeExonAlignment(
4814                         sequenceSelection, cf);
4815                 al.getCodonFrames().clear();
4816                 al.getCodonFrames().addAll(cf);
4817                 final StructureSelectionManager ssm = StructureSelectionManager
4818                         .getStructureSelectionManager(Desktop.instance);
4819                 ssm.registerMappings(cf);
4820               }
4821               else
4822               {
4823                 copyAlignment = new Alignment(new Alignment(
4824                         sequenceSelection));
4825               }
4826               AlignFrame copyThis = new AlignFrame(copyAlignment,
4827                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4828               copyThis.setTitle(AlignFrame.this.getTitle());
4829               // SplitFrame with dna above, protein below
4830               SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4831                       dna ? naf : copyThis);
4832               naf.setVisible(true);
4833               copyThis.setVisible(true);
4834               String linkedTitle = MessageManager
4835                       .getString("label.linked_view_title");
4836               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4837             }
4838             else
4839             {
4840               Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4841                       DEFAULT_HEIGHT);
4842             }
4843           }
4844           else
4845           {
4846             System.err.println("No Sequences generated for xRef type "
4847                     + source);
4848           }
4849         } catch (Exception e)
4850         {
4851           jalview.bin.Cache.log.error(
4852                   "Exception when finding crossreferences", e);
4853         } catch (OutOfMemoryError e)
4854         {
4855           new OOMWarning("whilst fetching crossreferences", e);
4856         } catch (Error e)
4857         {
4858           jalview.bin.Cache.log.error("Error when finding crossreferences",
4859                   e);
4860         }
4861         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4862                 "status.finished_searching_for_sequences_from",
4863                 new Object[] { source }), sttime);
4864       }
4865
4866     };
4867     Thread frunner = new Thread(foo);
4868     frunner.start();
4869   }
4870
4871   public boolean canShowTranslationProducts(SequenceI[] selection,
4872           AlignmentI alignment)
4873   {
4874     // old way
4875     try
4876     {
4877       return (jalview.analysis.Dna.canTranslate(selection,
4878               viewport.getViewAsVisibleContigs(true)));
4879     } catch (Exception e)
4880     {
4881       jalview.bin.Cache.log
4882               .warn("canTranslate threw an exception - please report to help@jalview.org",
4883                       e);
4884       return false;
4885     }
4886   }
4887
4888   /**
4889    * Construct and display a new frame containing the translation of this
4890    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4891    */
4892   @Override
4893   public void showTranslation_actionPerformed(ActionEvent e)
4894   {
4895     AlignmentI al = null;
4896     try
4897     {
4898       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4899
4900       al = dna.translateCdna();
4901     } catch (Exception ex)
4902     {
4903       jalview.bin.Cache.log.error(
4904               "Exception during translation. Please report this !", ex);
4905       final String msg = MessageManager
4906               .getString("label.error_when_translating_sequences_submit_bug_report");
4907       final String errorTitle = MessageManager
4908               .getString("label.implementation_error")
4909               + MessageManager.getString("translation_failed");
4910       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4911               JOptionPane.ERROR_MESSAGE);
4912       return;
4913     }
4914     if (al == null || al.getHeight() == 0)
4915     {
4916       final String msg = MessageManager
4917               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4918       final String errorTitle = MessageManager
4919               .getString("label.translation_failed");
4920       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4921               JOptionPane.WARNING_MESSAGE);
4922     }
4923     else
4924     {
4925       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4926       af.setFileFormat(this.currentFileFormat);
4927       final String newTitle = MessageManager.formatMessage(
4928               "label.translation_of_params",
4929               new Object[] { this.getTitle() });
4930       af.setTitle(newTitle);
4931       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4932       {
4933         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4934         viewport.openSplitFrame(af, new Alignment(seqs));
4935       }
4936       else
4937       {
4938         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4939                 DEFAULT_HEIGHT);
4940       }
4941     }
4942   }
4943
4944   /**
4945    * Set the file format
4946    *
4947    * @param fileFormat
4948    */
4949   public void setFileFormat(String fileFormat)
4950   {
4951     this.currentFileFormat = fileFormat;
4952   }
4953
4954   /**
4955    * Try to load a features file onto the alignment.
4956    *
4957    * @param file
4958    *          contents or path to retrieve file
4959    * @param type
4960    *          access mode of file (see jalview.io.AlignFile)
4961    * @return true if features file was parsed correctly.
