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.Vector;
 135
 136 import javax.swing.JCheckBoxMenuItem;
 137 import javax.swing.JEditorPane;
 138 import javax.swing.JInternalFrame;
 139 import javax.swing.JLayeredPane;
 140 import javax.swing.JMenu;
 141 import javax.swing.JMenuItem;
 142 import javax.swing.JOptionPane;
 143 import javax.swing.JRadioButtonMenuItem;
 144 import javax.swing.JScrollPane;
 145 import javax.swing.SwingUtilities;
 146
 147 /**
 148  * DOCUMENT ME!
 149  *
 150  * @author $author$
 151  * @version $Revision$
 152  */
 153 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 154         IProgressIndicator, AlignViewControllerGuiI
 155 {
 156
 157   public static final int DEFAULT_WIDTH = 700;
 158
 159   public static final int DEFAULT_HEIGHT = 500;
 160
 161   /*
 162    * The currently displayed panel (selected tabbed view if more than one)
 163    */
 164   public AlignmentPanel alignPanel;
 165
 166   AlignViewport viewport;
 167
 168   public AlignViewControllerI avc;
 169
 170   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 171
 172   /**
 173    * Last format used to load or save alignments in this window
 174    */
 175   String currentFileFormat = null;
 176
 177   /**
 178    * Current filename for this alignment
 179    */
 180   String fileName = null;
 181
 182   /**
 183    * Creates a new AlignFrame object with specific width and height.
 184    *
 185    * @param al
 186    * @param width
 187    * @param height
 188    */
 189   public AlignFrame(AlignmentI al, int width, int height)
 190   {
 191     this(al, null, width, height);
 192   }
 193
 194   /**
 195    * Creates a new AlignFrame object with specific width, height and
 196    * sequenceSetId
 197    *
 198    * @param al
 199    * @param width
 200    * @param height
 201    * @param sequenceSetId
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height,
 204           String sequenceSetId)
 205   {
 206     this(al, null, width, height, sequenceSetId);
 207   }
 208
 209   /**
 210    * Creates a new AlignFrame object with specific width, height and
 211    * sequenceSetId
 212    *
 213    * @param al
 214    * @param width
 215    * @param height
 216    * @param sequenceSetId
 217    * @param viewId
 218    */
 219   public AlignFrame(AlignmentI al, int width, int height,
 220           String sequenceSetId, String viewId)
 221   {
 222     this(al, null, width, height, sequenceSetId, viewId);
 223   }
 224
 225   /**
 226    * new alignment window with hidden columns
 227    *
 228    * @param al
 229    *          AlignmentI
 230    * @param hiddenColumns
 231    *          ColumnSelection or null
 232    * @param width
 233    *          Width of alignment frame
 234    * @param height
 235    *          height of frame.
 236    */
 237   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 238           int width, int height)
 239   {
 240     this(al, hiddenColumns, width, height, null);
 241   }
 242
 243   /**
 244    * Create alignment frame for al with hiddenColumns, a specific width and
 245    * height, and specific sequenceId
 246    *
 247    * @param al
 248    * @param hiddenColumns
 249    * @param width
 250    * @param height
 251    * @param sequenceSetId
 252    *          (may be null)
 253    */
 254   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 255           int width, int height, String sequenceSetId)
 256   {
 257     this(al, hiddenColumns, width, height, sequenceSetId, null);
 258   }
 259
 260   /**
 261    * Create alignment frame for al with hiddenColumns, a specific width and
 262    * height, and specific sequenceId
 263    *
 264    * @param al
 265    * @param hiddenColumns
 266    * @param width
 267    * @param height
 268    * @param sequenceSetId
 269    *          (may be null)
 270    * @param viewId
 271    *          (may be null)
 272    */
 273   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 274           int width, int height, String sequenceSetId, String viewId)
 275   {
 276     setSize(width, height);
 277
 278     if (al.getDataset() == null)
 279     {
 280       al.setDataset(null);
 281     }
 282
 283     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 284
 285     alignPanel = new AlignmentPanel(this, viewport);
 286
 287     addAlignmentPanel(alignPanel, true);
 288     init();
 289   }
 290
 291   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 292           ColumnSelection hiddenColumns, int width, int height)
 293   {
 294     setSize(width, height);
 295
 296     if (al.getDataset() == null)
 297     {
 298       al.setDataset(null);
 299     }
 300
 301     viewport = new AlignViewport(al, hiddenColumns);
 302
 303     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 304     {
 305       viewport.hideSequence(hiddenSeqs);
 306     }
 307     alignPanel = new AlignmentPanel(this, viewport);
 308     addAlignmentPanel(alignPanel, true);
 309     init();
 310   }
 311
 312   /**
 313    * Make a new AlignFrame from existing alignmentPanels
 314    *
 315    * @param ap
 316    *          AlignmentPanel
 317    * @param av
 318    *          AlignViewport
 319    */
 320   public AlignFrame(AlignmentPanel ap)
 321   {
 322     viewport = ap.av;
 323     alignPanel = ap;
 324     addAlignmentPanel(ap, false);
 325     init();
 326   }
 327
 328   /**
 329    * initalise the alignframe from the underlying viewport data and the
 330    * configurations
 331    */
 332   void init()
 333   {
 334     if (!Jalview.isHeadlessMode())
 335     {
 336       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 337     }
 338
 339     avc = new jalview.controller.AlignViewController(this, viewport,
 340             alignPanel);
 341     if (viewport.getAlignmentConservationAnnotation() == null)
 342     {
 343       BLOSUM62Colour.setEnabled(false);
 344       conservationMenuItem.setEnabled(false);
 345       modifyConservation.setEnabled(false);
 346       // PIDColour.setEnabled(false);
 347       // abovePIDThreshold.setEnabled(false);
 348       // modifyPID.setEnabled(false);
 349     }
 350
 351     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 352             "No sort");
 353
 354     if (sortby.equals("Id"))
 355     {
 356       sortIDMenuItem_actionPerformed(null);
 357     }
 358     else if (sortby.equals("Pairwise Identity"))
 359     {
 360       sortPairwiseMenuItem_actionPerformed(null);
 361     }
 362
 363     if (Desktop.desktop != null)
 364     {
 365       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 366       addServiceListeners();
 367       setGUINucleotide(viewport.getAlignment().isNucleotide());
 368     }
 369
 370     this.alignPanel.av
 371             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 372
 373     setMenusFromViewport(viewport);
 374     buildSortByAnnotationScoresMenu();
 375     buildTreeMenu();
 376
 377     if (viewport.getWrapAlignment())
 378     {
 379       wrapMenuItem_actionPerformed(null);
 380     }
 381
 382     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 383     {
 384       this.overviewMenuItem_actionPerformed(null);
 385     }
 386
 387     addKeyListener();
 388
 389     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 390     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 391     final String menuLabel = MessageManager
 392             .getString("label.copy_format_from");
 393     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 394             new ViewSetProvider()
 395             {
 396
 397               @Override
 398               public AlignmentPanel[] getAllAlignmentPanels()
 399               {
 400                 origview.clear();
 401                 origview.add(alignPanel);
 402                 // make an array of all alignment panels except for this one
 403                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 404                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 405                 aps.remove(AlignFrame.this.alignPanel);
 406                 return aps.toArray(new AlignmentPanel[aps.size()]);
 407               }
 408             }, selviews, new ItemListener()
 409             {
 410
 411               @Override
 412               public void itemStateChanged(ItemEvent e)
 413               {
 414                 if (origview.size() > 0)
 415                 {
 416                   final AlignmentPanel ap = origview.get(0);
 417
 418                   /*
 419                    * Copy the ViewStyle of the selected panel to 'this one'.
 420                    * Don't change value of 'scaleProteinAsCdna' unless copying
 421                    * from a SplitFrame.
 422                    */
 423                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 424                           .getViewStyle();
 425                   boolean fromSplitFrame = selviews.get(0)
 426                           .getAlignViewport().getCodingComplement() != null;
 427                   if (!fromSplitFrame)
 428                   {
 429                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 430                             .getViewStyle().isScaleProteinAsCdna());
 431                   }
 432                   ap.getAlignViewport().setViewStyle(vs);
 433
 434                   /*
 435                    * Also rescale ViewStyle of SplitFrame complement if there is
 436                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 437                    * the whole ViewStyle (allow cDNA protein to have different
 438                    * fonts)
 439                    */
 440                   AlignViewportI complement = ap.getAlignViewport()
 441                           .getCodingComplement();
 442                   if (complement != null && vs.isScaleProteinAsCdna())
 443                   {
 444                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 445                     ((SplitFrame) af.getSplitViewContainer())
 446                             .adjustLayout();
 447                     af.setMenusForViewport();
 448                   }
 449
 450                   ap.updateLayout();
 451                   ap.setSelected(true);
 452                   ap.alignFrame.setMenusForViewport();
 453
 454                 }
 455               }
 456             });
 457     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 458             .indexOf("devel") > -1
 459             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 460                     .indexOf("test") > -1)
 461     {
 462       formatMenu.add(vsel);
 463     }
 464
 465   }
 466
 467   /**
 468    * Change the filename and format for the alignment, and enable the 'reload'
 469    * button functionality.
 470    *
 471    * @param file
 472    *          valid filename
 473    * @param format
 474    *          format of file
 475    */
 476   public void setFileName(String file, String format)
 477   {
 478     fileName = file;
 479     setFileFormat(format);
 480     reload.setEnabled(true);
 481   }
 482
 483   /**
 484    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 485    * events
 486    */
 487   void addKeyListener()
 488   {
 489     addKeyListener(new KeyAdapter()
 490     {
 491       @Override
 492       public void keyPressed(KeyEvent evt)
 493       {
 494         if (viewport.cursorMode
 495                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 496                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 497                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 498                 && Character.isDigit(evt.getKeyChar()))
 499         {
 500           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 501         }
 502
 503         switch (evt.getKeyCode())
 504         {
 505
 506         case 27: // escape key
 507           deselectAllSequenceMenuItem_actionPerformed(null);
 508
 509           break;
 510
 511         case KeyEvent.VK_DOWN:
 512           if (evt.isAltDown() || !viewport.cursorMode)
 513           {
 514             moveSelectedSequences(false);
 515           }
 516           if (viewport.cursorMode)
 517           {
 518             alignPanel.getSeqPanel().moveCursor(0, 1);
 519           }
 520           break;
 521
 522         case KeyEvent.VK_UP:
 523           if (evt.isAltDown() || !viewport.cursorMode)
 524           {
 525             moveSelectedSequences(true);
 526           }
 527           if (viewport.cursorMode)
 528           {
 529             alignPanel.getSeqPanel().moveCursor(0, -1);
 530           }
 531
 532           break;
 533
 534         case KeyEvent.VK_LEFT:
 535           if (evt.isAltDown() || !viewport.cursorMode)
 536           {
 537             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 538           }
 539           else
 540           {
 541             alignPanel.getSeqPanel().moveCursor(-1, 0);
 542           }
 543
 544           break;
 545
 546         case KeyEvent.VK_RIGHT:
 547           if (evt.isAltDown() || !viewport.cursorMode)
 548           {
 549             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 550           }
 551           else
 552           {
 553             alignPanel.getSeqPanel().moveCursor(1, 0);
 554           }
 555           break;
 556
 557         case KeyEvent.VK_SPACE:
 558           if (viewport.cursorMode)
 559           {
 560             alignPanel.getSeqPanel().insertGapAtCursor(
 561                     evt.isControlDown() || evt.isShiftDown()
 562                             || evt.isAltDown());
 563           }
 564           break;
 565
 566         // case KeyEvent.VK_A:
 567         // if (viewport.cursorMode)
 568         // {
 569         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 570         // //System.out.println("A");
 571         // }
 572         // break;
 573         /*
 574          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 575          * System.out.println("closing bracket"); } break;
 576          */
 577         case KeyEvent.VK_DELETE:
 578         case KeyEvent.VK_BACK_SPACE:
 579           if (!viewport.cursorMode)
 580           {
 581             cut_actionPerformed(null);
 582           }
 583           else
 584           {
 585             alignPanel.getSeqPanel().deleteGapAtCursor(
 586                     evt.isControlDown() || evt.isShiftDown()
 587                             || evt.isAltDown());
 588           }
 589
 590           break;
 591
 592         case KeyEvent.VK_S:
 593           if (viewport.cursorMode)
 594           {
 595             alignPanel.getSeqPanel().setCursorRow();
 596           }
 597           break;
 598         case KeyEvent.VK_C:
 599           if (viewport.cursorMode && !evt.isControlDown())
 600           {
 601             alignPanel.getSeqPanel().setCursorColumn();
 602           }
 603           break;
 604         case KeyEvent.VK_P:
 605           if (viewport.cursorMode)
 606           {
 607             alignPanel.getSeqPanel().setCursorPosition();
 608           }
 609           break;
 610
 611         case KeyEvent.VK_ENTER:
 612         case KeyEvent.VK_COMMA:
 613           if (viewport.cursorMode)
 614           {
 615             alignPanel.getSeqPanel().setCursorRowAndColumn();
 616           }
 617           break;
 618
 619         case KeyEvent.VK_Q:
 620           if (viewport.cursorMode)
 621           {
 622             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 623           }
 624           break;
 625         case KeyEvent.VK_M:
 626           if (viewport.cursorMode)
 627           {
 628             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 629           }
 630           break;
 631
 632         case KeyEvent.VK_F2:
 633           viewport.cursorMode = !viewport.cursorMode;
 634           statusBar.setText(MessageManager.formatMessage(
 635                   "label.keyboard_editing_mode",
 636                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 640             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 641           }
 642           alignPanel.getSeqPanel().seqCanvas.repaint();
 643           break;
 644
 645         case KeyEvent.VK_F1:
 646           try
 647           {
 648             Help.showHelpWindow();
 649           } catch (Exception ex)
 650           {
 651             ex.printStackTrace();
 652           }
 653           break;
 654         case KeyEvent.VK_H:
 655         {
 656           boolean toggleSeqs = !evt.isControlDown();
 657           boolean toggleCols = !evt.isShiftDown();
 658           toggleHiddenRegions(toggleSeqs, toggleCols);
 659           break;
 660         }
 661         case KeyEvent.VK_PAGE_UP:
 662           if (viewport.getWrapAlignment())
 663           {
 664             alignPanel.scrollUp(true);
 665           }
 666           else
 667           {
 668             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 669                     - viewport.endSeq + viewport.startSeq);
 670           }
 671           break;
 672         case KeyEvent.VK_PAGE_DOWN:
 673           if (viewport.getWrapAlignment())
 674           {
 675             alignPanel.scrollUp(false);
 676           }
 677           else
 678           {
 679             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 680                     + viewport.endSeq - viewport.startSeq);
 681           }
 682           break;
 683         }
 684       }
 685
 686       @Override
 687       public void keyReleased(KeyEvent evt)
 688       {
 689         switch (evt.getKeyCode())
 690         {
 691         case KeyEvent.VK_LEFT:
 692           if (evt.isAltDown() || !viewport.cursorMode)
 693           {
 694             viewport.firePropertyChange("alignment", null, viewport
 695                     .getAlignment().getSequences());
 696           }
 697           break;
 698
 699         case KeyEvent.VK_RIGHT:
 700           if (evt.isAltDown() || !viewport.cursorMode)
 701           {
 702             viewport.firePropertyChange("alignment", null, viewport
 703                     .getAlignment().getSequences());
 704           }
 705           break;
 706         }
 707       }
 708     });
 709   }
 710
 711   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 712   {
 713     ap.alignFrame = this;
 714     avc = new jalview.controller.AlignViewController(this, viewport,
 715             alignPanel);
 716
 717     alignPanels.add(ap);
 718
 719     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 720
 721     int aSize = alignPanels.size();
 722
 723     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 724
 725     if (aSize == 1 && ap.av.viewName == null)
 726     {
 727       this.getContentPane().add(ap, BorderLayout.CENTER);
 728     }
 729     else
 730     {
 731       if (aSize == 2)
 732       {
 733         setInitialTabVisible();
 734       }
 735
 736       expandViews.setEnabled(true);
 737       gatherViews.setEnabled(true);
 738       tabbedPane.addTab(ap.av.viewName, ap);
 739
 740       ap.setVisible(false);
 741     }
 742
 743     if (newPanel)
 744     {
 745       if (ap.av.isPadGaps())
 746       {
 747         ap.av.getAlignment().padGaps();
 748       }
 749       ap.av.updateConservation(ap);
 750       ap.av.updateConsensus(ap);
 751       ap.av.updateStrucConsensus(ap);
 752     }
 753   }
 754
 755   public void setInitialTabVisible()
 756   {
 757     expandViews.setEnabled(true);
 758     gatherViews.setEnabled(true);
 759     tabbedPane.setVisible(true);
 760     AlignmentPanel first = alignPanels.get(0);
 761     tabbedPane.addTab(first.av.viewName, first);
 762     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 763   }
 764
 765   public AlignViewport getViewport()
 766   {
 767     return viewport;
 768   }
 769
 770   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 771   private void addServiceListeners()
 772   {
 773     final java.beans.PropertyChangeListener thisListener;
 774     Desktop.instance.addJalviewPropertyChangeListener("services",
 775             thisListener = new java.beans.PropertyChangeListener()
 776             {
 777               @Override
 778               public void propertyChange(PropertyChangeEvent evt)
 779               {
 780                 // // System.out.println("Discoverer property change.");
 781                 // if (evt.getPropertyName().equals("services"))
 782                 {
 783                   SwingUtilities.invokeLater(new Runnable()
 784                   {
 785
 786                     @Override
 787                     public void run()
 788                     {
 789                       System.err
 790                               .println("Rebuild WS Menu for service change");
 791                       BuildWebServiceMenu();
 792                     }
 793
 794                   });
 795                 }
 796               }
 797             });
 798     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 799     {
 800       @Override
 801       public void internalFrameClosed(
 802               javax.swing.event.InternalFrameEvent evt)
 803       {
 804         // System.out.println("deregistering discoverer listener");
 805         Desktop.instance.removeJalviewPropertyChangeListener("services",
 806                 thisListener);
 807         closeMenuItem_actionPerformed(true);
 808       };
 809     });
 810     // Finally, build the menu once to get current service state
 811     new Thread(new Runnable()
 812     {
 813       @Override
 814       public void run()
 815       {
 816         BuildWebServiceMenu();
 817       }
 818     }).start();
 819   }
 820
 821   /**
 822    * Configure menu items that vary according to whether the alignment is
 823    * nucleotide or protein
 824    *
 825    * @param nucleotide
 826    */
 827   public void setGUINucleotide(boolean nucleotide)
 828   {
 829     showTranslation.setVisible(nucleotide);
 830     showReverse.setVisible(nucleotide);
 831     showReverseComplement.setVisible(nucleotide);
 832     conservationMenuItem.setEnabled(!nucleotide);
 833     modifyConservation.setEnabled(!nucleotide);
 834     showGroupConservation.setEnabled(!nucleotide);
 835     rnahelicesColour.setEnabled(nucleotide);
 836     purinePyrimidineColour.setEnabled(nucleotide);
 837     showComplementMenuItem.setText(MessageManager
 838             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 839     setColourSelected(jalview.bin.Cache.getDefault(
 840             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 841                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 842   }
 843
 844   /**
 845    * set up menus for the current viewport. This may be called after any
 846    * operation that affects the data in the current view (selection changed,
 847    * etc) to update the menus to reflect the new state.
