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[2];
1313     int[] higestRange = new int[2];
1314
1315     for (int[] hiddenCol : hiddenCols)
1316     {
1317       // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
1318       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1319       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1320     }
1321     // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
1322     // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
1323
1324     if (lowestRange[0] == 0 && lowestRange[1] == 0)
1325     {
1326       startPos = aligmentStartEnd[0];
1327     }
1328     else
1329     {
1330       startPos = lowestRange[1] + 1;
1331     }
1332
1333     if (higestRange[0] == 0 && higestRange[1] == 0)
1334     {
1335       endPos = aligmentStartEnd[1];
1336     }
1337     else
1338     {
1339       endPos = higestRange[0];
1340     }
1341
1342     // System.out.println("Export range : " + minPos + " - " + maxPos);
1343     return new int[] { startPos, endPos };
1344   }
1345
1346   public static void main(String[] args)
1347   {
1348     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1349     hiddenCols.add(new int[] { 0, 4 });
1350     hiddenCols.add(new int[] { 6, 9 });
1351     hiddenCols.add(new int[] { 11, 12 });
1352     hiddenCols.add(new int[] { 33, 33 });
1353     hiddenCols.add(new int[] { 45, 50 });
1354
1355     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1356     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param e
1363    *          DOCUMENT ME!
1364    */
1365   @Override
1366   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1367   {
1368     new HtmlSvgOutput(null, alignPanel);
1369   }
1370
1371   @Override
1372   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1373   {
1374     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1375     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1376   }
1377
1378   public void createImageMap(File file, String image)
1379   {
1380     alignPanel.makePNGImageMap(file, image);
1381   }
1382
1383   /**
1384    * DOCUMENT ME!
1385    *
1386    * @param e
1387    *          DOCUMENT ME!
1388    */
1389   @Override
1390   public void createPNG(File f)
1391   {
1392     alignPanel.makePNG(f);
1393   }
1394
1395   /**
1396    * DOCUMENT ME!
1397    *
1398    * @param e
1399    *          DOCUMENT ME!
1400    */
1401   @Override
1402   public void createEPS(File f)
1403   {
1404     alignPanel.makeEPS(f);
1405   }
1406
1407   public void createSVG(File f)
1408   {
1409     alignPanel.makeSVG(f);
1410   }
1411
1412   @Override
1413   public void pageSetup_actionPerformed(ActionEvent e)
1414   {
1415     PrinterJob printJob = PrinterJob.getPrinterJob();
1416     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1417   }
1418
1419   /**
1420    * DOCUMENT ME!
1421    *
1422    * @param e
1423    *          DOCUMENT ME!
1424    */
1425   @Override
1426   public void printMenuItem_actionPerformed(ActionEvent e)
1427   {
1428     // Putting in a thread avoids Swing painting problems
1429     PrintThread thread = new PrintThread(alignPanel);
1430     thread.start();
1431   }
1432
1433   @Override
1434   public void exportFeatures_actionPerformed(ActionEvent e)
1435   {
1436     new AnnotationExporter().exportFeatures(alignPanel);
1437   }
1438
1439   @Override
1440   public void exportAnnotations_actionPerformed(ActionEvent e)
1441   {
1442     new AnnotationExporter().exportAnnotations(alignPanel);
1443   }
1444
1445   @Override
1446   public void associatedData_actionPerformed(ActionEvent e)
1447   {
1448     // Pick the tree file
1449     JalviewFileChooser chooser = new JalviewFileChooser(
1450             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1451     chooser.setFileView(new JalviewFileView());
1452     chooser.setDialogTitle(MessageManager
1453             .getString("label.load_jalview_annotations"));
1454     chooser.setToolTipText(MessageManager
1455             .getString("label.load_jalview_annotations"));
1456
1457     int value = chooser.showOpenDialog(null);
1458
1459     if (value == JalviewFileChooser.APPROVE_OPTION)
1460     {
1461       String choice = chooser.getSelectedFile().getPath();
1462       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1463       loadJalviewDataFile(choice, null, null, null);
1464     }
1465
1466   }
1467
1468   /**
1469    * Close the current view or all views in the alignment frame. If the frame
1470    * only contains one view then the alignment will be removed from memory.
1471    *
1472    * @param closeAllTabs
1473    */
1474   @Override
1475   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1476   {
1477     if (alignPanels != null && alignPanels.size() < 2)
1478     {
1479       closeAllTabs = true;
1480     }
1481
1482     try
1483     {
1484       if (alignPanels != null)
1485       {
1486         if (closeAllTabs)
1487         {
1488           if (this.isClosed())
1489           {
1490             // really close all the windows - otherwise wait till
1491             // setClosed(true) is called
1492             for (int i = 0; i < alignPanels.size(); i++)
1493             {
1494               AlignmentPanel ap = alignPanels.get(i);
1495               ap.closePanel();
1496             }
1497           }
1498         }
1499         else
1500         {
1501           closeView(alignPanel);
1502         }
1503       }
1504
1505       if (closeAllTabs)
1506       {
1507         /*
1508          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1509          * be called recursively, with the frame now in 'closed' state
1510          */
1511         this.setClosed(true);
1512       }
1513     } catch (Exception ex)
1514     {
1515       ex.printStackTrace();
1516     }
1517   }
1518
1519   /**
1520    * Close the specified panel and close up tabs appropriately.
1521    *
1522    * @param panelToClose
1523    */
1524   public void closeView(AlignmentPanel panelToClose)
1525   {
1526     int index = tabbedPane.getSelectedIndex();
1527     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1528     alignPanels.remove(panelToClose);
1529     panelToClose.closePanel();
1530     panelToClose = null;
1531
1532     tabbedPane.removeTabAt(closedindex);
1533     tabbedPane.validate();
1534
1535     if (index > closedindex || index == tabbedPane.getTabCount())
1536     {
1537       // modify currently selected tab index if necessary.
1538       index--;
1539     }
1540
1541     this.tabSelectionChanged(index);
1542   }
1543
1544   /**
1545    * DOCUMENT ME!
1546    */
1547   void updateEditMenuBar()
1548   {
1549
1550     if (viewport.getHistoryList().size() > 0)
1551     {
1552       undoMenuItem.setEnabled(true);
1553       CommandI command = viewport.getHistoryList().peek();
1554       undoMenuItem.setText(MessageManager.formatMessage(
1555               "label.undo_command",
1556               new Object[] { command.getDescription() }));
1557     }
1558     else
1559     {
1560       undoMenuItem.setEnabled(false);
1561       undoMenuItem.setText(MessageManager.getString("action.undo"));
1562     }
1563
1564     if (viewport.getRedoList().size() > 0)
1565     {
1566       redoMenuItem.setEnabled(true);
1567
1568       CommandI command = viewport.getRedoList().peek();
1569       redoMenuItem.setText(MessageManager.formatMessage(
1570               "label.redo_command",
1571               new Object[] { command.getDescription() }));
1572     }
1573     else
1574     {
1575       redoMenuItem.setEnabled(false);
1576       redoMenuItem.setText(MessageManager.getString("action.redo"));
1577     }
1578   }
1579
1580   public void addHistoryItem(CommandI command)
1581   {
1582     if (command.getSize() > 0)
1583     {
1584       viewport.addToHistoryList(command);
1585       viewport.clearRedoList();
1586       updateEditMenuBar();
1587       viewport.updateHiddenColumns();
1588       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1589       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1590       // viewport.getColumnSelection()
1591       // .getHiddenColumns().size() > 0);
1592     }
1593   }
1594
1595   /**
1596    *
1597    * @return alignment objects for all views
1598    */
1599   AlignmentI[] getViewAlignments()
1600   {
1601     if (alignPanels != null)
1602     {
1603       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1604       int i = 0;
1605       for (AlignmentPanel ap : alignPanels)
1606       {
1607         als[i++] = ap.av.getAlignment();
1608       }
1609       return als;
1610     }
1611     if (viewport != null)
1612     {
1613       return new AlignmentI[] { viewport.getAlignment() };
1614     }
1615     return null;
1616   }
1617
1618   /**
1619    * DOCUMENT ME!
1620    *
1621    * @param e
1622    *          DOCUMENT ME!
1623    */
1624   @Override
1625   protected void undoMenuItem_actionPerformed(ActionEvent e)
1626   {
1627     if (viewport.getHistoryList().isEmpty())
1628     {
1629       return;
1630     }
1631     CommandI command = viewport.getHistoryList().pop();
1632     viewport.addToRedoList(command);
1633     command.undoCommand(getViewAlignments());
1634
1635     AlignmentViewport originalSource = getOriginatingSource(command);
1636     updateEditMenuBar();
1637
1638     if (originalSource != null)
1639     {
1640       if (originalSource != viewport)
1641       {
1642         Cache.log
1643                 .warn("Implementation worry: mismatch of viewport origin for undo");
1644       }
1645       originalSource.updateHiddenColumns();
1646       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1647       // null
1648       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649       // viewport.getColumnSelection()
1650       // .getHiddenColumns().size() > 0);
1651       originalSource.firePropertyChange("alignment", null, originalSource
1652               .getAlignment().getSequences());
1653     }
1654   }
1655
1656   /**
1657    * DOCUMENT ME!
1658    *
1659    * @param e
1660    *          DOCUMENT ME!
1661    */
1662   @Override
1663   protected void redoMenuItem_actionPerformed(ActionEvent e)
1664   {
1665     if (viewport.getRedoList().size() < 1)
1666     {
1667       return;
1668     }
1669
1670     CommandI command = viewport.getRedoList().pop();
1671     viewport.addToHistoryList(command);
1672     command.doCommand(getViewAlignments());
1673
1674     AlignmentViewport originalSource = getOriginatingSource(command);
1675     updateEditMenuBar();
1676
1677     if (originalSource != null)
1678     {
1679
1680       if (originalSource != viewport)
1681       {
1682         Cache.log
1683                 .warn("Implementation worry: mismatch of viewport origin for redo");
1684       }
1685       originalSource.updateHiddenColumns();
1686       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1687       // null
1688       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1689       // viewport.getColumnSelection()
1690       // .getHiddenColumns().size() > 0);
1691       originalSource.firePropertyChange("alignment", null, originalSource
1692               .getAlignment().getSequences());
1693     }
1694   }
1695
1696   AlignmentViewport getOriginatingSource(CommandI command)
1697   {
1698     AlignmentViewport originalSource = null;
1699     // For sequence removal and addition, we need to fire
1700     // the property change event FROM the viewport where the
1701     // original alignment was altered
1702     AlignmentI al = null;
1703     if (command instanceof EditCommand)
1704     {
1705       EditCommand editCommand = (EditCommand) command;
1706       al = editCommand.getAlignment();
1707       List<Component> comps = PaintRefresher.components.get(viewport
1708               .getSequenceSetId());
1709
1710       for (Component comp : comps)
1711       {
1712         if (comp instanceof AlignmentPanel)
1713         {
1714           if (al == ((AlignmentPanel) comp).av.getAlignment())
1715           {
1716             originalSource = ((AlignmentPanel) comp).av;
1717             break;
1718           }
1719         }
1720       }
1721     }
1722
1723     if (originalSource == null)
1724     {
1725       // The original view is closed, we must validate
1726       // the current view against the closed view first
1727       if (al != null)
1728       {
1729         PaintRefresher.validateSequences(al, viewport.getAlignment());
1730       }
1731
1732       originalSource = viewport;
1733     }
1734
1735     return originalSource;
1736   }
1737
1738   /**
1739    * DOCUMENT ME!
1740    *
1741    * @param up
1742    *          DOCUMENT ME!
1743    */
1744   public void moveSelectedSequences(boolean up)
1745   {
1746     SequenceGroup sg = viewport.getSelectionGroup();
1747
1748     if (sg == null)
1749     {
1750       return;
1751     }
1752     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753             viewport.getHiddenRepSequences(), up);
1754     alignPanel.paintAlignment(true);
1755   }
1756
1757   synchronized void slideSequences(boolean right, int size)
1758   {
1759     List<SequenceI> sg = new ArrayList<SequenceI>();
1760     if (viewport.cursorMode)
1761     {
1762       sg.add(viewport.getAlignment().getSequenceAt(
1763               alignPanel.getSeqPanel().seqCanvas.cursorY));
1764     }
1765     else if (viewport.getSelectionGroup() != null
1766             && viewport.getSelectionGroup().getSize() != viewport
1767                     .getAlignment().getHeight())
1768     {
1769       sg = viewport.getSelectionGroup().getSequences(
1770               viewport.getHiddenRepSequences());
1771     }
1772
1773     if (sg.size() < 1)
1774     {
1775       return;
1776     }
1777
1778     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1779
1780     for (SequenceI seq : viewport.getAlignment().getSequences())
1781     {
1782       if (!sg.contains(seq))
1783       {
1784         invertGroup.add(seq);
1785       }
1786     }
1787
1788     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1789
1790     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1791     for (int i = 0; i < invertGroup.size(); i++)
1792     {
1793       seqs2[i] = invertGroup.get(i);
1794     }
1795
1796     SlideSequencesCommand ssc;
1797     if (right)
1798     {
1799       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1800               size, viewport.getGapCharacter());
1801     }
1802     else
1803     {
1804       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1805               size, viewport.getGapCharacter());
1806     }
1807
1808     int groupAdjustment = 0;
1809     if (ssc.getGapsInsertedBegin() && right)
1810     {
1811       if (viewport.cursorMode)
1812       {
1813         alignPanel.getSeqPanel().moveCursor(size, 0);
1814       }
1815       else
1816       {
1817         groupAdjustment = size;
1818       }
1819     }
1820     else if (!ssc.getGapsInsertedBegin() && !right)
1821     {
1822       if (viewport.cursorMode)
1823       {
1824         alignPanel.getSeqPanel().moveCursor(-size, 0);
1825       }
1826       else
1827       {
1828         groupAdjustment = -size;
1829       }
1830     }
1831
1832     if (groupAdjustment != 0)
1833     {
1834       viewport.getSelectionGroup().setStartRes(
1835               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1836       viewport.getSelectionGroup().setEndRes(
1837               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1838     }
1839
1840     /*
1841      * just extend the last slide command if compatible; but not if in
1842      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1843      */
1844     boolean appendHistoryItem = false;
1845     Deque<CommandI> historyList = viewport.getHistoryList();
1846     boolean inSplitFrame = getSplitViewContainer() != null;
1847     if (!inSplitFrame && historyList != null && historyList.size() > 0
1848             && historyList.peek() instanceof SlideSequencesCommand)
1849     {
1850       appendHistoryItem = ssc
1851               .appendSlideCommand((SlideSequencesCommand) historyList
1852                       .peek());
1853     }
1854
1855     if (!appendHistoryItem)
1856     {
1857       addHistoryItem(ssc);
1858     }
1859
1860     repaint();
1861   }
1862
1863   /**
1864    * DOCUMENT ME!
1865    *
1866    * @param e
1867    *          DOCUMENT ME!
1868    */
1869   @Override
1870   protected void copy_actionPerformed(ActionEvent e)
1871   {
1872     System.gc();
1873     if (viewport.getSelectionGroup() == null)
1874     {
1875       return;
1876     }
1877     // TODO: preserve the ordering of displayed alignment annotation in any
1878     // internal paste (particularly sequence associated annotation)
1879     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1880     String[] omitHidden = null;
1881
1882     if (viewport.hasHiddenColumns())
1883     {
1884       omitHidden = viewport.getViewAsString(true);
1885     }
1886
1887     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1888             omitHidden, null);
1889
1890     StringSelection ss = new StringSelection(output);
1891
1892     try
1893     {
1894       jalview.gui.Desktop.internalCopy = true;
1895       // Its really worth setting the clipboard contents
1896       // to empty before setting the large StringSelection!!