4962    */
4963   public boolean parseFeaturesFile(String file, String type)
4964   {
4965     return avc.parseFeaturesFile(file, type,
4966             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4967
4968   }
4969
4970   @Override
4971   public void refreshFeatureUI(boolean enableIfNecessary)
4972   {
4973     // note - currently this is only still here rather than in the controller
4974     // because of the featureSettings hard reference that is yet to be
4975     // abstracted
4976     if (enableIfNecessary)
4977     {
4978       viewport.setShowSequenceFeatures(true);
4979       showSeqFeatures.setSelected(true);
4980     }
4981
4982   }
4983
4984   @Override
4985   public void dragEnter(DropTargetDragEvent evt)
4986   {
4987   }
4988
4989   @Override
4990   public void dragExit(DropTargetEvent evt)
4991   {
4992   }
4993
4994   @Override
4995   public void dragOver(DropTargetDragEvent evt)
4996   {
4997   }
4998
4999   @Override
5000   public void dropActionChanged(DropTargetDragEvent evt)
5001   {
5002   }
5003
5004   @Override
5005   public void drop(DropTargetDropEvent evt)
5006   {
5007     Transferable t = evt.getTransferable();
5008     java.util.List files = null;
5009
5010     try
5011     {
5012       DataFlavor uriListFlavor = new DataFlavor(
5013               "text/uri-list;class=java.lang.String");
5014       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5015       {
5016         // Works on Windows and MacOSX
5017         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5018         files = (java.util.List) t
5019                 .getTransferData(DataFlavor.javaFileListFlavor);
5020       }
5021       else if (t.isDataFlavorSupported(uriListFlavor))
5022       {
5023         // This is used by Unix drag system
5024         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5025         String data = (String) t.getTransferData(uriListFlavor);
5026         files = new java.util.ArrayList(1);
5027         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5028                 data, "\r\n"); st.hasMoreTokens();)
5029         {
5030           String s = st.nextToken();
5031           if (s.startsWith("#"))
5032           {
5033             // the line is a comment (as per the RFC 2483)
5034             continue;
5035           }
5036
5037           java.net.URI uri = new java.net.URI(s);
5038           // check to see if we can handle this kind of URI
5039           if (uri.getScheme().toLowerCase().startsWith("http"))
5040           {
5041             files.add(uri.toString());
5042           }
5043           else
5044           {
5045             // otherwise preserve old behaviour: catch all for file objects
5046             java.io.File file = new java.io.File(uri);
5047             files.add(file.toString());
5048           }
5049         }
5050       }
5051     } catch (Exception e)
5052     {
5053       e.printStackTrace();
5054     }
5055     if (files != null)
5056     {
5057       try
5058       {
5059         // check to see if any of these files have names matching sequences in
5060         // the alignment
5061         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5062                 .getAlignment().getSequencesArray());
5063         /**
5064          * Object[] { String,SequenceI}
5065          */
5066         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5067         ArrayList<String> filesnotmatched = new ArrayList<String>();
5068         for (int i = 0; i < files.size(); i++)
5069         {
5070           String file = files.get(i).toString();
5071           String pdbfn = "";
5072           String protocol = FormatAdapter.checkProtocol(file);
5073           if (protocol == jalview.io.FormatAdapter.FILE)
5074           {
5075             File fl = new File(file);
5076             pdbfn = fl.getName();
5077           }
5078           else if (protocol == jalview.io.FormatAdapter.URL)
5079           {
5080             URL url = new URL(file);
5081             pdbfn = url.getFile();
5082           }
5083           if (pdbfn.length() > 0)
5084           {
5085             // attempt to find a match in the alignment
5086             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5087             int l = 0, c = pdbfn.indexOf(".");
5088             while (mtch == null && c != -1)
5089             {
5090               do
5091               {
5092                 l = c;
5093               } while ((c = pdbfn.indexOf(".", l)) > l);
5094               if (l > -1)
5095               {
5096                 pdbfn = pdbfn.substring(0, l);
5097               }
5098               mtch = idm.findAllIdMatches(pdbfn);
5099             }
5100             if (mtch != null)
5101             {
5102               String type = null;
5103               try
5104               {
5105                 type = new IdentifyFile().Identify(file, protocol);
5106               } catch (Exception ex)
5107               {
5108                 type = null;
5109               }
5110               if (type != null)
5111               {
5112                 if (type.equalsIgnoreCase("PDB"))
5113                 {
5114                   filesmatched.add(new Object[] { file, protocol, mtch });
5115                   continue;
5116                 }
5117               }
5118             }
5119             // File wasn't named like one of the sequences or wasn't a PDB file.