 848    */
 849   @Override
 850   public void setMenusForViewport()
 851   {
 852     setMenusFromViewport(viewport);
 853   }
 854
 855   /**
 856    * Need to call this method when tabs are selected for multiple views, or when
 857    * loading from Jalview2XML.java
 858    *
 859    * @param av
 860    *          AlignViewport
 861    */
 862   void setMenusFromViewport(AlignViewport av)
 863   {
 864     padGapsMenuitem.setSelected(av.isPadGaps());
 865     colourTextMenuItem.setSelected(av.isShowColourText());
 866     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 867     conservationMenuItem.setSelected(av.getConservationSelected());
 868     seqLimits.setSelected(av.getShowJVSuffix());
 869     idRightAlign.setSelected(av.isRightAlignIds());
 870     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 871     renderGapsMenuItem.setSelected(av.isRenderGaps());
 872     wrapMenuItem.setSelected(av.getWrapAlignment());
 873     scaleAbove.setVisible(av.getWrapAlignment());
 874     scaleLeft.setVisible(av.getWrapAlignment());
 875     scaleRight.setVisible(av.getWrapAlignment());
 876     annotationPanelMenuItem.setState(av.isShowAnnotation());
 877     /*
 878      * Show/hide annotations only enabled if annotation panel is shown
 879      */
 880     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 881     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 882     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 883     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 884     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 885     viewTextMenuItem.setSelected(av.getShowText());
 886     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 887     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 888     showGroupConservation.setSelected(av.isShowGroupConservation());
 889     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 890     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 891     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 892
 893     setColourSelected(ColourSchemeProperty.getColourName(av
 894             .getGlobalColourScheme()));
 895
 896     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 897     hiddenMarkers.setState(av.getShowHiddenMarkers());
 898     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 899     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 900     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 901     autoCalculate.setSelected(av.autoCalculateConsensus);
 902     sortByTree.setSelected(av.sortByTree);
 903     listenToViewSelections.setSelected(av.followSelection);
 904     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 905     rnahelicesColour
 906             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 907
 908     showProducts.setEnabled(canShowProducts());
 909
 910     updateEditMenuBar();
 911   }
 912
 913   private IProgressIndicator progressBar;
 914
 915   /*
 916    * (non-Javadoc)
 917    *
 918    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 919    */
 920   @Override
 921   public void setProgressBar(String message, long id)
 922   {
 923     progressBar.setProgressBar(message, id);
 924   }
 925
 926   @Override
 927   public void registerHandler(final long id,
 928           final IProgressIndicatorHandler handler)
 929   {
 930     progressBar.registerHandler(id, handler);
 931   }
 932
 933   /**
 934    *
 935    * @return true if any progress bars are still active
 936    */
 937   @Override
 938   public boolean operationInProgress()
 939   {
 940     return progressBar.operationInProgress();
 941   }
 942
 943   @Override
 944   public void setStatus(String text)
 945   {
 946     statusBar.setText(text);
 947   }
 948
 949   /*
 950    * Added so Castor Mapping file can obtain Jalview Version
 951    */
 952   public String getVersion()
 953   {
 954     return jalview.bin.Cache.getProperty("VERSION");
 955   }
 956
 957   public FeatureRenderer getFeatureRenderer()
 958   {
 959     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 960   }
 961
 962   @Override
 963   public void fetchSequence_actionPerformed(ActionEvent e)
 964   {
 965     new SequenceFetcher(this);
 966   }
 967
 968   @Override
 969   public void addFromFile_actionPerformed(ActionEvent e)
 970   {
 971     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 972   }
 973
 974   @Override
 975   public void reload_actionPerformed(ActionEvent e)
 976   {
 977     if (fileName != null)
 978     {
 979       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 980       // originating file's format
 981       // TODO: work out how to recover feature settings for correct view(s) when
 982       // file is reloaded.
 983       if (currentFileFormat.equals("Jalview"))
 984       {
 985         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 986         for (int i = 0; i < frames.length; i++)
 987         {
 988           if (frames[i] instanceof AlignFrame && frames[i] != this
 989                   && ((AlignFrame) frames[i]).fileName != null
 990                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 991           {
 992             try
 993             {
 994               frames[i].setSelected(true);
 995               Desktop.instance.closeAssociatedWindows();
 996             } catch (java.beans.PropertyVetoException ex)
 997             {
 998             }
 999           }
1000
1001         }
1002         Desktop.instance.closeAssociatedWindows();
1003
1004         FileLoader loader = new FileLoader();
1005         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1006         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1007       }
1008       else
1009       {
1010         Rectangle bounds = this.getBounds();
1011
1012         FileLoader loader = new FileLoader();
1013         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1014         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1015                 protocol, currentFileFormat);
1016
1017         newframe.setBounds(bounds);
1018         if (featureSettings != null && featureSettings.isShowing())
1019         {
1020           final Rectangle fspos = featureSettings.frame.getBounds();
1021           // TODO: need a 'show feature settings' function that takes bounds -
1022           // need to refactor Desktop.addFrame
1023           newframe.featureSettings_actionPerformed(null);
1024           final FeatureSettings nfs = newframe.featureSettings;
1025           SwingUtilities.invokeLater(new Runnable()
1026           {
1027             @Override
1028             public void run()
1029             {
1030               nfs.frame.setBounds(fspos);
1031             }
1032           });
1033           this.featureSettings.close();
1034           this.featureSettings = null;
1035         }
1036         this.closeMenuItem_actionPerformed(true);
1037       }
1038     }
1039   }
1040
1041   @Override
1042   public void addFromText_actionPerformed(ActionEvent e)
1043   {
1044     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1045             .getAlignPanel());
1046   }
1047
1048   @Override
1049   public void addFromURL_actionPerformed(ActionEvent e)
1050   {
1051     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1052   }
1053
1054   @Override
1055   public void save_actionPerformed(ActionEvent e)
1056   {
1057     if (fileName == null
1058             || (currentFileFormat == null || !jalview.io.FormatAdapter
1059                     .isValidIOFormat(currentFileFormat, true))
1060             || fileName.startsWith("http"))
1061     {
1062       saveAs_actionPerformed(null);
1063     }
1064     else
1065     {
1066       saveAlignment(fileName, currentFileFormat);
1067     }
1068   }
1069
1070   /**
1071    * DOCUMENT ME!
1072    *
1073    * @param e
1074    *          DOCUMENT ME!
1075    */
1076   @Override
1077   public void saveAs_actionPerformed(ActionEvent e)
1078   {
1079     JalviewFileChooser chooser = new JalviewFileChooser(
1080             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1081             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1082             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1083             currentFileFormat, false);
1084
1085     chooser.setFileView(new JalviewFileView());
1086     chooser.setDialogTitle(MessageManager
1087             .getString("label.save_alignment_to_file"));
1088     chooser.setToolTipText(MessageManager.getString("action.save"));
1089
1090     int value = chooser.showSaveDialog(this);
1091
1092     if (value == JalviewFileChooser.APPROVE_OPTION)
1093     {
1094       currentFileFormat = chooser.getSelectedFormat();
1095       while (currentFileFormat == null)
1096       {
1097         JOptionPane
1098                 .showInternalMessageDialog(
1099                         Desktop.desktop,
1100                         MessageManager
1101                                 .getString("label.select_file_format_before_saving"),
1102                         MessageManager
1103                                 .getString("label.file_format_not_specified"),
1104                         JOptionPane.WARNING_MESSAGE);
1105         currentFileFormat = chooser.getSelectedFormat();
1106         value = chooser.showSaveDialog(this);
1107         if (value != JalviewFileChooser.APPROVE_OPTION)
1108         {
1109           return;
1110         }
1111       }
1112
1113       fileName = chooser.getSelectedFile().getPath();
1114
1115       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1116               currentFileFormat);
1117
1118       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1119       if (currentFileFormat.indexOf(" ") > -1)
1120       {
1121         currentFileFormat = currentFileFormat.substring(0,
1122                 currentFileFormat.indexOf(" "));
1123       }
1124       saveAlignment(fileName, currentFileFormat);
1125     }
1126   }
1127
1128   public boolean saveAlignment(String file, String format)
1129   {
1130     boolean success = true;
1131
1132     if (format.equalsIgnoreCase("Jalview"))
1133     {
1134       String shortName = title;
1135
1136       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1137       {
1138         shortName = shortName.substring(shortName
1139                 .lastIndexOf(java.io.File.separatorChar) + 1);
1140       }
1141
1142       success = new Jalview2XML().saveAlignment(this, file, shortName);
1143
1144       statusBar.setText(MessageManager.formatMessage(
1145               "label.successfully_saved_to_file_in_format", new Object[] {
1146                   fileName, format }));
1147
1148     }
1149     else
1150     {
1151       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1152       {
1153         warningMessage("Cannot save file " + fileName + " using format "
1154                 + format, "Alignment output format not supported");
1155         if (!Jalview.isHeadlessMode())
1156         {
1157           saveAs_actionPerformed(null);
1158         }
1159         return false;
1160       }
1161
1162       AlignmentExportData exportData = getAlignmentForExport(format,
1163               viewport, null);
1164       if (exportData.getSettings().isCancelled())
1165       {
1166         return false;
1167       }
1168       FormatAdapter f = new FormatAdapter(alignPanel,
1169               exportData.getSettings());
1170       String output = f.formatSequences(
1171               format,
1172               exportData.getAlignment(), // class cast exceptions will
1173               // occur in the distant future
1174               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1175               f.getCacheSuffixDefault(format),
1176               viewport.getColumnSelection());
1177
1178       if (output == null)
1179       {
1180         success = false;
1181       }
1182       else
1183       {
1184         try
1185         {
1186           java.io.PrintWriter out = new java.io.PrintWriter(
1187                   new java.io.FileWriter(file));
1188
1189           out.print(output);
1190           out.close();
1191           this.setTitle(file);
1192           statusBar.setText(MessageManager.formatMessage(
1193                   "label.successfully_saved_to_file_in_format",
1194                   new Object[] { fileName, format }));
1195         } catch (Exception ex)
1196         {
1197           success = false;
1198           ex.printStackTrace();
1199         }
1200       }
1201     }
1202
1203     if (!success)
1204     {
1205       JOptionPane.showInternalMessageDialog(this, MessageManager
1206               .formatMessage("label.couldnt_save_file",
1207                       new Object[] { fileName }), MessageManager
1208               .getString("label.error_saving_file"),
1209               JOptionPane.WARNING_MESSAGE);
1210     }
1211
1212     return success;
1213   }
1214
1215   private void warningMessage(String warning, String title)
1216   {
1217     if (new jalview.util.Platform().isHeadless())
1218     {
1219       System.err.println("Warning: " + title + "\nWarning: " + warning);
1220
1221     }
1222     else
1223     {
1224       JOptionPane.showInternalMessageDialog(this, warning, title,
1225               JOptionPane.WARNING_MESSAGE);
1226     }
1227     return;
1228   }
1229
1230   /**
1231    * DOCUMENT ME!
1232    *
1233    * @param e
1234    *          DOCUMENT ME!
1235    */
1236   @Override
1237   protected void outputText_actionPerformed(ActionEvent e)
1238   {
1239
1240     AlignmentExportData exportData = getAlignmentForExport(
1241             e.getActionCommand(), viewport, null);
1242     if (exportData.getSettings().isCancelled())
1243     {
1244       return;
1245     }
1246     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1247     cap.setForInput(null);
1248     try
1249     {
1250       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1251               .formatSequences(e.getActionCommand(),
1252                       exportData.getAlignment(),
1253                       exportData.getOmitHidden(),
1254                       exportData.getStartEndPostions(),
1255                       viewport.getColumnSelection()));
1256       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1257               "label.alignment_output_command",
1258               new Object[] { e.getActionCommand() }), 600, 500);
1259     } catch (OutOfMemoryError oom)
1260     {
1261       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1262       cap.dispose();
1263     }
1264
1265   }
1266
1267   public static AlignmentExportData getAlignmentForExport(
1268           String exportFormat, AlignViewportI viewport,
1269           AlignExportSettingI exportSettings)
1270   {
1271     AlignmentI alignmentToExport = null;
1272     AlignExportSettingI settings = exportSettings;
1273     String[] omitHidden = null;
1274     int[] alignmentStartEnd = new int[2];
1275
1276     HiddenSequences hiddenSeqs = viewport.getAlignment()
1277             .getHiddenSequences();
1278
1279     alignmentToExport = viewport.getAlignment();
1280     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1281
1282     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1283     if (settings == null)
1284     {
1285       settings = new AlignExportSettings(hasHiddenSeqs,
1286               viewport.hasHiddenColumns(), exportFormat);
1287     }
1288     // settings.isExportAnnotations();
1289
1290     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1291     {
1292       omitHidden = viewport.getViewAsString(false);
1293     }
1294
1295     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1296     {
1297       alignmentToExport = hiddenSeqs.getFullAlignment();
1298     }
1299     else
1300     {
1301       alignmentToExport = viewport.getAlignment();
1302       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1303               .getColumnSelection().getHiddenColumns());
1304     }
1305     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1306             omitHidden, alignmentStartEnd, settings);
1307     return ed;
1308   }
1309
1310   public static int[] getStartEnd(int[] aligmentStartEnd,
1311           List<int[]> hiddenCols)
1312   {
1313     int startPos = aligmentStartEnd[0];
1314     int endPos = aligmentStartEnd[1];
1315
1316     int[] lowestRange = new int[] { -1, -1 };
1317     int[] higestRange = new int[] { -1, -1 };
1318
1319     for (int[] hiddenCol : hiddenCols)
1320     {
1321       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1322       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1323     }
1324
1325     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1326     {
1327       startPos = aligmentStartEnd[0];
1328     }
1329     else
1330     {
1331       startPos = lowestRange[1] + 1;
1332     }
1333
1334     if (higestRange[0] == -1 && higestRange[1] == -1)
1335     {
1336       endPos = aligmentStartEnd[1];
1337     }
1338     else
1339     {
1340       endPos = higestRange[0] - 1;
1341     }
1342
1343     // System.out.println("Export range : " + startPos + " - " + endPos);
1344     return new int[] { startPos, endPos };
1345   }
1346
1347   public static void main(String[] args)
1348   {
1349     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1350     hiddenCols.add(new int[] { 0, 0 });
1351     hiddenCols.add(new int[] { 6, 9 });
1352     hiddenCols.add(new int[] { 11, 12 });
1353     hiddenCols.add(new int[] { 33, 33 });
1354     hiddenCols.add(new int[] { 50, 50 });
1355
1356     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1357     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   @Override
1367   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1368   {
1369     new HtmlSvgOutput(null, alignPanel);
1370   }
1371
1372   @Override
1373   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1374   {
1375     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1376     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1377   }
1378
1379   public void createImageMap(File file, String image)
1380   {
1381     alignPanel.makePNGImageMap(file, image);
1382   }
1383
1384   /**
1385    * DOCUMENT ME!
1386    *
1387    * @param e
1388    *          DOCUMENT ME!
1389    */
1390   @Override
1391   public void createPNG(File f)
1392   {
1393     alignPanel.makePNG(f);
1394   }
1395
1396   /**
1397    * DOCUMENT ME!
1398    *
1399    * @param e
1400    *          DOCUMENT ME!
1401    */
1402   @Override
1403   public void createEPS(File f)
1404   {
1405     alignPanel.makeEPS(f);
1406   }
1407
1408   @Override
1409   public void createSVG(File f)
1410   {
1411     alignPanel.makeSVG(f);
1412   }
1413
1414   @Override
1415   public void pageSetup_actionPerformed(ActionEvent e)
1416   {
1417     PrinterJob printJob = PrinterJob.getPrinterJob();
1418     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1419   }
1420
1421   /**
1422    * DOCUMENT ME!
1423    *
1424    * @param e
1425    *          DOCUMENT ME!
1426    */
1427   @Override
1428   public void printMenuItem_actionPerformed(ActionEvent e)
1429   {
1430     // Putting in a thread avoids Swing painting problems
1431     PrintThread thread = new PrintThread(alignPanel);
1432     thread.start();
1433   }
1434
1435   @Override
1436   public void exportFeatures_actionPerformed(ActionEvent e)
1437   {
1438     new AnnotationExporter().exportFeatures(alignPanel);
1439   }
1440
1441   @Override
1442   public void exportAnnotations_actionPerformed(ActionEvent e)
1443   {
1444     new AnnotationExporter().exportAnnotations(alignPanel);
1445   }
1446
1447   @Override
1448   public void associatedData_actionPerformed(ActionEvent e)
1449   {
1450     // Pick the tree file
1451     JalviewFileChooser chooser = new JalviewFileChooser(
1452             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1453     chooser.setFileView(new JalviewFileView());
1454     chooser.setDialogTitle(MessageManager
1455             .getString("label.load_jalview_annotations"));
1456     chooser.setToolTipText(MessageManager
1457             .getString("label.load_jalview_annotations"));
1458
1459     int value = chooser.showOpenDialog(null);
1460
1461     if (value == JalviewFileChooser.APPROVE_OPTION)
1462     {
1463       String choice = chooser.getSelectedFile().getPath();
1464       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1465       loadJalviewDataFile(choice, null, null, null);
1466     }
1467
1468   }
1469
1470   /**
1471    * Close the current view or all views in the alignment frame. If the frame
1472    * only contains one view then the alignment will be removed from memory.
1473    *
1474    * @param closeAllTabs
1475    */
1476   @Override
1477   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1478   {
1479     if (alignPanels != null && alignPanels.size() < 2)
1480     {
1481       closeAllTabs = true;
1482     }
1483
1484     try
1485     {
1486       if (alignPanels != null)
1487       {
1488         if (closeAllTabs)
1489         {
1490           if (this.isClosed())
1491           {
1492             // really close all the windows - otherwise wait till
1493             // setClosed(true) is called
1494             for (int i = 0; i < alignPanels.size(); i++)
1495             {
1496               AlignmentPanel ap = alignPanels.get(i);
1497               ap.closePanel();
1498             }
1499           }
1500         }
1501         else
1502         {
1503           closeView(alignPanel);
1504         }
1505       }
1506
1507       if (closeAllTabs)
1508       {
1509         /*
1510          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1511          * be called recursively, with the frame now in 'closed' state
1512          */
1513         this.setClosed(true);
1514       }
1515     } catch (Exception ex)
1516     {
1517       ex.printStackTrace();
1518     }
1519   }
1520
1521   /**
1522    * Close the specified panel and close up tabs appropriately.
1523    *
1524    * @param panelToClose
1525    */
1526   public void closeView(AlignmentPanel panelToClose)
1527   {
1528     int index = tabbedPane.getSelectedIndex();
1529     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1530     alignPanels.remove(panelToClose);
1531     panelToClose.closePanel();
1532     panelToClose = null;
1533
1534     tabbedPane.removeTabAt(closedindex);
1535     tabbedPane.validate();
1536
1537     if (index > closedindex || index == tabbedPane.getTabCount())
1538     {
1539       // modify currently selected tab index if necessary.
1540       index--;
1541     }
1542
1543     this.tabSelectionChanged(index);
1544   }
1545
1546   /**
1547    * DOCUMENT ME!
1548    */
1549   void updateEditMenuBar()
1550   {
1551
1552     if (viewport.getHistoryList().size() > 0)
1553     {
1554       undoMenuItem.setEnabled(true);
1555       CommandI command = viewport.getHistoryList().peek();
1556       undoMenuItem.setText(MessageManager.formatMessage(
1557               "label.undo_command",
1558               new Object[] { command.getDescription() }));
1559     }
1560     else
1561     {
1562       undoMenuItem.setEnabled(false);
1563       undoMenuItem.setText(MessageManager.getString("action.undo"));
1564     }
1565
1566     if (viewport.getRedoList().size() > 0)
1567     {
1568       redoMenuItem.setEnabled(true);
1569
1570       CommandI command = viewport.getRedoList().peek();
1571       redoMenuItem.setText(MessageManager.formatMessage(
1572               "label.redo_command",
1573               new Object[] { command.getDescription() }));
1574     }
1575     else
1576     {
1577       redoMenuItem.setEnabled(false);
1578       redoMenuItem.setText(MessageManager.getString("action.redo"));
1579     }
1580   }
1581
1582   @Override
1583   public void addHistoryItem(CommandI command)
1584   {
1585     if (command.getSize() > 0)
1586     {
1587       viewport.addToHistoryList(command);
1588       viewport.clearRedoList();
1589       updateEditMenuBar();
1590       viewport.updateHiddenColumns();
1591       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1592       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1593       // viewport.getColumnSelection()
1594       // .getHiddenColumns().size() > 0);
1595     }
1596   }
1597
1598   /**
1599    *
1600    * @return alignment objects for all views
1601    */
1602   AlignmentI[] getViewAlignments()
1603   {
1604     if (alignPanels != null)
1605     {
1606       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1607       int i = 0;
1608       for (AlignmentPanel ap : alignPanels)
1609       {
1610         als[i++] = ap.av.getAlignment();
1611       }
1612       return als;
1613     }
1614     if (viewport != null)
1615     {
1616       return new AlignmentI[] { viewport.getAlignment() };
1617     }
1618     return null;
1619   }
1620
1621   /**
1622    * DOCUMENT ME!
1623    *
1624    * @param e
1625    *          DOCUMENT ME!
