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