5120             filesnotmatched.add(file);
5121           }
5122         }
5123         int assocfiles = 0;
5124         if (filesmatched.size() > 0)
5125         {
5126           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5127                   || JOptionPane
5128                           .showConfirmDialog(
5129                                   this,
5130                                   MessageManager
5131                                           .formatMessage(
5132                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5133                                                   new Object[] { Integer
5134                                                           .valueOf(
5135                                                                   filesmatched
5136                                                                           .size())
5137                                                           .toString() }),
5138                                   MessageManager
5139                                           .getString("label.automatically_associate_pdb_files_by_name"),
5140                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5141
5142           {
5143             for (Object[] fm : filesmatched)
5144             {
5145               // try and associate
5146               // TODO: may want to set a standard ID naming formalism for
5147               // associating PDB files which have no IDs.
5148               for (SequenceI toassoc : (SequenceI[]) fm[2])
5149               {
5150                 PDBEntry pe = new AssociatePdbFileWithSeq()
5151                         .associatePdbWithSeq((String) fm[0],
5152                                 (String) fm[1], toassoc, false,
5153                                 Desktop.instance);
5154                 if (pe != null)
5155                 {
5156                   System.err.println("Associated file : "
5157                           + ((String) fm[0]) + " with "
5158                           + toassoc.getDisplayId(true));
5159                   assocfiles++;
5160                 }
5161               }
5162               alignPanel.paintAlignment(true);
5163             }
5164           }
5165         }
5166         if (filesnotmatched.size() > 0)
5167         {
5168           if (assocfiles > 0
5169                   && (Cache.getDefault(
5170                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5171                           .showConfirmDialog(
5172                                   this,
5173                                   "<html>"
5174                                           + MessageManager
5175                                                   .formatMessage(
5176                                                           "label.ignore_unmatched_dropped_files_info",
5177                                                           new Object[] { Integer
5178                                                                   .valueOf(
5179                                                                           filesnotmatched
5180                                                                                   .size())
5181                                                                   .toString() })
5182                                           + "</html>",
5183                                   MessageManager
5184                                           .getString("label.ignore_unmatched_dropped_files"),
5185                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5186           {
5187             return;
5188           }
5189           for (String fn : filesnotmatched)
5190           {
5191             loadJalviewDataFile(fn, null, null, null);
5192           }
5193
5194         }
5195       } catch (Exception ex)
5196       {
5197         ex.printStackTrace();
5198       }
5199     }
5200   }
5201
5202   /**
5203    * Attempt to load a "dropped" file or URL string: First by testing whether
5204    * it's and Annotation file, then a JNet file, and finally a features file. If
5205    * all are false then the user may have dropped an alignment file onto this
5206    * AlignFrame.
5207    *
5208    * @param file
5209    *          either a filename or a URL string.
5210    */
5211   public void loadJalviewDataFile(String file, String protocol,
5212           String format, SequenceI assocSeq)
5213   {
5214     try
5215     {
5216       if (protocol == null)
5217       {
5218         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5219       }
5220       // if the file isn't identified, or not positively identified as some
5221       // other filetype (PFAM is default unidentified alignment file type) then
5222       // try to parse as annotation.
5223       boolean isAnnotation = (format == null || format
5224               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5225               .annotateAlignmentView(viewport, file, protocol) : false;
5226
5227       if (!isAnnotation)
5228       {
5229         // first see if its a T-COFFEE score file
5230         TCoffeeScoreFile tcf = null;
5231         try
5232         {
5233           tcf = new TCoffeeScoreFile(file, protocol);
5234           if (tcf.isValid())
5235           {
5236             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5237             {
5238               tcoffeeColour.setEnabled(true);
5239               tcoffeeColour.setSelected(true);
5240               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5241               isAnnotation = true;
5242               statusBar
5243                       .setText(MessageManager
5244                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5245             }
5246             else
5247             {
5248               // some problem - if no warning its probable that the ID matching
5249               // process didn't work
5250               JOptionPane
5251                       .showMessageDialog(
5252                               Desktop.desktop,
5253                               tcf.getWarningMessage() == null ? MessageManager
5254                                       .getString("label.check_file_matches_sequence_ids_alignment")
5255                                       : tcf.getWarningMessage(),
5256                               MessageManager
5257                                       .getString("label.problem_reading_tcoffee_score_file"),
5258                               JOptionPane.WARNING_MESSAGE);
5259             }
5260           }
5261           else
5262           {
5263             tcf = null;
5264           }
5265         } catch (Exception x)
5266         {
5267           Cache.log
5268                   .debug("Exception when processing data source as T-COFFEE score file",
5269                           x);
5270           tcf = null;
5271         }
5272         if (tcf == null)
5273         {
5274           // try to see if its a JNet 'concise' style annotation file *before*
5275           // we
5276           // try to parse it as a features file
5277           if (format == null)
5278           {
5279             format = new IdentifyFile().Identify(file, protocol);
5280           }
5281           if (format.equalsIgnoreCase("JnetFile"))
5282           {
5283             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5284                     file, protocol);
5285             new JnetAnnotationMaker();
5286             JnetAnnotationMaker.add_annotation(predictions,
5287                     viewport.getAlignment(), 0, false);
5288             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5289             viewport.getAlignment().setSeqrep(repseq);
5290             ColumnSelection cs = new ColumnSelection();
5291             cs.hideInsertionsFor(repseq);
5292             viewport.setColumnSelection(cs);
5293             isAnnotation = true;
5294           }
5295           else
5296           {
5297             /*
5298              * if (format.equalsIgnoreCase("PDB")) {
5299              *
5300              * String pdbfn = ""; // try to match up filename with sequence id
5301              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5302              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5303              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5304              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5305              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5306              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5307              * // attempt to find a match in the alignment SequenceI mtch =
5308              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5309              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5310              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5311              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5312              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5313              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5314              * { System.err.println("Associated file : " + file + " with " +
5315              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5316              * TODO: maybe need to load as normal otherwise return; } }
5317              */
5318             // try to parse it as a features file
5319             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5320             // if it wasn't a features file then we just treat it as a general
5321             // alignment file to load into the current view.
