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.util.MessageManager;
  95 import jalview.viewmodel.AlignmentViewport;
  96 import jalview.ws.DBRefFetcher;
  97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  98 import jalview.ws.jws1.Discoverer;
  99 import jalview.ws.jws2.Jws2Discoverer;
 100 import jalview.ws.jws2.jabaws2.Jws2Instance;
 101 import jalview.ws.seqfetcher.DbSourceProxy;
 102
 103 import java.awt.BorderLayout;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseAdapter;
 125 import java.awt.event.MouseEvent;
 126 import java.awt.print.PageFormat;
 127 import java.awt.print.PrinterJob;
 128 import java.beans.PropertyChangeEvent;
 129 import java.io.File;
 130 import java.net.URL;
 131 import java.util.ArrayList;
 132 import java.util.Arrays;
 133 import java.util.Deque;
 134 import java.util.Enumeration;
 135 import java.util.Hashtable;
 136 import java.util.List;
 137 import java.util.Vector;
 138
 139 import javax.swing.JCheckBoxMenuItem;
 140 import javax.swing.JEditorPane;
 141 import javax.swing.JInternalFrame;
 142 import javax.swing.JLayeredPane;
 143 import javax.swing.JMenu;
 144 import javax.swing.JMenuItem;
 145 import javax.swing.JOptionPane;
 146 import javax.swing.JRadioButtonMenuItem;
 147 import javax.swing.JScrollPane;
 148 import javax.swing.SwingUtilities;
 149
 150 /**
 151  * DOCUMENT ME!
 152  *
 153  * @author $author$
 154  * @version $Revision$
 155  */
 156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 157         IProgressIndicator, AlignViewControllerGuiI
 158 {
 159
 160   public static final int DEFAULT_WIDTH = 700;
 161
 162   public static final int DEFAULT_HEIGHT = 500;
 163
 164   /*
 165    * The currently displayed panel (selected tabbed view if more than one)
 166    */
 167   public AlignmentPanel alignPanel;
 168
 169   AlignViewport viewport;
 170
 171   public AlignViewControllerI avc;
 172
 173   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 174
 175   /**
 176    * Last format used to load or save alignments in this window
 177    */
 178   String currentFileFormat = null;
 179
 180   /**
 181    * Current filename for this alignment
 182    */
 183   String fileName = null;
 184
 185   /**
 186    * Creates a new AlignFrame object with specific width and height.
 187    *
 188    * @param al
 189    * @param width
 190    * @param height
 191    */
 192   public AlignFrame(AlignmentI al, int width, int height)
 193   {
 194     this(al, null, width, height);
 195   }
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width, height and
 199    * sequenceSetId
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    * @param sequenceSetId
 205    */
 206   public AlignFrame(AlignmentI al, int width, int height,
 207           String sequenceSetId)
 208   {
 209     this(al, null, width, height, sequenceSetId);
 210   }
 211
 212   /**
 213    * Creates a new AlignFrame object with specific width, height and
 214    * sequenceSetId
 215    *
 216    * @param al
 217    * @param width
 218    * @param height
 219    * @param sequenceSetId
 220    * @param viewId
 221    */
 222   public AlignFrame(AlignmentI al, int width, int height,
 223           String sequenceSetId, String viewId)
 224   {
 225     this(al, null, width, height, sequenceSetId, viewId);
 226   }
 227
 228   /**
 229    * new alignment window with hidden columns
 230    *
 231    * @param al
 232    *          AlignmentI
 233    * @param hiddenColumns
 234    *          ColumnSelection or null
 235    * @param width
 236    *          Width of alignment frame
 237    * @param height
 238    *          height of frame.
 239    */
 240   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 241           int width, int height)
 242   {
 243     this(al, hiddenColumns, width, height, null);
 244   }
 245
 246   /**
 247    * Create alignment frame for al with hiddenColumns, a specific width and
 248    * height, and specific sequenceId
 249    *
 250    * @param al
 251    * @param hiddenColumns
 252    * @param width
 253    * @param height
 254    * @param sequenceSetId
 255    *          (may be null)
 256    */
 257   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 258           int width, int height, String sequenceSetId)
 259   {
 260     this(al, hiddenColumns, width, height, sequenceSetId, null);
 261   }
 262
 263   /**
 264    * Create alignment frame for al with hiddenColumns, a specific width and
 265    * height, and specific sequenceId
 266    *
 267    * @param al
 268    * @param hiddenColumns
 269    * @param width
 270    * @param height
 271    * @param sequenceSetId
 272    *          (may be null)
 273    * @param viewId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 277           int width, int height, String sequenceSetId, String viewId)
 278   {
 279     setSize(width, height);
 280
 281     if (al.getDataset() == null)
 282     {
 283       al.setDataset(null);
 284     }
 285
 286     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 287
 288     alignPanel = new AlignmentPanel(this, viewport);
 289
 290     addAlignmentPanel(alignPanel, true);
 291     init();
 292   }
 293
 294   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 295           ColumnSelection hiddenColumns, int width, int height)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns);
 305
 306     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 307     {
 308       viewport.hideSequence(hiddenSeqs);
 309     }
 310     alignPanel = new AlignmentPanel(this, viewport);
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   /**
 316    * Make a new AlignFrame from existing alignmentPanels
 317    *
 318    * @param ap
 319    *          AlignmentPanel
 320    * @param av
 321    *          AlignViewport
 322    */
 323   public AlignFrame(AlignmentPanel ap)
 324   {
 325     viewport = ap.av;
 326     alignPanel = ap;
 327     addAlignmentPanel(ap, false);
 328     init();
 329   }
 330
 331   /**
 332    * initalise the alignframe from the underlying viewport data and the
 333    * configurations
 334    */
 335   void init()
 336   {
 337     if (!Jalview.isHeadlessMode())
 338     {
 339       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 340     }
 341
 342     avc = new jalview.controller.AlignViewController(this, viewport,
 343             alignPanel);
 344     if (viewport.getAlignmentConservationAnnotation() == null)
 345     {
 346       BLOSUM62Colour.setEnabled(false);
 347       conservationMenuItem.setEnabled(false);
 348       modifyConservation.setEnabled(false);
 349       // PIDColour.setEnabled(false);
 350       // abovePIDThreshold.setEnabled(false);
 351       // modifyPID.setEnabled(false);
 352     }
 353
 354     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 355             "No sort");
 356
 357     if (sortby.equals("Id"))
 358     {
 359       sortIDMenuItem_actionPerformed(null);
 360     }
 361     else if (sortby.equals("Pairwise Identity"))
 362     {
 363       sortPairwiseMenuItem_actionPerformed(null);
 364     }
 365
 366     if (Desktop.desktop != null)
 367     {
 368       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 369       addServiceListeners();
 370       setGUINucleotide(viewport.getAlignment().isNucleotide());
 371     }
 372
 373     this.alignPanel.av
 374             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 375
 376     setMenusFromViewport(viewport);
 377     buildSortByAnnotationScoresMenu();
 378     buildTreeMenu();
 379
 380     if (viewport.getWrapAlignment())
 381     {
 382       wrapMenuItem_actionPerformed(null);
 383     }
 384
 385     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 386     {
 387       this.overviewMenuItem_actionPerformed(null);
 388     }
 389
 390     addKeyListener();
 391
 392     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 393     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 394     final String menuLabel = MessageManager
 395             .getString("label.copy_format_from");
 396     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 397             new ViewSetProvider()
 398             {
 399
 400               @Override
 401               public AlignmentPanel[] getAllAlignmentPanels()
 402               {
 403                 origview.clear();
 404                 origview.add(alignPanel);
 405                 // make an array of all alignment panels except for this one
 406                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 407                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 408                 aps.remove(AlignFrame.this.alignPanel);
 409                 return aps.toArray(new AlignmentPanel[aps.size()]);
 410               }
 411             }, selviews, new ItemListener()
 412             {
 413
 414               @Override
 415               public void itemStateChanged(ItemEvent e)
 416               {
 417                 if (origview.size() > 0)
 418                 {
 419                   final AlignmentPanel ap = origview.get(0);
 420
 421                   /*
 422                    * Copy the ViewStyle of the selected panel to 'this one'.
 423                    * Don't change value of 'scaleProteinAsCdna' unless copying
 424                    * from a SplitFrame.
 425                    */
 426                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 427                           .getViewStyle();
 428                   boolean fromSplitFrame = selviews.get(0)
 429                           .getAlignViewport().getCodingComplement() != null;
 430                   if (!fromSplitFrame)
 431                   {
 432                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 433                             .getViewStyle().isScaleProteinAsCdna());
 434                   }
 435                   ap.getAlignViewport().setViewStyle(vs);
 436
 437                   /*
 438                    * Also rescale ViewStyle of SplitFrame complement if there is
 439                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 440                    * the whole ViewStyle (allow cDNA protein to have different
 441                    * fonts)
 442                    */
 443                   AlignViewportI complement = ap.getAlignViewport()
 444                           .getCodingComplement();
 445                   if (complement != null && vs.isScaleProteinAsCdna())
 446                   {
 447                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 448                     ((SplitFrame) af.getSplitViewContainer())
 449                             .adjustLayout();
 450                     af.setMenusForViewport();
 451                   }
 452
 453                   ap.updateLayout();
 454                   ap.setSelected(true);
 455                   ap.alignFrame.setMenusForViewport();
 456
 457                 }
 458               }
 459             });
 460     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 461             .indexOf("devel") > -1
 462             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 463                     .indexOf("test") > -1)
 464     {
 465       formatMenu.add(vsel);
 466     }
 467     addFocusListener(new FocusAdapter()
 468     {
 469       @Override
 470       public void focusGained(FocusEvent e)
 471       {
 472         Jalview.setCurrentAlignFrame(AlignFrame.this);
 473       }
 474     });
 475
 476   }
 477
 478   /**
 479    * Change the filename and format for the alignment, and enable the 'reload'
 480    * button functionality.
 481    *
 482    * @param file
 483    *          valid filename
 484    * @param format
 485    *          format of file
 486    */
 487   public void setFileName(String file, String format)
 488   {
 489     fileName = file;
 490     setFileFormat(format);
 491     reload.setEnabled(true);
 492   }
 493
 494   /**
 495    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 496    * events
 497    */
 498   void addKeyListener()
 499   {
 500     addKeyListener(new KeyAdapter()
 501     {
 502       @Override
 503       public void keyPressed(KeyEvent evt)
 504       {
 505         if (viewport.cursorMode
 506                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 507                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 508                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 509                 && Character.isDigit(evt.getKeyChar()))
 510         {
 511           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 512         }
 513
 514         switch (evt.getKeyCode())
 515         {
 516
 517         case 27: // escape key
 518           deselectAllSequenceMenuItem_actionPerformed(null);
 519
 520           break;
 521
 522         case KeyEvent.VK_DOWN:
 523           if (evt.isAltDown() || !viewport.cursorMode)
 524           {
 525             moveSelectedSequences(false);
 526           }
 527           if (viewport.cursorMode)
 528           {
 529             alignPanel.getSeqPanel().moveCursor(0, 1);
 530           }
 531           break;
 532
 533         case KeyEvent.VK_UP:
 534           if (evt.isAltDown() || !viewport.cursorMode)
 535           {
 536             moveSelectedSequences(true);
 537           }
 538           if (viewport.cursorMode)
 539           {
 540             alignPanel.getSeqPanel().moveCursor(0, -1);
 541           }
 542
 543           break;
 544
 545         case KeyEvent.VK_LEFT:
 546           if (evt.isAltDown() || !viewport.cursorMode)
 547           {
 548             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 549           }
 550           else
 551           {
 552             alignPanel.getSeqPanel().moveCursor(-1, 0);
 553           }
 554
 555           break;
 556
 557         case KeyEvent.VK_RIGHT:
 558           if (evt.isAltDown() || !viewport.cursorMode)
 559           {
 560             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 561           }
 562           else
 563           {
 564             alignPanel.getSeqPanel().moveCursor(1, 0);
 565           }
 566           break;
 567
 568         case KeyEvent.VK_SPACE:
 569           if (viewport.cursorMode)
 570           {
 571             alignPanel.getSeqPanel().insertGapAtCursor(
 572                     evt.isControlDown() || evt.isShiftDown()
 573                             || evt.isAltDown());
 574           }
 575           break;
 576
 577         // case KeyEvent.VK_A:
 578         // if (viewport.cursorMode)
 579         // {
 580         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 581         // //System.out.println("A");
 582         // }
 583         // break;
 584         /*
 585          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 586          * System.out.println("closing bracket"); } break;
 587          */
 588         case KeyEvent.VK_DELETE:
 589         case KeyEvent.VK_BACK_SPACE:
 590           if (!viewport.cursorMode)
 591           {
 592             cut_actionPerformed(null);
 593           }
 594           else
 595           {
 596             alignPanel.getSeqPanel().deleteGapAtCursor(
 597                     evt.isControlDown() || evt.isShiftDown()
 598                             || evt.isAltDown());
 599           }
 600
 601           break;
 602
 603         case KeyEvent.VK_S:
 604           if (viewport.cursorMode)
 605           {
 606             alignPanel.getSeqPanel().setCursorRow();
 607           }
 608           break;
 609         case KeyEvent.VK_C:
 610           if (viewport.cursorMode && !evt.isControlDown())
 611           {
 612             alignPanel.getSeqPanel().setCursorColumn();
 613           }
 614           break;
 615         case KeyEvent.VK_P:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().setCursorPosition();
 619           }
 620           break;
 621
 622         case KeyEvent.VK_ENTER:
 623         case KeyEvent.VK_COMMA:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setCursorRowAndColumn();
 627           }
 628           break;
 629
 630         case KeyEvent.VK_Q:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 634           }
 635           break;
 636         case KeyEvent.VK_M:
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 640           }
 641           break;
 642
 643         case KeyEvent.VK_F2:
 644           viewport.cursorMode = !viewport.cursorMode;
 645           statusBar.setText(MessageManager.formatMessage(
 646                   "label.keyboard_editing_mode",
 647                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 651             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 652           }
 653           alignPanel.getSeqPanel().seqCanvas.repaint();
 654           break;
 655
 656         case KeyEvent.VK_F1:
 657           try
 658           {
 659             Help.showHelpWindow();
 660           } catch (Exception ex)
 661           {
 662             ex.printStackTrace();
 663           }
 664           break;
 665         case KeyEvent.VK_H:
 666         {
 667           boolean toggleSeqs = !evt.isControlDown();
 668           boolean toggleCols = !evt.isShiftDown();
 669           toggleHiddenRegions(toggleSeqs, toggleCols);
 670           break;
 671         }
 672         case KeyEvent.VK_PAGE_UP:
 673           if (viewport.getWrapAlignment())
 674           {
 675             alignPanel.scrollUp(true);
 676           }
 677           else
 678           {
 679             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 680                     - viewport.endSeq + viewport.startSeq);
 681           }
 682           break;
 683         case KeyEvent.VK_PAGE_DOWN:
 684           if (viewport.getWrapAlignment())
 685           {
 686             alignPanel.scrollUp(false);
 687           }
 688           else
 689           {
 690             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 691                     + viewport.endSeq - viewport.startSeq);
 692           }
 693           break;
 694         }
 695       }
 696
 697       @Override
 698       public void keyReleased(KeyEvent evt)
 699       {
 700         switch (evt.getKeyCode())
 701         {
 702         case KeyEvent.VK_LEFT:
 703           if (evt.isAltDown() || !viewport.cursorMode)
 704           {
 705             viewport.firePropertyChange("alignment", null, viewport
 706                     .getAlignment().getSequences());
 707           }
 708           break;
 709
 710         case KeyEvent.VK_RIGHT:
 711           if (evt.isAltDown() || !viewport.cursorMode)
 712           {
 713             viewport.firePropertyChange("alignment", null, viewport
 714                     .getAlignment().getSequences());
 715           }
 716           break;
 717         }
 718       }
 719     });
 720   }
 721
 722   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 723   {
 724     ap.alignFrame = this;
 725     avc = new jalview.controller.AlignViewController(this, viewport,
 726             alignPanel);
 727
 728     alignPanels.add(ap);
 729
 730     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 731
 732     int aSize = alignPanels.size();
 733
 734     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 735
 736     if (aSize == 1 && ap.av.viewName == null)
 737     {
 738       this.getContentPane().add(ap, BorderLayout.CENTER);
 739     }
 740     else
 741     {
 742       if (aSize == 2)
 743       {
 744         setInitialTabVisible();
 745       }
 746
 747       expandViews.setEnabled(true);
 748       gatherViews.setEnabled(true);
 749       tabbedPane.addTab(ap.av.viewName, ap);
 750
 751       ap.setVisible(false);
 752     }
 753
 754     if (newPanel)
 755     {
 756       if (ap.av.isPadGaps())
 757       {
 758         ap.av.getAlignment().padGaps();
 759       }
 760       ap.av.updateConservation(ap);
 761       ap.av.updateConsensus(ap);
 762       ap.av.updateStrucConsensus(ap);
 763     }
 764   }
 765
 766   public void setInitialTabVisible()
 767   {
 768     expandViews.setEnabled(true);
 769     gatherViews.setEnabled(true);
 770     tabbedPane.setVisible(true);
 771     AlignmentPanel first = alignPanels.get(0);
 772     tabbedPane.addTab(first.av.viewName, first);
 773     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 774   }
 775
 776   public AlignViewport getViewport()
 777   {
 778     return viewport;
 779   }
 780
 781   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 782   private void addServiceListeners()
 783   {
 784     final java.beans.PropertyChangeListener thisListener;
 785     Desktop.instance.addJalviewPropertyChangeListener("services",
 786             thisListener = new java.beans.PropertyChangeListener()
 787             {
 788               @Override
 789               public void propertyChange(PropertyChangeEvent evt)
 790               {
 791                 // // System.out.println("Discoverer property change.");
 792                 // if (evt.getPropertyName().equals("services"))
 793                 {
 794                   SwingUtilities.invokeLater(new Runnable()
 795                   {
 796
 797                     @Override
 798                     public void run()
 799                     {
 800                       System.err
 801                               .println("Rebuild WS Menu for service change");
 802                       BuildWebServiceMenu();
 803                     }
 804
 805                   });
 806                 }
 807               }
 808             });
 809     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 810     {
 811       @Override
 812       public void internalFrameClosed(
 813               javax.swing.event.InternalFrameEvent evt)
 814       {
 815         // System.out.println("deregistering discoverer listener");
 816         Desktop.instance.removeJalviewPropertyChangeListener("services",
 817                 thisListener);
 818         closeMenuItem_actionPerformed(true);
 819       };
 820     });
 821     // Finally, build the menu once to get current service state
 822     new Thread(new Runnable()
 823     {
 824       @Override
 825       public void run()
 826       {
 827         BuildWebServiceMenu();
 828       }
 829     }).start();
 830   }
 831
 832   /**
 833    * Configure menu items that vary according to whether the alignment is
 834    * nucleotide or protein
 835    *
 836    * @param nucleotide
 837    */
 838   public void setGUINucleotide(boolean nucleotide)
 839   {
 840     showTranslation.setVisible(nucleotide);
 841     showReverse.setVisible(nucleotide);
 842     showReverseComplement.setVisible(nucleotide);
 843     conservationMenuItem.setEnabled(!nucleotide);
 844     modifyConservation.setEnabled(!nucleotide);
 845     showGroupConservation.setEnabled(!nucleotide);
 846     rnahelicesColour.setEnabled(nucleotide);
 847     purinePyrimidineColour.setEnabled(nucleotide);
 848     showComplementMenuItem.setText(nucleotide ? MessageManager
 849             .getString("label.protein") : MessageManager
 850             .getString("label.nucleotide"));
 851     setColourSelected(jalview.bin.Cache.getDefault(
 852             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 853                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 854   }
 855
 856   /**
 857    * set up menus for the current viewport. This may be called after any
 858    * operation that affects the data in the current view (selection changed,
 859    * etc) to update the menus to reflect the new state.