1626    */
1627   @Override
1628   protected void undoMenuItem_actionPerformed(ActionEvent e)
1629   {
1630     if (viewport.getHistoryList().isEmpty())
1631     {
1632       return;
1633     }
1634     CommandI command = viewport.getHistoryList().pop();
1635     viewport.addToRedoList(command);
1636     command.undoCommand(getViewAlignments());
1637
1638     AlignmentViewport originalSource = getOriginatingSource(command);
1639     updateEditMenuBar();
1640
1641     if (originalSource != null)
1642     {
1643       if (originalSource != viewport)
1644       {
1645         Cache.log
1646                 .warn("Implementation worry: mismatch of viewport origin for undo");
1647       }
1648       originalSource.updateHiddenColumns();
1649       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1650       // null
1651       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1652       // viewport.getColumnSelection()
1653       // .getHiddenColumns().size() > 0);
1654       originalSource.firePropertyChange("alignment", null, originalSource
1655               .getAlignment().getSequences());
1656     }
1657   }
1658
1659   /**
1660    * DOCUMENT ME!
1661    *
1662    * @param e
1663    *          DOCUMENT ME!
1664    */
1665   @Override
1666   protected void redoMenuItem_actionPerformed(ActionEvent e)
1667   {
1668     if (viewport.getRedoList().size() < 1)
1669     {
1670       return;
1671     }
1672
1673     CommandI command = viewport.getRedoList().pop();
1674     viewport.addToHistoryList(command);
1675     command.doCommand(getViewAlignments());
1676
1677     AlignmentViewport originalSource = getOriginatingSource(command);
1678     updateEditMenuBar();
1679
1680     if (originalSource != null)
1681     {
1682
1683       if (originalSource != viewport)
1684       {
1685         Cache.log
1686                 .warn("Implementation worry: mismatch of viewport origin for redo");
1687       }
1688       originalSource.updateHiddenColumns();
1689       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1690       // null
1691       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1692       // viewport.getColumnSelection()
1693       // .getHiddenColumns().size() > 0);
1694       originalSource.firePropertyChange("alignment", null, originalSource
1695               .getAlignment().getSequences());
1696     }
1697   }
1698
1699   AlignmentViewport getOriginatingSource(CommandI command)
1700   {
1701     AlignmentViewport originalSource = null;
1702     // For sequence removal and addition, we need to fire
1703     // the property change event FROM the viewport where the
1704     // original alignment was altered
1705     AlignmentI al = null;
1706     if (command instanceof EditCommand)
1707     {
1708       EditCommand editCommand = (EditCommand) command;
1709       al = editCommand.getAlignment();
1710       List<Component> comps = PaintRefresher.components.get(viewport
1711               .getSequenceSetId());
1712
1713       for (Component comp : comps)
1714       {
1715         if (comp instanceof AlignmentPanel)
1716         {
1717           if (al == ((AlignmentPanel) comp).av.getAlignment())
1718           {
1719             originalSource = ((AlignmentPanel) comp).av;
1720             break;
1721           }
1722         }
1723       }
1724     }
1725
1726     if (originalSource == null)
1727     {
1728       // The original view is closed, we must validate
1729       // the current view against the closed view first
1730       if (al != null)
1731       {
1732         PaintRefresher.validateSequences(al, viewport.getAlignment());
1733       }
1734
1735       originalSource = viewport;
1736     }
1737
1738     return originalSource;
1739   }
1740
1741   /**
1742    * DOCUMENT ME!
1743    *
1744    * @param up
1745    *          DOCUMENT ME!
1746    */
1747   public void moveSelectedSequences(boolean up)
1748   {
1749     SequenceGroup sg = viewport.getSelectionGroup();
1750
1751     if (sg == null)
1752     {
1753       return;
1754     }
1755     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1756             viewport.getHiddenRepSequences(), up);
1757     alignPanel.paintAlignment(true);
1758   }
1759
1760   synchronized void slideSequences(boolean right, int size)
1761   {
1762     List<SequenceI> sg = new ArrayList<SequenceI>();
1763     if (viewport.cursorMode)
1764     {
1765       sg.add(viewport.getAlignment().getSequenceAt(
1766               alignPanel.getSeqPanel().seqCanvas.cursorY));
1767     }
1768     else if (viewport.getSelectionGroup() != null
1769             && viewport.getSelectionGroup().getSize() != viewport
1770                     .getAlignment().getHeight())
1771     {
1772       sg = viewport.getSelectionGroup().getSequences(
1773               viewport.getHiddenRepSequences());
1774     }
1775
1776     if (sg.size() < 1)
1777     {
1778       return;
1779     }
1780
1781     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1782
1783     for (SequenceI seq : viewport.getAlignment().getSequences())
1784     {
1785       if (!sg.contains(seq))
1786       {
1787         invertGroup.add(seq);
1788       }
1789     }
1790
1791     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1792
1793     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1794     for (int i = 0; i < invertGroup.size(); i++)
1795     {
1796       seqs2[i] = invertGroup.get(i);
1797     }
1798
1799     SlideSequencesCommand ssc;
1800     if (right)
1801     {
1802       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1803               size, viewport.getGapCharacter());
1804     }
1805     else
1806     {
1807       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1808               size, viewport.getGapCharacter());
1809     }
1810
1811     int groupAdjustment = 0;
1812     if (ssc.getGapsInsertedBegin() && right)
1813     {
1814       if (viewport.cursorMode)
1815       {
1816         alignPanel.getSeqPanel().moveCursor(size, 0);
1817       }
1818       else
1819       {
1820         groupAdjustment = size;
1821       }
1822     }
1823     else if (!ssc.getGapsInsertedBegin() && !right)
1824     {
1825       if (viewport.cursorMode)
1826       {
1827         alignPanel.getSeqPanel().moveCursor(-size, 0);
1828       }
1829       else
1830       {
1831         groupAdjustment = -size;
1832       }
1833     }
1834
1835     if (groupAdjustment != 0)
1836     {
1837       viewport.getSelectionGroup().setStartRes(
1838               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1839       viewport.getSelectionGroup().setEndRes(
1840               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1841     }
1842
1843     /*
1844      * just extend the last slide command if compatible; but not if in
1845      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1846      */
1847     boolean appendHistoryItem = false;
1848     Deque<CommandI> historyList = viewport.getHistoryList();
1849     boolean inSplitFrame = getSplitViewContainer() != null;
1850     if (!inSplitFrame && historyList != null && historyList.size() > 0
1851             && historyList.peek() instanceof SlideSequencesCommand)
1852     {
1853       appendHistoryItem = ssc
1854               .appendSlideCommand((SlideSequencesCommand) historyList
1855                       .peek());
1856     }
1857
1858     if (!appendHistoryItem)
1859     {
1860       addHistoryItem(ssc);
1861     }
1862
1863     repaint();
1864   }
1865
1866   /**
1867    * DOCUMENT ME!
1868    *
1869    * @param e
1870    *          DOCUMENT ME!
1871    */
1872   @Override
1873   protected void copy_actionPerformed(ActionEvent e)
1874   {
1875     System.gc();
1876     if (viewport.getSelectionGroup() == null)
1877     {
1878       return;
1879     }
1880     // TODO: preserve the ordering of displayed alignment annotation in any
1881     // internal paste (particularly sequence associated annotation)
1882     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1883     String[] omitHidden = null;
1884
1885     if (viewport.hasHiddenColumns())
1886     {
1887       omitHidden = viewport.getViewAsString(true);
1888     }
1889
1890     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1891             omitHidden, null);
1892
1893     StringSelection ss = new StringSelection(output);
1894
1895     try
1896     {
1897       jalview.gui.Desktop.internalCopy = true;
1898       // Its really worth setting the clipboard contents
1899       // to empty before setting the large StringSelection!!
1900       Toolkit.getDefaultToolkit().getSystemClipboard()
1901               .setContents(new StringSelection(""), null);
1902
1903       Toolkit.getDefaultToolkit().getSystemClipboard()
1904               .setContents(ss, Desktop.instance);
1905     } catch (OutOfMemoryError er)
1906     {
1907       new OOMWarning("copying region", er);
1908       return;
1909     }
1910
1911     ArrayList<int[]> hiddenColumns = null;
1912     if (viewport.hasHiddenColumns())
1913     {
1914       hiddenColumns = new ArrayList<int[]>();
1915       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1916               .getSelectionGroup().getEndRes();
1917       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1918       {
1919         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1920         {
1921           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1922               region[1] - hiddenOffset });
1923         }
1924       }
1925     }
1926
1927     Desktop.jalviewClipboard = new Object[] { seqs,
1928         viewport.getAlignment().getDataset(), hiddenColumns };
1929     statusBar.setText(MessageManager.formatMessage(
1930             "label.copied_sequences_to_clipboard", new Object[] { Integer
1931                     .valueOf(seqs.length).toString() }));
1932   }
1933
1934   /**
1935    * DOCUMENT ME!
1936    *
1937    * @param e
1938    *          DOCUMENT ME!
1939    */
1940   @Override
1941   protected void pasteNew_actionPerformed(ActionEvent e)
1942   {
1943     paste(true);
1944   }
1945
1946   /**
1947    * DOCUMENT ME!
1948    *
1949    * @param e
1950    *          DOCUMENT ME!
1951    */
1952   @Override
1953   protected void pasteThis_actionPerformed(ActionEvent e)
1954   {
1955     paste(false);
1956   }
1957
1958   /**
1959    * Paste contents of Jalview clipboard
1960    *
1961    * @param newAlignment
1962    *          true to paste to a new alignment, otherwise add to this.
1963    */
1964   void paste(boolean newAlignment)
1965   {
1966     boolean externalPaste = true;
1967     try
1968     {
1969       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1970       Transferable contents = c.getContents(this);
1971
1972       if (contents == null)
1973       {
1974         return;
1975       }
1976
1977       String str, format;
1978       try
1979       {
1980         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1981         if (str.length() < 1)
1982         {
1983           return;
1984         }
1985
1986         format = new IdentifyFile().identify(str, "Paste");
1987
1988       } catch (OutOfMemoryError er)
1989       {
1990         new OOMWarning("Out of memory pasting sequences!!", er);
1991         return;
1992       }
1993
1994       SequenceI[] sequences;
1995       boolean annotationAdded = false;
1996       AlignmentI alignment = null;
1997
1998       if (Desktop.jalviewClipboard != null)
1999       {
2000         // The clipboard was filled from within Jalview, we must use the
2001         // sequences
2002         // And dataset from the copied alignment
2003         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2004         // be doubly sure that we create *new* sequence objects.
2005         sequences = new SequenceI[newseq.length];
2006         for (int i = 0; i < newseq.length; i++)
2007         {
2008           sequences[i] = new Sequence(newseq[i]);
2009         }
2010         alignment = new Alignment(sequences);
2011         externalPaste = false;
2012       }
2013       else
2014       {
2015         // parse the clipboard as an alignment.
2016         alignment = new FormatAdapter().readFile(str, "Paste", format);
2017         sequences = alignment.getSequencesArray();
2018       }
2019
2020       int alwidth = 0;
2021       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2022       int fgroup = -1;
2023
2024       if (newAlignment)
2025       {
2026
2027         if (Desktop.jalviewClipboard != null)
2028         {
2029           // dataset is inherited
2030           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2031         }
2032         else
2033         {
2034           // new dataset is constructed
2035           alignment.setDataset(null);
2036         }
2037         alwidth = alignment.getWidth() + 1;
2038       }
2039       else
2040       {
2041         AlignmentI pastedal = alignment; // preserve pasted alignment object
2042         // Add pasted sequences and dataset into existing alignment.
2043         alignment = viewport.getAlignment();
2044         alwidth = alignment.getWidth() + 1;
2045         // decide if we need to import sequences from an existing dataset
2046         boolean importDs = Desktop.jalviewClipboard != null
2047                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2048         // importDs==true instructs us to copy over new dataset sequences from
2049         // an existing alignment
2050         Vector newDs = (importDs) ? new Vector() : null; // used to create
2051         // minimum dataset set
2052
2053         for (int i = 0; i < sequences.length; i++)
2054         {
2055           if (importDs)
2056           {
2057             newDs.addElement(null);
2058           }
2059           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2060           // paste
2061           if (importDs && ds != null)
2062           {
2063             if (!newDs.contains(ds))
2064             {
2065               newDs.setElementAt(ds, i);
2066               ds = new Sequence(ds);
2067               // update with new dataset sequence
2068               sequences[i].setDatasetSequence(ds);
2069             }
2070             else
2071             {
2072               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2073             }
2074           }
2075           else
2076           {
2077             // copy and derive new dataset sequence
2078             sequences[i] = sequences[i].deriveSequence();
2079             alignment.getDataset().addSequence(
2080                     sequences[i].getDatasetSequence());
2081             // TODO: avoid creation of duplicate dataset sequences with a
2082             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2083           }
2084           alignment.addSequence(sequences[i]); // merges dataset
2085         }
2086         if (newDs != null)
2087         {
2088           newDs.clear(); // tidy up
2089         }
2090         if (alignment.getAlignmentAnnotation() != null)
2091         {
2092           for (AlignmentAnnotation alan : alignment
2093                   .getAlignmentAnnotation())
2094           {
2095             if (alan.graphGroup > fgroup)
2096             {
2097               fgroup = alan.graphGroup;
2098             }
2099           }
2100         }
2101         if (pastedal.getAlignmentAnnotation() != null)
2102         {
2103           // Add any annotation attached to alignment.
2104           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2105           for (int i = 0; i < alann.length; i++)
2106           {
2107             annotationAdded = true;
2108             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2109             {
2110               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2111               if (newann.graphGroup > -1)
2112               {
2113                 if (newGraphGroups.size() <= newann.graphGroup
2114                         || newGraphGroups.get(newann.graphGroup) == null)
2115                 {
2116                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2117                   {
2118                     newGraphGroups.add(q, null);
2119                   }
2120                   newGraphGroups.set(newann.graphGroup, new Integer(
2121                           ++fgroup));
2122                 }
2123                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2124                         .intValue();
2125               }
2126
2127               newann.padAnnotation(alwidth);
2128               alignment.addAnnotation(newann);
2129             }
2130           }
2131         }
2132       }
2133       if (!newAlignment)
2134       {
2135         // /////
2136         // ADD HISTORY ITEM
2137         //
2138         addHistoryItem(new EditCommand(
2139                 MessageManager.getString("label.add_sequences"),
2140                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2141       }
2142       // Add any annotations attached to sequences
2143       for (int i = 0; i < sequences.length; i++)
2144       {
2145         if (sequences[i].getAnnotation() != null)
2146         {
2147           AlignmentAnnotation newann;
2148           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2149           {
2150             annotationAdded = true;
2151             newann = sequences[i].getAnnotation()[a];
2152             newann.adjustForAlignment();
2153             newann.padAnnotation(alwidth);
2154             if (newann.graphGroup > -1)
2155             {
2156               if (newann.graphGroup > -1)
2157               {
2158                 if (newGraphGroups.size() <= newann.graphGroup
2159                         || newGraphGroups.get(newann.graphGroup) == null)
2160                 {
2161                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2162                   {
2163                     newGraphGroups.add(q, null);
2164                   }
2165                   newGraphGroups.set(newann.graphGroup, new Integer(
2166                           ++fgroup));
2167                 }
2168                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2169                         .intValue();
2170               }
2171             }
2172             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2173             // was
2174             // duplicated
2175             // earlier
2176             alignment
2177                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2178           }
2179         }
2180       }
2181       if (!newAlignment)
2182       {
2183
2184         // propagate alignment changed.
2185         viewport.setEndSeq(alignment.getHeight());
2186         if (annotationAdded)
2187         {
2188           // Duplicate sequence annotation in all views.
2189           AlignmentI[] alview = this.getViewAlignments();
2190           for (int i = 0; i < sequences.length; i++)
2191           {
2192             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2193             if (sann == null)
2194             {
2195               continue;
2196             }
2197             for (int avnum = 0; avnum < alview.length; avnum++)
2198             {
2199               if (alview[avnum] != alignment)
2200               {
2201                 // duplicate in a view other than the one with input focus
2202                 int avwidth = alview[avnum].getWidth() + 1;
2203                 // this relies on sann being preserved after we
2204                 // modify the sequence's annotation array for each duplication
2205                 for (int a = 0; a < sann.length; a++)
2206                 {
2207                   AlignmentAnnotation newann = new AlignmentAnnotation(
2208                           sann[a]);
2209                   sequences[i].addAlignmentAnnotation(newann);
2210                   newann.padAnnotation(avwidth);
2211                   alview[avnum].addAnnotation(newann); // annotation was
2212                   // duplicated earlier
2213                   // TODO JAL-1145 graphGroups are not updated for sequence
2214                   // annotation added to several views. This may cause
2215                   // strangeness
2216                   alview[avnum].setAnnotationIndex(newann, a);
2217                 }
2218               }
2219             }
2220           }
2221           buildSortByAnnotationScoresMenu();
2222         }
2223         viewport.firePropertyChange("alignment", null,
2224                 alignment.getSequences());
2225         if (alignPanels != null)
2226         {
2227           for (AlignmentPanel ap : alignPanels)
2228           {
2229             ap.validateAnnotationDimensions(false);
2230           }
2231         }
2232         else
2233         {
2234           alignPanel.validateAnnotationDimensions(false);
2235         }
2236
2237       }
2238       else
2239       {
2240         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2241                 DEFAULT_HEIGHT);
2242         String newtitle = new String("Copied sequences");
2243
2244         if (Desktop.jalviewClipboard != null
2245                 && Desktop.jalviewClipboard[2] != null)
2246         {
2247           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2248           for (int[] region : hc)
2249           {
2250             af.viewport.hideColumns(region[0], region[1]);
2251           }
2252         }
2253
2254         // >>>This is a fix for the moment, until a better solution is
2255         // found!!<<<
2256         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2257                 .transferSettings(
2258                         alignPanel.getSeqPanel().seqCanvas
2259                                 .getFeatureRenderer());
2260
2261         // TODO: maintain provenance of an alignment, rather than just make the
2262         // title a concatenation of operations.
2263         if (!externalPaste)
2264         {
2265           if (title.startsWith("Copied sequences"))
2266           {
2267             newtitle = title;
2268           }
2269           else
2270           {
2271             newtitle = newtitle.concat("- from " + title);
2272           }
2273         }
2274         else
2275         {
2276           newtitle = new String("Pasted sequences");
2277         }
2278
2279         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2280                 DEFAULT_HEIGHT);
2281
2282       }
2283
2284     } catch (Exception ex)
2285     {
2286       ex.printStackTrace();
2287       System.out.println("Exception whilst pasting: " + ex);
2288       // could be anything being pasted in here
2289     }
2290
2291   }
2292
2293   @Override
2294   protected void expand_newalign(ActionEvent e)
2295   {
2296     try
2297     {
2298       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2299               .getAlignment(), -1);
2300       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2301               DEFAULT_HEIGHT);
2302       String newtitle = new String("Flanking alignment");
2303
2304       if (Desktop.jalviewClipboard != null
2305               && Desktop.jalviewClipboard[2] != null)
2306       {
2307         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2308         for (int region[] : hc)
2309         {
2310           af.viewport.hideColumns(region[0], region[1]);
2311         }
2312       }
2313
2314       // >>>This is a fix for the moment, until a better solution is
2315       // found!!<<<
2316       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2317               .transferSettings(
2318                       alignPanel.getSeqPanel().seqCanvas
2319                               .getFeatureRenderer());
2320
2321       // TODO: maintain provenance of an alignment, rather than just make the
2322       // title a concatenation of operations.
2323       {
2324         if (title.startsWith("Copied sequences"))
2325         {
2326           newtitle = title;
2327         }
2328         else
2329         {
2330           newtitle = newtitle.concat("- from " + title);
2331         }
2332       }
2333
2334       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2335
2336     } catch (Exception ex)
2337     {
2338       ex.printStackTrace();
2339       System.out.println("Exception whilst pasting: " + ex);
2340       // could be anything being pasted in here
2341     } catch (OutOfMemoryError oom)
2342     {
2343       new OOMWarning("Viewing flanking region of alignment", oom);
2344     }
2345   }
2346
2347   /**
2348    * DOCUMENT ME!
2349    *
2350    * @param e
2351    *          DOCUMENT ME!
2352    */
2353   @Override
2354   protected void cut_actionPerformed(ActionEvent e)
2355   {
2356     copy_actionPerformed(null);
2357     delete_actionPerformed(null);
2358   }
2359
2360   /**
2361    * DOCUMENT ME!
2362    *
2363    * @param e
2364    *          DOCUMENT ME!