5322             if (!isGroupsFile)
5323             {
5324               new FileLoader().LoadFile(viewport, file, protocol, format);
5325             }
5326             else
5327             {
5328               alignPanel.paintAlignment(true);
5329             }
5330           }
5331         }
5332       }
5333       if (isAnnotation)
5334       {
5335
5336         alignPanel.adjustAnnotationHeight();
5337         viewport.updateSequenceIdColours();
5338         buildSortByAnnotationScoresMenu();
5339         alignPanel.paintAlignment(true);
5340       }
5341     } catch (Exception ex)
5342     {
5343       ex.printStackTrace();
5344     } catch (OutOfMemoryError oom)
5345     {
5346       try
5347       {
5348         System.gc();
5349       } catch (Exception x)
5350       {
5351       }
5352       ;
5353       new OOMWarning(
5354               "loading data "
5355                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5356                               : "using " + protocol + " from " + file)
5357                               : ".")
5358                       + (format != null ? "(parsing as '" + format
5359                               + "' file)" : ""), oom, Desktop.desktop);
5360     }
5361   }
5362
5363   /**
5364    * Method invoked by the ChangeListener on the tabbed pane, in other words
5365    * when a different tabbed pane is selected by the user or programmatically.
5366    */
5367   @Override
5368   public void tabSelectionChanged(int index)
5369   {
5370     if (index > -1)
5371     {
5372       alignPanel = alignPanels.get(index);
5373       viewport = alignPanel.av;
5374       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5375       setMenusFromViewport(viewport);
5376     }
5377
5378     /*
5379      * If there is a frame linked to this one in a SplitPane, switch it to the
5380      * same view tab index. No infinite recursion of calls should happen, since
5381      * tabSelectionChanged() should not get invoked on setting the selected
5382      * index to an unchanged value. Guard against setting an invalid index
5383      * before the new view peer tab has been created.
5384      */
5385     final AlignViewportI peer = viewport.getCodingComplement();
5386     if (peer != null)
5387     {
5388       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5389       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5390       {
5391         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5392       }
5393     }
5394   }
5395
5396   /**
5397    * On right mouse click on view tab, prompt for and set new view name.
5398    */
5399   @Override
5400   public void tabbedPane_mousePressed(MouseEvent e)
5401   {
5402     if (SwingUtilities.isRightMouseButton(e))
5403     {
5404       String msg = MessageManager.getString("label.enter_view_name");
5405       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5406               JOptionPane.QUESTION_MESSAGE);
5407
5408       if (reply != null)
5409       {
5410         viewport.viewName = reply;
5411         // TODO warn if reply is in getExistingViewNames()?
5412         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5413       }
5414     }
5415   }
5416
5417   public AlignViewport getCurrentView()
5418   {
5419     return viewport;
5420   }
5421
5422   /**
5423    * Open the dialog for regex description parsing.