 860    */
 861   @Override
 862   public void setMenusForViewport()
 863   {
 864     setMenusFromViewport(viewport);
 865   }
 866
 867   /**
 868    * Need to call this method when tabs are selected for multiple views, or when
 869    * loading from Jalview2XML.java
 870    *
 871    * @param av
 872    *          AlignViewport
 873    */
 874   void setMenusFromViewport(AlignViewport av)
 875   {
 876     padGapsMenuitem.setSelected(av.isPadGaps());
 877     colourTextMenuItem.setSelected(av.isShowColourText());
 878     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 879     conservationMenuItem.setSelected(av.getConservationSelected());
 880     seqLimits.setSelected(av.getShowJVSuffix());
 881     idRightAlign.setSelected(av.isRightAlignIds());
 882     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 883     renderGapsMenuItem.setSelected(av.isRenderGaps());
 884     wrapMenuItem.setSelected(av.getWrapAlignment());
 885     scaleAbove.setVisible(av.getWrapAlignment());
 886     scaleLeft.setVisible(av.getWrapAlignment());
 887     scaleRight.setVisible(av.getWrapAlignment());
 888     annotationPanelMenuItem.setState(av.isShowAnnotation());
 889     /*
 890      * Show/hide annotations only enabled if annotation panel is shown
 891      */
 892     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 893     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 894     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 895     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 897     viewTextMenuItem.setSelected(av.getShowText());
 898     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 899     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 900     showGroupConservation.setSelected(av.isShowGroupConservation());
 901     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 902     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 903     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 904
 905     setColourSelected(ColourSchemeProperty.getColourName(av
 906             .getGlobalColourScheme()));
 907
 908     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 909     hiddenMarkers.setState(av.getShowHiddenMarkers());
 910     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 911     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 912     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 913     autoCalculate.setSelected(av.autoCalculateConsensus);
 914     sortByTree.setSelected(av.sortByTree);
 915     listenToViewSelections.setSelected(av.followSelection);
 916     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 917     rnahelicesColour
 918             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 919
 920     showProducts.setEnabled(canShowProducts());
 921     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 922
 923     updateEditMenuBar();
 924   }
 925
 926   /**
 927    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 928    *
 929    * @param b
 930    */
 931   public void setGroovyEnabled(boolean b)
 932   {
 933     runGroovy.setEnabled(b);
 934   }
 935
 936   private IProgressIndicator progressBar;
 937
 938   /*
 939    * (non-Javadoc)
 940    *
 941    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 942    */
 943   @Override
 944   public void setProgressBar(String message, long id)
 945   {
 946     progressBar.setProgressBar(message, id);
 947   }
 948
 949   @Override
 950   public void registerHandler(final long id,
 951           final IProgressIndicatorHandler handler)
 952   {
 953     progressBar.registerHandler(id, handler);
 954   }
 955
 956   /**
 957    *
 958    * @return true if any progress bars are still active
 959    */
 960   @Override
 961   public boolean operationInProgress()
 962   {
 963     return progressBar.operationInProgress();
 964   }
 965
 966   @Override
 967   public void setStatus(String text)
 968   {
 969     statusBar.setText(text);
 970   }
 971
 972   /*
 973    * Added so Castor Mapping file can obtain Jalview Version
 974    */
 975   public String getVersion()
 976   {
 977     return jalview.bin.Cache.getProperty("VERSION");
 978   }
 979
 980   public FeatureRenderer getFeatureRenderer()
 981   {
 982     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 983   }
 984
 985   @Override
 986   public void fetchSequence_actionPerformed(ActionEvent e)
 987   {
 988     new jalview.gui.SequenceFetcher(this);
 989   }
 990
 991   @Override
 992   public void addFromFile_actionPerformed(ActionEvent e)
 993   {
 994     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 995   }
 996
 997   @Override
 998   public void reload_actionPerformed(ActionEvent e)
 999   {
1000     if (fileName != null)
1001     {
1002       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003       // originating file's format
1004       // TODO: work out how to recover feature settings for correct view(s) when
1005       // file is reloaded.
1006       if (currentFileFormat.equals("Jalview"))
1007       {
1008         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009         for (int i = 0; i < frames.length; i++)
1010         {
1011           if (frames[i] instanceof AlignFrame && frames[i] != this
1012                   && ((AlignFrame) frames[i]).fileName != null
1013                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014           {
1015             try
1016             {
1017               frames[i].setSelected(true);
1018               Desktop.instance.closeAssociatedWindows();
1019             } catch (java.beans.PropertyVetoException ex)
1020             {
1021             }
1022           }
1023
1024         }
1025         Desktop.instance.closeAssociatedWindows();
1026
1027         FileLoader loader = new FileLoader();
1028         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1029         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1030       }
1031       else
1032       {
1033         Rectangle bounds = this.getBounds();
1034
1035         FileLoader loader = new FileLoader();
1036         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1037         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1038                 protocol, currentFileFormat);
1039
1040         newframe.setBounds(bounds);
1041         if (featureSettings != null && featureSettings.isShowing())
1042         {
1043           final Rectangle fspos = featureSettings.frame.getBounds();
1044           // TODO: need a 'show feature settings' function that takes bounds -
1045           // need to refactor Desktop.addFrame
1046           newframe.featureSettings_actionPerformed(null);
1047           final FeatureSettings nfs = newframe.featureSettings;
1048           SwingUtilities.invokeLater(new Runnable()
1049           {
1050             @Override
1051             public void run()
1052             {
1053               nfs.frame.setBounds(fspos);
1054             }
1055           });
1056           this.featureSettings.close();
1057           this.featureSettings = null;
1058         }
1059         this.closeMenuItem_actionPerformed(true);
1060       }
1061     }
1062   }
1063
1064   @Override
1065   public void addFromText_actionPerformed(ActionEvent e)
1066   {
1067     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1068             .getAlignPanel());
1069   }
1070
1071   @Override
1072   public void addFromURL_actionPerformed(ActionEvent e)
1073   {
1074     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1075   }
1076
1077   @Override
1078   public void save_actionPerformed(ActionEvent e)
1079   {
1080     if (fileName == null
1081             || (currentFileFormat == null || !jalview.io.FormatAdapter
1082                     .isValidIOFormat(currentFileFormat, true))
1083             || fileName.startsWith("http"))
1084     {
1085       saveAs_actionPerformed(null);
1086     }
1087     else
1088     {
1089       saveAlignment(fileName, currentFileFormat);
1090     }
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @param e
1097    *          DOCUMENT ME!
1098    */
1099   @Override
1100   public void saveAs_actionPerformed(ActionEvent e)
1101   {
1102     JalviewFileChooser chooser = new JalviewFileChooser(
1103             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1104             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1105             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1106             currentFileFormat, false);
1107
1108     chooser.setFileView(new JalviewFileView());
1109     chooser.setDialogTitle(MessageManager
1110             .getString("label.save_alignment_to_file"));
1111     chooser.setToolTipText(MessageManager.getString("action.save"));
1112
1113     int value = chooser.showSaveDialog(this);
1114
1115     if (value == JalviewFileChooser.APPROVE_OPTION)
1116     {
1117       currentFileFormat = chooser.getSelectedFormat();
1118       while (currentFileFormat == null)
1119       {
1120         JOptionPane
1121                 .showInternalMessageDialog(
1122                         Desktop.desktop,
1123                         MessageManager
1124                                 .getString("label.select_file_format_before_saving"),
1125                         MessageManager
1126                                 .getString("label.file_format_not_specified"),
1127                         JOptionPane.WARNING_MESSAGE);
1128         currentFileFormat = chooser.getSelectedFormat();
1129         value = chooser.showSaveDialog(this);
1130         if (value != JalviewFileChooser.APPROVE_OPTION)
1131         {
1132           return;
1133         }
1134       }
1135
1136       fileName = chooser.getSelectedFile().getPath();
1137
1138       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1139               currentFileFormat);
1140
1141       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1142       if (currentFileFormat.indexOf(" ") > -1)
1143       {
1144         currentFileFormat = currentFileFormat.substring(0,
1145                 currentFileFormat.indexOf(" "));
1146       }
1147       saveAlignment(fileName, currentFileFormat);
1148     }
1149   }
1150
1151   public boolean saveAlignment(String file, String format)
1152   {
1153     boolean success = true;
1154
1155     if (format.equalsIgnoreCase("Jalview"))
1156     {
1157       String shortName = title;
1158
1159       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160       {
1161         shortName = shortName.substring(shortName
1162                 .lastIndexOf(java.io.File.separatorChar) + 1);
1163       }
1164
1165       success = new Jalview2XML().saveAlignment(this, file, shortName);
1166
1167       statusBar.setText(MessageManager.formatMessage(
1168               "label.successfully_saved_to_file_in_format", new Object[] {
1169                   fileName, format }));
1170
1171     }
1172     else
1173     {
1174       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1175       {
1176         warningMessage("Cannot save file " + fileName + " using format "
1177                 + format, "Alignment output format not supported");
1178         if (!Jalview.isHeadlessMode())
1179         {
1180           saveAs_actionPerformed(null);
1181         }
1182         return false;
1183       }
1184
1185       AlignmentExportData exportData = getAlignmentForExport(format,
1186               viewport, null);
1187       if (exportData.getSettings().isCancelled())
1188       {
1189         return false;
1190       }
1191       FormatAdapter f = new FormatAdapter(alignPanel,
1192               exportData.getSettings());
1193       String output = f.formatSequences(
1194               format,
1195               exportData.getAlignment(), // class cast exceptions will
1196               // occur in the distant future
1197               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1198               f.getCacheSuffixDefault(format),
1199               viewport.getColumnSelection());
1200
1201       if (output == null)
1202       {
1203         success = false;
1204       }
1205       else
1206       {
1207         try
1208         {
1209           java.io.PrintWriter out = new java.io.PrintWriter(
1210                   new java.io.FileWriter(file));
1211
1212           out.print(output);
1213           out.close();
1214           this.setTitle(file);
1215           statusBar.setText(MessageManager.formatMessage(
1216                   "label.successfully_saved_to_file_in_format",
1217                   new Object[] { fileName, format }));
1218         } catch (Exception ex)
1219         {
1220           success = false;
1221           ex.printStackTrace();
1222         }
1223       }
1224     }
1225
1226     if (!success)
1227     {
1228       JOptionPane.showInternalMessageDialog(this, MessageManager
1229               .formatMessage("label.couldnt_save_file",
1230                       new Object[] { fileName }), MessageManager
1231               .getString("label.error_saving_file"),
1232               JOptionPane.WARNING_MESSAGE);
1233     }
1234
1235     return success;
1236   }
1237
1238   private void warningMessage(String warning, String title)
1239   {
1240     if (new jalview.util.Platform().isHeadless())
1241     {
1242       System.err.println("Warning: " + title + "\nWarning: " + warning);
1243
1244     }
1245     else
1246     {
1247       JOptionPane.showInternalMessageDialog(this, warning, title,
1248               JOptionPane.WARNING_MESSAGE);
1249     }
1250     return;
1251   }
1252
1253   /**
1254    * DOCUMENT ME!
1255    *
1256    * @param e
1257    *          DOCUMENT ME!
1258    */
1259   @Override
1260   protected void outputText_actionPerformed(ActionEvent e)
1261   {
1262
1263     AlignmentExportData exportData = getAlignmentForExport(
1264             e.getActionCommand(), viewport, null);
1265     if (exportData.getSettings().isCancelled())
1266     {
1267       return;
1268     }
1269     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1270     cap.setForInput(null);
1271     try
1272     {
1273       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1274               .formatSequences(e.getActionCommand(),
1275                       exportData.getAlignment(),
1276                       exportData.getOmitHidden(),
1277                       exportData.getStartEndPostions(),
1278                       viewport.getColumnSelection()));
1279       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1280               "label.alignment_output_command",
1281               new Object[] { e.getActionCommand() }), 600, 500);
1282     } catch (OutOfMemoryError oom)
1283     {
1284       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1285       cap.dispose();
1286     }
1287
1288   }
1289
1290   public static AlignmentExportData getAlignmentForExport(
1291           String exportFormat, AlignViewportI viewport,
1292           AlignExportSettingI exportSettings)
1293   {
1294     AlignmentI alignmentToExport = null;
1295     AlignExportSettingI settings = exportSettings;
1296     String[] omitHidden = null;
1297
1298     HiddenSequences hiddenSeqs = viewport.getAlignment()
1299             .getHiddenSequences();
1300
1301     alignmentToExport = viewport.getAlignment();
1302
1303     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1304     if (settings == null)
1305     {
1306       settings = new AlignExportSettings(hasHiddenSeqs,
1307               viewport.hasHiddenColumns(), exportFormat);
1308     }
1309     // settings.isExportAnnotations();
1310
1311     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1312     {
1313       omitHidden = viewport.getViewAsString(false,
1314               settings.isExportHiddenSequences());
1315     }
1316
1317     int[] alignmentStartEnd = new int[2];
1318     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1319     {
1320       alignmentToExport = hiddenSeqs.getFullAlignment();
1321     }
1322     else
1323     {
1324       alignmentToExport = viewport.getAlignment();
1325     }
1326     alignmentStartEnd = alignmentToExport
1327             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1328                     .getHiddenColumns());
1329     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1330             omitHidden, alignmentStartEnd, settings);
1331     return ed;
1332   }
1333
1334   /**
1335    * DOCUMENT ME!
1336    *
1337    * @param e
1338    *          DOCUMENT ME!
1339    */
1340   @Override
1341   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1342   {
1343     new HtmlSvgOutput(null, alignPanel);
1344   }
1345
1346   @Override
1347   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348   {
1349     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1350     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1351   }
1352
1353   public void createImageMap(File file, String image)
1354   {
1355     alignPanel.makePNGImageMap(file, image);
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *          DOCUMENT ME!
1363    */
1364   @Override
1365   public void createPNG(File f)
1366   {
1367     alignPanel.makePNG(f);
1368   }
1369
1370   /**
1371    * DOCUMENT ME!
1372    *
1373    * @param e
1374    *          DOCUMENT ME!
1375    */
1376   @Override
1377   public void createEPS(File f)
1378   {
1379     alignPanel.makeEPS(f);
1380   }
1381
1382   @Override
1383   public void createSVG(File f)
1384   {
1385     alignPanel.makeSVG(f);
1386   }
1387
1388   @Override
1389   public void pageSetup_actionPerformed(ActionEvent e)
1390   {
1391     PrinterJob printJob = PrinterJob.getPrinterJob();
1392     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1393   }
1394
1395   /**
1396    * DOCUMENT ME!
1397    *
1398    * @param e
1399    *          DOCUMENT ME!
1400    */
1401   @Override
1402   public void printMenuItem_actionPerformed(ActionEvent e)
1403   {
1404     // Putting in a thread avoids Swing painting problems
1405     PrintThread thread = new PrintThread(alignPanel);
1406     thread.start();
1407   }
1408
1409   @Override
1410   public void exportFeatures_actionPerformed(ActionEvent e)
1411   {
1412     new AnnotationExporter().exportFeatures(alignPanel);
1413   }
1414
1415   @Override
1416   public void exportAnnotations_actionPerformed(ActionEvent e)
1417   {
1418     new AnnotationExporter().exportAnnotations(alignPanel);
1419   }
1420
1421   @Override
1422   public void associatedData_actionPerformed(ActionEvent e)
1423   {
1424     // Pick the tree file
1425     JalviewFileChooser chooser = new JalviewFileChooser(
1426             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427     chooser.setFileView(new JalviewFileView());
1428     chooser.setDialogTitle(MessageManager
1429             .getString("label.load_jalview_annotations"));
1430     chooser.setToolTipText(MessageManager
1431             .getString("label.load_jalview_annotations"));
1432
1433     int value = chooser.showOpenDialog(null);
1434
1435     if (value == JalviewFileChooser.APPROVE_OPTION)
1436     {
1437       String choice = chooser.getSelectedFile().getPath();
1438       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439       loadJalviewDataFile(choice, null, null, null);
1440     }
1441
1442   }
1443
1444   /**
1445    * Close the current view or all views in the alignment frame. If the frame
1446    * only contains one view then the alignment will be removed from memory.
1447    *
1448    * @param closeAllTabs
1449    */
1450   @Override
1451   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452   {
1453     if (alignPanels != null && alignPanels.size() < 2)
1454     {
1455       closeAllTabs = true;
1456     }
1457
1458     try
1459     {
1460       if (alignPanels != null)
1461       {
1462         if (closeAllTabs)
1463         {
1464           if (this.isClosed())
1465           {
1466             // really close all the windows - otherwise wait till
1467             // setClosed(true) is called
1468             for (int i = 0; i < alignPanels.size(); i++)
1469             {
1470               AlignmentPanel ap = alignPanels.get(i);
1471               ap.closePanel();
1472             }
1473           }
1474         }
1475         else
1476         {
1477           closeView(alignPanel);
1478         }
1479       }
1480
1481       if (closeAllTabs)
1482       {
1483         /*
1484          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485          * be called recursively, with the frame now in 'closed' state
1486          */
1487         this.setClosed(true);
1488       }
1489     } catch (Exception ex)
1490     {
1491       ex.printStackTrace();
1492     }
1493   }
1494
1495   /**
1496    * Close the specified panel and close up tabs appropriately.
1497    *
1498    * @param panelToClose
1499    */
1500   public void closeView(AlignmentPanel panelToClose)
1501   {
1502     int index = tabbedPane.getSelectedIndex();
1503     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504     alignPanels.remove(panelToClose);
1505     panelToClose.closePanel();
1506     panelToClose = null;
1507
1508     tabbedPane.removeTabAt(closedindex);
1509     tabbedPane.validate();
1510
1511     if (index > closedindex || index == tabbedPane.getTabCount())
1512     {
1513       // modify currently selected tab index if necessary.
1514       index--;
1515     }
1516
1517     this.tabSelectionChanged(index);
1518   }
1519
1520   /**
1521    * DOCUMENT ME!
1522    */
1523   void updateEditMenuBar()
1524   {
1525
1526     if (viewport.getHistoryList().size() > 0)
1527     {
1528       undoMenuItem.setEnabled(true);
1529       CommandI command = viewport.getHistoryList().peek();
1530       undoMenuItem.setText(MessageManager.formatMessage(
1531               "label.undo_command",
1532               new Object[] { command.getDescription() }));
1533     }
1534     else
1535     {
1536       undoMenuItem.setEnabled(false);
1537       undoMenuItem.setText(MessageManager.getString("action.undo"));
1538     }
1539
1540     if (viewport.getRedoList().size() > 0)
1541     {
1542       redoMenuItem.setEnabled(true);
1543
1544       CommandI command = viewport.getRedoList().peek();
1545       redoMenuItem.setText(MessageManager.formatMessage(
1546               "label.redo_command",
1547               new Object[] { command.getDescription() }));
1548     }
1549     else
1550     {
1551       redoMenuItem.setEnabled(false);
1552       redoMenuItem.setText(MessageManager.getString("action.redo"));
1553     }
1554   }
1555
1556   @Override
1557   public void addHistoryItem(CommandI command)
1558   {
1559     if (command.getSize() > 0)
1560     {
1561       viewport.addToHistoryList(command);
1562       viewport.clearRedoList();
1563       updateEditMenuBar();
1564       viewport.updateHiddenColumns();
1565       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567       // viewport.getColumnSelection()
1568       // .getHiddenColumns().size() > 0);
1569     }
1570   }
1571
1572   /**
1573    *
1574    * @return alignment objects for all views
1575    */
1576   AlignmentI[] getViewAlignments()
1577   {
1578     if (alignPanels != null)
1579     {
1580       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581       int i = 0;
1582       for (AlignmentPanel ap : alignPanels)
1583       {
1584         als[i++] = ap.av.getAlignment();
1585       }
1586       return als;
1587     }
1588     if (viewport != null)
1589     {
1590       return new AlignmentI[] { viewport.getAlignment() };
1591     }
1592     return null;
1593   }
1594
1595   /**
1596    * DOCUMENT ME!