1897       Toolkit.getDefaultToolkit().getSystemClipboard()
1898               .setContents(new StringSelection(""), null);
1899
1900       Toolkit.getDefaultToolkit().getSystemClipboard()
1901               .setContents(ss, Desktop.instance);
1902     } catch (OutOfMemoryError er)
1903     {
1904       new OOMWarning("copying region", er);
1905       return;
1906     }
1907
1908     ArrayList<int[]> hiddenColumns = null;
1909     if (viewport.hasHiddenColumns())
1910     {
1911       hiddenColumns = new ArrayList<int[]>();
1912       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1913               .getSelectionGroup().getEndRes();
1914       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1915       {
1916         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1917         {
1918           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1919               region[1] - hiddenOffset });
1920         }
1921       }
1922     }
1923
1924     Desktop.jalviewClipboard = new Object[] { seqs,
1925         viewport.getAlignment().getDataset(), hiddenColumns };
1926     statusBar.setText(MessageManager.formatMessage(
1927             "label.copied_sequences_to_clipboard", new Object[] { Integer
1928                     .valueOf(seqs.length).toString() }));
1929   }
1930
1931   /**
1932    * DOCUMENT ME!
1933    *
1934    * @param e
1935    *          DOCUMENT ME!
1936    */
1937   @Override
1938   protected void pasteNew_actionPerformed(ActionEvent e)
1939   {
1940     paste(true);
1941   }
1942
1943   /**
1944    * DOCUMENT ME!
1945    *
1946    * @param e
1947    *          DOCUMENT ME!
1948    */
1949   @Override
1950   protected void pasteThis_actionPerformed(ActionEvent e)
1951   {
1952     paste(false);
1953   }
1954
1955   /**
1956    * Paste contents of Jalview clipboard
1957    *
1958    * @param newAlignment
1959    *          true to paste to a new alignment, otherwise add to this.
1960    */
1961   void paste(boolean newAlignment)
1962   {
1963     boolean externalPaste = true;
1964     try
1965     {
1966       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1967       Transferable contents = c.getContents(this);
1968
1969       if (contents == null)
1970       {
1971         return;
1972       }
1973
1974       String str, format;
1975       try
1976       {
1977         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1978         if (str.length() < 1)
1979         {
1980           return;
1981         }
1982
1983         format = new IdentifyFile().Identify(str, "Paste");
1984
1985       } catch (OutOfMemoryError er)
1986       {
1987         new OOMWarning("Out of memory pasting sequences!!", er);
1988         return;
1989       }
1990
1991       SequenceI[] sequences;
1992       boolean annotationAdded = false;
1993       AlignmentI alignment = null;
1994
1995       if (Desktop.jalviewClipboard != null)
1996       {
1997         // The clipboard was filled from within Jalview, we must use the
1998         // sequences
1999         // And dataset from the copied alignment
2000         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2001         // be doubly sure that we create *new* sequence objects.
2002         sequences = new SequenceI[newseq.length];
2003         for (int i = 0; i < newseq.length; i++)
2004         {
2005           sequences[i] = new Sequence(newseq[i]);
2006         }
2007         alignment = new Alignment(sequences);
2008         externalPaste = false;
2009       }
2010       else
2011       {
2012         // parse the clipboard as an alignment.
2013         alignment = new FormatAdapter().readFile(str, "Paste", format);
2014         sequences = alignment.getSequencesArray();
2015       }
2016
2017       int alwidth = 0;
2018       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2019       int fgroup = -1;
2020
2021       if (newAlignment)
2022       {
2023
2024         if (Desktop.jalviewClipboard != null)
2025         {
2026           // dataset is inherited
2027           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2028         }
2029         else
2030         {
2031           // new dataset is constructed
2032           alignment.setDataset(null);
2033         }
2034         alwidth = alignment.getWidth() + 1;
2035       }
2036       else
2037       {
2038         AlignmentI pastedal = alignment; // preserve pasted alignment object
2039         // Add pasted sequences and dataset into existing alignment.
2040         alignment = viewport.getAlignment();
2041         alwidth = alignment.getWidth() + 1;
2042         // decide if we need to import sequences from an existing dataset
2043         boolean importDs = Desktop.jalviewClipboard != null
2044                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2045         // importDs==true instructs us to copy over new dataset sequences from
2046         // an existing alignment
2047         Vector newDs = (importDs) ? new Vector() : null; // used to create
2048         // minimum dataset set
2049
2050         for (int i = 0; i < sequences.length; i++)
2051         {
2052           if (importDs)
2053           {
2054             newDs.addElement(null);
2055           }
2056           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2057           // paste
2058           if (importDs && ds != null)
2059           {
2060             if (!newDs.contains(ds))
2061             {
2062               newDs.setElementAt(ds, i);
2063               ds = new Sequence(ds);
2064               // update with new dataset sequence
2065               sequences[i].setDatasetSequence(ds);
2066             }
2067             else
2068             {
2069               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2070             }
2071           }
2072           else
2073           {
2074             // copy and derive new dataset sequence
2075             sequences[i] = sequences[i].deriveSequence();
2076             alignment.getDataset().addSequence(
2077                     sequences[i].getDatasetSequence());
2078             // TODO: avoid creation of duplicate dataset sequences with a
2079             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2080           }
2081           alignment.addSequence(sequences[i]); // merges dataset
2082         }
2083         if (newDs != null)
2084         {
2085           newDs.clear(); // tidy up
2086         }
2087         if (alignment.getAlignmentAnnotation() != null)
2088         {
2089           for (AlignmentAnnotation alan : alignment
2090                   .getAlignmentAnnotation())
2091           {
2092             if (alan.graphGroup > fgroup)
2093             {
2094               fgroup = alan.graphGroup;
2095             }
2096           }
2097         }
2098         if (pastedal.getAlignmentAnnotation() != null)
2099         {
2100           // Add any annotation attached to alignment.
2101           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2102           for (int i = 0; i < alann.length; i++)
2103           {
2104             annotationAdded = true;
2105             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2106             {
2107               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2108               if (newann.graphGroup > -1)
2109               {
2110                 if (newGraphGroups.size() <= newann.graphGroup
2111                         || newGraphGroups.get(newann.graphGroup) == null)
2112                 {
2113                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2114                   {
2115                     newGraphGroups.add(q, null);
2116                   }
2117                   newGraphGroups.set(newann.graphGroup, new Integer(
2118                           ++fgroup));
2119                 }
2120                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2121                         .intValue();
2122               }
2123
2124               newann.padAnnotation(alwidth);
2125               alignment.addAnnotation(newann);
2126             }
2127           }
2128         }
2129       }
2130       if (!newAlignment)
2131       {
2132         // /////
2133         // ADD HISTORY ITEM
2134         //
2135         addHistoryItem(new EditCommand(
2136                 MessageManager.getString("label.add_sequences"),
2137                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2138       }
2139       // Add any annotations attached to sequences
2140       for (int i = 0; i < sequences.length; i++)
2141       {
2142         if (sequences[i].getAnnotation() != null)
2143         {
2144           AlignmentAnnotation newann;
2145           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2146           {
2147             annotationAdded = true;
2148             newann = sequences[i].getAnnotation()[a];
2149             newann.adjustForAlignment();
2150             newann.padAnnotation(alwidth);
2151             if (newann.graphGroup > -1)
2152             {
2153               if (newann.graphGroup > -1)
2154               {
2155                 if (newGraphGroups.size() <= newann.graphGroup
2156                         || newGraphGroups.get(newann.graphGroup) == null)
2157                 {
2158                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2159                   {
2160                     newGraphGroups.add(q, null);
2161                   }
2162                   newGraphGroups.set(newann.graphGroup, new Integer(
2163                           ++fgroup));
2164                 }
2165                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2166                         .intValue();
2167               }
2168             }
2169             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2170             // was
2171             // duplicated
2172             // earlier
2173             alignment
2174                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2175           }
2176         }
2177       }
2178       if (!newAlignment)
2179       {
2180
2181         // propagate alignment changed.
2182         viewport.setEndSeq(alignment.getHeight());
2183         if (annotationAdded)
2184         {
2185           // Duplicate sequence annotation in all views.
2186           AlignmentI[] alview = this.getViewAlignments();
2187           for (int i = 0; i < sequences.length; i++)
2188           {
2189             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2190             if (sann == null)
2191             {
2192               continue;
2193             }
2194             for (int avnum = 0; avnum < alview.length; avnum++)
2195             {
2196               if (alview[avnum] != alignment)
2197               {
2198                 // duplicate in a view other than the one with input focus
2199                 int avwidth = alview[avnum].getWidth() + 1;
2200                 // this relies on sann being preserved after we
2201                 // modify the sequence's annotation array for each duplication
2202                 for (int a = 0; a < sann.length; a++)
2203                 {
2204                   AlignmentAnnotation newann = new AlignmentAnnotation(
2205                           sann[a]);
2206                   sequences[i].addAlignmentAnnotation(newann);
2207                   newann.padAnnotation(avwidth);
2208                   alview[avnum].addAnnotation(newann); // annotation was
2209                   // duplicated earlier
2210                   // TODO JAL-1145 graphGroups are not updated for sequence
2211                   // annotation added to several views. This may cause
2212                   // strangeness
2213                   alview[avnum].setAnnotationIndex(newann, a);
2214                 }
2215               }
2216             }
2217           }
2218           buildSortByAnnotationScoresMenu();
2219         }
2220         viewport.firePropertyChange("alignment", null,
2221                 alignment.getSequences());
2222         if (alignPanels != null)
2223         {
2224           for (AlignmentPanel ap : alignPanels)
2225           {
2226             ap.validateAnnotationDimensions(false);
2227           }
2228         }
2229         else
2230         {
2231           alignPanel.validateAnnotationDimensions(false);
2232         }
2233
2234       }
2235       else
2236       {
2237         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2238                 DEFAULT_HEIGHT);
2239         String newtitle = new String("Copied sequences");
2240
2241         if (Desktop.jalviewClipboard != null
2242                 && Desktop.jalviewClipboard[2] != null)
2243         {
2244           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2245           for (int[] region : hc)
2246           {
2247             af.viewport.hideColumns(region[0], region[1]);
2248           }
2249         }
2250
2251         // >>>This is a fix for the moment, until a better solution is
2252         // found!!<<<
2253         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2254                 .transferSettings(
2255                         alignPanel.getSeqPanel().seqCanvas
2256                                 .getFeatureRenderer());
2257
2258         // TODO: maintain provenance of an alignment, rather than just make the
2259         // title a concatenation of operations.
2260         if (!externalPaste)
2261         {
2262           if (title.startsWith("Copied sequences"))
2263           {
2264             newtitle = title;
2265           }
2266           else
2267           {
2268             newtitle = newtitle.concat("- from " + title);
2269           }
2270         }
2271         else
2272         {
2273           newtitle = new String("Pasted sequences");
2274         }
2275
2276         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2277                 DEFAULT_HEIGHT);
2278
2279       }
2280
2281     } catch (Exception ex)
2282     {
2283       ex.printStackTrace();
2284       System.out.println("Exception whilst pasting: " + ex);
2285       // could be anything being pasted in here
2286     }
2287
2288   }
2289
2290   @Override
2291   protected void expand_newalign(ActionEvent e)
2292   {
2293     try
2294     {
2295       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2296               .getAlignment(), -1);
2297       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2298               DEFAULT_HEIGHT);
2299       String newtitle = new String("Flanking alignment");
2300
2301       if (Desktop.jalviewClipboard != null
2302               && Desktop.jalviewClipboard[2] != null)
2303       {
2304         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2305         for (int region[] : hc)
2306         {
2307           af.viewport.hideColumns(region[0], region[1]);
2308         }
2309       }
2310
2311       // >>>This is a fix for the moment, until a better solution is
2312       // found!!<<<
2313       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2314               .transferSettings(
2315                       alignPanel.getSeqPanel().seqCanvas
2316                               .getFeatureRenderer());
2317
2318       // TODO: maintain provenance of an alignment, rather than just make the
2319       // title a concatenation of operations.
2320       {
2321         if (title.startsWith("Copied sequences"))
2322         {
2323           newtitle = title;
2324         }
2325         else
2326         {
2327           newtitle = newtitle.concat("- from " + title);
2328         }
2329       }
2330
2331       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2332
2333     } catch (Exception ex)
2334     {
2335       ex.printStackTrace();
2336       System.out.println("Exception whilst pasting: " + ex);
2337       // could be anything being pasted in here
2338     } catch (OutOfMemoryError oom)
2339     {
2340       new OOMWarning("Viewing flanking region of alignment", oom);
2341     }
2342   }
2343
2344   /**
2345    * DOCUMENT ME!
2346    *
2347    * @param e
2348    *          DOCUMENT ME!
2349    */
2350   @Override
2351   protected void cut_actionPerformed(ActionEvent e)
2352   {
2353     copy_actionPerformed(null);
2354     delete_actionPerformed(null);
2355   }
2356
2357   /**
2358    * DOCUMENT ME!
2359    *
2360    * @param e
2361    *          DOCUMENT ME!
2362    */
2363   @Override
2364   protected void delete_actionPerformed(ActionEvent evt)
2365   {
2366
2367     SequenceGroup sg = viewport.getSelectionGroup();
2368     if (sg == null)
2369     {
2370       return;
2371     }
2372
2373     /*
2374      * If the cut affects all sequences, warn, remove highlighted columns
2375      */
2376     if (sg.getSize() == viewport.getAlignment().getHeight())
2377     {
2378       int confirm = JOptionPane.showConfirmDialog(this,
2379               MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2380               MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2381               JOptionPane.OK_CANCEL_OPTION);
2382
2383       if (confirm == JOptionPane.CANCEL_OPTION
2384               || confirm == JOptionPane.CLOSED_OPTION)
2385       {
2386         return;
2387       }
2388       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2389               sg.getEndRes() + 1);
2390     }
2391
2392     SequenceI[] cut = sg.getSequences()
2393             .toArray(new SequenceI[sg.getSize()]);
2394
2395     addHistoryItem(new EditCommand(
2396             MessageManager.getString("label.cut_sequences"), Action.CUT,
2397             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2398             viewport.getAlignment()));
2399
2400     viewport.setSelectionGroup(null);
2401     viewport.sendSelection();
2402     viewport.getAlignment().deleteGroup(sg);
2403
2404     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2405             .getSequences());
2406     if (viewport.getAlignment().getHeight() < 1)
2407     {
2408       try
2409       {
2410         this.setClosed(true);
2411       } catch (Exception ex)
2412       {
2413       }
2414     }
2415   }
2416
2417   /**
2418    * DOCUMENT ME!
2419    *
2420    * @param e
2421    *          DOCUMENT ME!
2422    */
2423   @Override
2424   protected void deleteGroups_actionPerformed(ActionEvent e)
2425   {
2426     if (avc.deleteGroups())
2427     {
2428       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2429       alignPanel.updateAnnotation();
2430       alignPanel.paintAlignment(true);
2431     }
2432   }
2433
2434   /**
2435    * DOCUMENT ME!
2436    *
2437    * @param e
2438    *          DOCUMENT ME!
2439    */
2440   @Override
2441   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2442   {
2443     SequenceGroup sg = new SequenceGroup();
2444
2445     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2446     {
2447       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2448     }
2449
2450     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2451     viewport.setSelectionGroup(sg);
2452     viewport.sendSelection();
2453     alignPanel.paintAlignment(true);
2454     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455   }
2456
2457   /**
2458    * DOCUMENT ME!
2459    *
2460    * @param e
2461    *          DOCUMENT ME!
2462    */
2463   @Override
2464   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2465   {
2466     if (viewport.cursorMode)
2467     {
2468       alignPanel.getSeqPanel().keyboardNo1 = null;
2469       alignPanel.getSeqPanel().keyboardNo2 = null;
2470     }
2471     viewport.setSelectionGroup(null);
2472     viewport.getColumnSelection().clear();
2473     viewport.setSelectionGroup(null);
2474     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2475     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2476     alignPanel.paintAlignment(true);
2477     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2478     viewport.sendSelection();
2479   }
2480
2481   /**
2482    * DOCUMENT ME!
2483    *
2484    * @param e
2485    *          DOCUMENT ME!
2486    */
2487   @Override
2488   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2489   {
2490     SequenceGroup sg = viewport.getSelectionGroup();
2491
2492     if (sg == null)
2493     {
2494       selectAllSequenceMenuItem_actionPerformed(null);
2495
2496       return;
2497     }
2498
2499     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2500     {
2501       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2502     }
2503
2504     alignPanel.paintAlignment(true);
2505     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2506     viewport.sendSelection();
2507   }
2508
2509   @Override
2510   public void invertColSel_actionPerformed(ActionEvent e)
2511   {
2512     viewport.invertColumnSelection();
2513     alignPanel.paintAlignment(true);
2514     viewport.sendSelection();
2515   }
2516
2517   /**
2518    * DOCUMENT ME!