2365    */
2366   @Override
2367   protected void delete_actionPerformed(ActionEvent evt)
2368   {
2369
2370     SequenceGroup sg = viewport.getSelectionGroup();
2371     if (sg == null)
2372     {
2373       return;
2374     }
2375
2376     /*
2377      * If the cut affects all sequences, warn, remove highlighted columns
2378      */
2379     if (sg.getSize() == viewport.getAlignment().getHeight())
2380     {
2381       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2382               .getAlignment().getWidth()) ? true : false;
2383       if (isEntireAlignWidth)
2384       {
2385         int confirm = JOptionPane.showConfirmDialog(this,
2386                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2387                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2388                 JOptionPane.OK_CANCEL_OPTION);
2389
2390         if (confirm == JOptionPane.CANCEL_OPTION
2391                 || confirm == JOptionPane.CLOSED_OPTION)
2392         {
2393           return;
2394         }
2395       }
2396       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2397               sg.getEndRes() + 1);
2398     }
2399     SequenceI[] cut = sg.getSequences()
2400             .toArray(new SequenceI[sg.getSize()]);
2401
2402     addHistoryItem(new EditCommand(
2403             MessageManager.getString("label.cut_sequences"), Action.CUT,
2404             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2405             viewport.getAlignment()));
2406
2407     viewport.setSelectionGroup(null);
2408     viewport.sendSelection();
2409     viewport.getAlignment().deleteGroup(sg);
2410
2411     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2412             .getSequences());
2413     if (viewport.getAlignment().getHeight() < 1)
2414     {
2415       try
2416       {
2417         this.setClosed(true);
2418       } catch (Exception ex)
2419       {
2420       }
2421     }
2422   }
2423
2424   /**
2425    * DOCUMENT ME!
2426    *
2427    * @param e
2428    *          DOCUMENT ME!
2429    */
2430   @Override
2431   protected void deleteGroups_actionPerformed(ActionEvent e)
2432   {
2433     if (avc.deleteGroups())
2434     {
2435       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2436       alignPanel.updateAnnotation();
2437       alignPanel.paintAlignment(true);
2438     }
2439   }
2440
2441   /**
2442    * DOCUMENT ME!
2443    *
2444    * @param e
2445    *          DOCUMENT ME!
2446    */
2447   @Override
2448   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449   {
2450     SequenceGroup sg = new SequenceGroup();
2451
2452     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2453     {
2454       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2455     }
2456
2457     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2458     viewport.setSelectionGroup(sg);
2459     viewport.sendSelection();
2460     alignPanel.paintAlignment(true);
2461     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2462   }
2463
2464   /**
2465    * DOCUMENT ME!
2466    *
2467    * @param e
2468    *          DOCUMENT ME!
2469    */
2470   @Override
2471   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2472   {
2473     if (viewport.cursorMode)
2474     {
2475       alignPanel.getSeqPanel().keyboardNo1 = null;
2476       alignPanel.getSeqPanel().keyboardNo2 = null;
2477     }
2478     viewport.setSelectionGroup(null);
2479     viewport.getColumnSelection().clear();
2480     viewport.setSelectionGroup(null);
2481     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2482     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2483     alignPanel.paintAlignment(true);
2484     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2485     viewport.sendSelection();
2486   }
2487
2488   /**
2489    * DOCUMENT ME!
2490    *
2491    * @param e
2492    *          DOCUMENT ME!
2493    */
2494   @Override
2495   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2496   {
2497     SequenceGroup sg = viewport.getSelectionGroup();
2498
2499     if (sg == null)
2500     {
2501       selectAllSequenceMenuItem_actionPerformed(null);
2502
2503       return;
2504     }
2505
2506     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2507     {
2508       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2509     }
2510
2511     alignPanel.paintAlignment(true);
2512     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2513     viewport.sendSelection();
2514   }
2515
2516   @Override
2517   public void invertColSel_actionPerformed(ActionEvent e)
2518   {
2519     viewport.invertColumnSelection();
2520     alignPanel.paintAlignment(true);
2521     viewport.sendSelection();
2522   }
2523
2524   /**
2525    * DOCUMENT ME!
2526    *
2527    * @param e
2528    *          DOCUMENT ME!
2529    */
2530   @Override
2531   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2532   {
2533     trimAlignment(true);
2534   }
2535
2536   /**
2537    * DOCUMENT ME!
2538    *
2539    * @param e
2540    *          DOCUMENT ME!
2541    */
2542   @Override
2543   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2544   {
2545     trimAlignment(false);
2546   }
2547
2548   void trimAlignment(boolean trimLeft)
2549   {
2550     ColumnSelection colSel = viewport.getColumnSelection();
2551     int column;
2552
2553     if (!colSel.isEmpty())
2554     {
2555       if (trimLeft)
2556       {
2557         column = colSel.getMin();
2558       }
2559       else
2560       {
2561         column = colSel.getMax();
2562       }
2563
2564       SequenceI[] seqs;
2565       if (viewport.getSelectionGroup() != null)
2566       {
2567         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2568                 viewport.getHiddenRepSequences());
2569       }
2570       else
2571       {
2572         seqs = viewport.getAlignment().getSequencesArray();
2573       }
2574
2575       TrimRegionCommand trimRegion;
2576       if (trimLeft)
2577       {
2578         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2579                 column, viewport.getAlignment());
2580         viewport.setStartRes(0);
2581       }
2582       else
2583       {
2584         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2585                 column, viewport.getAlignment());
2586       }
2587
2588       statusBar.setText(MessageManager.formatMessage(
2589               "label.removed_columns",
2590               new String[] { Integer.valueOf(trimRegion.getSize())
2591                       .toString() }));
2592
2593       addHistoryItem(trimRegion);
2594
2595       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2596       {
2597         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2598                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2599         {
2600           viewport.getAlignment().deleteGroup(sg);
2601         }
2602       }
2603
2604       viewport.firePropertyChange("alignment", null, viewport
2605               .getAlignment().getSequences());
2606     }
2607   }
2608
2609   /**
2610    * DOCUMENT ME!
2611    *
2612    * @param e
2613    *          DOCUMENT ME!
2614    */
2615   @Override
2616   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2617   {
2618     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2619
2620     SequenceI[] seqs;
2621     if (viewport.getSelectionGroup() != null)
2622     {
2623       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2624               viewport.getHiddenRepSequences());
2625       start = viewport.getSelectionGroup().getStartRes();
2626       end = viewport.getSelectionGroup().getEndRes();
2627     }
2628     else
2629     {
2630       seqs = viewport.getAlignment().getSequencesArray();
2631     }
2632
2633     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2634             "Remove Gapped Columns", seqs, start, end,
2635             viewport.getAlignment());
2636
2637     addHistoryItem(removeGapCols);
2638
2639     statusBar.setText(MessageManager.formatMessage(
2640             "label.removed_empty_columns",
2641             new Object[] { Integer.valueOf(removeGapCols.getSize())
2642                     .toString() }));
2643
2644     // This is to maintain viewport position on first residue
2645     // of first sequence
2646     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2647     int startRes = seq.findPosition(viewport.startRes);
2648     // ShiftList shifts;
2649     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2650     // edit.alColumnChanges=shifts.getInverse();
2651     // if (viewport.hasHiddenColumns)
2652     // viewport.getColumnSelection().compensateForEdits(shifts);
2653     viewport.setStartRes(seq.findIndex(startRes) - 1);
2654     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2655             .getSequences());
2656
2657   }
2658
2659   /**
2660    * DOCUMENT ME!
2661    *
2662    * @param e
2663    *          DOCUMENT ME!
2664    */
2665   @Override
2666   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2667   {
2668     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2669
2670     SequenceI[] seqs;
2671     if (viewport.getSelectionGroup() != null)
2672     {
2673       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2674               viewport.getHiddenRepSequences());
2675       start = viewport.getSelectionGroup().getStartRes();
2676       end = viewport.getSelectionGroup().getEndRes();
2677     }
2678     else
2679     {
2680       seqs = viewport.getAlignment().getSequencesArray();
2681     }
2682
2683     // This is to maintain viewport position on first residue
2684     // of first sequence
2685     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2686     int startRes = seq.findPosition(viewport.startRes);
2687
2688     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2689             viewport.getAlignment()));
2690
2691     viewport.setStartRes(seq.findIndex(startRes) - 1);
2692
2693     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2694             .getSequences());
2695
2696   }
2697
2698   /**
2699    * DOCUMENT ME!
2700    *
2701    * @param e
2702    *          DOCUMENT ME!
2703    */
2704   @Override
2705   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2706   {
2707     viewport.setPadGaps(padGapsMenuitem.isSelected());
2708     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2709             .getSequences());
2710   }
2711
2712   /**
2713    * DOCUMENT ME!
2714    *
2715    * @param e
2716    *          DOCUMENT ME!
2717    */
2718   @Override
2719   public void findMenuItem_actionPerformed(ActionEvent e)
2720   {
2721     new Finder();
2722   }
2723
2724   /**
2725    * Create a new view of the current alignment.
2726    */
2727   @Override
2728   public void newView_actionPerformed(ActionEvent e)
2729   {
2730     newView(null, true);
2731   }
2732
2733   /**
2734    * Creates and shows a new view of the current alignment.
2735    *
2736    * @param viewTitle
2737    *          title of newly created view; if null, one will be generated
2738    * @param copyAnnotation
2739    *          if true then duplicate all annnotation, groups and settings
2740    * @return new alignment panel, already displayed.
2741    */
2742   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2743   {
2744     /*
2745      * Create a new AlignmentPanel (with its own, new Viewport)
2746      */
2747     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2748             true);
2749     if (!copyAnnotation)
2750     {
2751       /*
2752        * remove all groups and annotation except for the automatic stuff
2753        */
2754       newap.av.getAlignment().deleteAllGroups();
2755       newap.av.getAlignment().deleteAllAnnotations(false);
2756     }
2757
2758     newap.av.setGatherViewsHere(false);
2759
2760     if (viewport.viewName == null)
2761     {
2762       viewport.viewName = MessageManager
2763               .getString("label.view_name_original");
2764     }
2765
2766     /*
2767      * Views share the same edits undo and redo stacks
2768      */
2769     newap.av.setHistoryList(viewport.getHistoryList());
2770     newap.av.setRedoList(viewport.getRedoList());
2771
2772     /*
2773      * Views share the same mappings; need to deregister any new mappings
2774      * created by copyAlignPanel, and register the new reference to the shared
2775      * mappings
2776      */
2777     newap.av.replaceMappings(viewport.getAlignment());
2778
2779     newap.av.viewName = getNewViewName(viewTitle);
2780
2781     addAlignmentPanel(newap, true);
2782     newap.alignmentChanged();
2783
2784     if (alignPanels.size() == 2)
2785     {
2786       viewport.setGatherViewsHere(true);
2787     }
2788     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2789     return newap;
2790   }
2791
2792   /**
2793    * Make a new name for the view, ensuring it is unique within the current
2794    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2795    * these now use viewId. Unique view names are still desirable for usability.)
2796    *
2797    * @param viewTitle
2798    * @return
2799    */
2800   protected String getNewViewName(String viewTitle)
2801   {
2802     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2803     boolean addFirstIndex = false;
2804     if (viewTitle == null || viewTitle.trim().length() == 0)
2805     {
2806       viewTitle = MessageManager.getString("action.view");
2807       addFirstIndex = true;
2808     }
2809     else
2810     {
2811       index = 1;// we count from 1 if given a specific name
2812     }
2813     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2814
2815     List<Component> comps = PaintRefresher.components.get(viewport
2816             .getSequenceSetId());
2817
2818     List<String> existingNames = getExistingViewNames(comps);
2819
2820     while (existingNames.contains(newViewName))
2821     {
2822       newViewName = viewTitle + " " + (++index);
2823     }
2824     return newViewName;
2825   }
2826
2827   /**
2828    * Returns a list of distinct view names found in the given list of
2829    * components. View names are held on the viewport of an AlignmentPanel.
2830    *
2831    * @param comps
2832    * @return
2833    */
2834   protected List<String> getExistingViewNames(List<Component> comps)
2835   {
2836     List<String> existingNames = new ArrayList<String>();
2837     for (Component comp : comps)
2838     {
2839       if (comp instanceof AlignmentPanel)
2840       {
2841         AlignmentPanel ap = (AlignmentPanel) comp;
2842         if (!existingNames.contains(ap.av.viewName))
2843         {
2844           existingNames.add(ap.av.viewName);
2845         }
2846       }
2847     }
2848     return existingNames;
2849   }
2850
2851   /**
2852    * Explode tabbed views into separate windows.
2853    */
2854   @Override
2855   public void expandViews_actionPerformed(ActionEvent e)
2856   {
2857     Desktop.instance.explodeViews(this);
2858   }
2859
2860   /**
2861    * Gather views in separate windows back into a tabbed presentation.
2862    */
2863   @Override
2864   public void gatherViews_actionPerformed(ActionEvent e)
2865   {
2866     Desktop.instance.gatherViews(this);
2867   }
2868
2869   /**
2870    * DOCUMENT ME!
2871    *
2872    * @param e
2873    *          DOCUMENT ME!
2874    */
2875   @Override
2876   public void font_actionPerformed(ActionEvent e)
2877   {
2878     new FontChooser(alignPanel);
2879   }
2880
2881   /**
2882    * DOCUMENT ME!
2883    *
2884    * @param e
2885    *          DOCUMENT ME!
2886    */
2887   @Override
2888   protected void seqLimit_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setShowJVSuffix(seqLimits.isSelected());
2891
2892     alignPanel.getIdPanel().getIdCanvas()
2893             .setPreferredSize(alignPanel.calculateIdWidth());
2894     alignPanel.paintAlignment(true);
2895   }
2896
2897   @Override
2898   public void idRightAlign_actionPerformed(ActionEvent e)
2899   {
2900     viewport.setRightAlignIds(idRightAlign.isSelected());
2901     alignPanel.paintAlignment(true);
2902   }
2903
2904   @Override
2905   public void centreColumnLabels_actionPerformed(ActionEvent e)
2906   {
2907     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2908     alignPanel.paintAlignment(true);
2909   }
2910
2911   /*
2912    * (non-Javadoc)
2913    *
2914    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2915    */
2916   @Override
2917   protected void followHighlight_actionPerformed()
2918   {
2919     /*
2920      * Set the 'follow' flag on the Viewport (and scroll to position if now
2921      * true).
2922      */
2923     final boolean state = this.followHighlightMenuItem.getState();
2924     viewport.setFollowHighlight(state);
2925     if (state)
2926     {
2927       alignPanel.scrollToPosition(
2928               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2929     }
2930   }
2931
2932   /**
2933    * DOCUMENT ME!
2934    *
2935    * @param e
2936    *          DOCUMENT ME!
2937    */
2938   @Override
2939   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2940   {
2941     viewport.setColourText(colourTextMenuItem.isSelected());
2942     alignPanel.paintAlignment(true);
2943   }
2944
2945   /**
2946    * DOCUMENT ME!
2947    *
2948    * @param e
2949    *          DOCUMENT ME!
2950    */
2951   @Override
2952   public void wrapMenuItem_actionPerformed(ActionEvent e)
2953   {
2954     scaleAbove.setVisible(wrapMenuItem.isSelected());
2955     scaleLeft.setVisible(wrapMenuItem.isSelected());
2956     scaleRight.setVisible(wrapMenuItem.isSelected());
2957     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2958     alignPanel.updateLayout();
2959   }
2960
2961   @Override
2962   public void showAllSeqs_actionPerformed(ActionEvent e)
2963   {
2964     viewport.showAllHiddenSeqs();
2965   }
2966
2967   @Override
2968   public void showAllColumns_actionPerformed(ActionEvent e)
2969   {
2970     viewport.showAllHiddenColumns();
2971     repaint();
2972     viewport.sendSelection();
2973   }
2974
2975   @Override
2976   public void hideSelSequences_actionPerformed(ActionEvent e)
2977   {
2978     viewport.hideAllSelectedSeqs();
2979     // alignPanel.paintAlignment(true);
2980   }
2981
2982   /**
2983    * called by key handler and the hide all/show all menu items
2984    *
2985    * @param toggleSeqs
2986    * @param toggleCols
2987    */
2988   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2989   {
2990
2991     boolean hide = false;
2992     SequenceGroup sg = viewport.getSelectionGroup();
2993     if (!toggleSeqs && !toggleCols)
2994     {
2995       // Hide everything by the current selection - this is a hack - we do the
2996       // invert and then hide
2997       // first check that there will be visible columns after the invert.
2998       if ((viewport.getColumnSelection() != null
2999               && viewport.getColumnSelection().getSelected() != null && viewport
3000               .getColumnSelection().getSelected().size() > 0)
3001               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3002                       .getEndRes()))
3003       {
3004         // now invert the sequence set, if required - empty selection implies
3005         // that no hiding is required.
3006         if (sg != null)
3007         {
3008           invertSequenceMenuItem_actionPerformed(null);
3009           sg = viewport.getSelectionGroup();
3010           toggleSeqs = true;
3011
3012         }
3013         viewport.expandColSelection(sg, true);
3014         // finally invert the column selection and get the new sequence
3015         // selection.
3016         invertColSel_actionPerformed(null);
3017         toggleCols = true;
3018       }
3019     }
3020
3021     if (toggleSeqs)
3022     {
3023       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3024       {
3025         hideSelSequences_actionPerformed(null);
3026         hide = true;
3027       }
3028       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3029               .size() > 0))
3030       {
3031         showAllSeqs_actionPerformed(null);
3032       }
3033     }
3034
3035     if (toggleCols)
3036     {
3037       if (viewport.getColumnSelection().getSelected().size() > 0)
3038       {
3039         hideSelColumns_actionPerformed(null);
3040         if (!toggleSeqs)
3041         {
3042           viewport.setSelectionGroup(sg);
3043         }
3044       }
3045       else if (!hide)
3046       {
3047         showAllColumns_actionPerformed(null);
3048       }
3049     }
3050   }
3051
3052   /*
3053    * (non-Javadoc)
3054    *
3055    * @see
3056    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3057    * event.ActionEvent)
3058    */
3059   @Override
3060   public void hideAllButSelection_actionPerformed(ActionEvent e)
3061   {
3062     toggleHiddenRegions(false, false);
3063     viewport.sendSelection();
3064   }
3065
3066   /*
3067    * (non-Javadoc)
3068    *
3069    * @see
3070    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3071    * .ActionEvent)
3072    */
3073   @Override
3074   public void hideAllSelection_actionPerformed(ActionEvent e)
3075   {
3076     SequenceGroup sg = viewport.getSelectionGroup();
3077     viewport.expandColSelection(sg, false);
3078     viewport.hideAllSelectedSeqs();
3079     viewport.hideSelectedColumns();
3080     alignPanel.paintAlignment(true);
3081     viewport.sendSelection();
3082   }
3083
3084   /*
3085    * (non-Javadoc)
3086    *
3087    * @see
3088    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3089    * ActionEvent)
3090    */
3091   @Override
3092   public void showAllhidden_actionPerformed(ActionEvent e)
3093   {
3094     viewport.showAllHiddenColumns();
3095     viewport.showAllHiddenSeqs();
3096     alignPanel.paintAlignment(true);
3097     viewport.sendSelection();
3098   }
3099
3100   @Override
3101   public void hideSelColumns_actionPerformed(ActionEvent e)
3102   {
3103     viewport.hideSelectedColumns();
3104     alignPanel.paintAlignment(true);
3105     viewport.sendSelection();
3106   }
3107
3108   @Override
3109   public void hiddenMarkers_actionPerformed(ActionEvent e)
3110   {
3111     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3112     repaint();
3113   }
3114
3115   /**
3116    * DOCUMENT ME!
3117    *
3118    * @param e
3119    *          DOCUMENT ME!
3120    */
3121   @Override
3122   protected void scaleAbove_actionPerformed(ActionEvent e)
3123   {
3124     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3125     alignPanel.paintAlignment(true);
3126   }
3127
3128   /**
3129    * DOCUMENT ME!
3130    *
3131    * @param e
3132    *          DOCUMENT ME!
3133    */
3134   @Override
3135   protected void scaleLeft_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3138     alignPanel.paintAlignment(true);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   protected void scaleRight_actionPerformed(ActionEvent e)
3149   {
3150     viewport.setScaleRightWrapped(scaleRight.isSelected());
3151     alignPanel.paintAlignment(true);
3152   }
3153
3154   /**
3155    * DOCUMENT ME!
3156    *
3157    * @param e
3158    *          DOCUMENT ME!
3159    */
3160   @Override
3161   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3162   {
3163     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3164     alignPanel.paintAlignment(true);
3165   }
3166
3167   /**
3168    * DOCUMENT ME!