1597    *
1598    * @param e
1599    *          DOCUMENT ME!
1600    */
1601   @Override
1602   protected void undoMenuItem_actionPerformed(ActionEvent e)
1603   {
1604     if (viewport.getHistoryList().isEmpty())
1605     {
1606       return;
1607     }
1608     CommandI command = viewport.getHistoryList().pop();
1609     viewport.addToRedoList(command);
1610     command.undoCommand(getViewAlignments());
1611
1612     AlignmentViewport originalSource = getOriginatingSource(command);
1613     updateEditMenuBar();
1614
1615     if (originalSource != null)
1616     {
1617       if (originalSource != viewport)
1618       {
1619         Cache.log
1620                 .warn("Implementation worry: mismatch of viewport origin for undo");
1621       }
1622       originalSource.updateHiddenColumns();
1623       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624       // null
1625       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626       // viewport.getColumnSelection()
1627       // .getHiddenColumns().size() > 0);
1628       originalSource.firePropertyChange("alignment", null, originalSource
1629               .getAlignment().getSequences());
1630     }
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   @Override
1640   protected void redoMenuItem_actionPerformed(ActionEvent e)
1641   {
1642     if (viewport.getRedoList().size() < 1)
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getRedoList().pop();
1648     viewport.addToHistoryList(command);
1649     command.doCommand(getViewAlignments());
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     updateEditMenuBar();
1653
1654     if (originalSource != null)
1655     {
1656
1657       if (originalSource != viewport)
1658       {
1659         Cache.log
1660                 .warn("Implementation worry: mismatch of viewport origin for redo");
1661       }
1662       originalSource.updateHiddenColumns();
1663       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664       // null
1665       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666       // viewport.getColumnSelection()
1667       // .getHiddenColumns().size() > 0);
1668       originalSource.firePropertyChange("alignment", null, originalSource
1669               .getAlignment().getSequences());
1670     }
1671   }
1672
1673   AlignmentViewport getOriginatingSource(CommandI command)
1674   {
1675     AlignmentViewport originalSource = null;
1676     // For sequence removal and addition, we need to fire
1677     // the property change event FROM the viewport where the
1678     // original alignment was altered
1679     AlignmentI al = null;
1680     if (command instanceof EditCommand)
1681     {
1682       EditCommand editCommand = (EditCommand) command;
1683       al = editCommand.getAlignment();
1684       List<Component> comps = PaintRefresher.components.get(viewport
1685               .getSequenceSetId());
1686
1687       for (Component comp : comps)
1688       {
1689         if (comp instanceof AlignmentPanel)
1690         {
1691           if (al == ((AlignmentPanel) comp).av.getAlignment())
1692           {
1693             originalSource = ((AlignmentPanel) comp).av;
1694             break;
1695           }
1696         }
1697       }
1698     }
1699
1700     if (originalSource == null)
1701     {
1702       // The original view is closed, we must validate
1703       // the current view against the closed view first
1704       if (al != null)
1705       {
1706         PaintRefresher.validateSequences(al, viewport.getAlignment());
1707       }
1708
1709       originalSource = viewport;
1710     }
1711
1712     return originalSource;
1713   }
1714
1715   /**
1716    * DOCUMENT ME!
1717    *
1718    * @param up
1719    *          DOCUMENT ME!
1720    */
1721   public void moveSelectedSequences(boolean up)
1722   {
1723     SequenceGroup sg = viewport.getSelectionGroup();
1724
1725     if (sg == null)
1726     {
1727       return;
1728     }
1729     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730             viewport.getHiddenRepSequences(), up);
1731     alignPanel.paintAlignment(true);
1732   }
1733
1734   synchronized void slideSequences(boolean right, int size)
1735   {
1736     List<SequenceI> sg = new ArrayList<SequenceI>();
1737     if (viewport.cursorMode)
1738     {
1739       sg.add(viewport.getAlignment().getSequenceAt(
1740               alignPanel.getSeqPanel().seqCanvas.cursorY));
1741     }
1742     else if (viewport.getSelectionGroup() != null
1743             && viewport.getSelectionGroup().getSize() != viewport
1744                     .getAlignment().getHeight())
1745     {
1746       sg = viewport.getSelectionGroup().getSequences(
1747               viewport.getHiddenRepSequences());
1748     }
1749
1750     if (sg.size() < 1)
1751     {
1752       return;
1753     }
1754
1755     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1756
1757     for (SequenceI seq : viewport.getAlignment().getSequences())
1758     {
1759       if (!sg.contains(seq))
1760       {
1761         invertGroup.add(seq);
1762       }
1763     }
1764
1765     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766
1767     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768     for (int i = 0; i < invertGroup.size(); i++)
1769     {
1770       seqs2[i] = invertGroup.get(i);
1771     }
1772
1773     SlideSequencesCommand ssc;
1774     if (right)
1775     {
1776       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1777               size, viewport.getGapCharacter());
1778     }
1779     else
1780     {
1781       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1782               size, viewport.getGapCharacter());
1783     }
1784
1785     int groupAdjustment = 0;
1786     if (ssc.getGapsInsertedBegin() && right)
1787     {
1788       if (viewport.cursorMode)
1789       {
1790         alignPanel.getSeqPanel().moveCursor(size, 0);
1791       }
1792       else
1793       {
1794         groupAdjustment = size;
1795       }
1796     }
1797     else if (!ssc.getGapsInsertedBegin() && !right)
1798     {
1799       if (viewport.cursorMode)
1800       {
1801         alignPanel.getSeqPanel().moveCursor(-size, 0);
1802       }
1803       else
1804       {
1805         groupAdjustment = -size;
1806       }
1807     }
1808
1809     if (groupAdjustment != 0)
1810     {
1811       viewport.getSelectionGroup().setStartRes(
1812               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813       viewport.getSelectionGroup().setEndRes(
1814               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1815     }
1816
1817     /*
1818      * just extend the last slide command if compatible; but not if in
1819      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820      */
1821     boolean appendHistoryItem = false;
1822     Deque<CommandI> historyList = viewport.getHistoryList();
1823     boolean inSplitFrame = getSplitViewContainer() != null;
1824     if (!inSplitFrame && historyList != null && historyList.size() > 0
1825             && historyList.peek() instanceof SlideSequencesCommand)
1826     {
1827       appendHistoryItem = ssc
1828               .appendSlideCommand((SlideSequencesCommand) historyList
1829                       .peek());
1830     }
1831
1832     if (!appendHistoryItem)
1833     {
1834       addHistoryItem(ssc);
1835     }
1836
1837     repaint();
1838   }
1839
1840   /**
1841    * DOCUMENT ME!
1842    *
1843    * @param e
1844    *          DOCUMENT ME!
1845    */
1846   @Override
1847   protected void copy_actionPerformed(ActionEvent e)
1848   {
1849     System.gc();
1850     if (viewport.getSelectionGroup() == null)
1851     {
1852       return;
1853     }
1854     // TODO: preserve the ordering of displayed alignment annotation in any
1855     // internal paste (particularly sequence associated annotation)
1856     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1857     String[] omitHidden = null;
1858
1859     if (viewport.hasHiddenColumns())
1860     {
1861       omitHidden = viewport.getViewAsString(true);
1862     }
1863
1864     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1865             omitHidden, null);
1866
1867     StringSelection ss = new StringSelection(output);
1868
1869     try
1870     {
1871       jalview.gui.Desktop.internalCopy = true;
1872       // Its really worth setting the clipboard contents
1873       // to empty before setting the large StringSelection!!
1874       Toolkit.getDefaultToolkit().getSystemClipboard()
1875               .setContents(new StringSelection(""), null);
1876
1877       Toolkit.getDefaultToolkit().getSystemClipboard()
1878               .setContents(ss, Desktop.instance);
1879     } catch (OutOfMemoryError er)
1880     {
1881       new OOMWarning("copying region", er);
1882       return;
1883     }
1884
1885     ArrayList<int[]> hiddenColumns = null;
1886     if (viewport.hasHiddenColumns())
1887     {
1888       hiddenColumns = new ArrayList<int[]>();
1889       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1890               .getSelectionGroup().getEndRes();
1891       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1892       {
1893         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1894         {
1895           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1896               region[1] - hiddenOffset });
1897         }
1898       }
1899     }
1900
1901     Desktop.jalviewClipboard = new Object[] { seqs,
1902         viewport.getAlignment().getDataset(), hiddenColumns };
1903     statusBar.setText(MessageManager.formatMessage(
1904             "label.copied_sequences_to_clipboard", new Object[] { Integer
1905                     .valueOf(seqs.length).toString() }));
1906   }
1907
1908   /**
1909    * DOCUMENT ME!
1910    *
1911    * @param e
1912    *          DOCUMENT ME!
1913    */
1914   @Override
1915   protected void pasteNew_actionPerformed(ActionEvent e)
1916   {
1917     paste(true);
1918   }
1919
1920   /**
1921    * DOCUMENT ME!
1922    *
1923    * @param e
1924    *          DOCUMENT ME!
1925    */
1926   @Override
1927   protected void pasteThis_actionPerformed(ActionEvent e)
1928   {
1929     paste(false);
1930   }
1931
1932   /**
1933    * Paste contents of Jalview clipboard
1934    *
1935    * @param newAlignment
1936    *          true to paste to a new alignment, otherwise add to this.
1937    */
1938   void paste(boolean newAlignment)
1939   {
1940     boolean externalPaste = true;
1941     try
1942     {
1943       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1944       Transferable contents = c.getContents(this);
1945
1946       if (contents == null)
1947       {
1948         return;
1949       }
1950
1951       String str, format;
1952       try
1953       {
1954         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1955         if (str.length() < 1)
1956         {
1957           return;
1958         }
1959
1960         format = new IdentifyFile().identify(str, "Paste");
1961
1962       } catch (OutOfMemoryError er)
1963       {
1964         new OOMWarning("Out of memory pasting sequences!!", er);
1965         return;
1966       }
1967
1968       SequenceI[] sequences;
1969       boolean annotationAdded = false;
1970       AlignmentI alignment = null;
1971
1972       if (Desktop.jalviewClipboard != null)
1973       {
1974         // The clipboard was filled from within Jalview, we must use the
1975         // sequences
1976         // And dataset from the copied alignment
1977         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1978         // be doubly sure that we create *new* sequence objects.
1979         sequences = new SequenceI[newseq.length];
1980         for (int i = 0; i < newseq.length; i++)
1981         {
1982           sequences[i] = new Sequence(newseq[i]);
1983         }
1984         alignment = new Alignment(sequences);
1985         externalPaste = false;
1986       }
1987       else
1988       {
1989         // parse the clipboard as an alignment.
1990         alignment = new FormatAdapter().readFile(str, "Paste", format);
1991         sequences = alignment.getSequencesArray();
1992       }
1993
1994       int alwidth = 0;
1995       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1996       int fgroup = -1;
1997
1998       if (newAlignment)
1999       {
2000
2001         if (Desktop.jalviewClipboard != null)
2002         {
2003           // dataset is inherited
2004           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2005         }
2006         else
2007         {
2008           // new dataset is constructed
2009           alignment.setDataset(null);
2010         }
2011         alwidth = alignment.getWidth() + 1;
2012       }
2013       else
2014       {
2015         AlignmentI pastedal = alignment; // preserve pasted alignment object
2016         // Add pasted sequences and dataset into existing alignment.
2017         alignment = viewport.getAlignment();
2018         alwidth = alignment.getWidth() + 1;
2019         // decide if we need to import sequences from an existing dataset
2020         boolean importDs = Desktop.jalviewClipboard != null
2021                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2022         // importDs==true instructs us to copy over new dataset sequences from
2023         // an existing alignment
2024         Vector newDs = (importDs) ? new Vector() : null; // used to create
2025         // minimum dataset set
2026
2027         for (int i = 0; i < sequences.length; i++)
2028         {
2029           if (importDs)
2030           {
2031             newDs.addElement(null);
2032           }
2033           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2034           // paste
2035           if (importDs && ds != null)
2036           {
2037             if (!newDs.contains(ds))
2038             {
2039               newDs.setElementAt(ds, i);
2040               ds = new Sequence(ds);
2041               // update with new dataset sequence
2042               sequences[i].setDatasetSequence(ds);
2043             }
2044             else
2045             {
2046               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2047             }
2048           }
2049           else
2050           {
2051             // copy and derive new dataset sequence
2052             sequences[i] = sequences[i].deriveSequence();
2053             alignment.getDataset().addSequence(
2054                     sequences[i].getDatasetSequence());
2055             // TODO: avoid creation of duplicate dataset sequences with a
2056             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2057           }
2058           alignment.addSequence(sequences[i]); // merges dataset
2059         }
2060         if (newDs != null)
2061         {
2062           newDs.clear(); // tidy up
2063         }
2064         if (alignment.getAlignmentAnnotation() != null)
2065         {
2066           for (AlignmentAnnotation alan : alignment
2067                   .getAlignmentAnnotation())
2068           {
2069             if (alan.graphGroup > fgroup)
2070             {
2071               fgroup = alan.graphGroup;
2072             }
2073           }
2074         }
2075         if (pastedal.getAlignmentAnnotation() != null)
2076         {
2077           // Add any annotation attached to alignment.
2078           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2079           for (int i = 0; i < alann.length; i++)
2080           {
2081             annotationAdded = true;
2082             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2083             {
2084               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2085               if (newann.graphGroup > -1)
2086               {
2087                 if (newGraphGroups.size() <= newann.graphGroup
2088                         || newGraphGroups.get(newann.graphGroup) == null)
2089                 {
2090                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2091                   {
2092                     newGraphGroups.add(q, null);
2093                   }
2094                   newGraphGroups.set(newann.graphGroup, new Integer(
2095                           ++fgroup));
2096                 }
2097                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2098                         .intValue();
2099               }
2100
2101               newann.padAnnotation(alwidth);
2102               alignment.addAnnotation(newann);
2103             }
2104           }
2105         }
2106       }
2107       if (!newAlignment)
2108       {
2109         // /////
2110         // ADD HISTORY ITEM
2111         //
2112         addHistoryItem(new EditCommand(
2113                 MessageManager.getString("label.add_sequences"),
2114                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2115       }
2116       // Add any annotations attached to sequences
2117       for (int i = 0; i < sequences.length; i++)
2118       {
2119         if (sequences[i].getAnnotation() != null)
2120         {
2121           AlignmentAnnotation newann;
2122           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123           {
2124             annotationAdded = true;
2125             newann = sequences[i].getAnnotation()[a];
2126             newann.adjustForAlignment();
2127             newann.padAnnotation(alwidth);
2128             if (newann.graphGroup > -1)
2129             {
2130               if (newann.graphGroup > -1)
2131               {
2132                 if (newGraphGroups.size() <= newann.graphGroup
2133                         || newGraphGroups.get(newann.graphGroup) == null)
2134                 {
2135                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2136                   {
2137                     newGraphGroups.add(q, null);
2138                   }
2139                   newGraphGroups.set(newann.graphGroup, new Integer(
2140                           ++fgroup));
2141                 }
2142                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2143                         .intValue();
2144               }
2145             }
2146             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2147             // was
2148             // duplicated
2149             // earlier
2150             alignment
2151                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2152           }
2153         }
2154       }
2155       if (!newAlignment)
2156       {
2157
2158         // propagate alignment changed.
2159         viewport.setEndSeq(alignment.getHeight());
2160         if (annotationAdded)
2161         {
2162           // Duplicate sequence annotation in all views.
2163           AlignmentI[] alview = this.getViewAlignments();
2164           for (int i = 0; i < sequences.length; i++)
2165           {
2166             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2167             if (sann == null)
2168             {
2169               continue;
2170             }
2171             for (int avnum = 0; avnum < alview.length; avnum++)
2172             {
2173               if (alview[avnum] != alignment)
2174               {
2175                 // duplicate in a view other than the one with input focus
2176                 int avwidth = alview[avnum].getWidth() + 1;
2177                 // this relies on sann being preserved after we
2178                 // modify the sequence's annotation array for each duplication
2179                 for (int a = 0; a < sann.length; a++)
2180                 {
2181                   AlignmentAnnotation newann = new AlignmentAnnotation(
2182                           sann[a]);
2183                   sequences[i].addAlignmentAnnotation(newann);
2184                   newann.padAnnotation(avwidth);
2185                   alview[avnum].addAnnotation(newann); // annotation was
2186                   // duplicated earlier
2187                   // TODO JAL-1145 graphGroups are not updated for sequence
2188                   // annotation added to several views. This may cause
2189                   // strangeness
2190                   alview[avnum].setAnnotationIndex(newann, a);
2191                 }
2192               }
2193             }
2194           }
2195           buildSortByAnnotationScoresMenu();
2196         }
2197         viewport.firePropertyChange("alignment", null,
2198                 alignment.getSequences());
2199         if (alignPanels != null)
2200         {
2201           for (AlignmentPanel ap : alignPanels)
2202           {
2203             ap.validateAnnotationDimensions(false);
2204           }
2205         }
2206         else
2207         {
2208           alignPanel.validateAnnotationDimensions(false);
2209         }
2210
2211       }
2212       else
2213       {
2214         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2215                 DEFAULT_HEIGHT);
2216         String newtitle = new String("Copied sequences");
2217
2218         if (Desktop.jalviewClipboard != null
2219                 && Desktop.jalviewClipboard[2] != null)
2220         {
2221           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2222           for (int[] region : hc)
2223           {
2224             af.viewport.hideColumns(region[0], region[1]);
2225           }
2226         }
2227
2228         // >>>This is a fix for the moment, until a better solution is
2229         // found!!<<<
2230         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2231                 .transferSettings(
2232                         alignPanel.getSeqPanel().seqCanvas
2233                                 .getFeatureRenderer());
2234
2235         // TODO: maintain provenance of an alignment, rather than just make the
2236         // title a concatenation of operations.
2237         if (!externalPaste)
2238         {
2239           if (title.startsWith("Copied sequences"))
2240           {
2241             newtitle = title;
2242           }
2243           else
2244           {
2245             newtitle = newtitle.concat("- from " + title);
2246           }
2247         }
2248         else
2249         {
2250           newtitle = new String("Pasted sequences");
2251         }
2252
2253         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2254                 DEFAULT_HEIGHT);
2255
2256       }
2257
2258     } catch (Exception ex)
2259     {
2260       ex.printStackTrace();
2261       System.out.println("Exception whilst pasting: " + ex);
2262       // could be anything being pasted in here
2263     }
2264
2265   }
2266
2267   @Override
2268   protected void expand_newalign(ActionEvent e)
2269   {
2270     try
2271     {
2272       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2273               .getAlignment(), -1);
2274       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2275               DEFAULT_HEIGHT);
2276       String newtitle = new String("Flanking alignment");
2277
2278       if (Desktop.jalviewClipboard != null
2279               && Desktop.jalviewClipboard[2] != null)
2280       {
2281         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2282         for (int region[] : hc)
2283         {
2284           af.viewport.hideColumns(region[0], region[1]);
2285         }
2286       }
2287
2288       // >>>This is a fix for the moment, until a better solution is
2289       // found!!<<<
2290       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291               .transferSettings(
2292                       alignPanel.getSeqPanel().seqCanvas
2293                               .getFeatureRenderer());
2294
2295       // TODO: maintain provenance of an alignment, rather than just make the
2296       // title a concatenation of operations.