2519    *
2520    * @param e
2521    *          DOCUMENT ME!
2522    */
2523   @Override
2524   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2525   {
2526     trimAlignment(true);
2527   }
2528
2529   /**
2530    * DOCUMENT ME!
2531    *
2532    * @param e
2533    *          DOCUMENT ME!
2534    */
2535   @Override
2536   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2537   {
2538     trimAlignment(false);
2539   }
2540
2541   void trimAlignment(boolean trimLeft)
2542   {
2543     ColumnSelection colSel = viewport.getColumnSelection();
2544     int column;
2545
2546     if (colSel.size() > 0)
2547     {
2548       if (trimLeft)
2549       {
2550         column = colSel.getMin();
2551       }
2552       else
2553       {
2554         column = colSel.getMax();
2555       }
2556
2557       SequenceI[] seqs;
2558       if (viewport.getSelectionGroup() != null)
2559       {
2560         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2561                 viewport.getHiddenRepSequences());
2562       }
2563       else
2564       {
2565         seqs = viewport.getAlignment().getSequencesArray();
2566       }
2567
2568       TrimRegionCommand trimRegion;
2569       if (trimLeft)
2570       {
2571         trimRegion = new TrimRegionCommand("Remove Left",
2572                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2573                 viewport.getAlignment(), viewport.getColumnSelection(),
2574                 viewport.getSelectionGroup());
2575         viewport.setStartRes(0);
2576       }
2577       else
2578       {
2579         trimRegion = new TrimRegionCommand("Remove Right",
2580                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2581                 viewport.getAlignment(), viewport.getColumnSelection(),
2582                 viewport.getSelectionGroup());
2583       }
2584
2585       statusBar.setText(MessageManager.formatMessage(
2586               "label.removed_columns",
2587               new String[] { Integer.valueOf(trimRegion.getSize())
2588                       .toString() }));
2589
2590       addHistoryItem(trimRegion);
2591
2592       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2593       {
2594         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2595                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2596         {
2597           viewport.getAlignment().deleteGroup(sg);
2598         }
2599       }
2600
2601       viewport.firePropertyChange("alignment", null, viewport
2602               .getAlignment().getSequences());
2603     }
2604   }
2605
2606   /**
2607    * DOCUMENT ME!
2608    *
2609    * @param e
2610    *          DOCUMENT ME!
2611    */
2612   @Override
2613   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2614   {
2615     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2616
2617     SequenceI[] seqs;
2618     if (viewport.getSelectionGroup() != null)
2619     {
2620       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2621               viewport.getHiddenRepSequences());
2622       start = viewport.getSelectionGroup().getStartRes();
2623       end = viewport.getSelectionGroup().getEndRes();
2624     }
2625     else
2626     {
2627       seqs = viewport.getAlignment().getSequencesArray();
2628     }
2629
2630     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2631             "Remove Gapped Columns", seqs, start, end,
2632             viewport.getAlignment());
2633
2634     addHistoryItem(removeGapCols);
2635
2636     statusBar.setText(MessageManager.formatMessage(
2637             "label.removed_empty_columns",
2638             new Object[] { Integer.valueOf(removeGapCols.getSize())
2639                     .toString() }));
2640
2641     // This is to maintain viewport position on first residue
2642     // of first sequence
2643     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644     int startRes = seq.findPosition(viewport.startRes);
2645     // ShiftList shifts;
2646     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2647     // edit.alColumnChanges=shifts.getInverse();
2648     // if (viewport.hasHiddenColumns)
2649     // viewport.getColumnSelection().compensateForEdits(shifts);
2650     viewport.setStartRes(seq.findIndex(startRes) - 1);
2651     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2652             .getSequences());
2653
2654   }
2655
2656   /**
2657    * DOCUMENT ME!
2658    *
2659    * @param e
2660    *          DOCUMENT ME!
2661    */
2662   @Override
2663   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2664   {
2665     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2666
2667     SequenceI[] seqs;
2668     if (viewport.getSelectionGroup() != null)
2669     {
2670       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2671               viewport.getHiddenRepSequences());
2672       start = viewport.getSelectionGroup().getStartRes();
2673       end = viewport.getSelectionGroup().getEndRes();
2674     }
2675     else
2676     {
2677       seqs = viewport.getAlignment().getSequencesArray();
2678     }
2679
2680     // This is to maintain viewport position on first residue
2681     // of first sequence
2682     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2683     int startRes = seq.findPosition(viewport.startRes);
2684
2685     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2686             viewport.getAlignment()));
2687
2688     viewport.setStartRes(seq.findIndex(startRes) - 1);
2689
2690     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2691             .getSequences());
2692
2693   }
2694
2695   /**
2696    * DOCUMENT ME!
2697    *
2698    * @param e
2699    *          DOCUMENT ME!
2700    */
2701   @Override
2702   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2703   {
2704     viewport.setPadGaps(padGapsMenuitem.isSelected());
2705     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2706             .getSequences());
2707   }
2708
2709   /**
2710    * DOCUMENT ME!
2711    *
2712    * @param e
2713    *          DOCUMENT ME!
2714    */
2715   @Override
2716   public void findMenuItem_actionPerformed(ActionEvent e)
2717   {
2718     new Finder();
2719   }
2720
2721   /**
2722    * Create a new view of the current alignment.
2723    */
2724   @Override
2725   public void newView_actionPerformed(ActionEvent e)
2726   {
2727     newView(null, true);
2728   }
2729
2730   /**
2731    * Creates and shows a new view of the current alignment.
2732    *
2733    * @param viewTitle
2734    *          title of newly created view; if null, one will be generated
2735    * @param copyAnnotation
2736    *          if true then duplicate all annnotation, groups and settings
2737    * @return new alignment panel, already displayed.
2738    */
2739   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2740   {
2741     /*
2742      * Create a new AlignmentPanel (with its own, new Viewport)
2743      */
2744     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2745             true);
2746     if (!copyAnnotation)
2747     {
2748       /*
2749        * remove all groups and annotation except for the automatic stuff
2750        */
2751       newap.av.getAlignment().deleteAllGroups();
2752       newap.av.getAlignment().deleteAllAnnotations(false);
2753     }
2754
2755     newap.av.setGatherViewsHere(false);
2756
2757     if (viewport.viewName == null)
2758     {
2759       viewport.viewName = MessageManager
2760               .getString("label.view_name_original");
2761     }
2762
2763     /*
2764      * Views share the same edits undo and redo stacks
2765      */
2766     newap.av.setHistoryList(viewport.getHistoryList());
2767     newap.av.setRedoList(viewport.getRedoList());
2768
2769     /*
2770      * Views share the same mappings; need to deregister any new mappings
2771      * created by copyAlignPanel, and register the new reference to the shared
2772      * mappings
2773      */
2774     newap.av.replaceMappings(viewport.getAlignment());
2775
2776     newap.av.viewName = getNewViewName(viewTitle);
2777
2778     addAlignmentPanel(newap, true);
2779     newap.alignmentChanged();
2780
2781     if (alignPanels.size() == 2)
2782     {
2783       viewport.setGatherViewsHere(true);
2784     }
2785     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2786     return newap;
2787   }
2788
2789   /**
2790    * Make a new name for the view, ensuring it is unique within the current
2791    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2792    * these now use viewId. Unique view names are still desirable for usability.)
2793    *
2794    * @param viewTitle
2795    * @return
2796    */
2797   protected String getNewViewName(String viewTitle)
2798   {
2799     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2800     boolean addFirstIndex = false;
2801     if (viewTitle == null || viewTitle.trim().length() == 0)
2802     {
2803       viewTitle = MessageManager.getString("action.view");
2804       addFirstIndex = true;
2805     }
2806     else
2807     {
2808       index = 1;// we count from 1 if given a specific name
2809     }
2810     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2811
2812     List<Component> comps = PaintRefresher.components.get(viewport
2813             .getSequenceSetId());
2814
2815     List<String> existingNames = getExistingViewNames(comps);
2816
2817     while (existingNames.contains(newViewName))
2818     {
2819       newViewName = viewTitle + " " + (++index);
2820     }
2821     return newViewName;
2822   }
2823
2824   /**
2825    * Returns a list of distinct view names found in the given list of
2826    * components. View names are held on the viewport of an AlignmentPanel.
2827    *
2828    * @param comps
2829    * @return
2830    */
2831   protected List<String> getExistingViewNames(List<Component> comps)
2832   {
2833     List<String> existingNames = new ArrayList<String>();
2834     for (Component comp : comps)
2835     {
2836       if (comp instanceof AlignmentPanel)
2837       {
2838         AlignmentPanel ap = (AlignmentPanel) comp;
2839         if (!existingNames.contains(ap.av.viewName))
2840         {
2841           existingNames.add(ap.av.viewName);
2842         }
2843       }
2844     }
2845     return existingNames;
2846   }
2847
2848   /**
2849    * Explode tabbed views into separate windows.
2850    */
2851   @Override
2852   public void expandViews_actionPerformed(ActionEvent e)
2853   {
2854     Desktop.instance.explodeViews(this);
2855   }
2856
2857   /**
2858    * Gather views in separate windows back into a tabbed presentation.
2859    */
2860   @Override
2861   public void gatherViews_actionPerformed(ActionEvent e)
2862   {
2863     Desktop.instance.gatherViews(this);
2864   }
2865
2866   /**
2867    * DOCUMENT ME!
2868    *
2869    * @param e
2870    *          DOCUMENT ME!
2871    */
2872   @Override
2873   public void font_actionPerformed(ActionEvent e)
2874   {
2875     new FontChooser(alignPanel);
2876   }
2877
2878   /**
2879    * DOCUMENT ME!
2880    *
2881    * @param e
2882    *          DOCUMENT ME!
2883    */
2884   @Override
2885   protected void seqLimit_actionPerformed(ActionEvent e)
2886   {
2887     viewport.setShowJVSuffix(seqLimits.isSelected());
2888
2889     alignPanel.getIdPanel().getIdCanvas()
2890             .setPreferredSize(alignPanel.calculateIdWidth());
2891     alignPanel.paintAlignment(true);
2892   }
2893
2894   @Override
2895   public void idRightAlign_actionPerformed(ActionEvent e)
2896   {
2897     viewport.setRightAlignIds(idRightAlign.isSelected());
2898     alignPanel.paintAlignment(true);
2899   }
2900
2901   @Override
2902   public void centreColumnLabels_actionPerformed(ActionEvent e)
2903   {
2904     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2905     alignPanel.paintAlignment(true);
2906   }
2907
2908   /*
2909    * (non-Javadoc)
2910    *
2911    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2912    */
2913   @Override
2914   protected void followHighlight_actionPerformed()
2915   {
2916     /*
2917      * Set the 'follow' flag on the Viewport (and scroll to position if now
2918      * true).
2919      */
2920     final boolean state = this.followHighlightMenuItem.getState();
2921     viewport.setFollowHighlight(state);
2922     if (state)
2923     {
2924       alignPanel.scrollToPosition(
2925               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2926     }
2927   }
2928
2929   /**
2930    * DOCUMENT ME!
2931    *
2932    * @param e
2933    *          DOCUMENT ME!
2934    */
2935   @Override
2936   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2937   {
2938     viewport.setColourText(colourTextMenuItem.isSelected());
2939     alignPanel.paintAlignment(true);
2940   }
2941
2942   /**
2943    * DOCUMENT ME!
2944    *
2945    * @param e
2946    *          DOCUMENT ME!
2947    */
2948   @Override
2949   public void wrapMenuItem_actionPerformed(ActionEvent e)
2950   {
2951     scaleAbove.setVisible(wrapMenuItem.isSelected());
2952     scaleLeft.setVisible(wrapMenuItem.isSelected());
2953     scaleRight.setVisible(wrapMenuItem.isSelected());
2954     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2955     alignPanel.updateLayout();
2956   }
2957
2958   @Override
2959   public void showAllSeqs_actionPerformed(ActionEvent e)
2960   {
2961     viewport.showAllHiddenSeqs();
2962   }
2963
2964   @Override
2965   public void showAllColumns_actionPerformed(ActionEvent e)
2966   {
2967     viewport.showAllHiddenColumns();
2968     repaint();
2969   }
2970
2971   @Override
2972   public void hideSelSequences_actionPerformed(ActionEvent e)
2973   {
2974     viewport.hideAllSelectedSeqs();
2975     // alignPanel.paintAlignment(true);
2976   }
2977
2978   /**
2979    * called by key handler and the hide all/show all menu items
2980    *
2981    * @param toggleSeqs
2982    * @param toggleCols
2983    */
2984   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2985   {
2986
2987     boolean hide = false;
2988     SequenceGroup sg = viewport.getSelectionGroup();
2989     if (!toggleSeqs && !toggleCols)
2990     {
2991       // Hide everything by the current selection - this is a hack - we do the
2992       // invert and then hide
2993       // first check that there will be visible columns after the invert.
2994       if ((viewport.getColumnSelection() != null
2995               && viewport.getColumnSelection().getSelected() != null && viewport
2996               .getColumnSelection().getSelected().size() > 0)
2997               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2998                       .getEndRes()))
2999       {
3000         // now invert the sequence set, if required - empty selection implies
3001         // that no hiding is required.
3002         if (sg != null)
3003         {
3004           invertSequenceMenuItem_actionPerformed(null);
3005           sg = viewport.getSelectionGroup();
3006           toggleSeqs = true;
3007
3008         }
3009         viewport.expandColSelection(sg, true);
3010         // finally invert the column selection and get the new sequence
3011         // selection.
3012         invertColSel_actionPerformed(null);
3013         toggleCols = true;
3014       }
3015     }
3016
3017     if (toggleSeqs)
3018     {
3019       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3020       {
3021         hideSelSequences_actionPerformed(null);
3022         hide = true;
3023       }
3024       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3025               .size() > 0))
3026       {
3027         showAllSeqs_actionPerformed(null);
3028       }
3029     }
3030
3031     if (toggleCols)
3032     {
3033       if (viewport.getColumnSelection().getSelected().size() > 0)
3034       {
3035         hideSelColumns_actionPerformed(null);
3036         if (!toggleSeqs)
3037         {
3038           viewport.setSelectionGroup(sg);
3039         }
3040       }
3041       else if (!hide)
3042       {
3043         showAllColumns_actionPerformed(null);
3044       }
3045     }
3046   }
3047
3048   /*
3049    * (non-Javadoc)
3050    *
3051    * @see
3052    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3053    * event.ActionEvent)
3054    */
3055   @Override
3056   public void hideAllButSelection_actionPerformed(ActionEvent e)
3057   {
3058     toggleHiddenRegions(false, false);
3059   }
3060
3061   /*
3062    * (non-Javadoc)
3063    *
3064    * @see
3065    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3066    * .ActionEvent)
3067    */
3068   @Override
3069   public void hideAllSelection_actionPerformed(ActionEvent e)
3070   {
3071     SequenceGroup sg = viewport.getSelectionGroup();
3072     viewport.expandColSelection(sg, false);
3073     viewport.hideAllSelectedSeqs();
3074     viewport.hideSelectedColumns();
3075     alignPanel.paintAlignment(true);
3076   }
3077
3078   /*
3079    * (non-Javadoc)
3080    *
3081    * @see
3082    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3083    * ActionEvent)
3084    */
3085   @Override
3086   public void showAllhidden_actionPerformed(ActionEvent e)
3087   {
3088     viewport.showAllHiddenColumns();
3089     viewport.showAllHiddenSeqs();
3090     alignPanel.paintAlignment(true);
3091   }
3092
3093   @Override
3094   public void hideSelColumns_actionPerformed(ActionEvent e)
3095   {
3096     viewport.hideSelectedColumns();
3097     alignPanel.paintAlignment(true);
3098   }
3099
3100   @Override
3101   public void hiddenMarkers_actionPerformed(ActionEvent e)
3102   {
3103     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3104     repaint();
3105   }
3106
3107   /**
3108    * DOCUMENT ME!
3109    *
3110    * @param e
3111    *          DOCUMENT ME!