3169    *
3170    * @param e
3171    *          DOCUMENT ME!
3172    */
3173   @Override
3174   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3175   {
3176     viewport.setShowText(viewTextMenuItem.isSelected());
3177     alignPanel.paintAlignment(true);
3178   }
3179
3180   /**
3181    * DOCUMENT ME!
3182    *
3183    * @param e
3184    *          DOCUMENT ME!
3185    */
3186   @Override
3187   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3188   {
3189     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3190     alignPanel.paintAlignment(true);
3191   }
3192
3193   public FeatureSettings featureSettings;
3194
3195   @Override
3196   public FeatureSettingsControllerI getFeatureSettingsUI()
3197   {
3198     return featureSettings;
3199   }
3200
3201   @Override
3202   public void featureSettings_actionPerformed(ActionEvent e)
3203   {
3204     if (featureSettings != null)
3205     {
3206       featureSettings.close();
3207       featureSettings = null;
3208     }
3209     if (!showSeqFeatures.isSelected())
3210     {
3211       // make sure features are actually displayed
3212       showSeqFeatures.setSelected(true);
3213       showSeqFeatures_actionPerformed(null);
3214     }
3215     featureSettings = new FeatureSettings(this);
3216   }
3217
3218   /**
3219    * Set or clear 'Show Sequence Features'
3220    *
3221    * @param evt
3222    *          DOCUMENT ME!
3223    */
3224   @Override
3225   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3226   {
3227     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3228     alignPanel.paintAlignment(true);
3229     if (alignPanel.getOverviewPanel() != null)
3230     {
3231       alignPanel.getOverviewPanel().updateOverviewImage();
3232     }
3233   }
3234
3235   /**
3236    * Set or clear 'Show Sequence Features'
3237    *
3238    * @param evt
3239    *          DOCUMENT ME!
3240    */
3241   @Override
3242   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3243   {
3244     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3245             .isSelected());
3246     if (viewport.isShowSequenceFeaturesHeight())
3247     {
3248       // ensure we're actually displaying features
3249       viewport.setShowSequenceFeatures(true);
3250       showSeqFeatures.setSelected(true);
3251     }
3252     alignPanel.paintAlignment(true);
3253     if (alignPanel.getOverviewPanel() != null)
3254     {
3255       alignPanel.getOverviewPanel().updateOverviewImage();
3256     }
3257   }
3258
3259   /**
3260    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3261    * the annotations panel as a whole.
3262    *
3263    * The options to show/hide all annotations should be enabled when the panel
3264    * is shown, and disabled when the panel is hidden.
3265    *
3266    * @param e
3267    */
3268   @Override
3269   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3270   {
3271     final boolean setVisible = annotationPanelMenuItem.isSelected();
3272     viewport.setShowAnnotation(setVisible);
3273     this.showAllSeqAnnotations.setEnabled(setVisible);
3274     this.hideAllSeqAnnotations.setEnabled(setVisible);
3275     this.showAllAlAnnotations.setEnabled(setVisible);
3276     this.hideAllAlAnnotations.setEnabled(setVisible);
3277     alignPanel.updateLayout();
3278   }
3279
3280   @Override
3281   public void alignmentProperties()
3282   {
3283     JEditorPane editPane = new JEditorPane("text/html", "");
3284     editPane.setEditable(false);
3285     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3286             .formatAsHtml();
3287     editPane.setText(MessageManager.formatMessage("label.html_content",
3288             new Object[] { contents.toString() }));
3289     JInternalFrame frame = new JInternalFrame();
3290     frame.getContentPane().add(new JScrollPane(editPane));
3291
3292     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3293             "label.alignment_properties", new Object[] { getTitle() }),
3294             500, 400);
3295   }
3296
3297   /**
3298    * DOCUMENT ME!
3299    *
3300    * @param e
3301    *          DOCUMENT ME!
3302    */
3303   @Override
3304   public void overviewMenuItem_actionPerformed(ActionEvent e)
3305   {
3306     if (alignPanel.overviewPanel != null)
3307     {
3308       return;
3309     }
3310
3311     JInternalFrame frame = new JInternalFrame();
3312     OverviewPanel overview = new OverviewPanel(alignPanel);
3313     frame.setContentPane(overview);
3314     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3315             "label.overview_params", new Object[] { this.getTitle() }),
3316             frame.getWidth(), frame.getHeight());
3317     frame.pack();
3318     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3319     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3320     {
3321       @Override
3322       public void internalFrameClosed(
3323               javax.swing.event.InternalFrameEvent evt)
3324       {
3325         alignPanel.setOverviewPanel(null);
3326       };
3327     });
3328
3329     alignPanel.setOverviewPanel(overview);
3330   }
3331
3332   @Override
3333   public void textColour_actionPerformed(ActionEvent e)
3334   {
3335     new TextColourChooser().chooseColour(alignPanel, null);
3336   }
3337
3338   /**
3339    * DOCUMENT ME!
3340    *
3341    * @param e
3342    *          DOCUMENT ME!
3343    */
3344   @Override
3345   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3346   {
3347     changeColour(null);
3348   }
3349
3350   /**
3351    * DOCUMENT ME!
3352    *
3353    * @param e
3354    *          DOCUMENT ME!
3355    */
3356   @Override
3357   public void clustalColour_actionPerformed(ActionEvent e)
3358   {
3359     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3360             viewport.getHiddenRepSequences()));
3361   }
3362
3363   /**
3364    * DOCUMENT ME!
3365    *
3366    * @param e
3367    *          DOCUMENT ME!
3368    */
3369   @Override
3370   public void zappoColour_actionPerformed(ActionEvent e)
3371   {
3372     changeColour(new ZappoColourScheme());
3373   }
3374
3375   /**
3376    * DOCUMENT ME!
3377    *
3378    * @param e
3379    *          DOCUMENT ME!
3380    */
3381   @Override
3382   public void taylorColour_actionPerformed(ActionEvent e)
3383   {
3384     changeColour(new TaylorColourScheme());
3385   }
3386
3387   /**
3388    * DOCUMENT ME!
3389    *
3390    * @param e
3391    *          DOCUMENT ME!
3392    */
3393   @Override
3394   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3395   {
3396     changeColour(new HydrophobicColourScheme());
3397   }
3398
3399   /**
3400    * DOCUMENT ME!
3401    *
3402    * @param e
3403    *          DOCUMENT ME!
3404    */
3405   @Override
3406   public void helixColour_actionPerformed(ActionEvent e)
3407   {
3408     changeColour(new HelixColourScheme());
3409   }
3410
3411   /**
3412    * DOCUMENT ME!
3413    *
3414    * @param e
3415    *          DOCUMENT ME!
3416    */
3417   @Override
3418   public void strandColour_actionPerformed(ActionEvent e)
3419   {
3420     changeColour(new StrandColourScheme());
3421   }
3422
3423   /**
3424    * DOCUMENT ME!
3425    *
3426    * @param e
3427    *          DOCUMENT ME!
3428    */
3429   @Override
3430   public void turnColour_actionPerformed(ActionEvent e)
3431   {
3432     changeColour(new TurnColourScheme());
3433   }
3434
3435   /**
3436    * DOCUMENT ME!
3437    *
3438    * @param e
3439    *          DOCUMENT ME!
3440    */
3441   @Override
3442   public void buriedColour_actionPerformed(ActionEvent e)
3443   {
3444     changeColour(new BuriedColourScheme());
3445   }
3446
3447   /**
3448    * DOCUMENT ME!
3449    *
3450    * @param e
3451    *          DOCUMENT ME!
3452    */
3453   @Override
3454   public void nucleotideColour_actionPerformed(ActionEvent e)
3455   {
3456     changeColour(new NucleotideColourScheme());
3457   }
3458
3459   @Override
3460   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3461   {
3462     changeColour(new PurinePyrimidineColourScheme());
3463   }
3464
3465   /*
3466    * public void covariationColour_actionPerformed(ActionEvent e) {
3467    * changeColour(new
3468    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3469    * ()[0])); }
3470    */
3471   @Override
3472   public void annotationColour_actionPerformed(ActionEvent e)
3473   {
3474     new AnnotationColourChooser(viewport, alignPanel);
3475   }
3476
3477   @Override
3478   public void annotationColumn_actionPerformed(ActionEvent e)
3479   {
3480     new AnnotationColumnChooser(viewport, alignPanel);
3481   }
3482
3483   @Override
3484   public void rnahelicesColour_actionPerformed(ActionEvent e)
3485   {
3486     new RNAHelicesColourChooser(viewport, alignPanel);
3487   }
3488
3489   /**
3490    * DOCUMENT ME!
3491    *
3492    * @param e
3493    *          DOCUMENT ME!
3494    */
3495   @Override
3496   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3497   {
3498     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3499   }
3500
3501   /**
3502    * DOCUMENT ME!
3503    *
3504    * @param cs
3505    *          DOCUMENT ME!
3506    */
3507   @Override
3508   public void changeColour(ColourSchemeI cs)
3509   {
3510     // TODO: pull up to controller method
3511
3512     if (cs != null)
3513     {
3514       // Make sure viewport is up to date w.r.t. any sliders
3515       if (viewport.getAbovePIDThreshold())
3516       {
3517         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3518                 "Background");
3519         viewport.setThreshold(threshold);
3520       }
3521
3522       if (viewport.getConservationSelected())
3523       {
3524         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3525                 cs, "Background"));
3526       }
3527       if (cs instanceof TCoffeeColourScheme)
3528       {
3529         tcoffeeColour.setEnabled(true);
3530         tcoffeeColour.setSelected(true);
3531       }
3532     }
3533
3534     viewport.setGlobalColourScheme(cs);
3535
3536     alignPanel.paintAlignment(true);
3537   }
3538
3539   /**
3540    * DOCUMENT ME!
3541    *
3542    * @param e
3543    *          DOCUMENT ME!
3544    */
3545   @Override
3546   protected void modifyPID_actionPerformed(ActionEvent e)
3547   {
3548     if (viewport.getAbovePIDThreshold()
3549             && viewport.getGlobalColourScheme() != null)
3550     {
3551       SliderPanel.setPIDSliderSource(alignPanel,
3552               viewport.getGlobalColourScheme(), "Background");
3553       SliderPanel.showPIDSlider();
3554     }
3555   }
3556
3557   /**
3558    * DOCUMENT ME!
3559    *
3560    * @param e
3561    *          DOCUMENT ME!
3562    */
3563   @Override
3564   protected void modifyConservation_actionPerformed(ActionEvent e)
3565   {
3566     if (viewport.getConservationSelected()
3567             && viewport.getGlobalColourScheme() != null)
3568     {
3569       SliderPanel.setConservationSlider(alignPanel,
3570               viewport.getGlobalColourScheme(), "Background");
3571       SliderPanel.showConservationSlider();
3572     }
3573   }
3574
3575   /**
3576    * DOCUMENT ME!
3577    *
3578    * @param e
3579    *          DOCUMENT ME!
3580    */
3581   @Override
3582   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3583   {
3584     viewport.setConservationSelected(conservationMenuItem.isSelected());
3585
3586     viewport.setAbovePIDThreshold(false);
3587     abovePIDThreshold.setSelected(false);
3588
3589     changeColour(viewport.getGlobalColourScheme());
3590
3591     modifyConservation_actionPerformed(null);
3592   }
3593
3594   /**
3595    * DOCUMENT ME!
3596    *
3597    * @param e
3598    *          DOCUMENT ME!
3599    */
3600   @Override
3601   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3602   {
3603     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3604
3605     conservationMenuItem.setSelected(false);
3606     viewport.setConservationSelected(false);
3607
3608     changeColour(viewport.getGlobalColourScheme());
3609
3610     modifyPID_actionPerformed(null);
3611   }
3612
3613   /**
3614    * DOCUMENT ME!
3615    *
3616    * @param e
3617    *          DOCUMENT ME!
3618    */
3619   @Override
3620   public void userDefinedColour_actionPerformed(ActionEvent e)
3621   {
3622     if (e.getActionCommand().equals(
3623             MessageManager.getString("action.user_defined")))
3624     {
3625       new UserDefinedColours(alignPanel, null);
3626     }
3627     else
3628     {
3629       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3630               .getUserColourSchemes().get(e.getActionCommand());
3631
3632       changeColour(udc);
3633     }
3634   }
3635
3636   public void updateUserColourMenu()
3637   {
3638
3639     Component[] menuItems = colourMenu.getMenuComponents();
3640     int iSize = menuItems.length;
3641     for (int i = 0; i < iSize; i++)
3642     {
3643       if (menuItems[i].getName() != null
3644               && menuItems[i].getName().equals("USER_DEFINED"))
3645       {
3646         colourMenu.remove(menuItems[i]);
3647         iSize--;
3648       }
3649     }
3650     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3651     {
3652       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3653               .getUserColourSchemes().keys();
3654
3655       while (userColours.hasMoreElements())
3656       {
3657         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3658                 userColours.nextElement().toString());
3659         radioItem.setName("USER_DEFINED");
3660         radioItem.addMouseListener(new MouseAdapter()
3661         {
3662           @Override
3663           public void mousePressed(MouseEvent evt)
3664           {
3665             if (evt.isControlDown()
3666                     || SwingUtilities.isRightMouseButton(evt))
3667             {
3668               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3669
3670               int option = JOptionPane.showInternalConfirmDialog(
3671                       jalview.gui.Desktop.desktop,
3672                       MessageManager
3673                               .getString("label.remove_from_default_list"),
3674                       MessageManager
3675                               .getString("label.remove_user_defined_colour"),
3676                       JOptionPane.YES_NO_OPTION);
3677               if (option == JOptionPane.YES_OPTION)
3678               {
3679                 jalview.gui.UserDefinedColours
3680                         .removeColourFromDefaults(radioItem.getText());
3681                 colourMenu.remove(radioItem);
3682               }
3683               else
3684               {
3685                 radioItem.addActionListener(new ActionListener()
3686                 {
3687                   @Override
3688                   public void actionPerformed(ActionEvent evt)
3689                   {
3690                     userDefinedColour_actionPerformed(evt);
3691                   }
3692                 });
3693               }
3694             }
3695           }
3696         });
3697         radioItem.addActionListener(new ActionListener()
3698         {
3699           @Override
3700           public void actionPerformed(ActionEvent evt)
3701           {
3702             userDefinedColour_actionPerformed(evt);
3703           }
3704         });
3705
3706         colourMenu.insert(radioItem, 15);
3707         colours.add(radioItem);
3708       }
3709     }
3710   }
3711
3712   /**
3713    * DOCUMENT ME!
3714    *
3715    * @param e
3716    *          DOCUMENT ME!
3717    */
3718   @Override
3719   public void PIDColour_actionPerformed(ActionEvent e)
3720   {
3721     changeColour(new PIDColourScheme());
3722   }
3723
3724   /**
3725    * DOCUMENT ME!
3726    *
3727    * @param e
3728    *          DOCUMENT ME!
3729    */
3730   @Override
3731   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3732   {
3733     changeColour(new Blosum62ColourScheme());
3734   }
3735
3736   /**
3737    * DOCUMENT ME!
3738    *
3739    * @param e
3740    *          DOCUMENT ME!
3741    */
3742   @Override
3743   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3744   {
3745     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3746     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3747             .getAlignment().getSequenceAt(0), null);
3748     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3749             viewport.getAlignment()));
3750     alignPanel.paintAlignment(true);
3751   }
3752
3753   /**
3754    * DOCUMENT ME!
3755    *
3756    * @param e
3757    *          DOCUMENT ME!
3758    */
3759   @Override
3760   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3761   {
3762     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3763     AlignmentSorter.sortByID(viewport.getAlignment());
3764     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3765             viewport.getAlignment()));
3766     alignPanel.paintAlignment(true);
3767   }
3768
3769   /**
3770    * DOCUMENT ME!
3771    *
3772    * @param e
3773    *          DOCUMENT ME!
3774    */
3775   @Override
3776   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3777   {
3778     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3779     AlignmentSorter.sortByLength(viewport.getAlignment());
3780     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3781             viewport.getAlignment()));
3782     alignPanel.paintAlignment(true);
3783   }
3784
3785   /**
3786    * DOCUMENT ME!
3787    *
3788    * @param e
3789    *          DOCUMENT ME!
3790    */
3791   @Override
3792   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3793   {
3794     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795     AlignmentSorter.sortByGroup(viewport.getAlignment());
3796     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3797             viewport.getAlignment()));
3798
3799     alignPanel.paintAlignment(true);
3800   }
3801
3802   /**
3803    * DOCUMENT ME!
3804    *
3805    * @param e
3806    *          DOCUMENT ME!
3807    */
3808   @Override
3809   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3810   {
3811     new RedundancyPanel(alignPanel, this);
3812   }
3813
3814   /**
3815    * DOCUMENT ME!
3816    *
3817    * @param e
3818    *          DOCUMENT ME!
3819    */
3820   @Override
3821   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3822   {
3823     if ((viewport.getSelectionGroup() == null)
3824             || (viewport.getSelectionGroup().getSize() < 2))
3825     {
3826       JOptionPane.showInternalMessageDialog(this, MessageManager
3827               .getString("label.you_must_select_least_two_sequences"),
3828               MessageManager.getString("label.invalid_selection"),
3829               JOptionPane.WARNING_MESSAGE);
3830     }
3831     else
3832     {
3833       JInternalFrame frame = new JInternalFrame();
3834       frame.setContentPane(new PairwiseAlignPanel(viewport));
3835       Desktop.addInternalFrame(frame,
3836               MessageManager.getString("action.pairwise_alignment"), 600,
3837               500);
3838     }
3839   }
3840
3841   /**
3842    * DOCUMENT ME!
3843    *
3844    * @param e
3845    *          DOCUMENT ME!
3846    */
3847   @Override
3848   public void PCAMenuItem_actionPerformed(ActionEvent e)
3849   {
3850     if (((viewport.getSelectionGroup() != null)
3851             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3852             .getSelectionGroup().getSize() > 0))
3853             || (viewport.getAlignment().getHeight() < 4))
3854     {
3855       JOptionPane
3856               .showInternalMessageDialog(
3857                       this,
3858                       MessageManager
3859                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3860                       MessageManager
3861                               .getString("label.sequence_selection_insufficient"),
3862                       JOptionPane.WARNING_MESSAGE);
3863
3864       return;
3865     }
3866
3867     new PCAPanel(alignPanel);
3868   }
3869
3870   @Override
3871   public void autoCalculate_actionPerformed(ActionEvent e)
3872   {
3873     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3874     if (viewport.autoCalculateConsensus)
3875     {
3876       viewport.firePropertyChange("alignment", null, viewport
3877               .getAlignment().getSequences());
3878     }
3879   }
3880
3881   @Override
3882   public void sortByTreeOption_actionPerformed(ActionEvent e)
3883   {
3884     viewport.sortByTree = sortByTree.isSelected();
3885   }
3886
3887   @Override
3888   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3889   {
3890     viewport.followSelection = listenToViewSelections.isSelected();
3891   }
3892
3893   /**
3894    * DOCUMENT ME!
3895    *
3896    * @param e
3897    *          DOCUMENT ME!
3898    */
3899   @Override
3900   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3901   {
3902     newTreePanel("AV", "PID", "Average distance tree using PID");
3903   }
3904
3905   /**
3906    * DOCUMENT ME!
3907    *
3908    * @param e
3909    *          DOCUMENT ME!
3910    */
3911   @Override
3912   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3913   {
3914     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3915   }
3916
3917   /**
3918    * DOCUMENT ME!
3919    *
3920    * @param e
3921    *          DOCUMENT ME!
3922    */
3923   @Override
3924   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3925   {
3926     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3927   }
3928
3929   /**
3930    * DOCUMENT ME!
3931    *
3932    * @param e
3933    *          DOCUMENT ME!
3934    */
3935   @Override
3936   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3937   {
3938     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3939   }
3940
3941   /**
3942    * DOCUMENT ME!
3943    *
3944    * @param type
3945    *          DOCUMENT ME!
3946    * @param pwType
3947    *          DOCUMENT ME!
3948    * @param title
3949    *          DOCUMENT ME!