2297       {
2298         if (title.startsWith("Copied sequences"))
2299         {
2300           newtitle = title;
2301         }
2302         else
2303         {
2304           newtitle = newtitle.concat("- from " + title);
2305         }
2306       }
2307
2308       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2309
2310     } catch (Exception ex)
2311     {
2312       ex.printStackTrace();
2313       System.out.println("Exception whilst pasting: " + ex);
2314       // could be anything being pasted in here
2315     } catch (OutOfMemoryError oom)
2316     {
2317       new OOMWarning("Viewing flanking region of alignment", oom);
2318     }
2319   }
2320
2321   /**
2322    * DOCUMENT ME!
2323    *
2324    * @param e
2325    *          DOCUMENT ME!
2326    */
2327   @Override
2328   protected void cut_actionPerformed(ActionEvent e)
2329   {
2330     copy_actionPerformed(null);
2331     delete_actionPerformed(null);
2332   }
2333
2334   /**
2335    * DOCUMENT ME!
2336    *
2337    * @param e
2338    *          DOCUMENT ME!
2339    */
2340   @Override
2341   protected void delete_actionPerformed(ActionEvent evt)
2342   {
2343
2344     SequenceGroup sg = viewport.getSelectionGroup();
2345     if (sg == null)
2346     {
2347       return;
2348     }
2349
2350     /*
2351      * If the cut affects all sequences, warn, remove highlighted columns
2352      */
2353     if (sg.getSize() == viewport.getAlignment().getHeight())
2354     {
2355       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2356               .getAlignment().getWidth()) ? true : false;
2357       if (isEntireAlignWidth)
2358       {
2359         int confirm = JOptionPane.showConfirmDialog(this,
2360                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2361                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2362                 JOptionPane.OK_CANCEL_OPTION);
2363
2364         if (confirm == JOptionPane.CANCEL_OPTION
2365                 || confirm == JOptionPane.CLOSED_OPTION)
2366         {
2367           return;
2368         }
2369       }
2370       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2371               sg.getEndRes() + 1);
2372     }
2373     SequenceI[] cut = sg.getSequences()
2374             .toArray(new SequenceI[sg.getSize()]);
2375
2376     addHistoryItem(new EditCommand(
2377             MessageManager.getString("label.cut_sequences"), Action.CUT,
2378             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2379             viewport.getAlignment()));
2380
2381     viewport.setSelectionGroup(null);
2382     viewport.sendSelection();
2383     viewport.getAlignment().deleteGroup(sg);
2384
2385     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386             .getSequences());
2387     if (viewport.getAlignment().getHeight() < 1)
2388     {
2389       try
2390       {
2391         this.setClosed(true);
2392       } catch (Exception ex)
2393       {
2394       }
2395     }
2396   }
2397
2398   /**
2399    * DOCUMENT ME!
2400    *
2401    * @param e
2402    *          DOCUMENT ME!
2403    */
2404   @Override
2405   protected void deleteGroups_actionPerformed(ActionEvent e)
2406   {
2407     if (avc.deleteGroups())
2408     {
2409       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2410       alignPanel.updateAnnotation();
2411       alignPanel.paintAlignment(true);
2412     }
2413   }
2414
2415   /**
2416    * DOCUMENT ME!
2417    *
2418    * @param e
2419    *          DOCUMENT ME!
2420    */
2421   @Override
2422   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2423   {
2424     SequenceGroup sg = new SequenceGroup();
2425
2426     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2427     {
2428       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2429     }
2430
2431     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2432     viewport.setSelectionGroup(sg);
2433     viewport.sendSelection();
2434     // JAL-2034 - should delegate to
2435     // alignPanel to decide if overview needs
2436     // updating.
2437     alignPanel.paintAlignment(false);
2438     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439   }
2440
2441   /**
2442    * DOCUMENT ME!
2443    *
2444    * @param e
2445    *          DOCUMENT ME!
2446    */
2447   @Override
2448   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449   {
2450     if (viewport.cursorMode)
2451     {
2452       alignPanel.getSeqPanel().keyboardNo1 = null;
2453       alignPanel.getSeqPanel().keyboardNo2 = null;
2454     }
2455     viewport.setSelectionGroup(null);
2456     viewport.getColumnSelection().clear();
2457     viewport.setSelectionGroup(null);
2458     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2459     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2460     // JAL-2034 - should delegate to
2461     // alignPanel to decide if overview needs
2462     // updating.
2463     alignPanel.paintAlignment(false);
2464     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465     viewport.sendSelection();
2466   }
2467
2468   /**
2469    * DOCUMENT ME!
2470    *
2471    * @param e
2472    *          DOCUMENT ME!
2473    */
2474   @Override
2475   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2476   {
2477     SequenceGroup sg = viewport.getSelectionGroup();
2478
2479     if (sg == null)
2480     {
2481       selectAllSequenceMenuItem_actionPerformed(null);
2482
2483       return;
2484     }
2485
2486     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487     {
2488       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2489     }
2490     // JAL-2034 - should delegate to
2491     // alignPanel to decide if overview needs
2492     // updating.
2493
2494     alignPanel.paintAlignment(true);
2495     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496     viewport.sendSelection();
2497   }
2498
2499   @Override
2500   public void invertColSel_actionPerformed(ActionEvent e)
2501   {
2502     viewport.invertColumnSelection();
2503     alignPanel.paintAlignment(true);
2504     viewport.sendSelection();
2505   }
2506
2507   /**
2508    * DOCUMENT ME!
2509    *
2510    * @param e
2511    *          DOCUMENT ME!
2512    */
2513   @Override
2514   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2515   {
2516     trimAlignment(true);
2517   }
2518
2519   /**
2520    * DOCUMENT ME!
2521    *
2522    * @param e
2523    *          DOCUMENT ME!
2524    */
2525   @Override
2526   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2527   {
2528     trimAlignment(false);
2529   }
2530
2531   void trimAlignment(boolean trimLeft)
2532   {
2533     ColumnSelection colSel = viewport.getColumnSelection();
2534     int column;
2535
2536     if (!colSel.isEmpty())
2537     {
2538       if (trimLeft)
2539       {
2540         column = colSel.getMin();
2541       }
2542       else
2543       {
2544         column = colSel.getMax();
2545       }
2546
2547       SequenceI[] seqs;
2548       if (viewport.getSelectionGroup() != null)
2549       {
2550         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2551                 viewport.getHiddenRepSequences());
2552       }
2553       else
2554       {
2555         seqs = viewport.getAlignment().getSequencesArray();
2556       }
2557
2558       TrimRegionCommand trimRegion;
2559       if (trimLeft)
2560       {
2561         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2562                 column, viewport.getAlignment());
2563         viewport.setStartRes(0);
2564       }
2565       else
2566       {
2567         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2568                 column, viewport.getAlignment());
2569       }
2570
2571       statusBar.setText(MessageManager.formatMessage(
2572               "label.removed_columns",
2573               new String[] { Integer.valueOf(trimRegion.getSize())
2574                       .toString() }));
2575
2576       addHistoryItem(trimRegion);
2577
2578       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2579       {
2580         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2581                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2582         {
2583           viewport.getAlignment().deleteGroup(sg);
2584         }
2585       }
2586
2587       viewport.firePropertyChange("alignment", null, viewport
2588               .getAlignment().getSequences());
2589     }
2590   }
2591
2592   /**
2593    * DOCUMENT ME!
2594    *
2595    * @param e
2596    *          DOCUMENT ME!
2597    */
2598   @Override
2599   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2600   {
2601     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2602
2603     SequenceI[] seqs;
2604     if (viewport.getSelectionGroup() != null)
2605     {
2606       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2607               viewport.getHiddenRepSequences());
2608       start = viewport.getSelectionGroup().getStartRes();
2609       end = viewport.getSelectionGroup().getEndRes();
2610     }
2611     else
2612     {
2613       seqs = viewport.getAlignment().getSequencesArray();
2614     }
2615
2616     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2617             "Remove Gapped Columns", seqs, start, end,
2618             viewport.getAlignment());
2619
2620     addHistoryItem(removeGapCols);
2621
2622     statusBar.setText(MessageManager.formatMessage(
2623             "label.removed_empty_columns",
2624             new Object[] { Integer.valueOf(removeGapCols.getSize())
2625                     .toString() }));
2626
2627     // This is to maintain viewport position on first residue
2628     // of first sequence
2629     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2630     int startRes = seq.findPosition(viewport.startRes);
2631     // ShiftList shifts;
2632     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2633     // edit.alColumnChanges=shifts.getInverse();
2634     // if (viewport.hasHiddenColumns)
2635     // viewport.getColumnSelection().compensateForEdits(shifts);
2636     viewport.setStartRes(seq.findIndex(startRes) - 1);
2637     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2638             .getSequences());
2639
2640   }
2641
2642   /**
2643    * DOCUMENT ME!
2644    *
2645    * @param e
2646    *          DOCUMENT ME!
2647    */
2648   @Override
2649   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2650   {
2651     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2652
2653     SequenceI[] seqs;
2654     if (viewport.getSelectionGroup() != null)
2655     {
2656       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2657               viewport.getHiddenRepSequences());
2658       start = viewport.getSelectionGroup().getStartRes();
2659       end = viewport.getSelectionGroup().getEndRes();
2660     }
2661     else
2662     {
2663       seqs = viewport.getAlignment().getSequencesArray();
2664     }
2665
2666     // This is to maintain viewport position on first residue
2667     // of first sequence
2668     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2669     int startRes = seq.findPosition(viewport.startRes);
2670
2671     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2672             viewport.getAlignment()));
2673
2674     viewport.setStartRes(seq.findIndex(startRes) - 1);
2675
2676     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2677             .getSequences());
2678
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2689   {
2690     viewport.setPadGaps(padGapsMenuitem.isSelected());
2691     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2692             .getSequences());
2693   }
2694
2695   /**
2696    * DOCUMENT ME!
2697    *
2698    * @param e
2699    *          DOCUMENT ME!
2700    */
2701   @Override
2702   public void findMenuItem_actionPerformed(ActionEvent e)
2703   {
2704     new Finder();
2705   }
2706
2707   /**
2708    * Create a new view of the current alignment.
2709    */
2710   @Override
2711   public void newView_actionPerformed(ActionEvent e)
2712   {
2713     newView(null, true);
2714   }
2715
2716   /**
2717    * Creates and shows a new view of the current alignment.
2718    *
2719    * @param viewTitle
2720    *          title of newly created view; if null, one will be generated
2721    * @param copyAnnotation
2722    *          if true then duplicate all annnotation, groups and settings
2723    * @return new alignment panel, already displayed.
2724    */
2725   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2726   {
2727     /*
2728      * Create a new AlignmentPanel (with its own, new Viewport)
2729      */
2730     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2731             true);
2732     if (!copyAnnotation)
2733     {
2734       /*
2735        * remove all groups and annotation except for the automatic stuff
2736        */
2737       newap.av.getAlignment().deleteAllGroups();
2738       newap.av.getAlignment().deleteAllAnnotations(false);
2739     }
2740
2741     newap.av.setGatherViewsHere(false);
2742
2743     if (viewport.viewName == null)
2744     {
2745       viewport.viewName = MessageManager
2746               .getString("label.view_name_original");
2747     }
2748
2749     /*
2750      * Views share the same edits undo and redo stacks
2751      */
2752     newap.av.setHistoryList(viewport.getHistoryList());
2753     newap.av.setRedoList(viewport.getRedoList());
2754
2755     /*
2756      * Views share the same mappings; need to deregister any new mappings
2757      * created by copyAlignPanel, and register the new reference to the shared
2758      * mappings
2759      */
2760     newap.av.replaceMappings(viewport.getAlignment());
2761
2762     newap.av.viewName = getNewViewName(viewTitle);
2763
2764     addAlignmentPanel(newap, true);
2765     newap.alignmentChanged();
2766
2767     if (alignPanels.size() == 2)
2768     {
2769       viewport.setGatherViewsHere(true);
2770     }
2771     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2772     return newap;
2773   }
2774
2775   /**
2776    * Make a new name for the view, ensuring it is unique within the current
2777    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2778    * these now use viewId. Unique view names are still desirable for usability.)
2779    *
2780    * @param viewTitle
2781    * @return
2782    */
2783   protected String getNewViewName(String viewTitle)
2784   {
2785     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2786     boolean addFirstIndex = false;
2787     if (viewTitle == null || viewTitle.trim().length() == 0)
2788     {
2789       viewTitle = MessageManager.getString("action.view");
2790       addFirstIndex = true;
2791     }
2792     else
2793     {
2794       index = 1;// we count from 1 if given a specific name
2795     }
2796     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2797
2798     List<Component> comps = PaintRefresher.components.get(viewport
2799             .getSequenceSetId());
2800
2801     List<String> existingNames = getExistingViewNames(comps);
2802
2803     while (existingNames.contains(newViewName))
2804     {
2805       newViewName = viewTitle + " " + (++index);
2806     }
2807     return newViewName;
2808   }
2809
2810   /**
2811    * Returns a list of distinct view names found in the given list of
2812    * components. View names are held on the viewport of an AlignmentPanel.
2813    *
2814    * @param comps
2815    * @return
2816    */
2817   protected List<String> getExistingViewNames(List<Component> comps)
2818   {
2819     List<String> existingNames = new ArrayList<String>();
2820     for (Component comp : comps)
2821     {
2822       if (comp instanceof AlignmentPanel)
2823       {
2824         AlignmentPanel ap = (AlignmentPanel) comp;
2825         if (!existingNames.contains(ap.av.viewName))
2826         {
2827           existingNames.add(ap.av.viewName);
2828         }
2829       }
2830     }
2831     return existingNames;
2832   }
2833
2834   /**
2835    * Explode tabbed views into separate windows.
2836    */
2837   @Override
2838   public void expandViews_actionPerformed(ActionEvent e)
2839   {
2840     Desktop.explodeViews(this);
2841   }
2842
2843   /**
2844    * Gather views in separate windows back into a tabbed presentation.
2845    */
2846   @Override
2847   public void gatherViews_actionPerformed(ActionEvent e)
2848   {
2849     Desktop.instance.gatherViews(this);
2850   }
2851
2852   /**
2853    * DOCUMENT ME!
2854    *
2855    * @param e
2856    *          DOCUMENT ME!
2857    */
2858   @Override
2859   public void font_actionPerformed(ActionEvent e)
2860   {
2861     new FontChooser(alignPanel);
2862   }
2863
2864   /**
2865    * DOCUMENT ME!
2866    *
2867    * @param e
2868    *          DOCUMENT ME!
2869    */
2870   @Override
2871   protected void seqLimit_actionPerformed(ActionEvent e)
2872   {
2873     viewport.setShowJVSuffix(seqLimits.isSelected());
2874
2875     alignPanel.getIdPanel().getIdCanvas()
2876             .setPreferredSize(alignPanel.calculateIdWidth());
2877     alignPanel.paintAlignment(true);
2878   }
2879
2880   @Override
2881   public void idRightAlign_actionPerformed(ActionEvent e)
2882   {
2883     viewport.setRightAlignIds(idRightAlign.isSelected());
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   @Override
2888   public void centreColumnLabels_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2891     alignPanel.paintAlignment(true);
2892   }
2893
2894   /*
2895    * (non-Javadoc)
2896    *
2897    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2898    */
2899   @Override
2900   protected void followHighlight_actionPerformed()
2901   {
2902     /*
2903      * Set the 'follow' flag on the Viewport (and scroll to position if now
2904      * true).
2905      */
2906     final boolean state = this.followHighlightMenuItem.getState();
2907     viewport.setFollowHighlight(state);
2908     if (state)
2909     {
2910       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2911     }
2912   }
2913
2914   /**
2915    * DOCUMENT ME!
2916    *
2917    * @param e
2918    *          DOCUMENT ME!
2919    */
2920   @Override
2921   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2922   {
2923     viewport.setColourText(colourTextMenuItem.isSelected());
2924     alignPanel.paintAlignment(true);
2925   }
2926
2927   /**
2928    * DOCUMENT ME!
2929    *
2930    * @param e
2931    *          DOCUMENT ME!
2932    */
2933   @Override
2934   public void wrapMenuItem_actionPerformed(ActionEvent e)
2935   {
2936     scaleAbove.setVisible(wrapMenuItem.isSelected());
2937     scaleLeft.setVisible(wrapMenuItem.isSelected());
2938     scaleRight.setVisible(wrapMenuItem.isSelected());
2939     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2940     alignPanel.updateLayout();
2941   }
2942
2943   @Override
2944   public void showAllSeqs_actionPerformed(ActionEvent e)
2945   {
2946     viewport.showAllHiddenSeqs();
2947   }
2948
2949   @Override
2950   public void showAllColumns_actionPerformed(ActionEvent e)
2951   {
2952     viewport.showAllHiddenColumns();
2953     repaint();
2954     viewport.sendSelection();
2955   }
2956
2957   @Override
2958   public void hideSelSequences_actionPerformed(ActionEvent e)
2959   {
2960     viewport.hideAllSelectedSeqs();
2961     // alignPanel.paintAlignment(true);
2962   }
2963
2964   /**
2965    * called by key handler and the hide all/show all menu items
2966    *
2967    * @param toggleSeqs
2968    * @param toggleCols
2969    */
2970   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2971   {
2972
2973     boolean hide = false;
2974     SequenceGroup sg = viewport.getSelectionGroup();
2975     if (!toggleSeqs && !toggleCols)
2976     {
2977       // Hide everything by the current selection - this is a hack - we do the
2978       // invert and then hide
2979       // first check that there will be visible columns after the invert.
2980       if (viewport.hasSelectedColumns()
2981               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2982                       .getEndRes()))
2983       {
2984         // now invert the sequence set, if required - empty selection implies
2985         // that no hiding is required.
2986         if (sg != null)
2987         {
2988           invertSequenceMenuItem_actionPerformed(null);
2989           sg = viewport.getSelectionGroup();
2990           toggleSeqs = true;
2991
2992         }
2993         viewport.expandColSelection(sg, true);
2994         // finally invert the column selection and get the new sequence
2995         // selection.
2996         invertColSel_actionPerformed(null);
2997         toggleCols = true;
2998       }
2999     }
3000
3001     if (toggleSeqs)
3002     {
3003       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3004       {
3005         hideSelSequences_actionPerformed(null);
3006         hide = true;
3007       }
3008       else if (!(toggleCols && viewport.hasSelectedColumns()))
3009       {
3010         showAllSeqs_actionPerformed(null);
3011       }
3012     }
3013
3014     if (toggleCols)
3015     {
3016       if (viewport.hasSelectedColumns())
3017       {
3018         hideSelColumns_actionPerformed(null);
3019         if (!toggleSeqs)
3020         {
3021           viewport.setSelectionGroup(sg);
3022         }
3023       }
3024       else if (!hide)
3025       {
3026         showAllColumns_actionPerformed(null);
3027       }
3028     }
3029   }
3030
3031   /*
3032    * (non-Javadoc)
3033    *
3034    * @see
3035    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036    * event.ActionEvent)
3037    */
3038   @Override
3039   public void hideAllButSelection_actionPerformed(ActionEvent e)
3040   {
3041     toggleHiddenRegions(false, false);
3042     viewport.sendSelection();
3043   }
3044
3045   /*
3046    * (non-Javadoc)
3047    *
3048    * @see
3049    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3050    * .ActionEvent)
3051    */
3052   @Override
3053   public void hideAllSelection_actionPerformed(ActionEvent e)
3054   {
3055     SequenceGroup sg = viewport.getSelectionGroup();
3056     viewport.expandColSelection(sg, false);
3057     viewport.hideAllSelectedSeqs();
3058     viewport.hideSelectedColumns();
3059     alignPanel.paintAlignment(true);
3060     viewport.sendSelection();
3061   }
3062
3063   /*
3064    * (non-Javadoc)
3065    *
3066    * @see
3067    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3068    * ActionEvent)
3069    */
3070   @Override
3071   public void showAllhidden_actionPerformed(ActionEvent e)
3072   {
3073     viewport.showAllHiddenColumns();
3074     viewport.showAllHiddenSeqs();
3075     alignPanel.paintAlignment(true);
3076     viewport.sendSelection();
3077   }
3078
3079   @Override
3080   public void hideSelColumns_actionPerformed(ActionEvent e)
3081   {
3082     viewport.hideSelectedColumns();
3083     alignPanel.paintAlignment(true);
3084     viewport.sendSelection();
3085   }
3086
3087   @Override
3088   public void hiddenMarkers_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3091     repaint();
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   protected void scaleAbove_actionPerformed(ActionEvent e)
3102   {
3103     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3104     alignPanel.paintAlignment(true);
3105   }
3106
3107   /**
3108    * DOCUMENT ME!