5424    */
5425   @Override
5426   protected void extractScores_actionPerformed(ActionEvent e)
5427   {
5428     ParseProperties pp = new jalview.analysis.ParseProperties(
5429             viewport.getAlignment());
5430     // TODO: verify regex and introduce GUI dialog for version 2.5
5431     // if (pp.getScoresFromDescription("col", "score column ",
5432     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5433     // true)>0)
5434     if (pp.getScoresFromDescription("description column",
5435             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5436     {
5437       buildSortByAnnotationScoresMenu();
5438     }
5439   }
5440
5441   /*
5442    * (non-Javadoc)
5443    *
5444    * @see
5445    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5446    * )
5447    */
5448   @Override
5449   protected void showDbRefs_actionPerformed(ActionEvent e)
5450   {
5451     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5452   }
5453
5454   /*
5455    * (non-Javadoc)
5456    *
5457    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5458    * ActionEvent)
5459    */
5460   @Override
5461   protected void showNpFeats_actionPerformed(ActionEvent e)
5462   {
5463     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5464   }
5465
5466   /**
5467    * find the viewport amongst the tabs in this alignment frame and close that
5468    * tab
5469    *
5470    * @param av
5471    */
5472   public boolean closeView(AlignViewportI av)
5473   {
5474     if (viewport == av)
5475     {
5476       this.closeMenuItem_actionPerformed(false);
5477       return true;
5478     }
5479     Component[] comp = tabbedPane.getComponents();
5480     for (int i = 0; comp != null && i < comp.length; i++)
5481     {
5482       if (comp[i] instanceof AlignmentPanel)
5483       {
5484         if (((AlignmentPanel) comp[i]).av == av)
5485         {
5486           // close the view.
5487           closeView((AlignmentPanel) comp[i]);
5488           return true;
5489         }
5490       }
5491     }
5492     return false;
5493   }
5494
5495   protected void build_fetchdbmenu(JMenu webService)
5496   {
5497     // Temporary hack - DBRef Fetcher always top level ws entry.
5498     // TODO We probably want to store a sequence database checklist in
5499     // preferences and have checkboxes.. rather than individual sources selected
5500     // here
5501     final JMenu rfetch = new JMenu(
5502             MessageManager.getString("action.fetch_db_references"));
5503     rfetch.setToolTipText(MessageManager
5504             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5505     webService.add(rfetch);
5506
5507     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5508             MessageManager.getString("option.trim_retrieved_seqs"));
5509     trimrs.setToolTipText(MessageManager
5510             .getString("label.trim_retrieved_sequences"));
5511     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5512     trimrs.addActionListener(new ActionListener()
5513     {
5514       @Override
5515       public void actionPerformed(ActionEvent e)
5516       {
5517         trimrs.setSelected(trimrs.isSelected());
5518         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5519                 Boolean.valueOf(trimrs.isSelected()).toString());
5520       };
5521     });
5522     rfetch.add(trimrs);
5523     JMenuItem fetchr = new JMenuItem(
5524             MessageManager.getString("label.standard_databases"));
5525     fetchr.setToolTipText(MessageManager
5526             .getString("label.fetch_embl_uniprot"));
5527     fetchr.addActionListener(new ActionListener()
5528     {
5529
5530       @Override
5531       public void actionPerformed(ActionEvent e)
5532       {
5533         new Thread(new Runnable()
5534         {
5535
5536           @Override
5537           public void run()
5538           {
5539             boolean isNuclueotide = alignPanel.alignFrame
5540                     .getViewport().getAlignment()
5541                     .isNucleotide();
5542             new jalview.ws.DBRefFetcher(alignPanel.av
5543                     .getSequenceSelection(),
5544                     alignPanel.alignFrame, null,
5545                     alignPanel.alignFrame.featureSettings,
5546                     isNuclueotide)
5547                     .fetchDBRefs(false);
5548           }
5549         }).start();
5550
5551       }
5552
5553     });
5554     rfetch.add(fetchr);
5555     final AlignFrame me = this;
5556     new Thread(new Runnable()
5557     {
5558       @Override
5559       public void run()
5560       {
5561         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5562                 .getSequenceFetcherSingleton(me);
5563         javax.swing.SwingUtilities.invokeLater(new Runnable()
5564         {
5565           @Override
5566           public void run()
5567           {
5568             String[] dbclasses = sf.getOrderedSupportedSources();
5569             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5570             // jalview.util.QuickSort.sort(otherdb, otherdb);
5571             List<DbSourceProxy> otherdb;
5572             JMenu dfetch = new JMenu();
5573             JMenu ifetch = new JMenu();
5574             JMenuItem fetchr = null;
5575             int comp = 0, icomp = 0, mcomp = 15;
5576             String mname = null;
5577             int dbi = 0;
5578             for (String dbclass : dbclasses)
5579             {
5580               otherdb = sf.getSourceProxy(dbclass);
5581               // add a single entry for this class, or submenu allowing 'fetch
5582               // all' or pick one
5583               if (otherdb == null || otherdb.size() < 1)
5584               {
5585                 continue;
5586               }
5587               // List<DbSourceProxy> dbs=otherdb;
5588               // otherdb=new ArrayList<DbSourceProxy>();
5589               // for (DbSourceProxy db:dbs)
5590               // {
5591               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5592               // }
5593               if (mname == null)
5594               {
5595                 mname = "From " + dbclass;
5596               }
5597               if (otherdb.size() == 1)
5598               {
5599                 final DbSourceProxy[] dassource = otherdb
5600                         .toArray(new DbSourceProxy[0]);
5601                 DbSourceProxy src = otherdb.get(0);
5602                 fetchr = new JMenuItem(src.getDbSource());
5603                 fetchr.addActionListener(new ActionListener()
5604                 {
5605
5606                   @Override
5607                   public void actionPerformed(ActionEvent e)
5608                   {
5609                     new Thread(new Runnable()
5610                     {
5611
5612                       @Override
5613                       public void run()
5614                       {