3112    */
3113   @Override
3114   protected void scaleAbove_actionPerformed(ActionEvent e)
3115   {
3116     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3117     alignPanel.paintAlignment(true);
3118   }
3119
3120   /**
3121    * DOCUMENT ME!
3122    *
3123    * @param e
3124    *          DOCUMENT ME!
3125    */
3126   @Override
3127   protected void scaleLeft_actionPerformed(ActionEvent e)
3128   {
3129     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3130     alignPanel.paintAlignment(true);
3131   }
3132
3133   /**
3134    * DOCUMENT ME!
3135    *
3136    * @param e
3137    *          DOCUMENT ME!
3138    */
3139   @Override
3140   protected void scaleRight_actionPerformed(ActionEvent e)
3141   {
3142     viewport.setScaleRightWrapped(scaleRight.isSelected());
3143     alignPanel.paintAlignment(true);
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3156     alignPanel.paintAlignment(true);
3157   }
3158
3159   /**
3160    * DOCUMENT ME!
3161    *
3162    * @param e
3163    *          DOCUMENT ME!
3164    */
3165   @Override
3166   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3167   {
3168     viewport.setShowText(viewTextMenuItem.isSelected());
3169     alignPanel.paintAlignment(true);
3170   }
3171
3172   /**
3173    * DOCUMENT ME!
3174    *
3175    * @param e
3176    *          DOCUMENT ME!
3177    */
3178   @Override
3179   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3180   {
3181     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3182     alignPanel.paintAlignment(true);
3183   }
3184
3185   public FeatureSettings featureSettings;
3186
3187   @Override
3188   public FeatureSettingsControllerI getFeatureSettingsUI()
3189   {
3190     return featureSettings;
3191   }
3192
3193   @Override
3194   public void featureSettings_actionPerformed(ActionEvent e)
3195   {
3196     if (featureSettings != null)
3197     {
3198       featureSettings.close();
3199       featureSettings = null;
3200     }
3201     if (!showSeqFeatures.isSelected())
3202     {
3203       // make sure features are actually displayed
3204       showSeqFeatures.setSelected(true);
3205       showSeqFeatures_actionPerformed(null);
3206     }
3207     featureSettings = new FeatureSettings(this);
3208   }
3209
3210   /**
3211    * Set or clear 'Show Sequence Features'
3212    *
3213    * @param evt
3214    *          DOCUMENT ME!
3215    */
3216   @Override
3217   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3218   {
3219     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3220     alignPanel.paintAlignment(true);
3221     if (alignPanel.getOverviewPanel() != null)
3222     {
3223       alignPanel.getOverviewPanel().updateOverviewImage();
3224     }
3225   }
3226
3227   /**
3228    * Set or clear 'Show Sequence Features'
3229    *
3230    * @param evt
3231    *          DOCUMENT ME!
3232    */
3233   @Override
3234   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3235   {
3236     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3237             .isSelected());
3238     if (viewport.isShowSequenceFeaturesHeight())
3239     {
3240       // ensure we're actually displaying features
3241       viewport.setShowSequenceFeatures(true);
3242       showSeqFeatures.setSelected(true);
3243     }
3244     alignPanel.paintAlignment(true);
3245     if (alignPanel.getOverviewPanel() != null)
3246     {
3247       alignPanel.getOverviewPanel().updateOverviewImage();
3248     }
3249   }
3250
3251   /**
3252    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3253    * the annotations panel as a whole.
3254    *
3255    * The options to show/hide all annotations should be enabled when the panel
3256    * is shown, and disabled when the panel is hidden.
3257    *
3258    * @param e
3259    */
3260   @Override
3261   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3262   {
3263     final boolean setVisible = annotationPanelMenuItem.isSelected();
3264     viewport.setShowAnnotation(setVisible);
3265     this.showAllSeqAnnotations.setEnabled(setVisible);
3266     this.hideAllSeqAnnotations.setEnabled(setVisible);
3267     this.showAllAlAnnotations.setEnabled(setVisible);
3268     this.hideAllAlAnnotations.setEnabled(setVisible);
3269     alignPanel.updateLayout();
3270   }
3271
3272   @Override
3273   public void alignmentProperties()
3274   {
3275     JEditorPane editPane = new JEditorPane("text/html", "");
3276     editPane.setEditable(false);
3277     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3278             .formatAsHtml();
3279     editPane.setText(MessageManager.formatMessage("label.html_content",
3280             new Object[] { contents.toString() }));
3281     JInternalFrame frame = new JInternalFrame();
3282     frame.getContentPane().add(new JScrollPane(editPane));
3283
3284     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3285             "label.alignment_properties", new Object[] { getTitle() }),
3286             500, 400);
3287   }
3288
3289   /**
3290    * DOCUMENT ME!
3291    *
3292    * @param e
3293    *          DOCUMENT ME!
3294    */
3295   @Override
3296   public void overviewMenuItem_actionPerformed(ActionEvent e)
3297   {
3298     if (alignPanel.overviewPanel != null)
3299     {
3300       return;
3301     }
3302
3303     JInternalFrame frame = new JInternalFrame();
3304     OverviewPanel overview = new OverviewPanel(alignPanel);
3305     frame.setContentPane(overview);
3306     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3307             "label.overview_params", new Object[] { this.getTitle() }),
3308             frame.getWidth(), frame.getHeight());
3309     frame.pack();
3310     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3311     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3312     {
3313       @Override
3314       public void internalFrameClosed(
3315               javax.swing.event.InternalFrameEvent evt)
3316       {
3317         alignPanel.setOverviewPanel(null);
3318       };
3319     });
3320
3321     alignPanel.setOverviewPanel(overview);
3322   }
3323
3324   @Override
3325   public void textColour_actionPerformed(ActionEvent e)
3326   {
3327     new TextColourChooser().chooseColour(alignPanel, null);
3328   }
3329
3330   /**
3331    * DOCUMENT ME!
3332    *
3333    * @param e
3334    *          DOCUMENT ME!
3335    */
3336   @Override
3337   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3338   {
3339     changeColour(null);
3340   }
3341
3342   /**
3343    * DOCUMENT ME!
3344    *
3345    * @param e
3346    *          DOCUMENT ME!
3347    */
3348   @Override
3349   public void clustalColour_actionPerformed(ActionEvent e)
3350   {
3351     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3352             viewport.getHiddenRepSequences()));
3353   }
3354
3355   /**
3356    * DOCUMENT ME!
3357    *
3358    * @param e
3359    *          DOCUMENT ME!
3360    */
3361   @Override
3362   public void zappoColour_actionPerformed(ActionEvent e)
3363   {
3364     changeColour(new ZappoColourScheme());
3365   }
3366
3367   /**
3368    * DOCUMENT ME!
3369    *
3370    * @param e
3371    *          DOCUMENT ME!
3372    */
3373   @Override
3374   public void taylorColour_actionPerformed(ActionEvent e)
3375   {
3376     changeColour(new TaylorColourScheme());
3377   }
3378
3379   /**
3380    * DOCUMENT ME!
3381    *
3382    * @param e
3383    *          DOCUMENT ME!
3384    */
3385   @Override
3386   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3387   {
3388     changeColour(new HydrophobicColourScheme());
3389   }
3390
3391   /**
3392    * DOCUMENT ME!
3393    *
3394    * @param e
3395    *          DOCUMENT ME!
3396    */
3397   @Override
3398   public void helixColour_actionPerformed(ActionEvent e)
3399   {
3400     changeColour(new HelixColourScheme());
3401   }
3402
3403   /**
3404    * DOCUMENT ME!
3405    *
3406    * @param e
3407    *          DOCUMENT ME!
3408    */
3409   @Override
3410   public void strandColour_actionPerformed(ActionEvent e)
3411   {
3412     changeColour(new StrandColourScheme());
3413   }
3414
3415   /**
3416    * DOCUMENT ME!
3417    *
3418    * @param e
3419    *          DOCUMENT ME!
3420    */
3421   @Override
3422   public void turnColour_actionPerformed(ActionEvent e)
3423   {
3424     changeColour(new TurnColourScheme());
3425   }
3426
3427   /**
3428    * DOCUMENT ME!
3429    *
3430    * @param e
3431    *          DOCUMENT ME!
3432    */
3433   @Override
3434   public void buriedColour_actionPerformed(ActionEvent e)
3435   {
3436     changeColour(new BuriedColourScheme());
3437   }
3438
3439   /**
3440    * DOCUMENT ME!
3441    *
3442    * @param e
3443    *          DOCUMENT ME!
3444    */
3445   @Override
3446   public void nucleotideColour_actionPerformed(ActionEvent e)
3447   {
3448     changeColour(new NucleotideColourScheme());
3449   }
3450
3451   @Override
3452   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3453   {
3454     changeColour(new PurinePyrimidineColourScheme());
3455   }
3456
3457   /*
3458    * public void covariationColour_actionPerformed(ActionEvent e) {
3459    * changeColour(new
3460    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3461    * ()[0])); }
3462    */
3463   @Override
3464   public void annotationColour_actionPerformed(ActionEvent e)
3465   {
3466     new AnnotationColourChooser(viewport, alignPanel);
3467   }
3468
3469   @Override
3470   public void annotationColumn_actionPerformed(ActionEvent e)
3471   {
3472     new AnnotationColumnChooser(viewport, alignPanel);
3473   }
3474
3475   @Override
3476   public void rnahelicesColour_actionPerformed(ActionEvent e)
3477   {
3478     new RNAHelicesColourChooser(viewport, alignPanel);
3479   }
3480
3481   /**
3482    * DOCUMENT ME!
3483    *
3484    * @param e
3485    *          DOCUMENT ME!
3486    */
3487   @Override
3488   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3489   {
3490     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3491   }
3492
3493   /**
3494    * DOCUMENT ME!
3495    *
3496    * @param cs
3497    *          DOCUMENT ME!
3498    */
3499   public void changeColour(ColourSchemeI cs)
3500   {
3501     // TODO: pull up to controller method
3502
3503     if (cs != null)
3504     {
3505       // Make sure viewport is up to date w.r.t. any sliders
3506       if (viewport.getAbovePIDThreshold())
3507       {
3508         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3509                 "Background");
3510         viewport.setThreshold(threshold);
3511       }
3512
3513       if (viewport.getConservationSelected())
3514       {
3515         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3516                 cs, "Background"));
3517       }
3518     }
3519
3520     viewport.setGlobalColourScheme(cs);
3521
3522     alignPanel.paintAlignment(true);
3523   }
3524
3525   /**
3526    * DOCUMENT ME!
3527    *
3528    * @param e
3529    *          DOCUMENT ME!
3530    */
3531   @Override
3532   protected void modifyPID_actionPerformed(ActionEvent e)
3533   {
3534     if (viewport.getAbovePIDThreshold()
3535             && viewport.getGlobalColourScheme() != null)
3536     {
3537       SliderPanel.setPIDSliderSource(alignPanel,
3538               viewport.getGlobalColourScheme(), "Background");
3539       SliderPanel.showPIDSlider();
3540     }
3541   }
3542
3543   /**
3544    * DOCUMENT ME!
3545    *
3546    * @param e
3547    *          DOCUMENT ME!
3548    */
3549   @Override
3550   protected void modifyConservation_actionPerformed(ActionEvent e)
3551   {
3552     if (viewport.getConservationSelected()
3553             && viewport.getGlobalColourScheme() != null)
3554     {
3555       SliderPanel.setConservationSlider(alignPanel,
3556               viewport.getGlobalColourScheme(), "Background");
3557       SliderPanel.showConservationSlider();
3558     }
3559   }
3560
3561   /**
3562    * DOCUMENT ME!
3563    *
3564    * @param e
3565    *          DOCUMENT ME!
3566    */
3567   @Override
3568   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3569   {
3570     viewport.setConservationSelected(conservationMenuItem.isSelected());
3571
3572     viewport.setAbovePIDThreshold(false);
3573     abovePIDThreshold.setSelected(false);
3574
3575     changeColour(viewport.getGlobalColourScheme());
3576
3577     modifyConservation_actionPerformed(null);
3578   }
3579
3580   /**
3581    * DOCUMENT ME!
3582    *
3583    * @param e
3584    *          DOCUMENT ME!
3585    */
3586   @Override
3587   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3588   {
3589     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3590
3591     conservationMenuItem.setSelected(false);
3592     viewport.setConservationSelected(false);
3593
3594     changeColour(viewport.getGlobalColourScheme());
3595
3596     modifyPID_actionPerformed(null);
3597   }
3598
3599   /**
3600    * DOCUMENT ME!
3601    *
3602    * @param e
3603    *          DOCUMENT ME!
3604    */
3605   @Override
3606   public void userDefinedColour_actionPerformed(ActionEvent e)
3607   {
3608     if (e.getActionCommand().equals(
3609             MessageManager.getString("action.user_defined")))
3610     {
3611       new UserDefinedColours(alignPanel, null);
3612     }
3613     else
3614     {
3615       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3616               .getUserColourSchemes().get(e.getActionCommand());
3617
3618       changeColour(udc);
3619     }
3620   }
3621
3622   public void updateUserColourMenu()
3623   {
3624
3625     Component[] menuItems = colourMenu.getMenuComponents();
3626     int iSize = menuItems.length;
3627     for (int i = 0; i < iSize; i++)
3628     {
3629       if (menuItems[i].getName() != null
3630               && menuItems[i].getName().equals("USER_DEFINED"))
3631       {
3632         colourMenu.remove(menuItems[i]);
3633         iSize--;
3634       }
3635     }
3636     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3637     {
3638       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3639               .getUserColourSchemes().keys();
3640
3641       while (userColours.hasMoreElements())
3642       {
3643         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3644                 userColours.nextElement().toString());
3645         radioItem.setName("USER_DEFINED");
3646         radioItem.addMouseListener(new MouseAdapter()
3647         {
3648           @Override
3649           public void mousePressed(MouseEvent evt)
3650           {
3651             if (evt.isControlDown()
3652                     || SwingUtilities.isRightMouseButton(evt))
3653             {
3654               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3655
3656               int option = JOptionPane.showInternalConfirmDialog(
3657                       jalview.gui.Desktop.desktop,
3658                       MessageManager
3659                               .getString("label.remove_from_default_list"),
3660                       MessageManager
3661                               .getString("label.remove_user_defined_colour"),
3662                       JOptionPane.YES_NO_OPTION);
3663               if (option == JOptionPane.YES_OPTION)
3664               {
3665                 jalview.gui.UserDefinedColours
3666                         .removeColourFromDefaults(radioItem.getText());
3667                 colourMenu.remove(radioItem);
3668               }
3669               else
3670               {
3671                 radioItem.addActionListener(new ActionListener()
3672                 {
3673                   @Override
3674                   public void actionPerformed(ActionEvent evt)
3675                   {
3676                     userDefinedColour_actionPerformed(evt);
3677                   }
3678                 });
3679               }
3680             }
3681           }
3682         });
3683         radioItem.addActionListener(new ActionListener()
3684         {
3685           @Override
3686           public void actionPerformed(ActionEvent evt)
3687           {
3688             userDefinedColour_actionPerformed(evt);
3689           }
3690         });
3691
3692         colourMenu.insert(radioItem, 15);
3693         colours.add(radioItem);
3694       }
3695     }
3696   }
3697
3698   /**
3699    * DOCUMENT ME!
3700    *
3701    * @param e
3702    *          DOCUMENT ME!
3703    */
3704   @Override
3705   public void PIDColour_actionPerformed(ActionEvent e)
3706   {
3707     changeColour(new PIDColourScheme());
3708   }
3709
3710   /**
3711    * DOCUMENT ME!
3712    *
3713    * @param e
3714    *          DOCUMENT ME!
3715    */
3716   @Override
3717   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3718   {
3719     changeColour(new Blosum62ColourScheme());
3720   }
3721
3722   /**
3723    * DOCUMENT ME!
3724    *
3725    * @param e
3726    *          DOCUMENT ME!
3727    */
3728   @Override
3729   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3730   {
3731     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3732     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3733             .getAlignment().getSequenceAt(0), null);
3734     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3735             viewport.getAlignment()));
3736     alignPanel.paintAlignment(true);
3737   }
3738
3739   /**
3740    * DOCUMENT ME!
3741    *
3742    * @param e
3743    *          DOCUMENT ME!