3109    *
3110    * @param e
3111    *          DOCUMENT ME!
3112    */
3113   @Override
3114   protected void scaleLeft_actionPerformed(ActionEvent e)
3115   {
3116     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3117     alignPanel.paintAlignment(true);
3118   }
3119
3120   /**
3121    * DOCUMENT ME!
3122    *
3123    * @param e
3124    *          DOCUMENT ME!
3125    */
3126   @Override
3127   protected void scaleRight_actionPerformed(ActionEvent e)
3128   {
3129     viewport.setScaleRightWrapped(scaleRight.isSelected());
3130     alignPanel.paintAlignment(true);
3131   }
3132
3133   /**
3134    * DOCUMENT ME!
3135    *
3136    * @param e
3137    *          DOCUMENT ME!
3138    */
3139   @Override
3140   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3141   {
3142     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3143     alignPanel.paintAlignment(true);
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setShowText(viewTextMenuItem.isSelected());
3156     alignPanel.paintAlignment(true);
3157   }
3158
3159   /**
3160    * DOCUMENT ME!
3161    *
3162    * @param e
3163    *          DOCUMENT ME!
3164    */
3165   @Override
3166   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3167   {
3168     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3169     alignPanel.paintAlignment(true);
3170   }
3171
3172   public FeatureSettings featureSettings;
3173
3174   @Override
3175   public FeatureSettingsControllerI getFeatureSettingsUI()
3176   {
3177     return featureSettings;
3178   }
3179
3180   @Override
3181   public void featureSettings_actionPerformed(ActionEvent e)
3182   {
3183     if (featureSettings != null)
3184     {
3185       featureSettings.close();
3186       featureSettings = null;
3187     }
3188     if (!showSeqFeatures.isSelected())
3189     {
3190       // make sure features are actually displayed
3191       showSeqFeatures.setSelected(true);
3192       showSeqFeatures_actionPerformed(null);
3193     }
3194     featureSettings = new FeatureSettings(this);
3195   }
3196
3197   /**
3198    * Set or clear 'Show Sequence Features'
3199    *
3200    * @param evt
3201    *          DOCUMENT ME!
3202    */
3203   @Override
3204   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3205   {
3206     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3207     alignPanel.paintAlignment(true);
3208     if (alignPanel.getOverviewPanel() != null)
3209     {
3210       alignPanel.getOverviewPanel().updateOverviewImage();
3211     }
3212   }
3213
3214   /**
3215    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3216    * the annotations panel as a whole.
3217    *
3218    * The options to show/hide all annotations should be enabled when the panel
3219    * is shown, and disabled when the panel is hidden.
3220    *
3221    * @param e
3222    */
3223   @Override
3224   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3225   {
3226     final boolean setVisible = annotationPanelMenuItem.isSelected();
3227     viewport.setShowAnnotation(setVisible);
3228     this.showAllSeqAnnotations.setEnabled(setVisible);
3229     this.hideAllSeqAnnotations.setEnabled(setVisible);
3230     this.showAllAlAnnotations.setEnabled(setVisible);
3231     this.hideAllAlAnnotations.setEnabled(setVisible);
3232     alignPanel.updateLayout();
3233   }
3234
3235   @Override
3236   public void alignmentProperties()
3237   {
3238     JEditorPane editPane = new JEditorPane("text/html", "");
3239     editPane.setEditable(false);
3240     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3241             .formatAsHtml();
3242     editPane.setText(MessageManager.formatMessage("label.html_content",
3243             new Object[] { contents.toString() }));
3244     JInternalFrame frame = new JInternalFrame();
3245     frame.getContentPane().add(new JScrollPane(editPane));
3246
3247     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3248             "label.alignment_properties", new Object[] { getTitle() }),
3249             500, 400);
3250   }
3251
3252   /**
3253    * DOCUMENT ME!
3254    *
3255    * @param e
3256    *          DOCUMENT ME!
3257    */
3258   @Override
3259   public void overviewMenuItem_actionPerformed(ActionEvent e)
3260   {
3261     if (alignPanel.overviewPanel != null)
3262     {
3263       return;
3264     }
3265
3266     JInternalFrame frame = new JInternalFrame();
3267     OverviewPanel overview = new OverviewPanel(alignPanel);
3268     frame.setContentPane(overview);
3269     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3270             "label.overview_params", new Object[] { this.getTitle() }),
3271             frame.getWidth(), frame.getHeight());
3272     frame.pack();
3273     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3274     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3275     {
3276       @Override
3277       public void internalFrameClosed(
3278               javax.swing.event.InternalFrameEvent evt)
3279       {
3280         alignPanel.setOverviewPanel(null);
3281       };
3282     });
3283
3284     alignPanel.setOverviewPanel(overview);
3285   }
3286
3287   @Override
3288   public void textColour_actionPerformed(ActionEvent e)
3289   {
3290     new TextColourChooser().chooseColour(alignPanel, null);
3291   }
3292
3293   /**
3294    * DOCUMENT ME!
3295    *
3296    * @param e
3297    *          DOCUMENT ME!
3298    */
3299   @Override
3300   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3301   {
3302     changeColour(null);
3303   }
3304
3305   /**
3306    * DOCUMENT ME!
3307    *
3308    * @param e
3309    *          DOCUMENT ME!
3310    */
3311   @Override
3312   public void clustalColour_actionPerformed(ActionEvent e)
3313   {
3314     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3315             viewport.getHiddenRepSequences()));
3316   }
3317
3318   /**
3319    * DOCUMENT ME!
3320    *
3321    * @param e
3322    *          DOCUMENT ME!
3323    */
3324   @Override
3325   public void zappoColour_actionPerformed(ActionEvent e)
3326   {
3327     changeColour(new ZappoColourScheme());
3328   }
3329
3330   /**
3331    * DOCUMENT ME!
3332    *
3333    * @param e
3334    *          DOCUMENT ME!
3335    */
3336   @Override
3337   public void taylorColour_actionPerformed(ActionEvent e)
3338   {
3339     changeColour(new TaylorColourScheme());
3340   }
3341
3342   /**
3343    * DOCUMENT ME!
3344    *
3345    * @param e
3346    *          DOCUMENT ME!
3347    */
3348   @Override
3349   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3350   {
3351     changeColour(new HydrophobicColourScheme());
3352   }
3353
3354   /**
3355    * DOCUMENT ME!
3356    *
3357    * @param e
3358    *          DOCUMENT ME!
3359    */
3360   @Override
3361   public void helixColour_actionPerformed(ActionEvent e)
3362   {
3363     changeColour(new HelixColourScheme());
3364   }
3365
3366   /**
3367    * DOCUMENT ME!
3368    *
3369    * @param e
3370    *          DOCUMENT ME!
3371    */
3372   @Override
3373   public void strandColour_actionPerformed(ActionEvent e)
3374   {
3375     changeColour(new StrandColourScheme());
3376   }
3377
3378   /**
3379    * DOCUMENT ME!
3380    *
3381    * @param e
3382    *          DOCUMENT ME!
3383    */
3384   @Override
3385   public void turnColour_actionPerformed(ActionEvent e)
3386   {
3387     changeColour(new TurnColourScheme());
3388   }
3389
3390   /**
3391    * DOCUMENT ME!
3392    *
3393    * @param e
3394    *          DOCUMENT ME!
3395    */
3396   @Override
3397   public void buriedColour_actionPerformed(ActionEvent e)
3398   {
3399     changeColour(new BuriedColourScheme());
3400   }
3401
3402   /**
3403    * DOCUMENT ME!
3404    *
3405    * @param e
3406    *          DOCUMENT ME!
3407    */
3408   @Override
3409   public void nucleotideColour_actionPerformed(ActionEvent e)
3410   {
3411     changeColour(new NucleotideColourScheme());
3412   }
3413
3414   @Override
3415   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3416   {
3417     changeColour(new PurinePyrimidineColourScheme());
3418   }
3419
3420   /*
3421    * public void covariationColour_actionPerformed(ActionEvent e) {
3422    * changeColour(new
3423    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3424    * ()[0])); }
3425    */
3426   @Override
3427   public void annotationColour_actionPerformed(ActionEvent e)
3428   {
3429     new AnnotationColourChooser(viewport, alignPanel);
3430   }
3431
3432   @Override
3433   public void annotationColumn_actionPerformed(ActionEvent e)
3434   {
3435     new AnnotationColumnChooser(viewport, alignPanel);
3436   }
3437
3438   @Override
3439   public void rnahelicesColour_actionPerformed(ActionEvent e)
3440   {
3441     new RNAHelicesColourChooser(viewport, alignPanel);
3442   }
3443
3444   /**
3445    * DOCUMENT ME!
3446    *
3447    * @param e
3448    *          DOCUMENT ME!
3449    */
3450   @Override
3451   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3452   {
3453     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3454   }
3455
3456   /**
3457    * DOCUMENT ME!
3458    *
3459    * @param cs
3460    *          DOCUMENT ME!
3461    */
3462   @Override
3463   public void changeColour(ColourSchemeI cs)
3464   {
3465     // TODO: pull up to controller method
3466
3467     if (cs != null)
3468     {
3469       // Make sure viewport is up to date w.r.t. any sliders
3470       if (viewport.getAbovePIDThreshold())
3471       {
3472         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3473                 "Background");
3474         viewport.setThreshold(threshold);
3475       }
3476
3477       if (viewport.getConservationSelected())
3478       {
3479         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3480                 cs, "Background"));
3481       }
3482       if (cs instanceof TCoffeeColourScheme)
3483       {
3484         tcoffeeColour.setEnabled(true);
3485         tcoffeeColour.setSelected(true);
3486       }
3487     }
3488
3489     viewport.setGlobalColourScheme(cs);
3490
3491     alignPanel.paintAlignment(true);
3492   }
3493
3494   /**
3495    * DOCUMENT ME!
3496    *
3497    * @param e
3498    *          DOCUMENT ME!
3499    */
3500   @Override
3501   protected void modifyPID_actionPerformed(ActionEvent e)
3502   {
3503     if (viewport.getAbovePIDThreshold()
3504             && viewport.getGlobalColourScheme() != null)
3505     {
3506       SliderPanel.setPIDSliderSource(alignPanel,
3507               viewport.getGlobalColourScheme(), "Background");
3508       SliderPanel.showPIDSlider();
3509     }
3510   }
3511
3512   /**
3513    * DOCUMENT ME!
3514    *
3515    * @param e
3516    *          DOCUMENT ME!
3517    */
3518   @Override
3519   protected void modifyConservation_actionPerformed(ActionEvent e)
3520   {
3521     if (viewport.getConservationSelected()
3522             && viewport.getGlobalColourScheme() != null)
3523     {
3524       SliderPanel.setConservationSlider(alignPanel,
3525               viewport.getGlobalColourScheme(), "Background");
3526       SliderPanel.showConservationSlider();
3527     }
3528   }
3529
3530   /**
3531    * DOCUMENT ME!
3532    *
3533    * @param e
3534    *          DOCUMENT ME!
3535    */
3536   @Override
3537   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3538   {
3539     viewport.setConservationSelected(conservationMenuItem.isSelected());
3540
3541     viewport.setAbovePIDThreshold(false);
3542     abovePIDThreshold.setSelected(false);
3543
3544     changeColour(viewport.getGlobalColourScheme());
3545
3546     modifyConservation_actionPerformed(null);
3547   }
3548
3549   /**
3550    * DOCUMENT ME!
3551    *
3552    * @param e
3553    *          DOCUMENT ME!
3554    */
3555   @Override
3556   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3557   {
3558     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3559
3560     conservationMenuItem.setSelected(false);
3561     viewport.setConservationSelected(false);
3562
3563     changeColour(viewport.getGlobalColourScheme());
3564
3565     modifyPID_actionPerformed(null);
3566   }
3567
3568   /**
3569    * DOCUMENT ME!
3570    *
3571    * @param e
3572    *          DOCUMENT ME!
3573    */
3574   @Override
3575   public void userDefinedColour_actionPerformed(ActionEvent e)
3576   {
3577     if (e.getActionCommand().equals(
3578             MessageManager.getString("action.user_defined")))
3579     {
3580       new UserDefinedColours(alignPanel, null);
3581     }
3582     else
3583     {
3584       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3585               .getUserColourSchemes().get(e.getActionCommand());
3586
3587       changeColour(udc);
3588     }
3589   }
3590
3591   public void updateUserColourMenu()
3592   {
3593
3594     Component[] menuItems = colourMenu.getMenuComponents();
3595     int iSize = menuItems.length;
3596     for (int i = 0; i < iSize; i++)
3597     {
3598       if (menuItems[i].getName() != null
3599               && menuItems[i].getName().equals("USER_DEFINED"))
3600       {
3601         colourMenu.remove(menuItems[i]);
3602         iSize--;
3603       }
3604     }
3605     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3606     {
3607       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3608               .getUserColourSchemes().keys();
3609
3610       while (userColours.hasMoreElements())
3611       {
3612         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3613                 userColours.nextElement().toString());
3614         radioItem.setName("USER_DEFINED");
3615         radioItem.addMouseListener(new MouseAdapter()
3616         {
3617           @Override
3618           public void mousePressed(MouseEvent evt)
3619           {
3620             if (evt.isPopupTrigger()) // Mac
3621             {
3622               offerRemoval(radioItem);
3623             }
3624           }
3625
3626           @Override
3627           public void mouseReleased(MouseEvent evt)
3628           {
3629             if (evt.isPopupTrigger()) // Windows
3630             {
3631               offerRemoval(radioItem);
3632             }
3633           }
3634
3635           /**
3636            * @param radioItem
3637            */
3638           void offerRemoval(final JRadioButtonMenuItem radioItem)
3639           {
3640             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3641
3642             int option = JOptionPane.showInternalConfirmDialog(
3643                     jalview.gui.Desktop.desktop, MessageManager
3644                             .getString("label.remove_from_default_list"),
3645                     MessageManager
3646                             .getString("label.remove_user_defined_colour"),
3647                     JOptionPane.YES_NO_OPTION);
3648             if (option == JOptionPane.YES_OPTION)
3649             {
3650               jalview.gui.UserDefinedColours
3651                       .removeColourFromDefaults(radioItem.getText());
3652               colourMenu.remove(radioItem);
3653             }
3654             else
3655             {
3656               radioItem.addActionListener(new ActionListener()
3657               {
3658                 @Override
3659                 public void actionPerformed(ActionEvent evt)
3660                 {
3661                   userDefinedColour_actionPerformed(evt);
3662                 }
3663               });
3664             }
3665           }
3666         });
3667         radioItem.addActionListener(new ActionListener()
3668         {
3669           @Override
3670           public void actionPerformed(ActionEvent evt)
3671           {
3672             userDefinedColour_actionPerformed(evt);
3673           }
3674         });
3675
3676         colourMenu.insert(radioItem, 15);
3677         colours.add(radioItem);
3678       }
3679     }
3680   }
3681
3682   /**
3683    * DOCUMENT ME!
3684    *
3685    * @param e
3686    *          DOCUMENT ME!
3687    */
3688   @Override
3689   public void PIDColour_actionPerformed(ActionEvent e)
3690   {
3691     changeColour(new PIDColourScheme());
3692   }
3693
3694   /**
3695    * DOCUMENT ME!
3696    *
3697    * @param e
3698    *          DOCUMENT ME!
3699    */
3700   @Override
3701   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3702   {
3703     changeColour(new Blosum62ColourScheme());
3704   }
3705
3706   /**
3707    * DOCUMENT ME!
3708    *
3709    * @param e
3710    *          DOCUMENT ME!
3711    */
3712   @Override
3713   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3714   {
3715     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3716     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3717             .getAlignment().getSequenceAt(0), null);
3718     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3719             viewport.getAlignment()));
3720     alignPanel.paintAlignment(true);
3721   }
3722
3723   /**
3724    * DOCUMENT ME!
3725    *
3726    * @param e
3727    *          DOCUMENT ME!
3728    */
3729   @Override
3730   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3731   {
3732     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3733     AlignmentSorter.sortByID(viewport.getAlignment());
3734     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3735             viewport.getAlignment()));
3736     alignPanel.paintAlignment(true);
3737   }
3738
3739   /**
3740    * DOCUMENT ME!
3741    *
3742    * @param e
3743    *          DOCUMENT ME!
3744    */
3745   @Override
3746   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3747   {
3748     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749     AlignmentSorter.sortByLength(viewport.getAlignment());
3750     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3751             viewport.getAlignment()));
3752     alignPanel.paintAlignment(true);
3753   }
3754
3755   /**
3756    * DOCUMENT ME!
3757    *
3758    * @param e
3759    *          DOCUMENT ME!
3760    */
3761   @Override
3762   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3763   {
3764     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3765     AlignmentSorter.sortByGroup(viewport.getAlignment());
3766     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3767             viewport.getAlignment()));
3768
3769     alignPanel.paintAlignment(true);
3770   }
3771
3772   /**
3773    * DOCUMENT ME!
3774    *
3775    * @param e
3776    *          DOCUMENT ME!
3777    */
3778   @Override
3779   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3780   {
3781     new RedundancyPanel(alignPanel, this);
3782   }
3783
3784   /**
3785    * DOCUMENT ME!
3786    *
3787    * @param e
3788    *          DOCUMENT ME!
3789    */
3790   @Override
3791   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3792   {
3793     if ((viewport.getSelectionGroup() == null)
3794             || (viewport.getSelectionGroup().getSize() < 2))
3795     {
3796       JOptionPane.showInternalMessageDialog(this, MessageManager
3797               .getString("label.you_must_select_least_two_sequences"),
3798               MessageManager.getString("label.invalid_selection"),
3799               JOptionPane.WARNING_MESSAGE);
3800     }
3801     else
3802     {
3803       JInternalFrame frame = new JInternalFrame();
3804       frame.setContentPane(new PairwiseAlignPanel(viewport));
3805       Desktop.addInternalFrame(frame,
3806               MessageManager.getString("action.pairwise_alignment"), 600,
3807               500);
3808     }
3809   }
3810
3811   /**
3812    * DOCUMENT ME!
3813    *
3814    * @param e
3815    *          DOCUMENT ME!