5615                         boolean isNuclueotide = alignPanel.alignFrame
5616                                 .getViewport().getAlignment()
5617                                 .isNucleotide();
5618                         new jalview.ws.DBRefFetcher(alignPanel.av
5619                                 .getSequenceSelection(),
5620                                 alignPanel.alignFrame, dassource,
5621                                 alignPanel.alignFrame.featureSettings,
5622                                 isNuclueotide)
5623                                 .fetchDBRefs(false);
5624                       }
5625                     }).start();
5626                   }
5627
5628                 });
5629                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5630                         MessageManager.formatMessage(
5631                                 "label.fetch_retrieve_from",
5632                                 new Object[] { src.getDbName() })));
5633                 dfetch.add(fetchr);
5634                 comp++;
5635               }
5636               else
5637               {
5638                 final DbSourceProxy[] dassource = otherdb
5639                         .toArray(new DbSourceProxy[0]);
5640                 // fetch all entry
5641                 DbSourceProxy src = otherdb.get(0);
5642                 fetchr = new JMenuItem(MessageManager.formatMessage(
5643                         "label.fetch_all_param",
5644                         new Object[] { src.getDbSource() }));
5645                 fetchr.addActionListener(new ActionListener()
5646                 {
5647                   @Override
5648                   public void actionPerformed(ActionEvent e)
5649                   {
5650                     new Thread(new Runnable()
5651                     {
5652
5653                       @Override
5654                       public void run()
5655                       {
5656                         boolean isNuclueotide = alignPanel.alignFrame
5657                                 .getViewport().getAlignment()
5658                                 .isNucleotide();
5659                         new jalview.ws.DBRefFetcher(alignPanel.av
5660                                 .getSequenceSelection(),
5661                                 alignPanel.alignFrame, dassource,
5662                                 alignPanel.alignFrame.featureSettings,
5663                                 isNuclueotide)
5664                                 .fetchDBRefs(false);
5665                       }
5666                     }).start();
5667                   }
5668                 });
5669
5670                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5671                         MessageManager.formatMessage(
5672                                 "label.fetch_retrieve_from_all_sources",
5673                                 new Object[] {
5674                                     Integer.valueOf(otherdb.size())
5675                                             .toString(), src.getDbSource(),
5676                                     src.getDbName() })));
5677                 dfetch.add(fetchr);
5678                 comp++;
5679                 // and then build the rest of the individual menus
5680                 ifetch = new JMenu(MessageManager.formatMessage(
5681                         "label.source_from_db_source",
5682                         new Object[] { src.getDbSource() }));
5683                 icomp = 0;
5684                 String imname = null;
5685                 int i = 0;
5686                 for (DbSourceProxy sproxy : otherdb)
5687                 {
5688                   String dbname = sproxy.getDbName();
5689                   String sname = dbname.length() > 5 ? dbname.substring(0,
5690                           5) + "..." : dbname;
5691                   String msname = dbname.length() > 10 ? dbname.substring(
5692                           0, 10) + "..." : dbname;
5693                   if (imname == null)
5694                   {
5695                     imname = MessageManager.formatMessage(
5696                             "label.from_msname", new Object[] { sname });
5697                   }
5698                   fetchr = new JMenuItem(msname);
5699                   final DbSourceProxy[] dassrc = { sproxy };
5700                   fetchr.addActionListener(new ActionListener()
5701                   {
5702
5703                     @Override
5704                     public void actionPerformed(ActionEvent e)
5705                     {
5706                       new Thread(new Runnable()
5707                       {
5708
5709                         @Override
5710                         public void run()
5711                         {
5712                           boolean isNuclueotide = alignPanel.alignFrame
5713                                   .getViewport().getAlignment()
5714                                   .isNucleotide();
5715                           new jalview.ws.DBRefFetcher(alignPanel.av
5716                                   .getSequenceSelection(),
5717                                   alignPanel.alignFrame, dassrc,
5718                                   alignPanel.alignFrame.featureSettings,
5719                                   isNuclueotide)
5720                                   .fetchDBRefs(false);
5721                         }
5722                       }).start();
5723                     }
5724
5725                   });
5726                   fetchr.setToolTipText("<html>"
5727                           + MessageManager.formatMessage(
5728                                   "label.fetch_retrieve_from", new Object[]
5729                                   { dbname }));
5730                   ifetch.add(fetchr);
5731                   ++i;
5732                   if (++icomp >= mcomp || i == (otherdb.size()))
5733                   {
5734                     ifetch.setText(MessageManager.formatMessage(
5735                             "label.source_to_target", imname, sname));
5736                     dfetch.add(ifetch);
5737                     ifetch = new JMenu();
5738                     imname = null;
5739                     icomp = 0;
5740                     comp++;
5741                   }
5742                 }
5743               }
5744               ++dbi;
5745               if (comp >= mcomp || dbi >= (dbclasses.length))
5746               {
5747                 dfetch.setText(MessageManager.formatMessage(
5748                         "label.source_to_target", mname, dbclass));
5749                 rfetch.add(dfetch);
5750                 dfetch = new JMenu();
5751                 mname = null;
5752                 comp = 0;
5753               }
5754             }
5755           }
5756         });
5757       }
5758     }).start();
5759
5760   }
5761
5762   /**
5763    * Left justify the whole alignment.