3744    */
3745   @Override
3746   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3747   {
3748     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749     AlignmentSorter.sortByID(viewport.getAlignment());
3750     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3751             viewport.getAlignment()));
3752     alignPanel.paintAlignment(true);
3753   }
3754
3755   /**
3756    * DOCUMENT ME!
3757    *
3758    * @param e
3759    *          DOCUMENT ME!
3760    */
3761   @Override
3762   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3763   {
3764     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3765     AlignmentSorter.sortByLength(viewport.getAlignment());
3766     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3767             viewport.getAlignment()));
3768     alignPanel.paintAlignment(true);
3769   }
3770
3771   /**
3772    * DOCUMENT ME!
3773    *
3774    * @param e
3775    *          DOCUMENT ME!
3776    */
3777   @Override
3778   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3779   {
3780     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3781     AlignmentSorter.sortByGroup(viewport.getAlignment());
3782     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3783             viewport.getAlignment()));
3784
3785     alignPanel.paintAlignment(true);
3786   }
3787
3788   /**
3789    * DOCUMENT ME!
3790    *
3791    * @param e
3792    *          DOCUMENT ME!
3793    */
3794   @Override
3795   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3796   {
3797     new RedundancyPanel(alignPanel, this);
3798   }
3799
3800   /**
3801    * DOCUMENT ME!
3802    *
3803    * @param e
3804    *          DOCUMENT ME!
3805    */
3806   @Override
3807   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3808   {
3809     if ((viewport.getSelectionGroup() == null)
3810             || (viewport.getSelectionGroup().getSize() < 2))
3811     {
3812       JOptionPane.showInternalMessageDialog(this, MessageManager
3813               .getString("label.you_must_select_least_two_sequences"),
3814               MessageManager.getString("label.invalid_selection"),
3815               JOptionPane.WARNING_MESSAGE);
3816     }
3817     else
3818     {
3819       JInternalFrame frame = new JInternalFrame();
3820       frame.setContentPane(new PairwiseAlignPanel(viewport));
3821       Desktop.addInternalFrame(frame,
3822               MessageManager.getString("action.pairwise_alignment"), 600,
3823               500);
3824     }
3825   }
3826
3827   /**
3828    * DOCUMENT ME!
3829    *
3830    * @param e
3831    *          DOCUMENT ME!
3832    */
3833   @Override
3834   public void PCAMenuItem_actionPerformed(ActionEvent e)
3835   {
3836     if (((viewport.getSelectionGroup() != null)
3837             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3838             .getSelectionGroup().getSize() > 0))
3839             || (viewport.getAlignment().getHeight() < 4))
3840     {
3841       JOptionPane
3842               .showInternalMessageDialog(
3843                       this,
3844                       MessageManager
3845                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3846                       MessageManager
3847                               .getString("label.sequence_selection_insufficient"),
3848                       JOptionPane.WARNING_MESSAGE);
3849
3850       return;
3851     }
3852
3853     new PCAPanel(alignPanel);
3854   }
3855
3856   @Override
3857   public void autoCalculate_actionPerformed(ActionEvent e)
3858   {
3859     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3860     if (viewport.autoCalculateConsensus)
3861     {
3862       viewport.firePropertyChange("alignment", null, viewport
3863               .getAlignment().getSequences());
3864     }
3865   }
3866
3867   @Override
3868   public void sortByTreeOption_actionPerformed(ActionEvent e)
3869   {
3870     viewport.sortByTree = sortByTree.isSelected();
3871   }
3872
3873   @Override
3874   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3875   {
3876     viewport.followSelection = listenToViewSelections.isSelected();
3877   }
3878
3879   /**
3880    * DOCUMENT ME!
3881    *
3882    * @param e
3883    *          DOCUMENT ME!
3884    */
3885   @Override
3886   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3887   {
3888     newTreePanel("AV", "PID", "Average distance tree using PID");
3889   }
3890
3891   /**
3892    * DOCUMENT ME!
3893    *
3894    * @param e
3895    *          DOCUMENT ME!
3896    */
3897   @Override
3898   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3899   {
3900     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3901   }
3902
3903   /**
3904    * DOCUMENT ME!
3905    *
3906    * @param e
3907    *          DOCUMENT ME!
3908    */
3909   @Override
3910   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3911   {
3912     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3913   }
3914
3915   /**
3916    * DOCUMENT ME!
3917    *
3918    * @param e
3919    *          DOCUMENT ME!
3920    */
3921   @Override
3922   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3923   {
3924     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3925   }
3926
3927   /**
3928    * DOCUMENT ME!
3929    *
3930    * @param type
3931    *          DOCUMENT ME!
3932    * @param pwType
3933    *          DOCUMENT ME!
3934    * @param title
3935    *          DOCUMENT ME!
3936    */
3937   void newTreePanel(String type, String pwType, String title)
3938   {
3939     TreePanel tp;
3940
3941     if (viewport.getSelectionGroup() != null
3942             && viewport.getSelectionGroup().getSize() > 0)
3943     {
3944       if (viewport.getSelectionGroup().getSize() < 3)
3945       {
3946         JOptionPane
3947                 .showMessageDialog(
3948                         Desktop.desktop,
3949                         MessageManager
3950                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3951                         MessageManager
3952                                 .getString("label.not_enough_sequences"),
3953                         JOptionPane.WARNING_MESSAGE);
3954         return;
3955       }
3956
3957       SequenceGroup sg = viewport.getSelectionGroup();
3958
3959       /* Decide if the selection is a column region */
3960       for (SequenceI _s : sg.getSequences())
3961       {
3962         if (_s.getLength() < sg.getEndRes())
3963         {
3964           JOptionPane
3965                   .showMessageDialog(
3966                           Desktop.desktop,
3967                           MessageManager
3968                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3969                           MessageManager
3970                                   .getString("label.sequences_selection_not_aligned"),
3971                           JOptionPane.WARNING_MESSAGE);
3972
3973           return;
3974         }
3975       }
3976
3977       title = title + " on region";
3978       tp = new TreePanel(alignPanel, type, pwType);
3979     }
3980     else
3981     {
3982       // are the visible sequences aligned?
3983       if (!viewport.getAlignment().isAligned(false))
3984       {
3985         JOptionPane
3986                 .showMessageDialog(
3987                         Desktop.desktop,
3988                         MessageManager
3989                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3990                         MessageManager
3991                                 .getString("label.sequences_not_aligned"),
3992                         JOptionPane.WARNING_MESSAGE);
3993
3994         return;
3995       }
3996
3997       if (viewport.getAlignment().getHeight() < 2)
3998       {
3999         return;
4000       }
4001
4002       tp = new TreePanel(alignPanel, type, pwType);
4003     }
4004
4005     title += " from ";
4006
4007     if (viewport.viewName != null)
4008     {
4009       title += viewport.viewName + " of ";
4010     }
4011
4012     title += this.title;
4013
4014     Desktop.addInternalFrame(tp, title, 600, 500);
4015   }
4016
4017   /**
4018    * DOCUMENT ME!
4019    *
4020    * @param title
4021    *          DOCUMENT ME!
4022    * @param order
4023    *          DOCUMENT ME!
4024    */
4025   public void addSortByOrderMenuItem(String title,
4026           final AlignmentOrder order)
4027   {
4028     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4029             "action.by_title_param", new Object[] { title }));
4030     sort.add(item);
4031     item.addActionListener(new java.awt.event.ActionListener()
4032     {
4033       @Override
4034       public void actionPerformed(ActionEvent e)
4035       {
4036         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4037
4038         // TODO: JBPNote - have to map order entries to curent SequenceI
4039         // pointers
4040         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4041
4042         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4043                 .getAlignment()));
4044
4045         alignPanel.paintAlignment(true);
4046       }
4047     });
4048   }
4049
4050   /**
4051    * Add a new sort by annotation score menu item
4052    *
4053    * @param sort
4054    *          the menu to add the option to
4055    * @param scoreLabel
4056    *          the label used to retrieve scores for each sequence on the
4057    *          alignment
4058    */
4059   public void addSortByAnnotScoreMenuItem(JMenu sort,
4060           final String scoreLabel)
4061   {
4062     final JMenuItem item = new JMenuItem(scoreLabel);
4063     sort.add(item);
4064     item.addActionListener(new java.awt.event.ActionListener()
4065     {
4066       @Override
4067       public void actionPerformed(ActionEvent e)
4068       {
4069         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4070         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4071                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4072         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4073                 viewport.getAlignment()));
4074         alignPanel.paintAlignment(true);
4075       }
4076     });
4077   }
4078
4079   /**
4080    * last hash for alignment's annotation array - used to minimise cost of
4081    * rebuild.
4082    */
4083   protected int _annotationScoreVectorHash;
4084
4085   /**
4086    * search the alignment and rebuild the sort by annotation score submenu the
4087    * last alignment annotation vector hash is stored to minimize cost of
4088    * rebuilding in subsequence calls.
4089    *
4090    */
4091   @Override
4092   public void buildSortByAnnotationScoresMenu()
4093   {
4094     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4095     {
4096       return;
4097     }
4098
4099     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4100     {
4101       sortByAnnotScore.removeAll();
4102       // almost certainly a quicker way to do this - but we keep it simple
4103       Hashtable scoreSorts = new Hashtable();
4104       AlignmentAnnotation aann[];
4105       for (SequenceI sqa : viewport.getAlignment().getSequences())
4106       {
4107         aann = sqa.getAnnotation();
4108         for (int i = 0; aann != null && i < aann.length; i++)
4109         {
4110           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4111           {
4112             scoreSorts.put(aann[i].label, aann[i].label);
4113           }
4114         }
4115       }
4116       Enumeration labels = scoreSorts.keys();
4117       while (labels.hasMoreElements())
4118       {
4119         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4120                 (String) labels.nextElement());
4121       }
4122       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4123       scoreSorts.clear();
4124
4125       _annotationScoreVectorHash = viewport.getAlignment()
4126               .getAlignmentAnnotation().hashCode();
4127     }
4128   }
4129
4130   /**
4131    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4132    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4133    * call. Listeners are added to remove the menu item when the treePanel is
4134    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4135    * modified.
4136    *
4137    * @param treePanel
4138    *          Displayed tree window.
4139    * @param title
4140    *          SortBy menu item title.
4141    */
4142   @Override
4143   public void buildTreeMenu()
4144   {
4145     calculateTree.removeAll();
4146     // build the calculate menu
4147
4148     for (final String type : new String[] { "NJ", "AV" })
4149     {
4150       String treecalcnm = MessageManager.getString("label.tree_calc_"
4151               + type.toLowerCase());
4152       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4153       {
4154         JMenuItem tm = new JMenuItem();
4155         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4156         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4157         {
4158           String smn = MessageManager.getStringOrReturn(
4159                   "label.score_model_", sm.getName());
4160           final String title = MessageManager.formatMessage(
4161                   "label.treecalc_title", treecalcnm, smn);
4162           tm.setText(title);//
4163           tm.addActionListener(new java.awt.event.ActionListener()
4164           {
4165             @Override
4166             public void actionPerformed(ActionEvent e)
4167             {
4168               newTreePanel(type, pwtype, title);
4169             }
4170           });
4171           calculateTree.add(tm);
4172         }
4173
4174       }
4175     }
4176     sortByTreeMenu.removeAll();
4177
4178     List<Component> comps = PaintRefresher.components.get(viewport
4179             .getSequenceSetId());
4180     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4181     for (Component comp : comps)
4182     {
4183       if (comp instanceof TreePanel)
4184       {
4185         treePanels.add((TreePanel) comp);
4186       }
4187     }
4188
4189     if (treePanels.size() < 1)
4190     {
4191       sortByTreeMenu.setVisible(false);
4192       return;
4193     }
4194
4195     sortByTreeMenu.setVisible(true);
4196
4197     for (final TreePanel tp : treePanels)
4198     {
4199       final JMenuItem item = new JMenuItem(tp.getTitle());
4200       item.addActionListener(new java.awt.event.ActionListener()
4201       {
4202         @Override
4203         public void actionPerformed(ActionEvent e)
4204         {
4205           tp.sortByTree_actionPerformed();
4206           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4207
4208         }
4209       });
4210
4211       sortByTreeMenu.add(item);
4212     }
4213   }
4214
4215   public boolean sortBy(AlignmentOrder alorder, String undoname)
4216   {
4217     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4218     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4219     if (undoname != null)
4220     {
4221       addHistoryItem(new OrderCommand(undoname, oldOrder,
4222               viewport.getAlignment()));
4223     }
4224     alignPanel.paintAlignment(true);
4225     return true;
4226   }
4227
4228   /**
4229    * Work out whether the whole set of sequences or just the selected set will
4230    * be submitted for multiple alignment.
4231    *
4232    */
4233   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4234   {
4235     // Now, check we have enough sequences
4236     AlignmentView msa = null;
4237
4238     if ((viewport.getSelectionGroup() != null)
4239             && (viewport.getSelectionGroup().getSize() > 1))
4240     {
4241       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4242       // some common interface!
4243       /*
4244        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4245        * SequenceI[sz = seqs.getSize(false)];
4246        *
4247        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4248        * seqs.getSequenceAt(i); }
4249        */
4250       msa = viewport.getAlignmentView(true);
4251     }
4252     else if (viewport.getSelectionGroup() != null
4253             && viewport.getSelectionGroup().getSize() == 1)
4254     {
4255       int option = JOptionPane.showConfirmDialog(this,
4256               MessageManager.getString("warn.oneseq_msainput_selection"),
4257               MessageManager.getString("label.invalid_selection"),
4258               JOptionPane.OK_CANCEL_OPTION);
4259       if (option == JOptionPane.OK_OPTION)
4260       {
4261         msa = viewport.getAlignmentView(false);
4262       }
4263     }
4264     else
4265     {
4266       msa = viewport.getAlignmentView(false);
4267     }
4268     return msa;
4269   }
4270
4271   /**
4272    * Decides what is submitted to a secondary structure prediction service: the
4273    * first sequence in the alignment, or in the current selection, or, if the
4274    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4275    * region or the whole alignment. (where the first sequence in the set is the
4276    * one that the prediction will be for).
4277    */
4278   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4279   {
4280     AlignmentView seqs = null;
4281
4282     if ((viewport.getSelectionGroup() != null)
4283             && (viewport.getSelectionGroup().getSize() > 0))
4284     {
4285       seqs = viewport.getAlignmentView(true);
4286     }
4287     else
4288     {
4289       seqs = viewport.getAlignmentView(false);
4290     }
4291     // limit sequences - JBPNote in future - could spawn multiple prediction
4292     // jobs
4293     // TODO: viewport.getAlignment().isAligned is a global state - the local
4294     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4295     if (!viewport.getAlignment().isAligned(false))
4296     {
4297       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4298       // TODO: if seqs.getSequences().length>1 then should really have warned
4299       // user!
4300
4301     }
4302     return seqs;
4303   }
4304
4305   /**
4306    * DOCUMENT ME!
4307    *
4308    * @param e
4309    *          DOCUMENT ME!