3816    */
3817   @Override
3818   public void PCAMenuItem_actionPerformed(ActionEvent e)
3819   {
3820     if (((viewport.getSelectionGroup() != null)
3821             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3822             .getSelectionGroup().getSize() > 0))
3823             || (viewport.getAlignment().getHeight() < 4))
3824     {
3825       JOptionPane
3826               .showInternalMessageDialog(
3827                       this,
3828                       MessageManager
3829                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3830                       MessageManager
3831                               .getString("label.sequence_selection_insufficient"),
3832                       JOptionPane.WARNING_MESSAGE);
3833
3834       return;
3835     }
3836
3837     new PCAPanel(alignPanel);
3838   }
3839
3840   @Override
3841   public void autoCalculate_actionPerformed(ActionEvent e)
3842   {
3843     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3844     if (viewport.autoCalculateConsensus)
3845     {
3846       viewport.firePropertyChange("alignment", null, viewport
3847               .getAlignment().getSequences());
3848     }
3849   }
3850
3851   @Override
3852   public void sortByTreeOption_actionPerformed(ActionEvent e)
3853   {
3854     viewport.sortByTree = sortByTree.isSelected();
3855   }
3856
3857   @Override
3858   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3859   {
3860     viewport.followSelection = listenToViewSelections.isSelected();
3861   }
3862
3863   /**
3864    * DOCUMENT ME!
3865    *
3866    * @param e
3867    *          DOCUMENT ME!
3868    */
3869   @Override
3870   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3871   {
3872     newTreePanel("AV", "PID", "Average distance tree using PID");
3873   }
3874
3875   /**
3876    * DOCUMENT ME!
3877    *
3878    * @param e
3879    *          DOCUMENT ME!
3880    */
3881   @Override
3882   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3883   {
3884     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3885   }
3886
3887   /**
3888    * DOCUMENT ME!
3889    *
3890    * @param e
3891    *          DOCUMENT ME!
3892    */
3893   @Override
3894   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3895   {
3896     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3897   }
3898
3899   /**
3900    * DOCUMENT ME!
3901    *
3902    * @param e
3903    *          DOCUMENT ME!
3904    */
3905   @Override
3906   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3907   {
3908     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3909   }
3910
3911   /**
3912    * DOCUMENT ME!
3913    *
3914    * @param type
3915    *          DOCUMENT ME!
3916    * @param pwType
3917    *          DOCUMENT ME!
3918    * @param title
3919    *          DOCUMENT ME!
3920    */
3921   void newTreePanel(String type, String pwType, String title)
3922   {
3923     TreePanel tp;
3924
3925     if (viewport.getSelectionGroup() != null
3926             && viewport.getSelectionGroup().getSize() > 0)
3927     {
3928       if (viewport.getSelectionGroup().getSize() < 3)
3929       {
3930         JOptionPane
3931                 .showMessageDialog(
3932                         Desktop.desktop,
3933                         MessageManager
3934                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3935                         MessageManager
3936                                 .getString("label.not_enough_sequences"),
3937                         JOptionPane.WARNING_MESSAGE);
3938         return;
3939       }
3940
3941       SequenceGroup sg = viewport.getSelectionGroup();
3942
3943       /* Decide if the selection is a column region */
3944       for (SequenceI _s : sg.getSequences())
3945       {
3946         if (_s.getLength() < sg.getEndRes())
3947         {
3948           JOptionPane
3949                   .showMessageDialog(
3950                           Desktop.desktop,
3951                           MessageManager
3952                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3953                           MessageManager
3954                                   .getString("label.sequences_selection_not_aligned"),
3955                           JOptionPane.WARNING_MESSAGE);
3956
3957           return;
3958         }
3959       }
3960
3961       title = title + " on region";
3962       tp = new TreePanel(alignPanel, type, pwType);
3963     }
3964     else
3965     {
3966       // are the visible sequences aligned?
3967       if (!viewport.getAlignment().isAligned(false))
3968       {
3969         JOptionPane
3970                 .showMessageDialog(
3971                         Desktop.desktop,
3972                         MessageManager
3973                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3974                         MessageManager
3975                                 .getString("label.sequences_not_aligned"),
3976                         JOptionPane.WARNING_MESSAGE);
3977
3978         return;
3979       }
3980
3981       if (viewport.getAlignment().getHeight() < 2)
3982       {
3983         return;
3984       }
3985
3986       tp = new TreePanel(alignPanel, type, pwType);
3987     }
3988
3989     title += " from ";
3990
3991     if (viewport.viewName != null)
3992     {
3993       title += viewport.viewName + " of ";
3994     }
3995
3996     title += this.title;
3997
3998     Desktop.addInternalFrame(tp, title, 600, 500);
3999   }
4000
4001   /**
4002    * DOCUMENT ME!
4003    *
4004    * @param title
4005    *          DOCUMENT ME!
4006    * @param order
4007    *          DOCUMENT ME!
4008    */
4009   public void addSortByOrderMenuItem(String title,
4010           final AlignmentOrder order)
4011   {
4012     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4013             "action.by_title_param", new Object[] { title }));
4014     sort.add(item);
4015     item.addActionListener(new java.awt.event.ActionListener()
4016     {
4017       @Override
4018       public void actionPerformed(ActionEvent e)
4019       {
4020         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4021
4022         // TODO: JBPNote - have to map order entries to curent SequenceI
4023         // pointers
4024         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4025
4026         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4027                 .getAlignment()));
4028
4029         alignPanel.paintAlignment(true);
4030       }
4031     });
4032   }
4033
4034   /**
4035    * Add a new sort by annotation score menu item
4036    *
4037    * @param sort
4038    *          the menu to add the option to
4039    * @param scoreLabel
4040    *          the label used to retrieve scores for each sequence on the
4041    *          alignment
4042    */
4043   public void addSortByAnnotScoreMenuItem(JMenu sort,
4044           final String scoreLabel)
4045   {
4046     final JMenuItem item = new JMenuItem(scoreLabel);
4047     sort.add(item);
4048     item.addActionListener(new java.awt.event.ActionListener()
4049     {
4050       @Override
4051       public void actionPerformed(ActionEvent e)
4052       {
4053         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4054         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4055                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4056         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4057                 viewport.getAlignment()));
4058         alignPanel.paintAlignment(true);
4059       }
4060     });
4061   }
4062
4063   /**
4064    * last hash for alignment's annotation array - used to minimise cost of
4065    * rebuild.
4066    */
4067   protected int _annotationScoreVectorHash;
4068
4069   /**
4070    * search the alignment and rebuild the sort by annotation score submenu the
4071    * last alignment annotation vector hash is stored to minimize cost of
4072    * rebuilding in subsequence calls.
4073    *
4074    */
4075   @Override
4076   public void buildSortByAnnotationScoresMenu()
4077   {
4078     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4079     {
4080       return;
4081     }
4082
4083     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4084     {
4085       sortByAnnotScore.removeAll();
4086       // almost certainly a quicker way to do this - but we keep it simple
4087       Hashtable scoreSorts = new Hashtable();
4088       AlignmentAnnotation aann[];
4089       for (SequenceI sqa : viewport.getAlignment().getSequences())
4090       {
4091         aann = sqa.getAnnotation();
4092         for (int i = 0; aann != null && i < aann.length; i++)
4093         {
4094           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4095           {
4096             scoreSorts.put(aann[i].label, aann[i].label);
4097           }
4098         }
4099       }
4100       Enumeration labels = scoreSorts.keys();
4101       while (labels.hasMoreElements())
4102       {
4103         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4104                 (String) labels.nextElement());
4105       }
4106       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4107       scoreSorts.clear();
4108
4109       _annotationScoreVectorHash = viewport.getAlignment()
4110               .getAlignmentAnnotation().hashCode();
4111     }
4112   }
4113
4114   /**
4115    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4116    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4117    * call. Listeners are added to remove the menu item when the treePanel is
4118    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4119    * modified.
4120    *
4121    * @param treePanel
4122    *          Displayed tree window.
4123    * @param title
4124    *          SortBy menu item title.
4125    */
4126   @Override
4127   public void buildTreeMenu()
4128   {
4129     calculateTree.removeAll();
4130     // build the calculate menu
4131
4132     for (final String type : new String[] { "NJ", "AV" })
4133     {
4134       String treecalcnm = MessageManager.getString("label.tree_calc_"
4135               + type.toLowerCase());
4136       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4137       {
4138         JMenuItem tm = new JMenuItem();
4139         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4140         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4141                 || sm.isProtein() == !viewport.getAlignment()
4142                         .isNucleotide())
4143         {
4144           String smn = MessageManager.getStringOrReturn(
4145                   "label.score_model_", sm.getName());
4146           final String title = MessageManager.formatMessage(
4147                   "label.treecalc_title", treecalcnm, smn);
4148           tm.setText(title);//
4149           tm.addActionListener(new java.awt.event.ActionListener()
4150           {
4151             @Override
4152             public void actionPerformed(ActionEvent e)
4153             {
4154               newTreePanel(type, pwtype, title);
4155             }
4156           });
4157           calculateTree.add(tm);
4158         }
4159
4160       }
4161     }
4162     sortByTreeMenu.removeAll();
4163
4164     List<Component> comps = PaintRefresher.components.get(viewport
4165             .getSequenceSetId());
4166     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4167     for (Component comp : comps)
4168     {
4169       if (comp instanceof TreePanel)
4170       {
4171         treePanels.add((TreePanel) comp);
4172       }
4173     }
4174
4175     if (treePanels.size() < 1)
4176     {
4177       sortByTreeMenu.setVisible(false);
4178       return;
4179     }
4180
4181     sortByTreeMenu.setVisible(true);
4182
4183     for (final TreePanel tp : treePanels)
4184     {
4185       final JMenuItem item = new JMenuItem(tp.getTitle());
4186       item.addActionListener(new java.awt.event.ActionListener()
4187       {
4188         @Override
4189         public void actionPerformed(ActionEvent e)
4190         {
4191           tp.sortByTree_actionPerformed();
4192           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4193
4194         }
4195       });
4196
4197       sortByTreeMenu.add(item);
4198     }
4199   }
4200
4201   public boolean sortBy(AlignmentOrder alorder, String undoname)
4202   {
4203     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4204     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4205     if (undoname != null)
4206     {
4207       addHistoryItem(new OrderCommand(undoname, oldOrder,
4208               viewport.getAlignment()));
4209     }
4210     alignPanel.paintAlignment(true);
4211     return true;
4212   }
4213
4214   /**
4215    * Work out whether the whole set of sequences or just the selected set will
4216    * be submitted for multiple alignment.
4217    *
4218    */
4219   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4220   {
4221     // Now, check we have enough sequences
4222     AlignmentView msa = null;
4223
4224     if ((viewport.getSelectionGroup() != null)
4225             && (viewport.getSelectionGroup().getSize() > 1))
4226     {
4227       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4228       // some common interface!
4229       /*
4230        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4231        * SequenceI[sz = seqs.getSize(false)];
4232        *
4233        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4234        * seqs.getSequenceAt(i); }
4235        */
4236       msa = viewport.getAlignmentView(true);
4237     }
4238     else if (viewport.getSelectionGroup() != null
4239             && viewport.getSelectionGroup().getSize() == 1)
4240     {
4241       int option = JOptionPane.showConfirmDialog(this,
4242               MessageManager.getString("warn.oneseq_msainput_selection"),
4243               MessageManager.getString("label.invalid_selection"),
4244               JOptionPane.OK_CANCEL_OPTION);
4245       if (option == JOptionPane.OK_OPTION)
4246       {
4247         msa = viewport.getAlignmentView(false);
4248       }
4249     }
4250     else
4251     {
4252       msa = viewport.getAlignmentView(false);
4253     }
4254     return msa;
4255   }
4256
4257   /**
4258    * Decides what is submitted to a secondary structure prediction service: the
4259    * first sequence in the alignment, or in the current selection, or, if the
4260    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4261    * region or the whole alignment. (where the first sequence in the set is the
4262    * one that the prediction will be for).
4263    */
4264   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4265   {
4266     AlignmentView seqs = null;
4267
4268     if ((viewport.getSelectionGroup() != null)
4269             && (viewport.getSelectionGroup().getSize() > 0))
4270     {
4271       seqs = viewport.getAlignmentView(true);
4272     }
4273     else
4274     {
4275       seqs = viewport.getAlignmentView(false);
4276     }
4277     // limit sequences - JBPNote in future - could spawn multiple prediction
4278     // jobs
4279     // TODO: viewport.getAlignment().isAligned is a global state - the local
4280     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4281     if (!viewport.getAlignment().isAligned(false))
4282     {
4283       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4284       // TODO: if seqs.getSequences().length>1 then should really have warned
4285       // user!
4286
4287     }
4288     return seqs;
4289   }
4290
4291   /**
4292    * DOCUMENT ME!
4293    *
4294    * @param e
4295    *          DOCUMENT ME!
4296    */
4297   @Override
4298   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4299   {
4300     // Pick the tree file
4301     JalviewFileChooser chooser = new JalviewFileChooser(
4302             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4303     chooser.setFileView(new JalviewFileView());
4304     chooser.setDialogTitle(MessageManager
4305             .getString("label.select_newick_like_tree_file"));
4306     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4307
4308     int value = chooser.showOpenDialog(null);
4309
4310     if (value == JalviewFileChooser.APPROVE_OPTION)
4311     {
4312       String choice = chooser.getSelectedFile().getPath();
4313       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4314       jalview.io.NewickFile fin = null;
4315       try
4316       {
4317         fin = new jalview.io.NewickFile(choice, "File");
4318         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4319       } catch (Exception ex)
4320       {
4321         JOptionPane
4322                 .showMessageDialog(
4323                         Desktop.desktop,
4324                         ex.getMessage(),
4325                         MessageManager
4326                                 .getString("label.problem_reading_tree_file"),
4327                         JOptionPane.WARNING_MESSAGE);
4328         ex.printStackTrace();
4329       }
4330       if (fin != null && fin.hasWarningMessage())
4331       {
4332         JOptionPane.showMessageDialog(Desktop.desktop, fin
4333                 .getWarningMessage(), MessageManager
4334                 .getString("label.possible_problem_with_tree_file"),
4335                 JOptionPane.WARNING_MESSAGE);
4336       }
4337     }
4338   }
4339
4340   @Override
4341   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4342   {
4343     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4344   }
4345
4346   public TreePanel ShowNewickTree(NewickFile nf, String title)
4347   {
4348     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4349   }
4350
4351   public TreePanel ShowNewickTree(NewickFile nf, String title,
4352           AlignmentView input)
4353   {
4354     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4355   }
4356
4357   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4358           int h, int x, int y)
4359   {
4360     return ShowNewickTree(nf, title, null, w, h, x, y);
4361   }
4362
4363   /**
4364    * Add a treeviewer for the tree extracted from a newick file object to the
4365    * current alignment view
4366    *
4367    * @param nf
4368    *          the tree
4369    * @param title
4370    *          tree viewer title
4371    * @param input
4372    *          Associated alignment input data (or null)
4373    * @param w
4374    *          width
4375    * @param h
4376    *          height
4377    * @param x
4378    *          position
4379    * @param y
4380    *          position
4381    * @return TreePanel handle
4382    */
4383   public TreePanel ShowNewickTree(NewickFile nf, String title,
4384           AlignmentView input, int w, int h, int x, int y)
4385   {
4386     TreePanel tp = null;
4387
4388     try
4389     {
4390       nf.parse();
4391
4392       if (nf.getTree() != null)
4393       {
4394         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4395
4396         tp.setSize(w, h);
4397
4398         if (x > 0 && y > 0)
4399         {
4400           tp.setLocation(x, y);
4401         }
4402
4403         Desktop.addInternalFrame(tp, title, w, h);
4404       }
4405     } catch (Exception ex)
4406     {
4407       ex.printStackTrace();
4408     }
4409
4410     return tp;
4411   }
4412
4413   private boolean buildingMenu = false;
4414
4415   /**
4416    * Generates menu items and listener event actions for web service clients
4417    *
4418    */
4419   public void BuildWebServiceMenu()
4420   {
4421     while (buildingMenu)
4422     {
4423       try
4424       {
4425         System.err.println("Waiting for building menu to finish.");
4426         Thread.sleep(10);
4427       } catch (Exception e)
4428       {
4429       }
4430     }
4431     final AlignFrame me = this;
4432     buildingMenu = true;
4433     new Thread(new Runnable()
4434     {
4435       @Override
4436       public void run()
4437       {
4438         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4439         try
4440         {
4441           // System.err.println("Building ws menu again "
4442           // + Thread.currentThread());
4443           // TODO: add support for context dependent disabling of services based
4444           // on
4445           // alignment and current selection
4446           // TODO: add additional serviceHandle parameter to specify abstract
4447           // handler
4448           // class independently of AbstractName
4449           // TODO: add in rediscovery GUI function to restart discoverer
4450           // TODO: group services by location as well as function and/or
4451           // introduce
4452           // object broker mechanism.
4453           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4454           final IProgressIndicator af = me;
4455
4456           /*
4457            * do not i18n these strings - they are hard-coded in class
4458            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4459            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4460            */
4461           final JMenu msawsmenu = new JMenu("Alignment");
4462           final JMenu secstrmenu = new JMenu(
4463                   "Secondary Structure Prediction");
4464           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4465           final JMenu analymenu = new JMenu("Analysis");
4466           final JMenu dismenu = new JMenu("Protein Disorder");
4467           // JAL-940 - only show secondary structure prediction services from
4468           // the legacy server
4469           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4470               // &&
4471           Discoverer.services != null && (Discoverer.services.size() > 0))
4472           {
4473             // TODO: refactor to allow list of AbstractName/Handler bindings to
4474             // be
4475             // stored or retrieved from elsewhere
4476             // No MSAWS used any more:
4477             // Vector msaws = null; // (Vector)
4478             // Discoverer.services.get("MsaWS");
4479             Vector secstrpr = (Vector) Discoverer.services
4480                     .get("SecStrPred");
4481             if (secstrpr != null)
4482             {
4483               // Add any secondary structure prediction services
4484               for (int i = 0, j = secstrpr.size(); i < j; i++)
4485               {
4486                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4487                         .get(i);
4488                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4489                         .getServiceClient(sh);
4490                 int p = secstrmenu.getItemCount();
4491                 impl.attachWSMenuEntry(secstrmenu, me);
4492                 int q = secstrmenu.getItemCount();
4493                 for (int litm = p; litm < q; litm++)
4494                 {
4495                   legacyItems.add(secstrmenu.getItem(litm));
4496                 }
4497               }
4498             }
4499           }
4500
4501           // Add all submenus in the order they should appear on the web
4502           // services menu
4503           wsmenu.add(msawsmenu);
4504           wsmenu.add(secstrmenu);
4505           wsmenu.add(dismenu);
4506           wsmenu.add(analymenu);
4507           // No search services yet
4508           // wsmenu.add(seqsrchmenu);
4509
4510           javax.swing.SwingUtilities.invokeLater(new Runnable()
4511           {
4512             @Override
4513             public void run()
4514             {
4515               try
4516               {
4517                 webService.removeAll();
4518                 // first, add discovered services onto the webservices menu
4519                 if (wsmenu.size() > 0)
4520                 {
4521                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4522                   {
4523                     webService.add(wsmenu.get(i));
4524                   }
4525                 }
4526                 else
4527                 {
4528                   webService.add(me.webServiceNoServices);
4529                 }
4530                 // TODO: move into separate menu builder class.