5764    */
5765   @Override
5766   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5767   {
5768     AlignmentI al = viewport.getAlignment();
5769     al.justify(false);
5770     viewport.firePropertyChange("alignment", null, al);
5771   }
5772
5773   /**
5774    * Right justify the whole alignment.
5775    */
5776   @Override
5777   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5778   {
5779     AlignmentI al = viewport.getAlignment();
5780     al.justify(true);
5781     viewport.firePropertyChange("alignment", null, al);
5782   }
5783
5784   @Override
5785   public void setShowSeqFeatures(boolean b)
5786   {
5787     showSeqFeatures.setSelected(b);
5788     viewport.setShowSequenceFeatures(b);
5789   }
5790
5791   /*
5792    * (non-Javadoc)
5793    *
5794    * @see
5795    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5796    * awt.event.ActionEvent)
5797    */
5798   @Override
5799   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5800   {
5801     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5802     alignPanel.paintAlignment(true);
5803   }
5804
5805   /*
5806    * (non-Javadoc)
5807    *
5808    * @see
5809    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5810    * .ActionEvent)
5811    */
5812   @Override
5813   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5814   {
5815     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5816     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5817
5818   }
5819
5820   /*
5821    * (non-Javadoc)
5822    *
5823    * @see
5824    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5825    * .event.ActionEvent)
5826    */
5827   @Override
5828   protected void showGroupConservation_actionPerformed(ActionEvent e)
5829   {
5830     viewport.setShowGroupConservation(showGroupConservation.getState());
5831     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5832   }
5833
5834   /*
5835    * (non-Javadoc)
5836    *
5837    * @see
5838    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5839    * .event.ActionEvent)
5840    */
5841   @Override
5842   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5843   {
5844     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5845     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5846   }
5847
5848   /*
5849    * (non-Javadoc)
5850    *
5851    * @see
5852    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5853    * .event.ActionEvent)
5854    */
5855   @Override
5856   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5857   {
5858     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5859     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5860   }
5861
5862   @Override
5863   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5864   {
5865     showSequenceLogo.setState(true);
5866     viewport.setShowSequenceLogo(true);
5867     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5868     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5869   }
5870
5871   @Override
5872   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5873   {
5874     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5875   }
5876
5877   /*
5878    * (non-Javadoc)
5879    *
5880    * @see
5881    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5882    * .event.ActionEvent)
5883    */
5884   @Override
5885   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5886   {
5887     if (avc.makeGroupsFromSelection())
5888     {
5889       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5890       alignPanel.updateAnnotation();
5891       alignPanel.paintAlignment(true);
5892     }
5893   }
5894
5895   public void clearAlignmentSeqRep()
5896   {
5897     // TODO refactor alignmentseqrep to controller
5898     if (viewport.getAlignment().hasSeqrep())
5899     {
5900       viewport.getAlignment().setSeqrep(null);
5901       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5902       alignPanel.updateAnnotation();
5903       alignPanel.paintAlignment(true);
5904     }
5905   }
5906
5907   @Override
5908   protected void createGroup_actionPerformed(ActionEvent e)
5909   {
5910     if (avc.createGroup())
5911     {
5912       alignPanel.alignmentChanged();
5913     }
5914   }
5915
5916   @Override
5917   protected void unGroup_actionPerformed(ActionEvent e)
5918   {
5919     if (avc.unGroup())
5920     {
5921       alignPanel.alignmentChanged();
5922     }
5923   }
5924
5925   /**
5926    * make the given alignmentPanel the currently selected tab
5927    *
5928    * @param alignmentPanel
5929    */
5930   public void setDisplayedView(AlignmentPanel alignmentPanel)
5931   {
5932     if (!viewport.getSequenceSetId().equals(
5933             alignmentPanel.av.getSequenceSetId()))
5934     {
5935       throw new Error(
5936               MessageManager
5937                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5938     }
5939     if (tabbedPane != null
5940             && tabbedPane.getTabCount() > 0
5941             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5942                     .getSelectedIndex())
5943     {
5944       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5945     }
5946   }
5947
5948   /**
5949    * Action on selection of menu options to Show or Hide annotations.