4310    */
4311   @Override
4312   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4313   {
4314     // Pick the tree file
4315     JalviewFileChooser chooser = new JalviewFileChooser(
4316             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4317     chooser.setFileView(new JalviewFileView());
4318     chooser.setDialogTitle(MessageManager
4319             .getString("label.select_newick_like_tree_file"));
4320     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4321
4322     int value = chooser.showOpenDialog(null);
4323
4324     if (value == JalviewFileChooser.APPROVE_OPTION)
4325     {
4326       String choice = chooser.getSelectedFile().getPath();
4327       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4328       jalview.io.NewickFile fin = null;
4329       try
4330       {
4331         fin = new jalview.io.NewickFile(choice, "File");
4332         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4333       } catch (Exception ex)
4334       {
4335         JOptionPane
4336                 .showMessageDialog(
4337                         Desktop.desktop,
4338                         ex.getMessage(),
4339                         MessageManager
4340                                 .getString("label.problem_reading_tree_file"),
4341                         JOptionPane.WARNING_MESSAGE);
4342         ex.printStackTrace();
4343       }
4344       if (fin != null && fin.hasWarningMessage())
4345       {
4346         JOptionPane.showMessageDialog(Desktop.desktop, fin
4347                 .getWarningMessage(), MessageManager
4348                 .getString("label.possible_problem_with_tree_file"),
4349                 JOptionPane.WARNING_MESSAGE);
4350       }
4351     }
4352   }
4353
4354   @Override
4355   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4356   {
4357     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4358   }
4359
4360   public TreePanel ShowNewickTree(NewickFile nf, String title)
4361   {
4362     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4363   }
4364
4365   public TreePanel ShowNewickTree(NewickFile nf, String title,
4366           AlignmentView input)
4367   {
4368     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4369   }
4370
4371   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4372           int h, int x, int y)
4373   {
4374     return ShowNewickTree(nf, title, null, w, h, x, y);
4375   }
4376
4377   /**
4378    * Add a treeviewer for the tree extracted from a newick file object to the
4379    * current alignment view
4380    *
4381    * @param nf
4382    *          the tree
4383    * @param title
4384    *          tree viewer title
4385    * @param input
4386    *          Associated alignment input data (or null)
4387    * @param w
4388    *          width
4389    * @param h
4390    *          height
4391    * @param x
4392    *          position
4393    * @param y
4394    *          position
4395    * @return TreePanel handle
4396    */
4397   public TreePanel ShowNewickTree(NewickFile nf, String title,
4398           AlignmentView input, int w, int h, int x, int y)
4399   {
4400     TreePanel tp = null;
4401
4402     try
4403     {
4404       nf.parse();
4405
4406       if (nf.getTree() != null)
4407       {
4408         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4409
4410         tp.setSize(w, h);
4411
4412         if (x > 0 && y > 0)
4413         {
4414           tp.setLocation(x, y);
4415         }
4416
4417         Desktop.addInternalFrame(tp, title, w, h);
4418       }
4419     } catch (Exception ex)
4420     {
4421       ex.printStackTrace();
4422     }
4423
4424     return tp;
4425   }
4426
4427   private boolean buildingMenu = false;
4428
4429   /**
4430    * Generates menu items and listener event actions for web service clients
4431    *
4432    */
4433   public void BuildWebServiceMenu()
4434   {
4435     while (buildingMenu)
4436     {
4437       try
4438       {
4439         System.err.println("Waiting for building menu to finish.");
4440         Thread.sleep(10);
4441       } catch (Exception e)
4442       {
4443       }
4444     }
4445     final AlignFrame me = this;
4446     buildingMenu = true;
4447     new Thread(new Runnable()
4448     {
4449       @Override
4450       public void run()
4451       {
4452         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4453         try
4454         {
4455           // System.err.println("Building ws menu again "
4456           // + Thread.currentThread());
4457           // TODO: add support for context dependent disabling of services based
4458           // on
4459           // alignment and current selection
4460           // TODO: add additional serviceHandle parameter to specify abstract
4461           // handler
4462           // class independently of AbstractName
4463           // TODO: add in rediscovery GUI function to restart discoverer
4464           // TODO: group services by location as well as function and/or
4465           // introduce
4466           // object broker mechanism.
4467           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4468           final IProgressIndicator af = me;
4469           final JMenu msawsmenu = new JMenu("Alignment");
4470           final JMenu secstrmenu = new JMenu(
4471                   "Secondary Structure Prediction");
4472           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4473           final JMenu analymenu = new JMenu("Analysis");
4474           final JMenu dismenu = new JMenu("Protein Disorder");
4475           // final JMenu msawsmenu = new
4476           // JMenu(MessageManager.getString("label.alignment"));
4477           // final JMenu secstrmenu = new
4478           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4479           // final JMenu seqsrchmenu = new
4480           // JMenu(MessageManager.getString("label.sequence_database_search"));
4481           // final JMenu analymenu = new
4482           // JMenu(MessageManager.getString("label.analysis"));
4483           // final JMenu dismenu = new
4484           // JMenu(MessageManager.getString("label.protein_disorder"));
4485           // JAL-940 - only show secondary structure prediction services from
4486           // the legacy server
4487           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4488               // &&
4489           Discoverer.services != null && (Discoverer.services.size() > 0))
4490           {
4491             // TODO: refactor to allow list of AbstractName/Handler bindings to
4492             // be
4493             // stored or retrieved from elsewhere
4494             // No MSAWS used any more:
4495             // Vector msaws = null; // (Vector)
4496             // Discoverer.services.get("MsaWS");
4497             Vector secstrpr = (Vector) Discoverer.services
4498                     .get("SecStrPred");
4499             if (secstrpr != null)
4500             {
4501               // Add any secondary structure prediction services
4502               for (int i = 0, j = secstrpr.size(); i < j; i++)
4503               {
4504                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4505                         .get(i);
4506                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4507                         .getServiceClient(sh);
4508                 int p = secstrmenu.getItemCount();
4509                 impl.attachWSMenuEntry(secstrmenu, me);
4510                 int q = secstrmenu.getItemCount();
4511                 for (int litm = p; litm < q; litm++)
4512                 {
4513                   legacyItems.add(secstrmenu.getItem(litm));
4514                 }
4515               }
4516             }
4517           }
4518
4519           // Add all submenus in the order they should appear on the web
4520           // services menu
4521           wsmenu.add(msawsmenu);
4522           wsmenu.add(secstrmenu);
4523           wsmenu.add(dismenu);
4524           wsmenu.add(analymenu);
4525           // No search services yet
4526           // wsmenu.add(seqsrchmenu);
4527
4528           javax.swing.SwingUtilities.invokeLater(new Runnable()
4529           {
4530             @Override
4531             public void run()
4532             {
4533               try
4534               {
4535                 webService.removeAll();
4536                 // first, add discovered services onto the webservices menu
4537                 if (wsmenu.size() > 0)
4538                 {
4539                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4540                   {
4541                     webService.add(wsmenu.get(i));
4542                   }
4543                 }
4544                 else
4545                 {
4546                   webService.add(me.webServiceNoServices);
4547                 }
4548                 // TODO: move into separate menu builder class.
4549                 boolean new_sspred = false;
4550                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4551                 {
4552                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4553                   if (jws2servs != null)
4554                   {
4555                     if (jws2servs.hasServices())
4556                     {
4557                       jws2servs.attachWSMenuEntry(webService, me);
4558                       for (Jws2Instance sv : jws2servs.getServices())
4559                       {
4560                         if (sv.description.toLowerCase().contains("jpred"))
4561                         {
4562                           for (JMenuItem jmi : legacyItems)
4563                           {
4564                             jmi.setVisible(false);
4565                           }
4566                         }
4567                       }
4568
4569                     }
4570                     if (jws2servs.isRunning())
4571                     {
4572                       JMenuItem tm = new JMenuItem(
4573                               "Still discovering JABA Services");
4574                       tm.setEnabled(false);
4575                       webService.add(tm);
4576                     }
4577                   }
4578                 }
4579                 build_urlServiceMenu(me.webService);
4580                 build_fetchdbmenu(webService);
4581                 for (JMenu item : wsmenu)
4582                 {
4583                   if (item.getItemCount() == 0)
4584                   {
4585                     item.setEnabled(false);
4586                   }
4587                   else
4588                   {
4589                     item.setEnabled(true);
4590                   }
4591                 }
4592               } catch (Exception e)
4593               {
4594                 Cache.log
4595                         .debug("Exception during web service menu building process.",
4596                                 e);
4597               }
4598             }
4599           });
4600         } catch (Exception e)
4601         {
4602         }
4603         buildingMenu = false;
4604       }
4605     }).start();
4606
4607   }
4608
4609   /**
4610    * construct any groupURL type service menu entries.
4611    *
4612    * @param webService
4613    */
4614   private void build_urlServiceMenu(JMenu webService)
4615   {
4616     // TODO: remove this code when 2.7 is released
4617     // DEBUG - alignmentView
4618     /*
4619      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4620      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4621      *
4622      * @Override public void actionPerformed(ActionEvent e) {
4623      * jalview.datamodel.AlignmentView
4624      * .testSelectionViews(af.viewport.getAlignment(),
4625      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4626      *
4627      * }); webService.add(testAlView);
4628      */
4629     // TODO: refactor to RestClient discoverer and merge menu entries for
4630     // rest-style services with other types of analysis/calculation service
4631     // SHmmr test client - still being implemented.
4632     // DEBUG - alignmentView
4633
4634     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4635             .getRestClients())
4636     {
4637       client.attachWSMenuEntry(
4638               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4639               this);
4640     }
4641   }
4642
4643   /*
4644    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4645    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4646    * getProperty("LAST_DIRECTORY"));
4647    *
4648    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4649    * to Vamsas file"); chooser.setToolTipText("Export");
4650    *
4651    * int value = chooser.showSaveDialog(this);
4652    *
4653    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4654    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4655    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4656    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4657    */
4658   /**
4659    * prototype of an automatically enabled/disabled analysis function
4660    *
4661    */
4662   protected void setShowProductsEnabled()
4663   {
4664     SequenceI[] selection = viewport.getSequenceSelection();
4665     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4666             viewport.getAlignment().getDataset()))
4667     {
4668       showProducts.setEnabled(true);
4669
4670     }
4671     else
4672     {
4673       showProducts.setEnabled(false);
4674     }
4675   }
4676
4677   /**
4678    * search selection for sequence xRef products and build the show products
4679    * menu.
4680    *
4681    * @param selection
4682    * @param dataset
4683    * @return true if showProducts menu should be enabled.
4684    */
4685   public boolean canShowProducts(SequenceI[] selection,
4686           boolean isRegionSelection, Alignment dataset)
4687   {
4688     boolean showp = false;
4689     try
4690     {
4691       showProducts.removeAll();
4692       final boolean dna = viewport.getAlignment().isNucleotide();
4693       final Alignment ds = dataset;
4694       String[] ptypes = (selection == null || selection.length == 0) ? null
4695               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4696       // Object[] prods =
4697       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4698       // selection, dataset, true);
4699       final SequenceI[] sel = selection;
4700       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4701       {
4702         showp = true;
4703         final boolean isRegSel = isRegionSelection;
4704         final AlignFrame af = this;
4705         final String source = ptypes[t];
4706         JMenuItem xtype = new JMenuItem(ptypes[t]);
4707         xtype.addActionListener(new ActionListener()
4708         {
4709
4710           @Override
4711           public void actionPerformed(ActionEvent e)
4712           {
4713             // TODO: new thread for this call with vis-delay
4714             af.showProductsFor(af.viewport.getSequenceSelection(),
4715                     isRegSel, dna, source);
4716           }
4717
4718         });
4719         showProducts.add(xtype);
4720       }
4721       showProducts.setVisible(showp);
4722       showProducts.setEnabled(showp);
4723     } catch (Exception e)
4724     {
4725       jalview.bin.Cache.log
4726               .warn("canTranslate threw an exception - please report to help@jalview.org",
4727                       e);
4728       return false;
4729     }
4730     return showp;
4731   }
4732
4733   protected void showProductsFor(final SequenceI[] sel,
4734           final boolean isRegSel, final boolean dna, final String source)
4735   {
4736     Runnable foo = new Runnable()
4737     {
4738
4739       @Override
4740       public void run()
4741       {
4742         final long sttime = System.currentTimeMillis();
4743         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4744                 "status.searching_for_sequences_from",
4745                 new Object[] { source }), sttime);
4746         try
4747         {
4748           // update our local dataset reference
4749           Alignment ds = AlignFrame.this.getViewport().getAlignment()
4750                   .getDataset();
4751           Alignment prods = CrossRef
4752                   .findXrefSequences(sel, dna, source, ds);
4753           if (prods != null)
4754           {
4755             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4756             for (int s = 0; s < sprods.length; s++)
4757             {
4758               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4759               if (ds.getSequences() == null
4760                       || !ds.getSequences().contains(
4761                               sprods[s].getDatasetSequence()))
4762               {
4763                 ds.addSequence(sprods[s].getDatasetSequence());
4764               }
4765               sprods[s].updatePDBIds();
4766             }
4767             Alignment al = new Alignment(sprods);
4768             al.setDataset(ds);
4769
4770             /*
4771              * Copy dna-to-protein mappings to new alignment
4772              */
4773             // TODO 1: no mappings are set up for EMBL product
4774             // TODO 2: if they were, should add them to protein alignment, not
4775             // dna
4776             Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4777             for (AlignedCodonFrame acf : cf)
4778             {
4779               al.addCodonFrame(acf);
4780             }
4781             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4782                     DEFAULT_HEIGHT);
4783             String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4784                     + " for " + ((isRegSel) ? "selected region of " : "")
4785                     + getTitle();
4786             naf.setTitle(newtitle);
4787
4788             // temporary flag until SplitFrame is released
4789             boolean asSplitFrame = Cache.getDefault(
4790                     Preferences.ENABLE_SPLIT_FRAME, true);
4791             if (asSplitFrame)
4792             {
4793               /*
4794                * Make a copy of this alignment (sharing the same dataset
4795                * sequences). If we are DNA, drop introns and update mappings
4796                */
4797               AlignmentI copyAlignment = null;
4798               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4799                       .getSequenceSelection();
4800               if (dna)
4801               {
4802                 copyAlignment = AlignmentUtils.makeExonAlignment(
4803                         sequenceSelection, cf);
4804                 al.getCodonFrames().clear();
4805                 al.getCodonFrames().addAll(cf);
4806                 final StructureSelectionManager ssm = StructureSelectionManager
4807                         .getStructureSelectionManager(Desktop.instance);
4808                 ssm.registerMappings(cf);
4809               }
4810               else
4811               {
4812                 copyAlignment = new Alignment(new Alignment(
4813                         sequenceSelection));
4814               }
4815               AlignFrame copyThis = new AlignFrame(copyAlignment,
4816                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4817               copyThis.setTitle(AlignFrame.this.getTitle());
4818               // SplitFrame with dna above, protein below
4819               SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4820                       dna ? naf : copyThis);
4821               naf.setVisible(true);
4822               copyThis.setVisible(true);
4823               String linkedTitle = MessageManager
4824                       .getString("label.linked_view_title");
4825               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4826             }
4827             else
4828             {
4829               Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4830                       DEFAULT_HEIGHT);
4831             }
4832           }
4833           else
4834           {
4835             System.err.println("No Sequences generated for xRef type "
4836                     + source);
4837           }
4838         } catch (Exception e)
4839         {
4840           jalview.bin.Cache.log.error(
4841                   "Exception when finding crossreferences", e);
4842         } catch (OutOfMemoryError e)
4843         {
4844           new OOMWarning("whilst fetching crossreferences", e);
4845         } catch (Error e)
4846         {
4847           jalview.bin.Cache.log.error("Error when finding crossreferences",
4848                   e);
4849         }
4850         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4851                 "status.finished_searching_for_sequences_from",
4852                 new Object[] { source }), sttime);
4853       }
4854
4855     };
4856     Thread frunner = new Thread(foo);
4857     frunner.start();
4858   }
4859
4860   public boolean canShowTranslationProducts(SequenceI[] selection,
4861           AlignmentI alignment)
4862   {
4863     // old way
4864     try
4865     {
4866       return (jalview.analysis.Dna.canTranslate(selection,
4867               viewport.getViewAsVisibleContigs(true)));
4868     } catch (Exception e)
4869     {
4870       jalview.bin.Cache.log
4871               .warn("canTranslate threw an exception - please report to help@jalview.org",
4872                       e);
4873       return false;
4874     }
4875   }
4876
4877   /**
4878    * Construct and display a new frame containing the translation of this
4879    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4880    */
4881   @Override
4882   public void showTranslation_actionPerformed(ActionEvent e)
4883   {
4884     AlignmentI al = null;
4885     try
4886     {
4887       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4888
4889       al = dna.translateCdna();
4890     } catch (Exception ex)
4891     {
4892       jalview.bin.Cache.log.error(
4893               "Exception during translation. Please report this !", ex);
4894       final String msg = MessageManager
4895               .getString("label.error_when_translating_sequences_submit_bug_report");
4896       final String errorTitle = MessageManager
4897               .getString("label.implementation_error")
4898               + MessageManager.getString("translation_failed");
4899       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4900               JOptionPane.ERROR_MESSAGE);
4901       return;
4902     }
4903     if (al == null || al.getHeight() == 0)
4904     {
4905       final String msg = MessageManager
4906               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4907       final String errorTitle = MessageManager
4908               .getString("label.translation_failed");
4909       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4910               JOptionPane.WARNING_MESSAGE);
4911     }
4912     else
4913     {
4914       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4915       af.setFileFormat(this.currentFileFormat);
4916       final String newTitle = MessageManager.formatMessage(
4917               "label.translation_of_params",
4918               new Object[] { this.getTitle() });
4919       af.setTitle(newTitle);
4920       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4921       {
4922         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4923         viewport.openSplitFrame(af, new Alignment(seqs));
4924       }
4925       else
4926       {
4927         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4928                 DEFAULT_HEIGHT);
4929       }
4930     }
4931   }
4932
4933   /**
4934    * Set the file format
4935    *
4936    * @param fileFormat
4937    */
4938   public void setFileFormat(String fileFormat)
4939   {
4940     this.currentFileFormat = fileFormat;
4941   }
4942
4943   /**
4944    * Try to load a features file onto the alignment.