4531                 boolean new_sspred = false;
4532                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4533                 {
4534                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4535                   if (jws2servs != null)
4536                   {
4537                     if (jws2servs.hasServices())
4538                     {
4539                       jws2servs.attachWSMenuEntry(webService, me);
4540                       for (Jws2Instance sv : jws2servs.getServices())
4541                       {
4542                         if (sv.description.toLowerCase().contains("jpred"))
4543                         {
4544                           for (JMenuItem jmi : legacyItems)
4545                           {
4546                             jmi.setVisible(false);
4547                           }
4548                         }
4549                       }
4550
4551                     }
4552                     if (jws2servs.isRunning())
4553                     {
4554                       JMenuItem tm = new JMenuItem(
4555                               "Still discovering JABA Services");
4556                       tm.setEnabled(false);
4557                       webService.add(tm);
4558                     }
4559                   }
4560                 }
4561                 build_urlServiceMenu(me.webService);
4562                 build_fetchdbmenu(webService);
4563                 for (JMenu item : wsmenu)
4564                 {
4565                   if (item.getItemCount() == 0)
4566                   {
4567                     item.setEnabled(false);
4568                   }
4569                   else
4570                   {
4571                     item.setEnabled(true);
4572                   }
4573                 }
4574               } catch (Exception e)
4575               {
4576                 Cache.log
4577                         .debug("Exception during web service menu building process.",
4578                                 e);
4579               }
4580             }
4581           });
4582         } catch (Exception e)
4583         {
4584         }
4585         buildingMenu = false;
4586       }
4587     }).start();
4588
4589   }
4590
4591   /**
4592    * construct any groupURL type service menu entries.
4593    *
4594    * @param webService
4595    */
4596   private void build_urlServiceMenu(JMenu webService)
4597   {
4598     // TODO: remove this code when 2.7 is released
4599     // DEBUG - alignmentView
4600     /*
4601      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4602      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4603      *
4604      * @Override public void actionPerformed(ActionEvent e) {
4605      * jalview.datamodel.AlignmentView
4606      * .testSelectionViews(af.viewport.getAlignment(),
4607      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4608      *
4609      * }); webService.add(testAlView);
4610      */
4611     // TODO: refactor to RestClient discoverer and merge menu entries for
4612     // rest-style services with other types of analysis/calculation service
4613     // SHmmr test client - still being implemented.
4614     // DEBUG - alignmentView
4615
4616     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4617             .getRestClients())
4618     {
4619       client.attachWSMenuEntry(
4620               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4621               this);
4622     }
4623   }
4624
4625   /**
4626    * Searches the alignment sequences for xRefs and builds the Show
4627    * Cross-References menu (formerly called Show Products), with database
4628    * sources for which cross-references are found (protein sources for a
4629    * nucleotide alignment and vice versa)
4630    *
4631    * @return true if Show Cross-references menu should be enabled
4632    */
4633   public boolean canShowProducts()
4634   {
4635     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4636     AlignmentI dataset = viewport.getAlignment().getDataset();
4637
4638     showProducts.removeAll();
4639     final boolean dna = viewport.getAlignment().isNucleotide();
4640
4641     if (seqs == null || seqs.length == 0)
4642     {
4643       // nothing to see here.
4644       return false;
4645     }
4646
4647     boolean showp = false;
4648     try
4649     {
4650       List<String> ptypes = new CrossRef(seqs, dataset)
4651               .findXrefSourcesForSequences(dna);
4652
4653       for (final String source : ptypes)
4654       {
4655         showp = true;
4656         final AlignFrame af = this;
4657         JMenuItem xtype = new JMenuItem(source);
4658         xtype.addActionListener(new ActionListener()
4659         {
4660           @Override
4661           public void actionPerformed(ActionEvent e)
4662           {
4663             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4664           }
4665         });
4666         showProducts.add(xtype);
4667       }
4668       showProducts.setVisible(showp);
4669       showProducts.setEnabled(showp);
4670     } catch (Exception e)
4671     {
4672       Cache.log
4673               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4674                       e);
4675       return false;
4676     }
4677     return showp;
4678   }
4679
4680   /**
4681    * Finds and displays cross-references for the selected sequences (protein
4682    * products for nucleotide sequences, dna coding sequences for peptides).
4683    *
4684    * @param sel
4685    *          the sequences to show cross-references for
4686    * @param dna
4687    *          true if from a nucleotide alignment (so showing proteins)
4688    * @param source
4689    *          the database to show cross-references for
4690    */
4691   protected void showProductsFor(final SequenceI[] sel,
4692           final boolean _odna, final String source)
4693   {
4694     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4695             .start();
4696   }
4697
4698   /**
4699    * Construct and display a new frame containing the translation of this
4700    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4701    */
4702   @Override
4703   public void showTranslation_actionPerformed(ActionEvent e)
4704   {
4705     AlignmentI al = null;
4706     try
4707     {
4708       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4709
4710       al = dna.translateCdna();
4711     } catch (Exception ex)
4712     {
4713       jalview.bin.Cache.log.error(
4714               "Exception during translation. Please report this !", ex);
4715       final String msg = MessageManager
4716               .getString("label.error_when_translating_sequences_submit_bug_report");
4717       final String errorTitle = MessageManager
4718               .getString("label.implementation_error")
4719               + MessageManager.getString("label.translation_failed");
4720       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4721               JOptionPane.ERROR_MESSAGE);
4722       return;
4723     }
4724     if (al == null || al.getHeight() == 0)
4725     {
4726       final String msg = MessageManager
4727               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4728       final String errorTitle = MessageManager
4729               .getString("label.translation_failed");
4730       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4731               JOptionPane.WARNING_MESSAGE);
4732     }
4733     else
4734     {
4735       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4736       af.setFileFormat(this.currentFileFormat);
4737       final String newTitle = MessageManager.formatMessage(
4738               "label.translation_of_params",
4739               new Object[] { this.getTitle() });
4740       af.setTitle(newTitle);
4741       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4742       {
4743         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4744         viewport.openSplitFrame(af, new Alignment(seqs));
4745       }
4746       else
4747       {
4748         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4749                 DEFAULT_HEIGHT);
4750       }
4751     }
4752   }
4753
4754   /**
4755    * Set the file format
4756    *
4757    * @param fileFormat
4758    */
4759   public void setFileFormat(String fileFormat)
4760   {
4761     this.currentFileFormat = fileFormat;
4762   }
4763
4764   /**
4765    * Try to load a features file onto the alignment.
4766    *
4767    * @param file
4768    *          contents or path to retrieve file
4769    * @param type
4770    *          access mode of file (see jalview.io.AlignFile)
4771    * @return true if features file was parsed correctly.
4772    */
4773   public boolean parseFeaturesFile(String file, String type)
4774   {
4775     return avc.parseFeaturesFile(file, type,
4776             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4777
4778   }
4779
4780   @Override
4781   public void refreshFeatureUI(boolean enableIfNecessary)
4782   {
4783     // note - currently this is only still here rather than in the controller
4784     // because of the featureSettings hard reference that is yet to be
4785     // abstracted
4786     if (enableIfNecessary)
4787     {
4788       viewport.setShowSequenceFeatures(true);
4789       showSeqFeatures.setSelected(true);
4790     }
4791
4792   }
4793
4794   @Override
4795   public void dragEnter(DropTargetDragEvent evt)
4796   {
4797   }
4798
4799   @Override
4800   public void dragExit(DropTargetEvent evt)
4801   {
4802   }
4803
4804   @Override
4805   public void dragOver(DropTargetDragEvent evt)
4806   {
4807   }
4808
4809   @Override
4810   public void dropActionChanged(DropTargetDragEvent evt)
4811   {
4812   }
4813
4814   @Override
4815   public void drop(DropTargetDropEvent evt)
4816   {
4817     // JAL-1552 - acceptDrop required before getTransferable call for
4818     // Java's Transferable for native dnd
4819     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4820     Transferable t = evt.getTransferable();
4821     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4822
4823     try
4824     {
4825       Desktop.transferFromDropTarget(files, protocols, evt, t);
4826     } catch (Exception e)
4827     {
4828       e.printStackTrace();
4829     }
4830     if (files != null)
4831     {
4832       try
4833       {
4834         // check to see if any of these files have names matching sequences in
4835         // the alignment
4836         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4837                 .getAlignment().getSequencesArray());
4838         /**
4839          * Object[] { String,SequenceI}
4840          */
4841         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4842         ArrayList<String> filesnotmatched = new ArrayList<String>();
4843         for (int i = 0; i < files.size(); i++)
4844         {
4845           String file = files.get(i).toString();
4846           String pdbfn = "";
4847           String protocol = FormatAdapter.checkProtocol(file);
4848           if (protocol == jalview.io.FormatAdapter.FILE)
4849           {
4850             File fl = new File(file);
4851             pdbfn = fl.getName();
4852           }
4853           else if (protocol == jalview.io.FormatAdapter.URL)
4854           {
4855             URL url = new URL(file);
4856             pdbfn = url.getFile();
4857           }
4858           if (pdbfn.length() > 0)
4859           {
4860             // attempt to find a match in the alignment
4861             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4862             int l = 0, c = pdbfn.indexOf(".");
4863             while (mtch == null && c != -1)
4864             {
4865               do
4866               {
4867                 l = c;
4868               } while ((c = pdbfn.indexOf(".", l)) > l);
4869               if (l > -1)
4870               {
4871                 pdbfn = pdbfn.substring(0, l);
4872               }
4873               mtch = idm.findAllIdMatches(pdbfn);
4874             }
4875             if (mtch != null)
4876             {
4877               String type = null;
4878               try
4879               {
4880                 type = new IdentifyFile().identify(file, protocol);
4881               } catch (Exception ex)
4882               {
4883                 type = null;
4884               }
4885               if (type != null)
4886               {
4887                 if (type.equalsIgnoreCase("PDB"))
4888                 {
4889                   filesmatched.add(new Object[] { file, protocol, mtch });
4890                   continue;
4891                 }
4892               }
4893             }
4894             // File wasn't named like one of the sequences or wasn't a PDB file.
4895             filesnotmatched.add(file);
4896           }
4897         }
4898         int assocfiles = 0;
4899         if (filesmatched.size() > 0)
4900         {
4901           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4902                   || JOptionPane
4903                           .showConfirmDialog(
4904                                   this,
4905                                   MessageManager
4906                                           .formatMessage(
4907                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
4908                                                   new Object[] { Integer
4909                                                           .valueOf(
4910                                                                   filesmatched
4911                                                                           .size())
4912                                                           .toString() }),
4913                                   MessageManager
4914                                           .getString("label.automatically_associate_pdb_files_by_name"),
4915                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4916
4917           {
4918             for (Object[] fm : filesmatched)
4919             {
4920               // try and associate
4921               // TODO: may want to set a standard ID naming formalism for
4922               // associating PDB files which have no IDs.
4923               for (SequenceI toassoc : (SequenceI[]) fm[2])
4924               {
4925                 PDBEntry pe = new AssociatePdbFileWithSeq()
4926                         .associatePdbWithSeq((String) fm[0],
4927                                 (String) fm[1], toassoc, false,
4928                                 Desktop.instance);
4929                 if (pe != null)
4930                 {
4931                   System.err.println("Associated file : "
4932                           + ((String) fm[0]) + " with "
4933                           + toassoc.getDisplayId(true));
4934                   assocfiles++;
4935                 }
4936               }
4937               alignPanel.paintAlignment(true);
4938             }
4939           }
4940         }
4941         if (filesnotmatched.size() > 0)
4942         {
4943           if (assocfiles > 0
4944                   && (Cache.getDefault(
4945                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4946                           .showConfirmDialog(
4947                                   this,
4948                                   "<html>"
4949                                           + MessageManager
4950                                                   .formatMessage(
4951                                                           "label.ignore_unmatched_dropped_files_info",
4952                                                           new Object[] { Integer
4953                                                                   .valueOf(
4954                                                                           filesnotmatched
4955                                                                                   .size())
4956                                                                   .toString() })
4957                                           + "</html>",
4958                                   MessageManager
4959                                           .getString("label.ignore_unmatched_dropped_files"),
4960                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4961           {
4962             return;
4963           }
4964           for (String fn : filesnotmatched)
4965           {
4966             loadJalviewDataFile(fn, null, null, null);
4967           }
4968
4969         }
4970       } catch (Exception ex)
4971       {
4972         ex.printStackTrace();
4973       }
4974     }
4975   }
4976
4977   /**
4978    * Attempt to load a "dropped" file or URL string: First by testing whether
4979    * it's an Annotation file, then a JNet file, and finally a features file. If
4980    * all are false then the user may have dropped an alignment file onto this
4981    * AlignFrame.
4982    *
4983    * @param file
4984    *          either a filename or a URL string.
4985    */
4986   public void loadJalviewDataFile(String file, String protocol,
4987           String format, SequenceI assocSeq)
4988   {
4989     try
4990     {
4991       if (protocol == null)
4992       {
4993         protocol = FormatAdapter.checkProtocol(file);
4994       }
4995       // if the file isn't identified, or not positively identified as some
4996       // other filetype (PFAM is default unidentified alignment file type) then
4997       // try to parse as annotation.
4998       boolean isAnnotation = (format == null || format
4999               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5000               .annotateAlignmentView(viewport, file, protocol) : false;
5001
5002       if (!isAnnotation)
5003       {
5004         // first see if its a T-COFFEE score file
5005         TCoffeeScoreFile tcf = null;
5006         try
5007         {
5008           tcf = new TCoffeeScoreFile(file, protocol);
5009           if (tcf.isValid())
5010           {
5011             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5012             {
5013               tcoffeeColour.setEnabled(true);
5014               tcoffeeColour.setSelected(true);
5015               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5016               isAnnotation = true;
5017               statusBar
5018                       .setText(MessageManager
5019                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5020             }
5021             else
5022             {
5023               // some problem - if no warning its probable that the ID matching
5024               // process didn't work
5025               JOptionPane
5026                       .showMessageDialog(
5027                               Desktop.desktop,
5028                               tcf.getWarningMessage() == null ? MessageManager
5029                                       .getString("label.check_file_matches_sequence_ids_alignment")
5030                                       : tcf.getWarningMessage(),
5031                               MessageManager
5032                                       .getString("label.problem_reading_tcoffee_score_file"),
5033                               JOptionPane.WARNING_MESSAGE);
5034             }
5035           }
5036           else
5037           {
5038             tcf = null;
5039           }
5040         } catch (Exception x)
5041         {
5042           Cache.log
5043                   .debug("Exception when processing data source as T-COFFEE score file",
5044                           x);
5045           tcf = null;
5046         }
5047         if (tcf == null)
5048         {
5049           // try to see if its a JNet 'concise' style annotation file *before*
5050           // we
5051           // try to parse it as a features file
5052           if (format == null)
5053           {
5054             format = new IdentifyFile().identify(file, protocol);
5055           }
5056           if (format.equalsIgnoreCase("JnetFile"))
5057           {
5058             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5059                     file, protocol);
5060             new JnetAnnotationMaker();
5061             JnetAnnotationMaker.add_annotation(predictions,
5062                     viewport.getAlignment(), 0, false);
5063             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5064             viewport.getAlignment().setSeqrep(repseq);
5065             ColumnSelection cs = new ColumnSelection();
5066             cs.hideInsertionsFor(repseq);
5067             viewport.setColumnSelection(cs);
5068             isAnnotation = true;
5069           }
5070           else if (IdentifyFile.FeaturesFile.equals(format))
5071           {
5072             if (parseFeaturesFile(file, protocol))
5073             {
5074               alignPanel.paintAlignment(true);
5075             }
5076           }
5077           else
5078           {
5079             new FileLoader().LoadFile(viewport, file, protocol, format);
5080           }
5081         }
5082       }
5083       if (isAnnotation)
5084       {
5085
5086         alignPanel.adjustAnnotationHeight();
5087         viewport.updateSequenceIdColours();
5088         buildSortByAnnotationScoresMenu();
5089         alignPanel.paintAlignment(true);
5090       }
5091     } catch (Exception ex)
5092     {
5093       ex.printStackTrace();
5094     } catch (OutOfMemoryError oom)
5095     {
5096       try
5097       {
5098         System.gc();
5099       } catch (Exception x)
5100       {
5101       }
5102       new OOMWarning(
5103               "loading data "
5104                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5105                               : "using " + protocol + " from " + file)
5106                               : ".")
5107                       + (format != null ? "(parsing as '" + format
5108                               + "' file)" : ""), oom, Desktop.desktop);
5109     }
5110   }
5111
5112   /**
5113    * Method invoked by the ChangeListener on the tabbed pane, in other words
5114    * when a different tabbed pane is selected by the user or programmatically.
5115    */
5116   @Override
5117   public void tabSelectionChanged(int index)
5118   {
5119     if (index > -1)
5120     {
5121       alignPanel = alignPanels.get(index);
5122       viewport = alignPanel.av;
5123       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5124       setMenusFromViewport(viewport);
5125     }
5126
5127     /*
5128      * If there is a frame linked to this one in a SplitPane, switch it to the
5129      * same view tab index. No infinite recursion of calls should happen, since
5130      * tabSelectionChanged() should not get invoked on setting the selected
5131      * index to an unchanged value. Guard against setting an invalid index
5132      * before the new view peer tab has been created.
5133      */
5134     final AlignViewportI peer = viewport.getCodingComplement();
5135     if (peer != null)
5136     {
5137       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5138       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5139       {
5140         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5141       }
5142     }
5143   }
5144
5145   /**
5146    * On right mouse click on view tab, prompt for and set new view name.
5147    */
5148   @Override
5149   public void tabbedPane_mousePressed(MouseEvent e)
5150   {
5151     if (e.isPopupTrigger())
5152     {
5153       String msg = MessageManager.getString("label.enter_view_name");
5154       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5155               JOptionPane.QUESTION_MESSAGE);
5156
5157       if (reply != null)
5158       {
5159         viewport.viewName = reply;
5160         // TODO warn if reply is in getExistingViewNames()?
5161         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5162       }
5163     }
5164   }
5165
5166   public AlignViewport getCurrentView()
5167   {
5168     return viewport;
5169   }
5170
5171   /**
5172    * Open the dialog for regex description parsing.
5173    */
5174   @Override
5175   protected void extractScores_actionPerformed(ActionEvent e)
5176   {
5177     ParseProperties pp = new jalview.analysis.ParseProperties(
5178             viewport.getAlignment());
5179     // TODO: verify regex and introduce GUI dialog for version 2.5
5180     // if (pp.getScoresFromDescription("col", "score column ",
5181     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5182     // true)>0)
5183     if (pp.getScoresFromDescription("description column",
5184             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5185     {
5186       buildSortByAnnotationScoresMenu();
5187     }
5188   }
5189
5190   /*
5191    * (non-Javadoc)
5192    *
5193    * @see
5194    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5195    * )
5196    */
5197   @Override
5198   protected void showDbRefs_actionPerformed(ActionEvent e)
5199   {
5200     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5201   }
5202
5203   /*
5204    * (non-Javadoc)
5205    *
5206    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5207    * ActionEvent)
5208    */
5209   @Override
5210   protected void showNpFeats_actionPerformed(ActionEvent e)
5211   {
5212     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5213   }
5214
5215   /**
5216    * find the viewport amongst the tabs in this alignment frame and close that
5217    * tab
5218    *
5219    * @param av
5220    */
5221   public boolean closeView(AlignViewportI av)
5222   {
5223     if (viewport == av)
5224     {
5225       this.closeMenuItem_actionPerformed(false);
5226       return true;
5227     }
5228     Component[] comp = tabbedPane.getComponents();
5229     for (int i = 0; comp != null && i < comp.length; i++)
5230     {
5231       if (comp[i] instanceof AlignmentPanel)
5232       {
5233         if (((AlignmentPanel) comp[i]).av == av)
5234         {
5235           // close the view.
5236           closeView((AlignmentPanel) comp[i]);
5237           return true;
5238         }
5239       }
5240     }
5241     return false;
5242   }
5243
5244   protected void build_fetchdbmenu(JMenu webService)
5245   {
5246     // Temporary hack - DBRef Fetcher always top level ws entry.