5950    *
5951    * @param visible
5952    * @param forSequences
5953    *          update sequence-related annotations
5954    * @param forAlignment
5955    *          update non-sequence-related annotations
5956    */
5957   @Override
5958   protected void setAnnotationsVisibility(boolean visible,
5959           boolean forSequences, boolean forAlignment)
5960   {
5961     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5962             .getAlignmentAnnotation())
5963     {
5964       /*
5965        * don't display non-positional annotations on an alignment
5966        */
5967       if (aa.annotations == null)
5968       {
5969         continue;
5970       }
5971       boolean apply = (aa.sequenceRef == null && forAlignment)
5972               || (aa.sequenceRef != null && forSequences);
5973       if (apply)
5974       {
5975         aa.visible = visible;
5976       }
5977     }
5978     alignPanel.validateAnnotationDimensions(true);
5979     alignPanel.alignmentChanged();
5980   }
5981
5982   /**
5983    * Store selected annotation sort order for the view and repaint.
5984    */
5985   @Override
5986   protected void sortAnnotations_actionPerformed()
5987   {
5988     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5989     this.alignPanel.av
5990             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5991     alignPanel.paintAlignment(true);
5992   }
5993
5994   /**
5995    *
5996    * @return alignment panels in this alignment frame
5997    */
5998   public List<? extends AlignmentViewPanel> getAlignPanels()
5999   {
6000     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6001   }
6002
6003   /**
6004    * Open a new alignment window, with the cDNA associated with this (protein)
6005    * alignment, aligned as is the protein.
6006    */
6007   protected void viewAsCdna_actionPerformed()
6008   {
6009     // TODO no longer a menu action - refactor as required
6010     final AlignmentI alignment = getViewport().getAlignment();
6011     Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6012     if (mappings == null)
6013     {
6014       return;
6015     }
6016     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6017     for (SequenceI aaSeq : alignment.getSequences())
6018     {
6019       for (AlignedCodonFrame acf : mappings)
6020       {
6021         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6022         if (dnaSeq != null)
6023         {
6024           /*
6025            * There is a cDNA mapping for this protein sequence - add to new
6026            * alignment. It will share the same dataset sequence as other mapped
6027            * cDNA (no new mappings need to be created).
6028            */
6029           final Sequence newSeq = new Sequence(dnaSeq);
6030           newSeq.setDatasetSequence(dnaSeq);
6031           cdnaSeqs.add(newSeq);
6032         }
6033       }
6034     }
6035     if (cdnaSeqs.size() == 0)
6036     {
6037       // show a warning dialog no mapped cDNA
6038       return;
6039     }
6040     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6041             .size()]));
6042     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6043             AlignFrame.DEFAULT_HEIGHT);
6044     cdna.alignAs(alignment);
6045     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6046             + this.title;
6047     Desktop.addInternalFrame(alignFrame, newtitle,
6048             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6049   }
6050
6051   /**
6052    * Set visibility of dna/protein complement view (available when shown in a
6053    * split frame).
6054    *
6055    * @param show
6056    */
6057   @Override
6058   protected void showComplement_actionPerformed(boolean show)
6059   {
6060     SplitContainerI sf = getSplitViewContainer();
6061     if (sf != null)
6062     {
6063       sf.setComplementVisible(this, show);
6064     }
6065   }
6066 }
6067
6068 class PrintThread extends Thread
6069 {
6070   AlignmentPanel ap;
6071
6072   public PrintThread(AlignmentPanel ap)
6073   {
6074     this.ap = ap;
6075   }
6076
6077   static PageFormat pf;
6078
6079   @Override
6080   public void run()
6081   {
6082     PrinterJob printJob = PrinterJob.getPrinterJob();
6083
6084     if (pf != null)
6085     {
6086       printJob.setPrintable(ap, pf);
6087     }
6088     else
6089     {
6090       printJob.setPrintable(ap);
6091     }
6092
6093     if (printJob.printDialog())
6094     {
6095       try
6096       {
6097         printJob.print();
6098       } catch (Exception PrintException)
6099       {
6100         PrintException.printStackTrace();
6101       }
6102     }
6103   }
6104 }