3950    */
3951   void newTreePanel(String type, String pwType, String title)
3952   {
3953     TreePanel tp;
3954
3955     if (viewport.getSelectionGroup() != null
3956             && viewport.getSelectionGroup().getSize() > 0)
3957     {
3958       if (viewport.getSelectionGroup().getSize() < 3)
3959       {
3960         JOptionPane
3961                 .showMessageDialog(
3962                         Desktop.desktop,
3963                         MessageManager
3964                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3965                         MessageManager
3966                                 .getString("label.not_enough_sequences"),
3967                         JOptionPane.WARNING_MESSAGE);
3968         return;
3969       }
3970
3971       SequenceGroup sg = viewport.getSelectionGroup();
3972
3973       /* Decide if the selection is a column region */
3974       for (SequenceI _s : sg.getSequences())
3975       {
3976         if (_s.getLength() < sg.getEndRes())
3977         {
3978           JOptionPane
3979                   .showMessageDialog(
3980                           Desktop.desktop,
3981                           MessageManager
3982                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3983                           MessageManager
3984                                   .getString("label.sequences_selection_not_aligned"),
3985                           JOptionPane.WARNING_MESSAGE);
3986
3987           return;
3988         }
3989       }
3990
3991       title = title + " on region";
3992       tp = new TreePanel(alignPanel, type, pwType);
3993     }
3994     else
3995     {
3996       // are the visible sequences aligned?
3997       if (!viewport.getAlignment().isAligned(false))
3998       {
3999         JOptionPane
4000                 .showMessageDialog(
4001                         Desktop.desktop,
4002                         MessageManager
4003                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4004                         MessageManager
4005                                 .getString("label.sequences_not_aligned"),
4006                         JOptionPane.WARNING_MESSAGE);
4007
4008         return;
4009       }
4010
4011       if (viewport.getAlignment().getHeight() < 2)
4012       {
4013         return;
4014       }
4015
4016       tp = new TreePanel(alignPanel, type, pwType);
4017     }
4018
4019     title += " from ";
4020
4021     if (viewport.viewName != null)
4022     {
4023       title += viewport.viewName + " of ";
4024     }
4025
4026     title += this.title;
4027
4028     Desktop.addInternalFrame(tp, title, 600, 500);
4029   }
4030
4031   /**
4032    * DOCUMENT ME!
4033    *
4034    * @param title
4035    *          DOCUMENT ME!
4036    * @param order
4037    *          DOCUMENT ME!
4038    */
4039   public void addSortByOrderMenuItem(String title,
4040           final AlignmentOrder order)
4041   {
4042     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4043             "action.by_title_param", new Object[] { title }));
4044     sort.add(item);
4045     item.addActionListener(new java.awt.event.ActionListener()
4046     {
4047       @Override
4048       public void actionPerformed(ActionEvent e)
4049       {
4050         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4051
4052         // TODO: JBPNote - have to map order entries to curent SequenceI
4053         // pointers
4054         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4055
4056         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4057                 .getAlignment()));
4058
4059         alignPanel.paintAlignment(true);
4060       }
4061     });
4062   }
4063
4064   /**
4065    * Add a new sort by annotation score menu item
4066    *
4067    * @param sort
4068    *          the menu to add the option to
4069    * @param scoreLabel
4070    *          the label used to retrieve scores for each sequence on the
4071    *          alignment
4072    */
4073   public void addSortByAnnotScoreMenuItem(JMenu sort,
4074           final String scoreLabel)
4075   {
4076     final JMenuItem item = new JMenuItem(scoreLabel);
4077     sort.add(item);
4078     item.addActionListener(new java.awt.event.ActionListener()
4079     {
4080       @Override
4081       public void actionPerformed(ActionEvent e)
4082       {
4083         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4084         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4085                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4086         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4087                 viewport.getAlignment()));
4088         alignPanel.paintAlignment(true);
4089       }
4090     });
4091   }
4092
4093   /**
4094    * last hash for alignment's annotation array - used to minimise cost of
4095    * rebuild.
4096    */
4097   protected int _annotationScoreVectorHash;
4098
4099   /**
4100    * search the alignment and rebuild the sort by annotation score submenu the
4101    * last alignment annotation vector hash is stored to minimize cost of
4102    * rebuilding in subsequence calls.
4103    *
4104    */
4105   @Override
4106   public void buildSortByAnnotationScoresMenu()
4107   {
4108     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4109     {
4110       return;
4111     }
4112
4113     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4114     {
4115       sortByAnnotScore.removeAll();
4116       // almost certainly a quicker way to do this - but we keep it simple
4117       Hashtable scoreSorts = new Hashtable();
4118       AlignmentAnnotation aann[];
4119       for (SequenceI sqa : viewport.getAlignment().getSequences())
4120       {
4121         aann = sqa.getAnnotation();
4122         for (int i = 0; aann != null && i < aann.length; i++)
4123         {
4124           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4125           {
4126             scoreSorts.put(aann[i].label, aann[i].label);
4127           }
4128         }
4129       }
4130       Enumeration labels = scoreSorts.keys();
4131       while (labels.hasMoreElements())
4132       {
4133         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4134                 (String) labels.nextElement());
4135       }
4136       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4137       scoreSorts.clear();
4138
4139       _annotationScoreVectorHash = viewport.getAlignment()
4140               .getAlignmentAnnotation().hashCode();
4141     }
4142   }
4143
4144   /**
4145    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4146    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4147    * call. Listeners are added to remove the menu item when the treePanel is
4148    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4149    * modified.
4150    *
4151    * @param treePanel
4152    *          Displayed tree window.
4153    * @param title
4154    *          SortBy menu item title.
4155    */
4156   @Override
4157   public void buildTreeMenu()
4158   {
4159     calculateTree.removeAll();
4160     // build the calculate menu
4161
4162     for (final String type : new String[] { "NJ", "AV" })
4163     {
4164       String treecalcnm = MessageManager.getString("label.tree_calc_"
4165               + type.toLowerCase());
4166       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4167       {
4168         JMenuItem tm = new JMenuItem();
4169         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4170         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4171         {
4172           String smn = MessageManager.getStringOrReturn(
4173                   "label.score_model_", sm.getName());
4174           final String title = MessageManager.formatMessage(
4175                   "label.treecalc_title", treecalcnm, smn);
4176           tm.setText(title);//
4177           tm.addActionListener(new java.awt.event.ActionListener()
4178           {
4179             @Override
4180             public void actionPerformed(ActionEvent e)
4181             {
4182               newTreePanel(type, pwtype, title);
4183             }
4184           });
4185           calculateTree.add(tm);
4186         }
4187
4188       }
4189     }
4190     sortByTreeMenu.removeAll();
4191
4192     List<Component> comps = PaintRefresher.components.get(viewport
4193             .getSequenceSetId());
4194     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4195     for (Component comp : comps)
4196     {
4197       if (comp instanceof TreePanel)
4198       {
4199         treePanels.add((TreePanel) comp);
4200       }
4201     }
4202
4203     if (treePanels.size() < 1)
4204     {
4205       sortByTreeMenu.setVisible(false);
4206       return;
4207     }
4208
4209     sortByTreeMenu.setVisible(true);
4210
4211     for (final TreePanel tp : treePanels)
4212     {
4213       final JMenuItem item = new JMenuItem(tp.getTitle());
4214       item.addActionListener(new java.awt.event.ActionListener()
4215       {
4216         @Override
4217         public void actionPerformed(ActionEvent e)
4218         {
4219           tp.sortByTree_actionPerformed();
4220           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4221
4222         }
4223       });
4224
4225       sortByTreeMenu.add(item);
4226     }
4227   }
4228
4229   public boolean sortBy(AlignmentOrder alorder, String undoname)
4230   {
4231     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4232     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4233     if (undoname != null)
4234     {
4235       addHistoryItem(new OrderCommand(undoname, oldOrder,
4236               viewport.getAlignment()));
4237     }
4238     alignPanel.paintAlignment(true);
4239     return true;
4240   }
4241
4242   /**
4243    * Work out whether the whole set of sequences or just the selected set will
4244    * be submitted for multiple alignment.
4245    *
4246    */
4247   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4248   {
4249     // Now, check we have enough sequences
4250     AlignmentView msa = null;
4251
4252     if ((viewport.getSelectionGroup() != null)
4253             && (viewport.getSelectionGroup().getSize() > 1))
4254     {
4255       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4256       // some common interface!
4257       /*
4258        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4259        * SequenceI[sz = seqs.getSize(false)];
4260        *
4261        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4262        * seqs.getSequenceAt(i); }
4263        */
4264       msa = viewport.getAlignmentView(true);
4265     }
4266     else if (viewport.getSelectionGroup() != null
4267             && viewport.getSelectionGroup().getSize() == 1)
4268     {
4269       int option = JOptionPane.showConfirmDialog(this,
4270               MessageManager.getString("warn.oneseq_msainput_selection"),
4271               MessageManager.getString("label.invalid_selection"),
4272               JOptionPane.OK_CANCEL_OPTION);
4273       if (option == JOptionPane.OK_OPTION)
4274       {
4275         msa = viewport.getAlignmentView(false);
4276       }
4277     }
4278     else
4279     {
4280       msa = viewport.getAlignmentView(false);
4281     }
4282     return msa;
4283   }
4284
4285   /**
4286    * Decides what is submitted to a secondary structure prediction service: the
4287    * first sequence in the alignment, or in the current selection, or, if the
4288    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4289    * region or the whole alignment. (where the first sequence in the set is the
4290    * one that the prediction will be for).
4291    */
4292   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4293   {
4294     AlignmentView seqs = null;
4295
4296     if ((viewport.getSelectionGroup() != null)
4297             && (viewport.getSelectionGroup().getSize() > 0))
4298     {
4299       seqs = viewport.getAlignmentView(true);
4300     }
4301     else
4302     {
4303       seqs = viewport.getAlignmentView(false);
4304     }
4305     // limit sequences - JBPNote in future - could spawn multiple prediction
4306     // jobs
4307     // TODO: viewport.getAlignment().isAligned is a global state - the local
4308     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4309     if (!viewport.getAlignment().isAligned(false))
4310     {
4311       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4312       // TODO: if seqs.getSequences().length>1 then should really have warned
4313       // user!
4314
4315     }
4316     return seqs;
4317   }
4318
4319   /**
4320    * DOCUMENT ME!
4321    *
4322    * @param e
4323    *          DOCUMENT ME!
4324    */
4325   @Override
4326   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4327   {
4328     // Pick the tree file
4329     JalviewFileChooser chooser = new JalviewFileChooser(
4330             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4331     chooser.setFileView(new JalviewFileView());
4332     chooser.setDialogTitle(MessageManager
4333             .getString("label.select_newick_like_tree_file"));
4334     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4335
4336     int value = chooser.showOpenDialog(null);
4337
4338     if (value == JalviewFileChooser.APPROVE_OPTION)
4339     {
4340       String choice = chooser.getSelectedFile().getPath();
4341       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4342       jalview.io.NewickFile fin = null;
4343       try
4344       {
4345         fin = new jalview.io.NewickFile(choice, "File");
4346         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4347       } catch (Exception ex)
4348       {
4349         JOptionPane
4350                 .showMessageDialog(
4351                         Desktop.desktop,
4352                         ex.getMessage(),
4353                         MessageManager
4354                                 .getString("label.problem_reading_tree_file"),
4355                         JOptionPane.WARNING_MESSAGE);
4356         ex.printStackTrace();
4357       }
4358       if (fin != null && fin.hasWarningMessage())
4359       {
4360         JOptionPane.showMessageDialog(Desktop.desktop, fin
4361                 .getWarningMessage(), MessageManager
4362                 .getString("label.possible_problem_with_tree_file"),
4363                 JOptionPane.WARNING_MESSAGE);
4364       }
4365     }
4366   }
4367
4368   @Override
4369   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4370   {
4371     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4372   }
4373
4374   public TreePanel ShowNewickTree(NewickFile nf, String title)
4375   {
4376     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4377   }
4378
4379   public TreePanel ShowNewickTree(NewickFile nf, String title,
4380           AlignmentView input)
4381   {
4382     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4383   }
4384
4385   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4386           int h, int x, int y)
4387   {
4388     return ShowNewickTree(nf, title, null, w, h, x, y);
4389   }
4390
4391   /**
4392    * Add a treeviewer for the tree extracted from a newick file object to the
4393    * current alignment view
4394    *
4395    * @param nf
4396    *          the tree
4397    * @param title
4398    *          tree viewer title
4399    * @param input
4400    *          Associated alignment input data (or null)
4401    * @param w
4402    *          width
4403    * @param h
4404    *          height
4405    * @param x
4406    *          position
4407    * @param y
4408    *          position
4409    * @return TreePanel handle
4410    */
4411   public TreePanel ShowNewickTree(NewickFile nf, String title,
4412           AlignmentView input, int w, int h, int x, int y)
4413   {
4414     TreePanel tp = null;
4415
4416     try
4417     {
4418       nf.parse();
4419
4420       if (nf.getTree() != null)
4421       {
4422         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4423
4424         tp.setSize(w, h);
4425
4426         if (x > 0 && y > 0)
4427         {
4428           tp.setLocation(x, y);
4429         }
4430
4431         Desktop.addInternalFrame(tp, title, w, h);
4432       }
4433     } catch (Exception ex)
4434     {
4435       ex.printStackTrace();
4436     }
4437
4438     return tp;
4439   }
4440
4441   private boolean buildingMenu = false;
4442
4443   /**
4444    * Generates menu items and listener event actions for web service clients
4445    *
4446    */
4447   public void BuildWebServiceMenu()
4448   {
4449     while (buildingMenu)
4450     {
4451       try
4452       {
4453         System.err.println("Waiting for building menu to finish.");
4454         Thread.sleep(10);
4455       } catch (Exception e)
4456       {
4457       }
4458     }
4459     final AlignFrame me = this;
4460     buildingMenu = true;
4461     new Thread(new Runnable()
4462     {
4463       @Override
4464       public void run()
4465       {
4466         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4467         try
4468         {
4469           // System.err.println("Building ws menu again "
4470           // + Thread.currentThread());
4471           // TODO: add support for context dependent disabling of services based
4472           // on
4473           // alignment and current selection
4474           // TODO: add additional serviceHandle parameter to specify abstract
4475           // handler
4476           // class independently of AbstractName
4477           // TODO: add in rediscovery GUI function to restart discoverer
4478           // TODO: group services by location as well as function and/or
4479           // introduce
4480           // object broker mechanism.
4481           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4482           final IProgressIndicator af = me;
4483           final JMenu msawsmenu = new JMenu("Alignment");
4484           final JMenu secstrmenu = new JMenu(
4485                   "Secondary Structure Prediction");
4486           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4487           final JMenu analymenu = new JMenu("Analysis");
4488           final JMenu dismenu = new JMenu("Protein Disorder");
4489           // final JMenu msawsmenu = new
4490           // JMenu(MessageManager.getString("label.alignment"));
4491           // final JMenu secstrmenu = new
4492           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4493           // final JMenu seqsrchmenu = new
4494           // JMenu(MessageManager.getString("label.sequence_database_search"));
4495           // final JMenu analymenu = new
4496           // JMenu(MessageManager.getString("label.analysis"));
4497           // final JMenu dismenu = new
4498           // JMenu(MessageManager.getString("label.protein_disorder"));
4499           // JAL-940 - only show secondary structure prediction services from
4500           // the legacy server
4501           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4502               // &&
4503           Discoverer.services != null && (Discoverer.services.size() > 0))
4504           {
4505             // TODO: refactor to allow list of AbstractName/Handler bindings to
4506             // be
4507             // stored or retrieved from elsewhere
4508             // No MSAWS used any more:
4509             // Vector msaws = null; // (Vector)
4510             // Discoverer.services.get("MsaWS");
4511             Vector secstrpr = (Vector) Discoverer.services
4512                     .get("SecStrPred");
4513             if (secstrpr != null)
4514             {
4515               // Add any secondary structure prediction services
4516               for (int i = 0, j = secstrpr.size(); i < j; i++)
4517               {
4518                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4519                         .get(i);
4520                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4521                         .getServiceClient(sh);
4522                 int p = secstrmenu.getItemCount();
4523                 impl.attachWSMenuEntry(secstrmenu, me);
4524                 int q = secstrmenu.getItemCount();
4525                 for (int litm = p; litm < q; litm++)
4526                 {
4527                   legacyItems.add(secstrmenu.getItem(litm));
4528                 }
4529               }
4530             }
4531           }
4532
4533           // Add all submenus in the order they should appear on the web
4534           // services menu
4535           wsmenu.add(msawsmenu);
4536           wsmenu.add(secstrmenu);
4537           wsmenu.add(dismenu);
4538           wsmenu.add(analymenu);
4539           // No search services yet
4540           // wsmenu.add(seqsrchmenu);
4541
4542           javax.swing.SwingUtilities.invokeLater(new Runnable()
4543           {
4544             @Override
4545             public void run()
4546             {
4547               try
4548               {
4549                 webService.removeAll();
4550                 // first, add discovered services onto the webservices menu
4551                 if (wsmenu.size() > 0)
4552                 {
4553                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4554                   {
4555                     webService.add(wsmenu.get(i));
4556                   }
4557                 }
4558                 else
4559                 {
4560                   webService.add(me.webServiceNoServices);
4561                 }
4562                 // TODO: move into separate menu builder class.
4563                 boolean new_sspred = false;
4564                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4565                 {
4566                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4567                   if (jws2servs != null)
4568                   {
4569                     if (jws2servs.hasServices())
4570                     {
4571                       jws2servs.attachWSMenuEntry(webService, me);
4572                       for (Jws2Instance sv : jws2servs.getServices())
4573                       {
4574                         if (sv.description.toLowerCase().contains("jpred"))
4575                         {
4576                           for (JMenuItem jmi : legacyItems)
4577                           {
4578                             jmi.setVisible(false);
4579                           }
4580                         }
4581                       }
4582
4583                     }
4584                     if (jws2servs.isRunning())
4585                     {
4586                       JMenuItem tm = new JMenuItem(
4587                               "Still discovering JABA Services");
4588                       tm.setEnabled(false);
4589                       webService.add(tm);
4590                     }
4591                   }
4592                 }
4593                 build_urlServiceMenu(me.webService);
4594                 build_fetchdbmenu(webService);
4595                 for (JMenu item : wsmenu)
4596                 {
4597                   if (item.getItemCount() == 0)
4598                   {
4599                     item.setEnabled(false);
4600                   }
4601                   else
4602                   {
4603                     item.setEnabled(true);
4604                   }
4605                 }
4606               } catch (Exception e)
4607               {
4608                 Cache.log
4609                         .debug("Exception during web service menu building process.",
4610                                 e);
4611               }
4612             }
4613           });
4614         } catch (Exception e)
4615         {
4616         }
4617         buildingMenu = false;
4618       }
4619     }).start();
4620
4621   }
4622
4623   /**
4624    * construct any groupURL type service menu entries.
4625    *
4626    * @param webService
4627    */
4628   private void build_urlServiceMenu(JMenu webService)
4629   {
4630     // TODO: remove this code when 2.7 is released
4631     // DEBUG - alignmentView
4632     /*
4633      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4634      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4635      *
4636      * @Override public void actionPerformed(ActionEvent e) {
4637      * jalview.datamodel.AlignmentView
4638      * .testSelectionViews(af.viewport.getAlignment(),
4639      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4640      *
4641      * }); webService.add(testAlView);
4642      */
4643     // TODO: refactor to RestClient discoverer and merge menu entries for
4644     // rest-style services with other types of analysis/calculation service
4645     // SHmmr test client - still being implemented.
4646     // DEBUG - alignmentView
4647
4648     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4649             .getRestClients())
4650     {
4651       client.attachWSMenuEntry(
4652               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4653               this);
4654     }
4655   }
4656
4657   /**
4658    * Searches selected sequences for xRef products and builds the Show
4659    * Cross-References menu (formerly called Show Products)
4660    *
4661    * @return true if Show Cross-references menu should be enabled.