4945    *
4946    * @param file
4947    *          contents or path to retrieve file
4948    * @param type
4949    *          access mode of file (see jalview.io.AlignFile)
4950    * @return true if features file was parsed correctly.
4951    */
4952   public boolean parseFeaturesFile(String file, String type)
4953   {
4954     return avc.parseFeaturesFile(file, type,
4955             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4956
4957   }
4958
4959   @Override
4960   public void refreshFeatureUI(boolean enableIfNecessary)
4961   {
4962     // note - currently this is only still here rather than in the controller
4963     // because of the featureSettings hard reference that is yet to be
4964     // abstracted
4965     if (enableIfNecessary)
4966     {
4967       viewport.setShowSequenceFeatures(true);
4968       showSeqFeatures.setSelected(true);
4969     }
4970
4971   }
4972
4973   @Override
4974   public void dragEnter(DropTargetDragEvent evt)
4975   {
4976   }
4977
4978   @Override
4979   public void dragExit(DropTargetEvent evt)
4980   {
4981   }
4982
4983   @Override
4984   public void dragOver(DropTargetDragEvent evt)
4985   {
4986   }
4987
4988   @Override
4989   public void dropActionChanged(DropTargetDragEvent evt)
4990   {
4991   }
4992
4993   @Override
4994   public void drop(DropTargetDropEvent evt)
4995   {
4996     Transferable t = evt.getTransferable();
4997     java.util.List files = null;
4998
4999     try
5000     {
5001       DataFlavor uriListFlavor = new DataFlavor(
5002               "text/uri-list;class=java.lang.String");
5003       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5004       {
5005         // Works on Windows and MacOSX
5006         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5007         files = (java.util.List) t
5008                 .getTransferData(DataFlavor.javaFileListFlavor);
5009       }
5010       else if (t.isDataFlavorSupported(uriListFlavor))
5011       {
5012         // This is used by Unix drag system
5013         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5014         String data = (String) t.getTransferData(uriListFlavor);
5015         files = new java.util.ArrayList(1);
5016         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5017                 data, "\r\n"); st.hasMoreTokens();)
5018         {
5019           String s = st.nextToken();
5020           if (s.startsWith("#"))
5021           {
5022             // the line is a comment (as per the RFC 2483)
5023             continue;
5024           }
5025
5026           java.net.URI uri = new java.net.URI(s);
5027           // check to see if we can handle this kind of URI
5028           if (uri.getScheme().toLowerCase().startsWith("http"))
5029           {
5030             files.add(uri.toString());
5031           }
5032           else
5033           {
5034             // otherwise preserve old behaviour: catch all for file objects
5035             java.io.File file = new java.io.File(uri);
5036             files.add(file.toString());
5037           }
5038         }
5039       }
5040     } catch (Exception e)
5041     {
5042       e.printStackTrace();
5043     }
5044     if (files != null)
5045     {
5046       try
5047       {
5048         // check to see if any of these files have names matching sequences in
5049         // the alignment
5050         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5051                 .getAlignment().getSequencesArray());
5052         /**
5053          * Object[] { String,SequenceI}
5054          */
5055         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5056         ArrayList<String> filesnotmatched = new ArrayList<String>();
5057         for (int i = 0; i < files.size(); i++)
5058         {
5059           String file = files.get(i).toString();
5060           String pdbfn = "";
5061           String protocol = FormatAdapter.checkProtocol(file);
5062           if (protocol == jalview.io.FormatAdapter.FILE)
5063           {
5064             File fl = new File(file);
5065             pdbfn = fl.getName();
5066           }
5067           else if (protocol == jalview.io.FormatAdapter.URL)
5068           {
5069             URL url = new URL(file);
5070             pdbfn = url.getFile();
5071           }
5072           if (pdbfn.length() > 0)
5073           {
5074             // attempt to find a match in the alignment
5075             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5076             int l = 0, c = pdbfn.indexOf(".");
5077             while (mtch == null && c != -1)
5078             {
5079               do
5080               {
5081                 l = c;
5082               } while ((c = pdbfn.indexOf(".", l)) > l);
5083               if (l > -1)
5084               {
5085                 pdbfn = pdbfn.substring(0, l);
5086               }
5087               mtch = idm.findAllIdMatches(pdbfn);
5088             }
5089             if (mtch != null)
5090             {
5091               String type = null;
5092               try
5093               {
5094                 type = new IdentifyFile().Identify(file, protocol);
5095               } catch (Exception ex)
5096               {
5097                 type = null;
5098               }
5099               if (type != null)
5100               {
5101                 if (type.equalsIgnoreCase("PDB"))
5102                 {
5103                   filesmatched.add(new Object[] { file, protocol, mtch });
5104                   continue;
5105                 }
5106               }
5107             }
5108             // File wasn't named like one of the sequences or wasn't a PDB file.
5109             filesnotmatched.add(file);
5110           }
5111         }
5112         int assocfiles = 0;
5113         if (filesmatched.size() > 0)
5114         {
5115           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5116                   || JOptionPane
5117                           .showConfirmDialog(
5118                                   this,
5119                                   MessageManager
5120                                           .formatMessage(
5121                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5122                                                   new Object[] { Integer
5123                                                           .valueOf(
5124                                                                   filesmatched
5125                                                                           .size())
5126                                                           .toString() }),
5127                                   MessageManager
5128                                           .getString("label.automatically_associate_pdb_files_by_name"),
5129                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5130
5131           {
5132             for (Object[] fm : filesmatched)
5133             {
5134               // try and associate
5135               // TODO: may want to set a standard ID naming formalism for
5136               // associating PDB files which have no IDs.
5137               for (SequenceI toassoc : (SequenceI[]) fm[2])
5138               {
5139                 PDBEntry pe = new AssociatePdbFileWithSeq()
5140                         .associatePdbWithSeq((String) fm[0],
5141                                 (String) fm[1], toassoc, false,
5142                                 Desktop.instance);
5143                 if (pe != null)
5144                 {
5145                   System.err.println("Associated file : "
5146                           + ((String) fm[0]) + " with "
5147                           + toassoc.getDisplayId(true));
5148                   assocfiles++;
5149                 }
5150               }
5151               alignPanel.paintAlignment(true);
5152             }
5153           }
5154         }
5155         if (filesnotmatched.size() > 0)
5156         {
5157           if (assocfiles > 0
5158                   && (Cache.getDefault(
5159                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5160                           .showConfirmDialog(
5161                                   this,
5162                                   "<html>"
5163                                           + MessageManager
5164                                                   .formatMessage(
5165                                                           "label.ignore_unmatched_dropped_files_info",
5166                                                           new Object[] { Integer
5167                                                                   .valueOf(
5168                                                                           filesnotmatched
5169                                                                                   .size())
5170                                                                   .toString() })
5171                                           + "</html>",
5172                                   MessageManager
5173                                           .getString("label.ignore_unmatched_dropped_files"),
5174                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5175           {
5176             return;
5177           }
5178           for (String fn : filesnotmatched)
5179           {
5180             loadJalviewDataFile(fn, null, null, null);
5181           }
5182
5183         }
5184       } catch (Exception ex)
5185       {
5186         ex.printStackTrace();
5187       }
5188     }
5189   }
5190
5191   /**
5192    * Attempt to load a "dropped" file or URL string: First by testing whether
5193    * it's and Annotation file, then a JNet file, and finally a features file. If
5194    * all are false then the user may have dropped an alignment file onto this
5195    * AlignFrame.
5196    *
5197    * @param file
5198    *          either a filename or a URL string.
5199    */
5200   public void loadJalviewDataFile(String file, String protocol,
5201           String format, SequenceI assocSeq)
5202   {
5203     try
5204     {
5205       if (protocol == null)
5206       {
5207         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5208       }
5209       // if the file isn't identified, or not positively identified as some
5210       // other filetype (PFAM is default unidentified alignment file type) then
5211       // try to parse as annotation.
5212       boolean isAnnotation = (format == null || format
5213               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5214               .annotateAlignmentView(viewport, file, protocol) : false;
5215
5216       if (!isAnnotation)
5217       {
5218         // first see if its a T-COFFEE score file
5219         TCoffeeScoreFile tcf = null;
5220         try
5221         {
5222           tcf = new TCoffeeScoreFile(file, protocol);
5223           if (tcf.isValid())
5224           {
5225             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5226             {
5227               tcoffeeColour.setEnabled(true);
5228               tcoffeeColour.setSelected(true);
5229               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5230               isAnnotation = true;
5231               statusBar
5232                       .setText(MessageManager
5233                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5234             }
5235             else
5236             {
5237               // some problem - if no warning its probable that the ID matching
5238               // process didn't work
5239               JOptionPane
5240                       .showMessageDialog(
5241                               Desktop.desktop,
5242                               tcf.getWarningMessage() == null ? MessageManager
5243                                       .getString("label.check_file_matches_sequence_ids_alignment")
5244                                       : tcf.getWarningMessage(),
5245                               MessageManager
5246                                       .getString("label.problem_reading_tcoffee_score_file"),
5247                               JOptionPane.WARNING_MESSAGE);
5248             }
5249           }
5250           else
5251           {
5252             tcf = null;
5253           }
5254         } catch (Exception x)
5255         {
5256           Cache.log
5257                   .debug("Exception when processing data source as T-COFFEE score file",
5258                           x);
5259           tcf = null;
5260         }
5261         if (tcf == null)
5262         {
5263           // try to see if its a JNet 'concise' style annotation file *before*
5264           // we
5265           // try to parse it as a features file
5266           if (format == null)
5267           {
5268             format = new IdentifyFile().Identify(file, protocol);
5269           }
5270           if (format.equalsIgnoreCase("JnetFile"))
5271           {
5272             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5273                     file, protocol);
5274             new JnetAnnotationMaker();
5275             JnetAnnotationMaker.add_annotation(predictions,
5276                     viewport.getAlignment(), 0, false);
5277             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5278             viewport.getAlignment().setSeqrep(repseq);
5279             ColumnSelection cs = new ColumnSelection();
5280             cs.hideInsertionsFor(repseq);
5281             viewport.setColumnSelection(cs);
5282             isAnnotation = true;
5283           }
5284           else
5285           {
5286             /*
5287              * if (format.equalsIgnoreCase("PDB")) {
5288              *
5289              * String pdbfn = ""; // try to match up filename with sequence id
5290              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5291              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5292              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5293              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5294              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5295              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5296              * // attempt to find a match in the alignment SequenceI mtch =
5297              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5298              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5299              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5300              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5301              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5302              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5303              * { System.err.println("Associated file : " + file + " with " +
5304              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5305              * TODO: maybe need to load as normal otherwise return; } }
5306              */
5307             // try to parse it as a features file
5308             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5309             // if it wasn't a features file then we just treat it as a general
5310             // alignment file to load into the current view.
5311             if (!isGroupsFile)
5312             {
5313               new FileLoader().LoadFile(viewport, file, protocol, format);
5314             }
5315             else
5316             {
5317               alignPanel.paintAlignment(true);
5318             }
5319           }
5320         }
5321       }
5322       if (isAnnotation)
5323       {
5324
5325         alignPanel.adjustAnnotationHeight();
5326         viewport.updateSequenceIdColours();
5327         buildSortByAnnotationScoresMenu();
5328         alignPanel.paintAlignment(true);
5329       }
5330     } catch (Exception ex)
5331     {
5332       ex.printStackTrace();
5333     } catch (OutOfMemoryError oom)
5334     {
5335       try
5336       {
5337         System.gc();
5338       } catch (Exception x)
5339       {
5340       }
5341       ;
5342       new OOMWarning(
5343               "loading data "
5344                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5345                               : "using " + protocol + " from " + file)
5346                               : ".")
5347                       + (format != null ? "(parsing as '" + format
5348                               + "' file)" : ""), oom, Desktop.desktop);
5349     }
5350   }
5351
5352   /**
5353    * Method invoked by the ChangeListener on the tabbed pane, in other words
5354    * when a different tabbed pane is selected by the user or programmatically.
5355    */
5356   @Override
5357   public void tabSelectionChanged(int index)
5358   {
5359     if (index > -1)
5360     {
5361       alignPanel = alignPanels.get(index);
5362       viewport = alignPanel.av;
5363       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5364       setMenusFromViewport(viewport);
5365     }
5366
5367     /*
5368      * If there is a frame linked to this one in a SplitPane, switch it to the
5369      * same view tab index. No infinite recursion of calls should happen, since
5370      * tabSelectionChanged() should not get invoked on setting the selected
5371      * index to an unchanged value. Guard against setting an invalid index
5372      * before the new view peer tab has been created.
5373      */
5374     final AlignViewportI peer = viewport.getCodingComplement();
5375     if (peer != null)
5376     {
5377       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5378       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5379       {
5380         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5381       }
5382     }
5383   }
5384
5385   /**
5386    * On right mouse click on view tab, prompt for and set new view name.
5387    */
5388   @Override
5389   public void tabbedPane_mousePressed(MouseEvent e)
5390   {
5391     if (SwingUtilities.isRightMouseButton(e))
5392     {
5393       String msg = MessageManager.getString("label.enter_view_name");
5394       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5395               JOptionPane.QUESTION_MESSAGE);
5396
5397       if (reply != null)
5398       {
5399         viewport.viewName = reply;
5400         // TODO warn if reply is in getExistingViewNames()?
5401         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5402       }
5403     }
5404   }
5405
5406   public AlignViewport getCurrentView()
5407   {
5408     return viewport;
5409   }
5410
5411   /**
5412    * Open the dialog for regex description parsing.
5413    */
5414   @Override
5415   protected void extractScores_actionPerformed(ActionEvent e)
5416   {
5417     ParseProperties pp = new jalview.analysis.ParseProperties(
5418             viewport.getAlignment());
5419     // TODO: verify regex and introduce GUI dialog for version 2.5
5420     // if (pp.getScoresFromDescription("col", "score column ",
5421     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5422     // true)>0)
5423     if (pp.getScoresFromDescription("description column",
5424             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5425     {
5426       buildSortByAnnotationScoresMenu();
5427     }
5428   }
5429
5430   /*
5431    * (non-Javadoc)
5432    *
5433    * @see
5434    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5435    * )
5436    */
5437   @Override
5438   protected void showDbRefs_actionPerformed(ActionEvent e)
5439   {
5440     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5441   }
5442
5443   /*
5444    * (non-Javadoc)
5445    *
5446    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5447    * ActionEvent)
5448    */
5449   @Override
5450   protected void showNpFeats_actionPerformed(ActionEvent e)
5451   {
5452     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5453   }
5454
5455   /**
5456    * find the viewport amongst the tabs in this alignment frame and close that
5457    * tab
5458    *
5459    * @param av
5460    */
5461   public boolean closeView(AlignViewportI av)
5462   {
5463     if (viewport == av)
5464     {
5465       this.closeMenuItem_actionPerformed(false);
5466       return true;
5467     }
5468     Component[] comp = tabbedPane.getComponents();
5469     for (int i = 0; comp != null && i < comp.length; i++)
5470     {
5471       if (comp[i] instanceof AlignmentPanel)
5472       {
5473         if (((AlignmentPanel) comp[i]).av == av)
5474         {
5475           // close the view.
5476           closeView((AlignmentPanel) comp[i]);
5477           return true;
5478         }
5479       }
5480     }
5481     return false;
5482   }
5483
5484   protected void build_fetchdbmenu(JMenu webService)
5485   {
5486     // Temporary hack - DBRef Fetcher always top level ws entry.