4662    */
4663   public boolean canShowProducts()
4664   {
4665     SequenceI[] selection = viewport.getSequenceSelection();
4666     AlignmentI dataset = viewport.getAlignment().getDataset();
4667     boolean showp = false;
4668     try
4669     {
4670       showProducts.removeAll();
4671       final boolean dna = viewport.getAlignment().isNucleotide();
4672       String[] ptypes = (selection == null || selection.length == 0) ? null
4673               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4674
4675       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4676       {
4677         showp = true;
4678         final AlignFrame af = this;
4679         final String source = ptypes[t];
4680         JMenuItem xtype = new JMenuItem(ptypes[t]);
4681         xtype.addActionListener(new ActionListener()
4682         {
4683
4684           @Override
4685           public void actionPerformed(ActionEvent e)
4686           {
4687             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4688           }
4689
4690         });
4691         showProducts.add(xtype);
4692       }
4693       showProducts.setVisible(showp);
4694       showProducts.setEnabled(showp);
4695     } catch (Exception e)
4696     {
4697       jalview.bin.Cache.log
4698               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4699                       e);
4700       return false;
4701     }
4702     return showp;
4703   }
4704
4705   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4706           final String source)
4707   {
4708     Runnable foo = new Runnable()
4709     {
4710
4711       @Override
4712       public void run()
4713       {
4714         final long sttime = System.currentTimeMillis();
4715         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4716                 "status.searching_for_sequences_from",
4717                 new Object[] { source }), sttime);
4718         try
4719         {
4720           /*
4721            * 'peer' sequences are any to add to this alignment, for example
4722            * alternative protein products for my protein's gene
4723            */
4724           List<SequenceI> addedPeers = new ArrayList<SequenceI>();
4725           AlignmentI alignment = AlignFrame.this.getViewport().getAlignment();
4726           Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
4727                   alignment, addedPeers);
4728           if (xrefs != null)
4729           {
4730             Alignment al = makeCrossReferencesAlignment(
4731                     alignment.getDataset(), xrefs);
4732
4733             /*
4734              * Copy dna-to-protein mappings to new alignment
4735              */
4736             // TODO 1: no mappings are set up for EMBL product
4737             // TODO 2: if they were, should add them to protein alignment, not
4738             // dna
4739             // List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4740             // for (AlignedCodonFrame acf : cf)
4741             // {
4742             // al.addCodonFrame(acf);
4743             // }
4744             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4745                     DEFAULT_HEIGHT);
4746             String newtitle = String.format("%s %s %s",
4747                     MessageManager.getString(dna ? "label.proteins"
4748                             : "label.nucleotides"), MessageManager
4749                             .getString("label.for"), getTitle());
4750             newFrame.setTitle(newtitle);
4751
4752             boolean asSplitFrame = Cache.getDefault(
4753                     Preferences.ENABLE_SPLIT_FRAME, true);
4754             if (asSplitFrame)
4755             {
4756               /*
4757                * Make a copy of this alignment (sharing the same dataset
4758                * sequences). If we are DNA, drop introns and update mappings
4759                */
4760               AlignmentI copyAlignment = null;
4761               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4762                       .getSequenceSelection();
4763               List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4764               if (dna)
4765               {
4766                 copyAlignment = AlignmentUtils.makeCdsAlignment(
4767                         sequenceSelection, cf);
4768                 al.getCodonFrames().clear();
4769                 al.getCodonFrames().addAll(cf);
4770               }
4771               else
4772               {
4773                 copyAlignment = new Alignment(new Alignment(
4774                         sequenceSelection));
4775                 copyAlignment.getCodonFrames().addAll(cf);
4776               }
4777               StructureSelectionManager ssm = StructureSelectionManager
4778                       .getStructureSelectionManager(Desktop.instance);
4779               ssm.registerMappings(cf);
4780
4781               /*
4782                * add in any extra 'peer' sequences discovered
4783                * (e.g. alternative protein products)
4784                */
4785               for (SequenceI peer : addedPeers)
4786               {
4787                 copyAlignment.addSequence(peer);
4788               }
4789
4790               /*
4791                * align protein to dna
4792                */
4793               // TODO needs debugging
4794               // if (dna)
4795               // {
4796               // al.alignAs(copyAlignment);
4797               // }
4798               // else
4799               // {
4800               // copyAlignment.alignAs(al);
4801               // }
4802
4803               AlignFrame copyThis = new AlignFrame(copyAlignment,
4804                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4805               copyThis.setTitle(AlignFrame.this.getTitle());
4806
4807               boolean showSequenceFeatures = viewport
4808                       .isShowSequenceFeatures();
4809               newFrame.setShowSeqFeatures(showSequenceFeatures);
4810               copyThis.setShowSeqFeatures(showSequenceFeatures);
4811               FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4812                       .getFeatureRenderer();
4813               /*
4814                * copy feature rendering settings to split frame
4815                */
4816               newFrame.alignPanel.getSeqPanel().seqCanvas
4817                       .getFeatureRenderer().transferSettings(
4818                               myFeatureStyling);
4819               copyThis.alignPanel.getSeqPanel().seqCanvas
4820                       .getFeatureRenderer().transferSettings(
4821                               myFeatureStyling);
4822               SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4823                       dna ? newFrame : copyThis);
4824               newFrame.setVisible(true);
4825               copyThis.setVisible(true);
4826               String linkedTitle = MessageManager
4827                       .getString("label.linked_view_title");
4828               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4829               sf.adjustDivider();
4830             }
4831             else
4832             {
4833               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4834                       DEFAULT_HEIGHT);
4835             }
4836           }
4837           else
4838           {
4839             System.err.println("No Sequences generated for xRef type "
4840                     + source);
4841           }
4842         } catch (Exception e)
4843         {
4844           jalview.bin.Cache.log.error(
4845                   "Exception when finding crossreferences", e);
4846         } catch (OutOfMemoryError e)
4847         {
4848           new OOMWarning("whilst fetching crossreferences", e);
4849         } catch (Error e)
4850         {
4851           jalview.bin.Cache.log.error("Error when finding crossreferences",
4852                   e);
4853         }
4854         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4855                 "status.finished_searching_for_sequences_from",
4856                 new Object[] { source }), sttime);
4857       }
4858
4859       /**
4860        * @param alignment
4861        * @param prods
4862        * @return
4863        */
4864       protected Alignment makeCrossReferencesAlignment(
4865 Alignment dataset,
4866               Alignment prods)
4867       {
4868         SequenceI[] sprods = new SequenceI[prods.getHeight()];
4869         for (int s = 0; s < sprods.length; s++)
4870         {
4871           sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4872           if (dataset.getSequences() == null
4873                   || !dataset.getSequences().contains(
4874                           sprods[s].getDatasetSequence()))
4875           {
4876             dataset.addSequence(sprods[s].getDatasetSequence());
4877           }
4878           sprods[s].updatePDBIds();
4879         }
4880         Alignment al = new Alignment(sprods);
4881         al.setDataset(dataset);
4882         return al;
4883       }
4884
4885     };
4886     Thread frunner = new Thread(foo);
4887     frunner.start();
4888   }
4889
4890   public boolean canShowTranslationProducts(SequenceI[] selection,
4891           AlignmentI alignment)
4892   {
4893     // old way
4894     try
4895     {
4896       return (jalview.analysis.Dna.canTranslate(selection,
4897               viewport.getViewAsVisibleContigs(true)));
4898     } catch (Exception e)
4899     {
4900       jalview.bin.Cache.log
4901               .warn("canTranslate threw an exception - please report to help@jalview.org",
4902                       e);
4903       return false;
4904     }
4905   }
4906
4907   /**
4908    * Construct and display a new frame containing the translation of this
4909    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4910    */
4911   @Override
4912   public void showTranslation_actionPerformed(ActionEvent e)
4913   {
4914     AlignmentI al = null;
4915     try
4916     {
4917       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4918
4919       al = dna.translateCdna();
4920     } catch (Exception ex)
4921     {
4922       jalview.bin.Cache.log.error(
4923               "Exception during translation. Please report this !", ex);
4924       final String msg = MessageManager
4925               .getString("label.error_when_translating_sequences_submit_bug_report");
4926       final String errorTitle = MessageManager
4927               .getString("label.implementation_error")
4928               + MessageManager.getString("translation_failed");
4929       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4930               JOptionPane.ERROR_MESSAGE);
4931       return;
4932     }
4933     if (al == null || al.getHeight() == 0)
4934     {
4935       final String msg = MessageManager
4936               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4937       final String errorTitle = MessageManager
4938               .getString("label.translation_failed");
4939       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4940               JOptionPane.WARNING_MESSAGE);
4941     }
4942     else
4943     {
4944       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4945       af.setFileFormat(this.currentFileFormat);
4946       final String newTitle = MessageManager.formatMessage(
4947               "label.translation_of_params",
4948               new Object[] { this.getTitle() });
4949       af.setTitle(newTitle);
4950       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4951       {
4952         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4953         viewport.openSplitFrame(af, new Alignment(seqs));
4954       }
4955       else
4956       {
4957         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4958                 DEFAULT_HEIGHT);
4959       }
4960     }
4961   }
4962
4963   /**
4964    * Set the file format
4965    *
4966    * @param fileFormat
4967    */
4968   public void setFileFormat(String fileFormat)
4969   {
4970     this.currentFileFormat = fileFormat;
4971   }
4972
4973   /**
4974    * Try to load a features file onto the alignment.
4975    *
4976    * @param file
4977    *          contents or path to retrieve file
4978    * @param type
4979    *          access mode of file (see jalview.io.AlignFile)
4980    * @return true if features file was parsed correctly.
4981    */
4982   public boolean parseFeaturesFile(String file, String type)
4983   {
4984     return avc.parseFeaturesFile(file, type,
4985             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4986
4987   }
4988
4989   @Override
4990   public void refreshFeatureUI(boolean enableIfNecessary)
4991   {
4992     // note - currently this is only still here rather than in the controller
4993     // because of the featureSettings hard reference that is yet to be
4994     // abstracted
4995     if (enableIfNecessary)
4996     {
4997       viewport.setShowSequenceFeatures(true);
4998       showSeqFeatures.setSelected(true);
4999     }
5000
5001   }
5002
5003   @Override
5004   public void dragEnter(DropTargetDragEvent evt)
5005   {
5006   }
5007
5008   @Override
5009   public void dragExit(DropTargetEvent evt)
5010   {
5011   }
5012
5013   @Override
5014   public void dragOver(DropTargetDragEvent evt)
5015   {
5016   }
5017
5018   @Override
5019   public void dropActionChanged(DropTargetDragEvent evt)
5020   {
5021   }
5022
5023   @Override
5024   public void drop(DropTargetDropEvent evt)
5025   {
5026     Transferable t = evt.getTransferable();
5027     java.util.List files = null;
5028
5029     try
5030     {
5031       DataFlavor uriListFlavor = new DataFlavor(
5032               "text/uri-list;class=java.lang.String");
5033       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5034       {
5035         // Works on Windows and MacOSX
5036         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5037         files = (java.util.List) t
5038                 .getTransferData(DataFlavor.javaFileListFlavor);
5039       }
5040       else if (t.isDataFlavorSupported(uriListFlavor))
5041       {
5042         // This is used by Unix drag system
5043         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5044         String data = (String) t.getTransferData(uriListFlavor);
5045         files = new java.util.ArrayList(1);
5046         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5047                 data, "\r\n"); st.hasMoreTokens();)
5048         {
5049           String s = st.nextToken();
5050           if (s.startsWith("#"))
5051           {
5052             // the line is a comment (as per the RFC 2483)
5053             continue;
5054           }
5055
5056           java.net.URI uri = new java.net.URI(s);
5057           // check to see if we can handle this kind of URI
5058           if (uri.getScheme().toLowerCase().startsWith("http"))
5059           {
5060             files.add(uri.toString());
5061           }
5062           else
5063           {
5064             // otherwise preserve old behaviour: catch all for file objects
5065             java.io.File file = new java.io.File(uri);
5066             files.add(file.toString());
5067           }
5068         }
5069       }
5070     } catch (Exception e)
5071     {
5072       e.printStackTrace();
5073     }
5074     if (files != null)
5075     {
5076       try
5077       {
5078         // check to see if any of these files have names matching sequences in
5079         // the alignment
5080         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5081                 .getAlignment().getSequencesArray());
5082         /**
5083          * Object[] { String,SequenceI}
5084          */
5085         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5086         ArrayList<String> filesnotmatched = new ArrayList<String>();
5087         for (int i = 0; i < files.size(); i++)
5088         {
5089           String file = files.get(i).toString();
5090           String pdbfn = "";
5091           String protocol = FormatAdapter.checkProtocol(file);
5092           if (protocol == jalview.io.FormatAdapter.FILE)
5093           {
5094             File fl = new File(file);
5095             pdbfn = fl.getName();
5096           }
5097           else if (protocol == jalview.io.FormatAdapter.URL)
5098           {
5099             URL url = new URL(file);
5100             pdbfn = url.getFile();
5101           }
5102           if (pdbfn.length() > 0)
5103           {
5104             // attempt to find a match in the alignment
5105             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5106             int l = 0, c = pdbfn.indexOf(".");
5107             while (mtch == null && c != -1)
5108             {
5109               do
5110               {
5111                 l = c;
5112               } while ((c = pdbfn.indexOf(".", l)) > l);
5113               if (l > -1)
5114               {
5115                 pdbfn = pdbfn.substring(0, l);
5116               }
5117               mtch = idm.findAllIdMatches(pdbfn);
5118             }
5119             if (mtch != null)
5120             {
5121               String type = null;
5122               try
5123               {
5124                 type = new IdentifyFile().identify(file, protocol);
5125               } catch (Exception ex)
5126               {
5127                 type = null;
5128               }
5129               if (type != null)
5130               {
5131                 if (type.equalsIgnoreCase("PDB"))
5132                 {
5133                   filesmatched.add(new Object[] { file, protocol, mtch });
5134                   continue;
5135                 }
5136               }
5137             }
5138             // File wasn't named like one of the sequences or wasn't a PDB file.
5139             filesnotmatched.add(file);
5140           }
5141         }
5142         int assocfiles = 0;
5143         if (filesmatched.size() > 0)
5144         {
5145           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5146                   || JOptionPane
5147                           .showConfirmDialog(
5148                                   this,
5149                                   MessageManager
5150                                           .formatMessage(
5151                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5152                                                   new Object[] { Integer
5153                                                           .valueOf(
5154                                                                   filesmatched
5155                                                                           .size())
5156                                                           .toString() }),
5157                                   MessageManager
5158                                           .getString("label.automatically_associate_pdb_files_by_name"),
5159                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5160
5161           {
5162             for (Object[] fm : filesmatched)
5163             {
5164               // try and associate
5165               // TODO: may want to set a standard ID naming formalism for
5166               // associating PDB files which have no IDs.
5167               for (SequenceI toassoc : (SequenceI[]) fm[2])
5168               {
5169                 PDBEntry pe = new AssociatePdbFileWithSeq()
5170                         .associatePdbWithSeq((String) fm[0],
5171                                 (String) fm[1], toassoc, false,
5172                                 Desktop.instance);
5173                 if (pe != null)
5174                 {
5175                   System.err.println("Associated file : "
5176                           + ((String) fm[0]) + " with "
5177                           + toassoc.getDisplayId(true));
5178                   assocfiles++;
5179                 }
5180               }
5181               alignPanel.paintAlignment(true);
5182             }
5183           }
5184         }
5185         if (filesnotmatched.size() > 0)
5186         {
5187           if (assocfiles > 0
5188                   && (Cache.getDefault(
5189                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5190                           .showConfirmDialog(
5191                                   this,
5192                                   "<html>"
5193                                           + MessageManager
5194                                                   .formatMessage(
5195                                                           "label.ignore_unmatched_dropped_files_info",
5196                                                           new Object[] { Integer
5197                                                                   .valueOf(
5198                                                                           filesnotmatched
5199                                                                                   .size())
5200                                                                   .toString() })
5201                                           + "</html>",
5202                                   MessageManager
5203                                           .getString("label.ignore_unmatched_dropped_files"),
5204                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5205           {
5206             return;
5207           }
5208           for (String fn : filesnotmatched)
5209           {
5210             loadJalviewDataFile(fn, null, null, null);
5211           }
5212
5213         }
5214       } catch (Exception ex)
5215       {
5216         ex.printStackTrace();
5217       }
5218     }
5219   }
5220
5221   /**
5222    * Attempt to load a "dropped" file or URL string: First by testing whether
5223    * it's an Annotation file, then a JNet file, and finally a features file. If
5224    * all are false then the user may have dropped an alignment file onto this
5225    * AlignFrame.
5226    *
5227    * @param file
5228    *          either a filename or a URL string.
5229    */
5230   public void loadJalviewDataFile(String file, String protocol,
5231           String format, SequenceI assocSeq)
5232   {
5233     try
5234     {
5235       if (protocol == null)
5236       {
5237         protocol = FormatAdapter.checkProtocol(file);
5238       }
5239       // if the file isn't identified, or not positively identified as some
5240       // other filetype (PFAM is default unidentified alignment file type) then
5241       // try to parse as annotation.
5242       boolean isAnnotation = (format == null || format
5243               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5244               .annotateAlignmentView(viewport, file, protocol) : false;
5245
5246       if (!isAnnotation)
5247       {
5248         // first see if its a T-COFFEE score file
5249         TCoffeeScoreFile tcf = null;
5250         try
5251         {
5252           tcf = new TCoffeeScoreFile(file, protocol);
5253           if (tcf.isValid())
5254           {
5255             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5256             {
5257               tcoffeeColour.setEnabled(true);
5258               tcoffeeColour.setSelected(true);
5259               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5260               isAnnotation = true;
5261               statusBar
5262                       .setText(MessageManager
5263                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5264             }
5265             else
5266             {
5267               // some problem - if no warning its probable that the ID matching
5268               // process didn't work
5269               JOptionPane
5270                       .showMessageDialog(
5271                               Desktop.desktop,
5272                               tcf.getWarningMessage() == null ? MessageManager
5273                                       .getString("label.check_file_matches_sequence_ids_alignment")
5274                                       : tcf.getWarningMessage(),
5275                               MessageManager
5276                                       .getString("label.problem_reading_tcoffee_score_file"),
5277                               JOptionPane.WARNING_MESSAGE);
5278             }
5279           }
5280           else
5281           {
5282             tcf = null;
5283           }
5284         } catch (Exception x)
5285         {
5286           Cache.log
5287                   .debug("Exception when processing data source as T-COFFEE score file",
5288                           x);
5289           tcf = null;
5290         }
5291         if (tcf == null)
5292         {
5293           // try to see if its a JNet 'concise' style annotation file *before*
5294           // we
5295           // try to parse it as a features file
5296           if (format == null)
5297           {
5298             format = new IdentifyFile().identify(file, protocol);
5299           }
5300           if (format.equalsIgnoreCase("JnetFile"))
5301           {
5302             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5303                     file, protocol);
5304             new JnetAnnotationMaker();
5305             JnetAnnotationMaker.add_annotation(predictions,
5306                     viewport.getAlignment(), 0, false);
5307             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5308             viewport.getAlignment().setSeqrep(repseq);
5309             ColumnSelection cs = new ColumnSelection();
5310             cs.hideInsertionsFor(repseq);
5311             viewport.setColumnSelection(cs);
5312             isAnnotation = true;
5313           }
5314           else if (IdentifyFile.FeaturesFile.equals(format))
5315           {
5316             if (parseFeaturesFile(file, protocol))
5317             {
5318               alignPanel.paintAlignment(true);
5319             }
5320           }
5321             else
5322             {
5323               new FileLoader().LoadFile(viewport, file, protocol, format);
5324             }
5325         }
5326       }
5327       if (isAnnotation)
5328       {
5329
5330         alignPanel.adjustAnnotationHeight();
5331         viewport.updateSequenceIdColours();
5332         buildSortByAnnotationScoresMenu();
5333         alignPanel.paintAlignment(true);
5334       }
5335     } catch (Exception ex)
5336     {
5337       ex.printStackTrace();
5338     } catch (OutOfMemoryError oom)
5339     {
5340       try
5341       {
5342         System.gc();
5343       } catch (Exception x)
5344       {
5345       }
5346       new OOMWarning(
5347               "loading data "
5348                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5349                               : "using " + protocol + " from " + file)
5350                               : ".")
5351                       + (format != null ? "(parsing as '" + format
5352                               + "' file)" : ""), oom, Desktop.desktop);
5353     }
5354   }
5355
5356   /**
5357    * Method invoked by the ChangeListener on the tabbed pane, in other words
5358    * when a different tabbed pane is selected by the user or programmatically.
5359    */
5360   @Override
5361   public void tabSelectionChanged(int index)
5362   {
5363     if (index > -1)
5364     {
5365       alignPanel = alignPanels.get(index);
5366       viewport = alignPanel.av;
5367       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5368       setMenusFromViewport(viewport);
5369     }
5370
5371     /*
5372      * If there is a frame linked to this one in a SplitPane, switch it to the
5373      * same view tab index. No infinite recursion of calls should happen, since
5374      * tabSelectionChanged() should not get invoked on setting the selected
5375      * index to an unchanged value. Guard against setting an invalid index
5376      * before the new view peer tab has been created.
5377      */
5378     final AlignViewportI peer = viewport.getCodingComplement();
5379     if (peer != null)
5380     {
5381       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5382       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5383       {
5384         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5385       }
5386     }
5387   }
5388
5389   /**
5390    * On right mouse click on view tab, prompt for and set new view name.
5391    */
5392   @Override
5393   public void tabbedPane_mousePressed(MouseEvent e)
5394   {
5395     if (SwingUtilities.isRightMouseButton(e))
5396     {
5397       String msg = MessageManager.getString("label.enter_view_name");
5398       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5399               JOptionPane.QUESTION_MESSAGE);
5400
5401       if (reply != null)
5402       {
5403         viewport.viewName = reply;
5404         // TODO warn if reply is in getExistingViewNames()?
5405         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5406       }
5407     }
5408   }
5409
5410   public AlignViewport getCurrentView()
5411   {
5412     return viewport;
5413   }
5414
5415   /**
5416    * Open the dialog for regex description parsing.
5417    */
5418   @Override
5419   protected void extractScores_actionPerformed(ActionEvent e)
5420   {
5421     ParseProperties pp = new jalview.analysis.ParseProperties(
5422             viewport.getAlignment());
5423     // TODO: verify regex and introduce GUI dialog for version 2.5
5424     // if (pp.getScoresFromDescription("col", "score column ",
5425     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5426     // true)>0)
5427     if (pp.getScoresFromDescription("description column",
5428             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5429     {
5430       buildSortByAnnotationScoresMenu();
5431     }
5432   }
5433
5434   /*
5435    * (non-Javadoc)
5436    *
5437    * @see
5438    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5439    * )
5440    */
5441   @Override
5442   protected void showDbRefs_actionPerformed(ActionEvent e)
5443   {
5444     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5445   }
5446
5447   /*
5448    * (non-Javadoc)
5449    *
5450    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5451    * ActionEvent)
5452    */
5453   @Override
5454   protected void showNpFeats_actionPerformed(ActionEvent e)
5455   {
5456     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5457   }
5458
5459   /**
5460    * find the viewport amongst the tabs in this alignment frame and close that
5461    * tab
5462    *
5463    * @param av
5464    */
5465   public boolean closeView(AlignViewportI av)
5466   {
5467     if (viewport == av)
5468     {
5469       this.closeMenuItem_actionPerformed(false);
5470       return true;
5471     }
5472     Component[] comp = tabbedPane.getComponents();
5473     for (int i = 0; comp != null && i < comp.length; i++)
5474     {
5475       if (comp[i] instanceof AlignmentPanel)
5476       {
5477         if (((AlignmentPanel) comp[i]).av == av)
5478         {
5479           // close the view.
5480           closeView((AlignmentPanel) comp[i]);
5481           return true;
5482         }
5483       }
5484     }
5485     return false;
5486   }
5487
5488   protected void build_fetchdbmenu(JMenu webService)
5489   {
5490     // Temporary hack - DBRef Fetcher always top level ws entry.
5491     // TODO We probably want to store a sequence database checklist in
5492     // preferences and have checkboxes.. rather than individual sources selected
5493     // here
5494     final JMenu rfetch = new JMenu(
5495             MessageManager.getString("action.fetch_db_references"));
5496     rfetch.setToolTipText(MessageManager
5497             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5498     webService.add(rfetch);
5499
5500     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5501             MessageManager.getString("option.trim_retrieved_seqs"));
5502     trimrs.setToolTipText(MessageManager
5503             .getString("label.trim_retrieved_sequences"));
5504     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5505     trimrs.addActionListener(new ActionListener()
5506     {
5507       @Override
5508       public void actionPerformed(ActionEvent e)
5509       {
5510         trimrs.setSelected(trimrs.isSelected());
5511         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5512                 Boolean.valueOf(trimrs.isSelected()).toString());
5513       };
5514     });
5515     rfetch.add(trimrs);
5516     JMenuItem fetchr = new JMenuItem(
5517             MessageManager.getString("label.standard_databases"));
5518     fetchr.setToolTipText(MessageManager
5519             .getString("label.fetch_embl_uniprot"));
5520     fetchr.addActionListener(new ActionListener()
5521     {
5522
5523       @Override
5524       public void actionPerformed(ActionEvent e)
5525       {
5526         new Thread(new Runnable()
5527         {
5528
5529           @Override
5530           public void run()
5531           {
5532             boolean isNuclueotide = alignPanel.alignFrame
5533                     .getViewport().getAlignment()
5534                     .isNucleotide();
5535             new jalview.ws.DBRefFetcher(alignPanel.av
5536                     .getSequenceSelection(),
5537                     alignPanel.alignFrame, null,
5538                     alignPanel.alignFrame.featureSettings,
5539                     isNuclueotide)
5540                     .fetchDBRefs(false);
5541           }
5542         }).start();
5543
5544       }
5545
5546     });
5547     rfetch.add(fetchr);
5548     final AlignFrame me = this;
5549     new Thread(new Runnable()
5550     {
5551       @Override
5552       public void run()
5553       {
5554         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5555                 .getSequenceFetcherSingleton(me);
5556         javax.swing.SwingUtilities.invokeLater(new Runnable()
5557         {
5558           @Override
5559           public void run()
5560           {
5561             String[] dbclasses = sf.getOrderedSupportedSources();
5562             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5563             // jalview.util.QuickSort.sort(otherdb, otherdb);
5564             List<DbSourceProxy> otherdb;
5565             JMenu dfetch = new JMenu();
5566             JMenu ifetch = new JMenu();
5567             JMenuItem fetchr = null;
5568             int comp = 0, icomp = 0, mcomp = 15;
5569             String mname = null;
5570             int dbi = 0;
5571             for (String dbclass : dbclasses)
5572             {
5573               otherdb = sf.getSourceProxy(dbclass);
5574               // add a single entry for this class, or submenu allowing 'fetch
5575               // all' or pick one
5576               if (otherdb == null || otherdb.size() < 1)
5577               {
5578                 continue;
5579               }
5580               // List<DbSourceProxy> dbs=otherdb;
5581               // otherdb=new ArrayList<DbSourceProxy>();
5582               // for (DbSourceProxy db:dbs)
5583               // {
5584               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5585               // }
5586               if (mname == null)
5587               {
5588                 mname = "From " + dbclass;
5589               }
5590               if (otherdb.size() == 1)
5591               {
5592                 final DbSourceProxy[] dassource = otherdb
5593                         .toArray(new DbSourceProxy[0]);
5594                 DbSourceProxy src = otherdb.get(0);
5595                 fetchr = new JMenuItem(src.getDbSource());
5596                 fetchr.addActionListener(new ActionListener()
5597                 {
5598
5599                   @Override
5600                   public void actionPerformed(ActionEvent e)
5601                   {
5602                     new Thread(new Runnable()
5603                     {
5604
5605                       @Override
5606                       public void run()
5607                       {
5608                         boolean isNuclueotide = alignPanel.alignFrame
5609                                 .getViewport().getAlignment()
5610                                 .isNucleotide();
5611                         new jalview.ws.DBRefFetcher(alignPanel.av
5612                                 .getSequenceSelection(),
5613                                 alignPanel.alignFrame, dassource,
5614                                 alignPanel.alignFrame.featureSettings,
5615                                 isNuclueotide)
5616                                 .fetchDBRefs(false);
5617                       }
5618                     }).start();
5619                   }
5620
5621                 });
5622                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5623                         MessageManager.formatMessage(
5624                                 "label.fetch_retrieve_from",
5625                                 new Object[] { src.getDbName() })));
5626                 dfetch.add(fetchr);
5627                 comp++;
5628               }
5629               else
5630               {
5631                 final DbSourceProxy[] dassource = otherdb
5632                         .toArray(new DbSourceProxy[0]);
5633                 // fetch all entry
5634                 DbSourceProxy src = otherdb.get(0);
5635                 fetchr = new JMenuItem(MessageManager.formatMessage(
5636                         "label.fetch_all_param",
5637                         new Object[] { src.getDbSource() }));
5638                 fetchr.addActionListener(new ActionListener()
5639                 {
5640                   @Override
5641                   public void actionPerformed(ActionEvent e)
5642                   {
5643                     new Thread(new Runnable()
5644                     {
5645
5646                       @Override
5647                       public void run()
5648                       {
5649                         boolean isNuclueotide = alignPanel.alignFrame
5650                                 .getViewport().getAlignment()
5651                                 .isNucleotide();
5652                         new jalview.ws.DBRefFetcher(alignPanel.av
5653                                 .getSequenceSelection(),
5654                                 alignPanel.alignFrame, dassource,
5655                                 alignPanel.alignFrame.featureSettings,
5656                                 isNuclueotide)
5657                                 .fetchDBRefs(false);
5658                       }
5659                     }).start();
5660                   }
5661                 });
5662
5663                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5664                         MessageManager.formatMessage(
5665                                 "label.fetch_retrieve_from_all_sources",
5666                                 new Object[] {
5667                                     Integer.valueOf(otherdb.size())
5668                                             .toString(), src.getDbSource(),
5669                                     src.getDbName() })));
5670                 dfetch.add(fetchr);
5671                 comp++;
5672                 // and then build the rest of the individual menus
5673                 ifetch = new JMenu(MessageManager.formatMessage(
5674                         "label.source_from_db_source",
5675                         new Object[] { src.getDbSource() }));
5676                 icomp = 0;
5677                 String imname = null;
5678                 int i = 0;
5679                 for (DbSourceProxy sproxy : otherdb)
5680                 {
5681                   String dbname = sproxy.getDbName();
5682                   String sname = dbname.length() > 5 ? dbname.substring(0,
5683                           5) + "..." : dbname;
5684                   String msname = dbname.length() > 10 ? dbname.substring(
5685                           0, 10) + "..." : dbname;
5686                   if (imname == null)
5687                   {
5688                     imname = MessageManager.formatMessage(
5689                             "label.from_msname", new Object[] { sname });
5690                   }
5691                   fetchr = new JMenuItem(msname);
5692                   final DbSourceProxy[] dassrc = { sproxy };
5693                   fetchr.addActionListener(new ActionListener()
5694                   {
5695
5696                     @Override
5697                     public void actionPerformed(ActionEvent e)
5698                     {
5699                       new Thread(new Runnable()
5700                       {
5701
5702                         @Override
5703                         public void run()
5704                         {
5705                           boolean isNuclueotide = alignPanel.alignFrame
5706                                   .getViewport().getAlignment()
5707                                   .isNucleotide();
5708                           new jalview.ws.DBRefFetcher(alignPanel.av
5709                                   .getSequenceSelection(),
5710                                   alignPanel.alignFrame, dassrc,
5711                                   alignPanel.alignFrame.featureSettings,
5712                                   isNuclueotide)
5713                                   .fetchDBRefs(false);
5714                         }
5715                       }).start();
5716                     }
5717
5718                   });
5719                   fetchr.setToolTipText("<html>"
5720                           + MessageManager.formatMessage(
5721                                   "label.fetch_retrieve_from", new Object[]
5722                                   { dbname }));
5723                   ifetch.add(fetchr);
5724                   ++i;
5725                   if (++icomp >= mcomp || i == (otherdb.size()))
5726                   {
5727                     ifetch.setText(MessageManager.formatMessage(
5728                             "label.source_to_target", imname, sname));
5729                     dfetch.add(ifetch);
5730                     ifetch = new JMenu();
5731                     imname = null;
5732                     icomp = 0;
5733                     comp++;
5734                   }
5735                 }
5736               }
5737               ++dbi;
5738               if (comp >= mcomp || dbi >= (dbclasses.length))
5739               {
5740                 dfetch.setText(MessageManager.formatMessage(
5741                         "label.source_to_target", mname, dbclass));
5742                 rfetch.add(dfetch);
5743                 dfetch = new JMenu();
5744                 mname = null;
5745                 comp = 0;
5746               }
5747             }
5748           }
5749         });
5750       }
5751     }).start();
5752
5753   }
5754
5755   /**
5756    * Left justify the whole alignment.
5757    */
5758   @Override
5759   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5760   {
5761     AlignmentI al = viewport.getAlignment();
5762     al.justify(false);
5763     viewport.firePropertyChange("alignment", null, al);
5764   }
5765
5766   /**
5767    * Right justify the whole alignment.
5768    */
5769   @Override
5770   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5771   {
5772     AlignmentI al = viewport.getAlignment();
5773     al.justify(true);
5774     viewport.firePropertyChange("alignment", null, al);
5775   }
5776
5777   @Override
5778   public void setShowSeqFeatures(boolean b)
5779   {
5780     showSeqFeatures.setSelected(b);
5781     viewport.setShowSequenceFeatures(b);
5782   }
5783
5784   /*
5785    * (non-Javadoc)
5786    *
5787    * @see
5788    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5789    * awt.event.ActionEvent)
5790    */
5791   @Override
5792   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5793   {
5794     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5795     alignPanel.paintAlignment(true);
5796   }
5797
5798   /*
5799    * (non-Javadoc)
5800    *
5801    * @see
5802    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5803    * .ActionEvent)
5804    */
5805   @Override
5806   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5807   {
5808     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5809     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5810
5811   }
5812
5813   /*
5814    * (non-Javadoc)
5815    *
5816    * @see
5817    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5818    * .event.ActionEvent)
5819    */
5820   @Override
5821   protected void showGroupConservation_actionPerformed(ActionEvent e)
5822   {
5823     viewport.setShowGroupConservation(showGroupConservation.getState());
5824     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5825   }
5826
5827   /*
5828    * (non-Javadoc)
5829    *
5830    * @see
5831    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5832    * .event.ActionEvent)
5833    */
5834   @Override
5835   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5836   {
5837     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5838     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5839   }
5840
5841   /*
5842    * (non-Javadoc)
5843    *
5844    * @see
5845    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5846    * .event.ActionEvent)
5847    */
5848   @Override
5849   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5850   {
5851     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5852     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5853   }
5854
5855   @Override
5856   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5857   {
5858     showSequenceLogo.setState(true);
5859     viewport.setShowSequenceLogo(true);
5860     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5861     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5862   }
5863
5864   @Override
5865   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5866   {
5867     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5868   }
5869
5870   /*
5871    * (non-Javadoc)
5872    *
5873    * @see
5874    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5875    * .event.ActionEvent)
5876    */
5877   @Override
5878   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5879   {
5880     if (avc.makeGroupsFromSelection())
5881     {
5882       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5883       alignPanel.updateAnnotation();
5884       alignPanel.paintAlignment(true);
5885     }
5886   }
5887
5888   public void clearAlignmentSeqRep()
5889   {
5890     // TODO refactor alignmentseqrep to controller
5891     if (viewport.getAlignment().hasSeqrep())
5892     {
5893       viewport.getAlignment().setSeqrep(null);
5894       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5895       alignPanel.updateAnnotation();
5896       alignPanel.paintAlignment(true);
5897     }
5898   }
5899
5900   @Override
5901   protected void createGroup_actionPerformed(ActionEvent e)
5902   {
5903     if (avc.createGroup())
5904     {
5905       alignPanel.alignmentChanged();
5906     }
5907   }
5908
5909   @Override
5910   protected void unGroup_actionPerformed(ActionEvent e)
5911   {
5912     if (avc.unGroup())
5913     {
5914       alignPanel.alignmentChanged();
5915     }
5916   }
5917
5918   /**
5919    * make the given alignmentPanel the currently selected tab
5920    *
5921    * @param alignmentPanel
5922    */
5923   public void setDisplayedView(AlignmentPanel alignmentPanel)
5924   {
5925     if (!viewport.getSequenceSetId().equals(
5926             alignmentPanel.av.getSequenceSetId()))
5927     {
5928       throw new Error(
5929               MessageManager
5930                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5931     }
5932     if (tabbedPane != null
5933             && tabbedPane.getTabCount() > 0
5934             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5935                     .getSelectedIndex())
5936     {
5937       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5938     }
5939   }
5940
5941   /**
5942    * Action on selection of menu options to Show or Hide annotations.
5943    *
5944    * @param visible
5945    * @param forSequences
5946    *          update sequence-related annotations
5947    * @param forAlignment
5948    *          update non-sequence-related annotations
5949    */
5950   @Override
5951   protected void setAnnotationsVisibility(boolean visible,
5952           boolean forSequences, boolean forAlignment)
5953   {
5954     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5955             .getAlignmentAnnotation())
5956     {
5957       /*
5958        * don't display non-positional annotations on an alignment
5959        */
5960       if (aa.annotations == null)
5961       {
5962         continue;
5963       }
5964       boolean apply = (aa.sequenceRef == null && forAlignment)
5965               || (aa.sequenceRef != null && forSequences);
5966       if (apply)
5967       {
5968         aa.visible = visible;
5969       }
5970     }
5971     alignPanel.validateAnnotationDimensions(true);
5972     alignPanel.alignmentChanged();
5973   }
5974
5975   /**
5976    * Store selected annotation sort order for the view and repaint.
5977    */
5978   @Override
5979   protected void sortAnnotations_actionPerformed()
5980   {
5981     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5982     this.alignPanel.av
5983             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5984     alignPanel.paintAlignment(true);
5985   }
5986
5987   /**
5988    *
5989    * @return alignment panels in this alignment frame
5990    */
5991   public List<? extends AlignmentViewPanel> getAlignPanels()
5992   {
5993     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5994   }
5995
5996   /**
5997    * Open a new alignment window, with the cDNA associated with this (protein)
5998    * alignment, aligned as is the protein.
5999    */
6000   protected void viewAsCdna_actionPerformed()
6001   {
6002     // TODO no longer a menu action - refactor as required
6003     final AlignmentI alignment = getViewport().getAlignment();
6004     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6005     if (mappings == null)
6006     {
6007       return;
6008     }
6009     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6010     for (SequenceI aaSeq : alignment.getSequences())
6011     {
6012       for (AlignedCodonFrame acf : mappings)
6013       {
6014         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6015         if (dnaSeq != null)
6016         {
6017           /*
6018            * There is a cDNA mapping for this protein sequence - add to new
6019            * alignment. It will share the same dataset sequence as other mapped
6020            * cDNA (no new mappings need to be created).
6021            */
6022           final Sequence newSeq = new Sequence(dnaSeq);
6023           newSeq.setDatasetSequence(dnaSeq);
6024           cdnaSeqs.add(newSeq);
6025         }
6026       }
6027     }
6028     if (cdnaSeqs.size() == 0)
6029     {
6030       // show a warning dialog no mapped cDNA
6031       return;
6032     }
6033     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6034             .size()]));
6035     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6036             AlignFrame.DEFAULT_HEIGHT);
6037     cdna.alignAs(alignment);
6038     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6039             + this.title;
6040     Desktop.addInternalFrame(alignFrame, newtitle,
6041             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6042   }
6043
6044   /**
6045    * Set visibility of dna/protein complement view (available when shown in a
6046    * split frame).
6047    *
6048    * @param show
6049    */
6050   @Override
6051   protected void showComplement_actionPerformed(boolean show)
6052   {
6053     SplitContainerI sf = getSplitViewContainer();
6054     if (sf != null)
6055     {
6056       sf.setComplementVisible(this, show);
6057     }
6058   }
6059
6060   /**
6061    * Generate the reverse (optionally complemented) of the selected sequences,
6062    * and add them to the alignment
6063    */
6064   @Override
6065   protected void showReverse_actionPerformed(boolean complement)
6066   {
6067     AlignmentI al = null;
6068     try
6069     {
6070       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6071
6072       al = dna.reverseCdna(complement);
6073       viewport.addAlignment(al, "");
6074     } catch (Exception ex)
6075     {
6076       System.err.println(ex.getMessage());
6077       return;
6078     }
6079   }
6080 }
6081
6082 class PrintThread extends Thread
6083 {
6084   AlignmentPanel ap;
6085
6086   public PrintThread(AlignmentPanel ap)
6087   {
6088     this.ap = ap;
6089   }
6090
6091   static PageFormat pf;
6092
6093   @Override
6094   public void run()
6095   {
6096     PrinterJob printJob = PrinterJob.getPrinterJob();
6097
6098     if (pf != null)
6099     {
6100       printJob.setPrintable(ap, pf);
6101     }
6102     else
6103     {
6104       printJob.setPrintable(ap);
6105     }
6106
6107     if (printJob.printDialog())
6108     {
6109       try
6110       {
6111         printJob.print();
6112       } catch (Exception PrintException)
6113       {
6114         PrintException.printStackTrace();
6115       }
6116     }
6117   }
6118 }