5487     // TODO We probably want to store a sequence database checklist in
5488     // preferences and have checkboxes.. rather than individual sources selected
5489     // here
5490     final JMenu rfetch = new JMenu(
5491             MessageManager.getString("action.fetch_db_references"));
5492     rfetch.setToolTipText(MessageManager
5493             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5494     webService.add(rfetch);
5495
5496     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5497             MessageManager.getString("option.trim_retrieved_seqs"));
5498     trimrs.setToolTipText(MessageManager
5499             .getString("label.trim_retrieved_sequences"));
5500     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5501     trimrs.addActionListener(new ActionListener()
5502     {
5503       @Override
5504       public void actionPerformed(ActionEvent e)
5505       {
5506         trimrs.setSelected(trimrs.isSelected());
5507         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5508                 Boolean.valueOf(trimrs.isSelected()).toString());
5509       };
5510     });
5511     rfetch.add(trimrs);
5512     JMenuItem fetchr = new JMenuItem(
5513             MessageManager.getString("label.standard_databases"));
5514     fetchr.setToolTipText(MessageManager
5515             .getString("label.fetch_embl_uniprot"));
5516     fetchr.addActionListener(new ActionListener()
5517     {
5518
5519       @Override
5520       public void actionPerformed(ActionEvent e)
5521       {
5522         new Thread(new Runnable()
5523         {
5524
5525           @Override
5526           public void run()
5527           {
5528             new jalview.ws.DBRefFetcher(alignPanel.av
5529                     .getSequenceSelection(), alignPanel.alignFrame)
5530                     .fetchDBRefs(false);
5531           }
5532         }).start();
5533
5534       }
5535
5536     });
5537     rfetch.add(fetchr);
5538     final AlignFrame me = this;
5539     new Thread(new Runnable()
5540     {
5541       @Override
5542       public void run()
5543       {
5544         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5545                 .getSequenceFetcherSingleton(me);
5546         javax.swing.SwingUtilities.invokeLater(new Runnable()
5547         {
5548           @Override
5549           public void run()
5550           {
5551             String[] dbclasses = sf.getOrderedSupportedSources();
5552             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5553             // jalview.util.QuickSort.sort(otherdb, otherdb);
5554             List<DbSourceProxy> otherdb;
5555             JMenu dfetch = new JMenu();
5556             JMenu ifetch = new JMenu();
5557             JMenuItem fetchr = null;
5558             int comp = 0, icomp = 0, mcomp = 15;
5559             String mname = null;
5560             int dbi = 0;
5561             for (String dbclass : dbclasses)
5562             {
5563               otherdb = sf.getSourceProxy(dbclass);
5564               // add a single entry for this class, or submenu allowing 'fetch
5565               // all' or pick one
5566               if (otherdb == null || otherdb.size() < 1)
5567               {
5568                 continue;
5569               }
5570               // List<DbSourceProxy> dbs=otherdb;
5571               // otherdb=new ArrayList<DbSourceProxy>();
5572               // for (DbSourceProxy db:dbs)
5573               // {
5574               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5575               // }
5576               if (mname == null)
5577               {
5578                 mname = "From " + dbclass;
5579               }
5580               if (otherdb.size() == 1)
5581               {
5582                 final DbSourceProxy[] dassource = otherdb
5583                         .toArray(new DbSourceProxy[0]);
5584                 DbSourceProxy src = otherdb.get(0);
5585                 fetchr = new JMenuItem(src.getDbSource());
5586                 fetchr.addActionListener(new ActionListener()
5587                 {
5588
5589                   @Override
5590                   public void actionPerformed(ActionEvent e)
5591                   {
5592                     new Thread(new Runnable()
5593                     {
5594
5595                       @Override
5596                       public void run()
5597                       {
5598                         new jalview.ws.DBRefFetcher(alignPanel.av
5599                                 .getSequenceSelection(),
5600                                 alignPanel.alignFrame, dassource)
5601                                 .fetchDBRefs(false);
5602                       }
5603                     }).start();
5604                   }
5605
5606                 });
5607                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5608                         MessageManager.formatMessage(
5609                                 "label.fetch_retrieve_from",
5610                                 new Object[] { src.getDbName() })));
5611                 dfetch.add(fetchr);
5612                 comp++;
5613               }
5614               else
5615               {
5616                 final DbSourceProxy[] dassource = otherdb
5617                         .toArray(new DbSourceProxy[0]);
5618                 // fetch all entry
5619                 DbSourceProxy src = otherdb.get(0);
5620                 fetchr = new JMenuItem(MessageManager.formatMessage(
5621                         "label.fetch_all_param",
5622                         new Object[] { src.getDbSource() }));
5623                 fetchr.addActionListener(new ActionListener()
5624                 {
5625                   @Override
5626                   public void actionPerformed(ActionEvent e)
5627                   {
5628                     new Thread(new Runnable()
5629                     {
5630
5631                       @Override
5632                       public void run()
5633                       {
5634                         new jalview.ws.DBRefFetcher(alignPanel.av
5635                                 .getSequenceSelection(),
5636                                 alignPanel.alignFrame, dassource)
5637                                 .fetchDBRefs(false);
5638                       }
5639                     }).start();
5640                   }
5641                 });
5642
5643                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5644                         MessageManager.formatMessage(
5645                                 "label.fetch_retrieve_from_all_sources",
5646                                 new Object[] {
5647                                     Integer.valueOf(otherdb.size())
5648                                             .toString(), src.getDbSource(),
5649                                     src.getDbName() })));
5650                 dfetch.add(fetchr);
5651                 comp++;
5652                 // and then build the rest of the individual menus
5653                 ifetch = new JMenu(MessageManager.formatMessage(
5654                         "label.source_from_db_source",
5655                         new Object[] { src.getDbSource() }));
5656                 icomp = 0;
5657                 String imname = null;
5658                 int i = 0;
5659                 for (DbSourceProxy sproxy : otherdb)
5660                 {
5661                   String dbname = sproxy.getDbName();
5662                   String sname = dbname.length() > 5 ? dbname.substring(0,
5663                           5) + "..." : dbname;
5664                   String msname = dbname.length() > 10 ? dbname.substring(
5665                           0, 10) + "..." : dbname;
5666                   if (imname == null)
5667                   {
5668                     imname = MessageManager.formatMessage(
5669                             "label.from_msname", new Object[] { sname });
5670                   }
5671                   fetchr = new JMenuItem(msname);
5672                   final DbSourceProxy[] dassrc = { sproxy };
5673                   fetchr.addActionListener(new ActionListener()
5674                   {
5675
5676                     @Override
5677                     public void actionPerformed(ActionEvent e)
5678                     {
5679                       new Thread(new Runnable()
5680                       {
5681
5682                         @Override
5683                         public void run()
5684                         {
5685                           new jalview.ws.DBRefFetcher(alignPanel.av
5686                                   .getSequenceSelection(),
5687                                   alignPanel.alignFrame, dassrc)
5688                                   .fetchDBRefs(false);
5689                         }
5690                       }).start();
5691                     }
5692
5693                   });
5694                   fetchr.setToolTipText("<html>"
5695                           + MessageManager.formatMessage(
5696                                   "label.fetch_retrieve_from", new Object[]
5697                                   { dbname }));
5698                   ifetch.add(fetchr);
5699                   ++i;
5700                   if (++icomp >= mcomp || i == (otherdb.size()))
5701                   {
5702                     ifetch.setText(MessageManager.formatMessage(
5703                             "label.source_to_target", imname, sname));
5704                     dfetch.add(ifetch);
5705                     ifetch = new JMenu();
5706                     imname = null;
5707                     icomp = 0;
5708                     comp++;
5709                   }
5710                 }
5711               }
5712               ++dbi;
5713               if (comp >= mcomp || dbi >= (dbclasses.length))
5714               {
5715                 dfetch.setText(MessageManager.formatMessage(
5716                         "label.source_to_target", mname, dbclass));
5717                 rfetch.add(dfetch);
5718                 dfetch = new JMenu();
5719                 mname = null;
5720                 comp = 0;
5721               }
5722             }
5723           }
5724         });
5725       }
5726     }).start();
5727
5728   }
5729
5730   /**
5731    * Left justify the whole alignment.
5732    */
5733   @Override
5734   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5735   {
5736     AlignmentI al = viewport.getAlignment();
5737     al.justify(false);
5738     viewport.firePropertyChange("alignment", null, al);
5739   }
5740
5741   /**
5742    * Right justify the whole alignment.
5743    */
5744   @Override
5745   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5746   {
5747     AlignmentI al = viewport.getAlignment();
5748     al.justify(true);
5749     viewport.firePropertyChange("alignment", null, al);
5750   }
5751
5752   public void setShowSeqFeatures(boolean b)
5753   {
5754     showSeqFeatures.setSelected(b);
5755     viewport.setShowSequenceFeatures(b);
5756   }
5757
5758   /*
5759    * (non-Javadoc)
5760    *
5761    * @see
5762    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5763    * awt.event.ActionEvent)
5764    */
5765   @Override
5766   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5767   {
5768     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5769     alignPanel.paintAlignment(true);
5770   }
5771
5772   /*
5773    * (non-Javadoc)
5774    *
5775    * @see
5776    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5777    * .ActionEvent)
5778    */
5779   @Override
5780   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5781   {
5782     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5783     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5784
5785   }
5786
5787   /*
5788    * (non-Javadoc)
5789    *
5790    * @see
5791    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5792    * .event.ActionEvent)
5793    */
5794   @Override
5795   protected void showGroupConservation_actionPerformed(ActionEvent e)
5796   {
5797     viewport.setShowGroupConservation(showGroupConservation.getState());
5798     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5799   }
5800
5801   /*
5802    * (non-Javadoc)
5803    *
5804    * @see
5805    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5806    * .event.ActionEvent)
5807    */
5808   @Override
5809   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5810   {
5811     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5812     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5813   }
5814
5815   /*
5816    * (non-Javadoc)
5817    *
5818    * @see
5819    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5820    * .event.ActionEvent)
5821    */
5822   @Override
5823   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5824   {
5825     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5826     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5827   }
5828
5829   @Override
5830   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5831   {
5832     showSequenceLogo.setState(true);
5833     viewport.setShowSequenceLogo(true);
5834     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5835     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5836   }
5837
5838   @Override
5839   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5840   {
5841     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5842   }
5843
5844   /*
5845    * (non-Javadoc)
5846    *
5847    * @see
5848    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5849    * .event.ActionEvent)
5850    */
5851   @Override
5852   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5853   {
5854     if (avc.makeGroupsFromSelection())
5855     {
5856       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5857       alignPanel.updateAnnotation();
5858       alignPanel.paintAlignment(true);
5859     }
5860   }
5861
5862   public void clearAlignmentSeqRep()
5863   {
5864     // TODO refactor alignmentseqrep to controller
5865     if (viewport.getAlignment().hasSeqrep())
5866     {
5867       viewport.getAlignment().setSeqrep(null);
5868       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5869       alignPanel.updateAnnotation();
5870       alignPanel.paintAlignment(true);
5871     }
5872   }
5873
5874   @Override
5875   protected void createGroup_actionPerformed(ActionEvent e)
5876   {
5877     if (avc.createGroup())
5878     {
5879       alignPanel.alignmentChanged();
5880     }
5881   }
5882
5883   @Override
5884   protected void unGroup_actionPerformed(ActionEvent e)
5885   {
5886     if (avc.unGroup())
5887     {
5888       alignPanel.alignmentChanged();
5889     }
5890   }
5891
5892   /**
5893    * make the given alignmentPanel the currently selected tab
5894    *
5895    * @param alignmentPanel
5896    */
5897   public void setDisplayedView(AlignmentPanel alignmentPanel)
5898   {
5899     if (!viewport.getSequenceSetId().equals(
5900             alignmentPanel.av.getSequenceSetId()))
5901     {
5902       throw new Error(
5903               MessageManager
5904                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5905     }
5906     if (tabbedPane != null
5907             && tabbedPane.getTabCount() > 0
5908             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5909                     .getSelectedIndex())
5910     {
5911       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5912     }
5913   }
5914
5915   /**
5916    * Action on selection of menu options to Show or Hide annotations.
5917    *
5918    * @param visible
5919    * @param forSequences
5920    *          update sequence-related annotations
5921    * @param forAlignment
5922    *          update non-sequence-related annotations
5923    */
5924   @Override
5925   protected void setAnnotationsVisibility(boolean visible,
5926           boolean forSequences, boolean forAlignment)
5927   {
5928     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5929             .getAlignmentAnnotation())
5930     {
5931       /*
5932        * don't display non-positional annotations on an alignment
5933        */
5934       if (aa.annotations == null)
5935       {
5936         continue;
5937       }
5938       boolean apply = (aa.sequenceRef == null && forAlignment)
5939               || (aa.sequenceRef != null && forSequences);
5940       if (apply)
5941       {
5942         aa.visible = visible;
5943       }
5944     }
5945     alignPanel.validateAnnotationDimensions(true);
5946     alignPanel.alignmentChanged();
5947   }
5948
5949   /**
5950    * Store selected annotation sort order for the view and repaint.
5951    */
5952   @Override
5953   protected void sortAnnotations_actionPerformed()
5954   {
5955     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5956     this.alignPanel.av
5957             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5958     alignPanel.paintAlignment(true);
5959   }
5960
5961   /**
5962    *
5963    * @return alignment panels in this alignment frame
5964    */
5965   public List<? extends AlignmentViewPanel> getAlignPanels()
5966   {
5967     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5968   }
5969
5970   /**
5971    * Open a new alignment window, with the cDNA associated with this (protein)
5972    * alignment, aligned as is the protein.
5973    */
5974   protected void viewAsCdna_actionPerformed()
5975   {
5976     // TODO no longer a menu action - refactor as required
5977     final AlignmentI alignment = getViewport().getAlignment();
5978     Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5979     if (mappings == null)
5980     {
5981       return;
5982     }
5983     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5984     for (SequenceI aaSeq : alignment.getSequences())
5985     {
5986       for (AlignedCodonFrame acf : mappings)
5987       {
5988         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5989         if (dnaSeq != null)
5990         {
5991           /*
5992            * There is a cDNA mapping for this protein sequence - add to new
5993            * alignment. It will share the same dataset sequence as other mapped
5994            * cDNA (no new mappings need to be created).
5995            */
5996           final Sequence newSeq = new Sequence(dnaSeq);
5997           newSeq.setDatasetSequence(dnaSeq);
5998           cdnaSeqs.add(newSeq);
5999         }
6000       }
6001     }
6002     if (cdnaSeqs.size() == 0)
6003     {
6004       // show a warning dialog no mapped cDNA
6005       return;
6006     }
6007     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6008             .size()]));
6009     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6010             AlignFrame.DEFAULT_HEIGHT);
6011     cdna.alignAs(alignment);
6012     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6013             + this.title;
6014     Desktop.addInternalFrame(alignFrame, newtitle,
6015             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6016   }
6017
6018   /**
6019    * Set visibility of dna/protein complement view (available when shown in a
6020    * split frame).
6021    *
6022    * @param show
6023    */
6024   @Override
6025   protected void showComplement_actionPerformed(boolean show)
6026   {
6027     SplitContainerI sf = getSplitViewContainer();
6028     if (sf != null)
6029     {
6030       sf.setComplementVisible(this, show);
6031     }
6032   }
6033 }
6034
6035 class PrintThread extends Thread
6036 {
6037   AlignmentPanel ap;
6038
6039   public PrintThread(AlignmentPanel ap)
6040   {
6041     this.ap = ap;
6042   }
6043
6044   static PageFormat pf;
6045
6046   @Override
6047   public void run()
6048   {
6049     PrinterJob printJob = PrinterJob.getPrinterJob();
6050
6051     if (pf != null)
6052     {
6053       printJob.setPrintable(ap, pf);
6054     }
6055     else
6056     {
6057       printJob.setPrintable(ap);
6058     }
6059
6060     if (printJob.printDialog())
6061     {
6062       try
6063       {
6064         printJob.print();
6065       } catch (Exception PrintException)
6066       {
6067         PrintException.printStackTrace();
6068       }
6069     }
6070   }
6071 }