5247     // TODO We probably want to store a sequence database checklist in
5248     // preferences and have checkboxes.. rather than individual sources selected
5249     // here
5250     final JMenu rfetch = new JMenu(
5251             MessageManager.getString("action.fetch_db_references"));
5252     rfetch.setToolTipText(MessageManager
5253             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5254     webService.add(rfetch);
5255
5256     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5257             MessageManager.getString("option.trim_retrieved_seqs"));
5258     trimrs.setToolTipText(MessageManager
5259             .getString("label.trim_retrieved_sequences"));
5260     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5261     trimrs.addActionListener(new ActionListener()
5262     {
5263       @Override
5264       public void actionPerformed(ActionEvent e)
5265       {
5266         trimrs.setSelected(trimrs.isSelected());
5267         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5268                 Boolean.valueOf(trimrs.isSelected()).toString());
5269       };
5270     });
5271     rfetch.add(trimrs);
5272     JMenuItem fetchr = new JMenuItem(
5273             MessageManager.getString("label.standard_databases"));
5274     fetchr.setToolTipText(MessageManager
5275             .getString("label.fetch_embl_uniprot"));
5276     fetchr.addActionListener(new ActionListener()
5277     {
5278
5279       @Override
5280       public void actionPerformed(ActionEvent e)
5281       {
5282         new Thread(new Runnable()
5283         {
5284           @Override
5285           public void run()
5286           {
5287             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5288                     .getAlignment().isNucleotide();
5289             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5290                     .getSequenceSelection(), alignPanel.alignFrame, null,
5291                     alignPanel.alignFrame.featureSettings, isNucleotide);
5292             dbRefFetcher.addListener(new FetchFinishedListenerI()
5293             {
5294               @Override
5295               public void finished()
5296               {
5297                 AlignFrame.this.setMenusForViewport();
5298               }
5299             });
5300             dbRefFetcher.fetchDBRefs(false);
5301           }
5302         }).start();
5303
5304       }
5305
5306     });
5307     rfetch.add(fetchr);
5308     final AlignFrame me = this;
5309     new Thread(new Runnable()
5310     {
5311       @Override
5312       public void run()
5313       {
5314         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5315                 .getSequenceFetcherSingleton(me);
5316         javax.swing.SwingUtilities.invokeLater(new Runnable()
5317         {
5318           @Override
5319           public void run()
5320           {
5321             String[] dbclasses = sf.getOrderedSupportedSources();
5322             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5323             // jalview.util.QuickSort.sort(otherdb, otherdb);
5324             List<DbSourceProxy> otherdb;
5325             JMenu dfetch = new JMenu();
5326             JMenu ifetch = new JMenu();
5327             JMenuItem fetchr = null;
5328             int comp = 0, icomp = 0, mcomp = 15;
5329             String mname = null;
5330             int dbi = 0;
5331             for (String dbclass : dbclasses)
5332             {
5333               otherdb = sf.getSourceProxy(dbclass);
5334               // add a single entry for this class, or submenu allowing 'fetch
5335               // all' or pick one
5336               if (otherdb == null || otherdb.size() < 1)
5337               {
5338                 continue;
5339               }
5340               // List<DbSourceProxy> dbs=otherdb;
5341               // otherdb=new ArrayList<DbSourceProxy>();
5342               // for (DbSourceProxy db:dbs)
5343               // {
5344               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5345               // }
5346               if (mname == null)
5347               {
5348                 mname = "From " + dbclass;
5349               }
5350               if (otherdb.size() == 1)
5351               {
5352                 final DbSourceProxy[] dassource = otherdb
5353                         .toArray(new DbSourceProxy[0]);
5354                 DbSourceProxy src = otherdb.get(0);
5355                 fetchr = new JMenuItem(src.getDbSource());
5356                 fetchr.addActionListener(new ActionListener()
5357                 {
5358
5359                   @Override
5360                   public void actionPerformed(ActionEvent e)
5361                   {
5362                     new Thread(new Runnable()
5363                     {
5364
5365                       @Override
5366                       public void run()
5367                       {
5368                         boolean isNucleotide = alignPanel.alignFrame
5369                                 .getViewport().getAlignment()
5370                                 .isNucleotide();
5371                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5372                                 alignPanel.av.getSequenceSelection(),
5373                                 alignPanel.alignFrame, dassource,
5374                                 alignPanel.alignFrame.featureSettings,
5375                                 isNucleotide);
5376                         dbRefFetcher
5377                                 .addListener(new FetchFinishedListenerI()
5378                                 {
5379                                   @Override
5380                                   public void finished()
5381                                   {
5382                                     AlignFrame.this.setMenusForViewport();
5383                                   }
5384                                 });
5385                         dbRefFetcher.fetchDBRefs(false);
5386                       }
5387                     }).start();
5388                   }
5389
5390                 });
5391                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5392                         MessageManager.formatMessage(
5393                                 "label.fetch_retrieve_from",
5394                                 new Object[] { src.getDbName() })));
5395                 dfetch.add(fetchr);
5396                 comp++;
5397               }
5398               else
5399               {
5400                 final DbSourceProxy[] dassource = otherdb
5401                         .toArray(new DbSourceProxy[0]);
5402                 // fetch all entry
5403                 DbSourceProxy src = otherdb.get(0);
5404                 fetchr = new JMenuItem(MessageManager.formatMessage(
5405                         "label.fetch_all_param",
5406                         new Object[] { src.getDbSource() }));
5407                 fetchr.addActionListener(new ActionListener()
5408                 {
5409                   @Override
5410                   public void actionPerformed(ActionEvent e)
5411                   {
5412                     new Thread(new Runnable()
5413                     {
5414
5415                       @Override
5416                       public void run()
5417                       {
5418                         boolean isNucleotide = alignPanel.alignFrame
5419                                 .getViewport().getAlignment()
5420                                 .isNucleotide();
5421                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5422                                 alignPanel.av.getSequenceSelection(),
5423                                 alignPanel.alignFrame, dassource,
5424                                 alignPanel.alignFrame.featureSettings,
5425                                 isNucleotide);
5426                         dbRefFetcher
5427                                 .addListener(new FetchFinishedListenerI()
5428                                 {
5429                                   @Override
5430                                   public void finished()
5431                                   {
5432                                     AlignFrame.this.setMenusForViewport();
5433                                   }
5434                                 });
5435                         dbRefFetcher.fetchDBRefs(false);
5436                       }
5437                     }).start();
5438                   }
5439                 });
5440
5441                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5442                         MessageManager.formatMessage(
5443                                 "label.fetch_retrieve_from_all_sources",
5444                                 new Object[] {
5445                                     Integer.valueOf(otherdb.size())
5446                                             .toString(), src.getDbSource(),
5447                                     src.getDbName() })));
5448                 dfetch.add(fetchr);
5449                 comp++;
5450                 // and then build the rest of the individual menus
5451                 ifetch = new JMenu(MessageManager.formatMessage(
5452                         "label.source_from_db_source",
5453                         new Object[] { src.getDbSource() }));
5454                 icomp = 0;
5455                 String imname = null;
5456                 int i = 0;
5457                 for (DbSourceProxy sproxy : otherdb)
5458                 {
5459                   String dbname = sproxy.getDbName();
5460                   String sname = dbname.length() > 5 ? dbname.substring(0,
5461                           5) + "..." : dbname;
5462                   String msname = dbname.length() > 10 ? dbname.substring(
5463                           0, 10) + "..." : dbname;
5464                   if (imname == null)
5465                   {
5466                     imname = MessageManager.formatMessage(
5467                             "label.from_msname", new Object[] { sname });
5468                   }
5469                   fetchr = new JMenuItem(msname);
5470                   final DbSourceProxy[] dassrc = { sproxy };
5471                   fetchr.addActionListener(new ActionListener()
5472                   {
5473
5474                     @Override
5475                     public void actionPerformed(ActionEvent e)
5476                     {
5477                       new Thread(new Runnable()
5478                       {
5479
5480                         @Override
5481                         public void run()
5482                         {
5483                           boolean isNucleotide = alignPanel.alignFrame
5484                                   .getViewport().getAlignment()
5485                                   .isNucleotide();
5486                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5487                                   alignPanel.av.getSequenceSelection(),
5488                                   alignPanel.alignFrame, dassrc,
5489                                   alignPanel.alignFrame.featureSettings,
5490                                   isNucleotide);
5491                           dbRefFetcher
5492                                   .addListener(new FetchFinishedListenerI()
5493                                   {
5494                                     @Override
5495                                     public void finished()
5496                                     {
5497                                       AlignFrame.this.setMenusForViewport();
5498                                     }
5499                                   });
5500                           dbRefFetcher.fetchDBRefs(false);
5501                         }
5502                       }).start();
5503                     }
5504
5505                   });
5506                   fetchr.setToolTipText("<html>"
5507                           + MessageManager.formatMessage(
5508                                   "label.fetch_retrieve_from", new Object[]
5509                                   { dbname }));
5510                   ifetch.add(fetchr);
5511                   ++i;
5512                   if (++icomp >= mcomp || i == (otherdb.size()))
5513                   {
5514                     ifetch.setText(MessageManager.formatMessage(
5515                             "label.source_to_target", imname, sname));
5516                     dfetch.add(ifetch);
5517                     ifetch = new JMenu();
5518                     imname = null;
5519                     icomp = 0;
5520                     comp++;
5521                   }
5522                 }
5523               }
5524               ++dbi;
5525               if (comp >= mcomp || dbi >= (dbclasses.length))
5526               {
5527                 dfetch.setText(MessageManager.formatMessage(
5528                         "label.source_to_target", mname, dbclass));
5529                 rfetch.add(dfetch);
5530                 dfetch = new JMenu();
5531                 mname = null;
5532                 comp = 0;
5533               }
5534             }
5535           }
5536         });
5537       }
5538     }).start();
5539
5540   }
5541
5542   /**
5543    * Left justify the whole alignment.
5544    */
5545   @Override
5546   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5547   {
5548     AlignmentI al = viewport.getAlignment();
5549     al.justify(false);
5550     viewport.firePropertyChange("alignment", null, al);
5551   }
5552
5553   /**
5554    * Right justify the whole alignment.
5555    */
5556   @Override
5557   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5558   {
5559     AlignmentI al = viewport.getAlignment();
5560     al.justify(true);
5561     viewport.firePropertyChange("alignment", null, al);
5562   }
5563
5564   @Override
5565   public void setShowSeqFeatures(boolean b)
5566   {
5567     showSeqFeatures.setSelected(b);
5568     viewport.setShowSequenceFeatures(b);
5569   }
5570
5571   /*
5572    * (non-Javadoc)
5573    *
5574    * @see
5575    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5576    * awt.event.ActionEvent)
5577    */
5578   @Override
5579   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5580   {
5581     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5582     alignPanel.paintAlignment(true);
5583   }
5584
5585   /*
5586    * (non-Javadoc)
5587    *
5588    * @see
5589    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5590    * .ActionEvent)
5591    */
5592   @Override
5593   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5594   {
5595     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5596     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5597
5598   }
5599
5600   /*
5601    * (non-Javadoc)
5602    *
5603    * @see
5604    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5605    * .event.ActionEvent)
5606    */
5607   @Override
5608   protected void showGroupConservation_actionPerformed(ActionEvent e)
5609   {
5610     viewport.setShowGroupConservation(showGroupConservation.getState());
5611     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5612   }
5613
5614   /*
5615    * (non-Javadoc)
5616    *
5617    * @see
5618    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5619    * .event.ActionEvent)
5620    */
5621   @Override
5622   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5623   {
5624     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5625     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5626   }
5627
5628   /*
5629    * (non-Javadoc)
5630    *
5631    * @see
5632    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5633    * .event.ActionEvent)
5634    */
5635   @Override
5636   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5637   {
5638     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5639     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5640   }
5641
5642   @Override
5643   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5644   {
5645     showSequenceLogo.setState(true);
5646     viewport.setShowSequenceLogo(true);
5647     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5648     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5649   }
5650
5651   @Override
5652   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5653   {
5654     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5655   }
5656
5657   /*
5658    * (non-Javadoc)
5659    *
5660    * @see
5661    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5662    * .event.ActionEvent)
5663    */
5664   @Override
5665   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5666   {
5667     if (avc.makeGroupsFromSelection())
5668     {
5669       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5670       alignPanel.updateAnnotation();
5671       alignPanel.paintAlignment(true);
5672     }
5673   }
5674
5675   public void clearAlignmentSeqRep()
5676   {
5677     // TODO refactor alignmentseqrep to controller
5678     if (viewport.getAlignment().hasSeqrep())
5679     {
5680       viewport.getAlignment().setSeqrep(null);
5681       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5682       alignPanel.updateAnnotation();
5683       alignPanel.paintAlignment(true);
5684     }
5685   }
5686
5687   @Override
5688   protected void createGroup_actionPerformed(ActionEvent e)
5689   {
5690     if (avc.createGroup())
5691     {
5692       alignPanel.alignmentChanged();
5693     }
5694   }
5695
5696   @Override
5697   protected void unGroup_actionPerformed(ActionEvent e)
5698   {
5699     if (avc.unGroup())
5700     {
5701       alignPanel.alignmentChanged();
5702     }
5703   }
5704
5705   /**
5706    * make the given alignmentPanel the currently selected tab
5707    *
5708    * @param alignmentPanel
5709    */
5710   public void setDisplayedView(AlignmentPanel alignmentPanel)
5711   {
5712     if (!viewport.getSequenceSetId().equals(
5713             alignmentPanel.av.getSequenceSetId()))
5714     {
5715       throw new Error(
5716               MessageManager
5717                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5718     }
5719     if (tabbedPane != null
5720             && tabbedPane.getTabCount() > 0
5721             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5722                     .getSelectedIndex())
5723     {
5724       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5725     }
5726   }
5727
5728   /**
5729    * Action on selection of menu options to Show or Hide annotations.
5730    *
5731    * @param visible
5732    * @param forSequences
5733    *          update sequence-related annotations
5734    * @param forAlignment
5735    *          update non-sequence-related annotations
5736    */
5737   @Override
5738   protected void setAnnotationsVisibility(boolean visible,
5739           boolean forSequences, boolean forAlignment)
5740   {
5741     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5742             .getAlignmentAnnotation();
5743     if (anns == null)
5744     {
5745       return;
5746     }
5747     for (AlignmentAnnotation aa : anns)
5748     {
5749       /*
5750        * don't display non-positional annotations on an alignment
5751        */
5752       if (aa.annotations == null)
5753       {
5754         continue;
5755       }
5756       boolean apply = (aa.sequenceRef == null && forAlignment)
5757               || (aa.sequenceRef != null && forSequences);
5758       if (apply)
5759       {
5760         aa.visible = visible;
5761       }
5762     }
5763     alignPanel.validateAnnotationDimensions(true);
5764     alignPanel.alignmentChanged();
5765   }
5766
5767   /**
5768    * Store selected annotation sort order for the view and repaint.
5769    */
5770   @Override
5771   protected void sortAnnotations_actionPerformed()
5772   {
5773     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5774     this.alignPanel.av
5775             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5776     alignPanel.paintAlignment(true);
5777   }
5778
5779   /**
5780    *
5781    * @return alignment panels in this alignment frame
5782    */
5783   public List<? extends AlignmentViewPanel> getAlignPanels()
5784   {
5785     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5786   }
5787
5788   /**
5789    * Open a new alignment window, with the cDNA associated with this (protein)
5790    * alignment, aligned as is the protein.
5791    */
5792   protected void viewAsCdna_actionPerformed()
5793   {
5794     // TODO no longer a menu action - refactor as required
5795     final AlignmentI alignment = getViewport().getAlignment();
5796     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5797     if (mappings == null)
5798     {
5799       return;
5800     }
5801     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5802     for (SequenceI aaSeq : alignment.getSequences())
5803     {
5804       for (AlignedCodonFrame acf : mappings)
5805       {
5806         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5807         if (dnaSeq != null)
5808         {
5809           /*
5810            * There is a cDNA mapping for this protein sequence - add to new
5811            * alignment. It will share the same dataset sequence as other mapped
5812            * cDNA (no new mappings need to be created).
5813            */
5814           final Sequence newSeq = new Sequence(dnaSeq);
5815           newSeq.setDatasetSequence(dnaSeq);
5816           cdnaSeqs.add(newSeq);
5817         }
5818       }
5819     }
5820     if (cdnaSeqs.size() == 0)
5821     {
5822       // show a warning dialog no mapped cDNA
5823       return;
5824     }
5825     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5826             .size()]));
5827     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5828             AlignFrame.DEFAULT_HEIGHT);
5829     cdna.alignAs(alignment);
5830     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5831             + this.title;
5832     Desktop.addInternalFrame(alignFrame, newtitle,
5833             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5834   }
5835
5836   /**
5837    * Set visibility of dna/protein complement view (available when shown in a
5838    * split frame).
5839    *
5840    * @param show
5841    */
5842   @Override
5843   protected void showComplement_actionPerformed(boolean show)
5844   {
5845     SplitContainerI sf = getSplitViewContainer();
5846     if (sf != null)
5847     {
5848       sf.setComplementVisible(this, show);
5849     }
5850   }
5851
5852   /**
5853    * Generate the reverse (optionally complemented) of the selected sequences,
5854    * and add them to the alignment
5855    */
5856   @Override
5857   protected void showReverse_actionPerformed(boolean complement)
5858   {
5859     AlignmentI al = null;
5860     try
5861     {
5862       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5863       al = dna.reverseCdna(complement);
5864       viewport.addAlignment(al, "");
5865       addHistoryItem(new EditCommand(
5866               MessageManager.getString("label.add_sequences"),
5867               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5868               viewport.getAlignment()));
5869     } catch (Exception ex)
5870     {
5871       System.err.println(ex.getMessage());
5872       return;
5873     }
5874   }
5875
5876   /**
5877    * Try to run a script in the Groovy console, having first ensured that this
5878    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5879    * be targeted at this alignment.
5880    */
5881   @Override
5882   protected void runGroovy_actionPerformed()
5883   {
5884     Jalview.setCurrentAlignFrame(this);
5885     groovy.ui.Console console = Desktop.getGroovyConsole();
5886     if (console != null)
5887     {
5888       try
5889       {
5890         console.runScript();
5891       } catch (Exception ex)
5892       {
5893         System.err.println((ex.toString()));
5894         JOptionPane
5895                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5896                         .getString("label.couldnt_run_groovy_script"),
5897                         MessageManager
5898                                 .getString("label.groovy_support_failed"),
5899                         JOptionPane.ERROR_MESSAGE);
5900       }
5901     }
5902     else
5903     {
5904       System.err.println("Can't run Groovy script as console not found");
5905     }
5906   }
5907
5908   /**
5909    * Hides columns containing (or not containing) a specified feature, provided
5910    * that would not leave all columns hidden
5911    *
5912    * @param featureType
5913    * @param columnsContaining
5914    * @return
5915    */
5916   public boolean hideFeatureColumns(String featureType,
5917           boolean columnsContaining)
5918   {
5919     boolean notForHiding = avc.markColumnsContainingFeatures(
5920             columnsContaining, false, false, featureType);
5921     if (notForHiding)
5922     {
5923       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5924               false, featureType))
5925       {
5926         getViewport().hideSelectedColumns();
5927         return true;
5928       }
5929     }
5930     return false;
5931   }
5932 }
5933
5934 class PrintThread extends Thread
5935 {
5936   AlignmentPanel ap;
5937
5938   public PrintThread(AlignmentPanel ap)
5939   {
5940     this.ap = ap;
5941   }
5942
5943   static PageFormat pf;
5944
5945   @Override
5946   public void run()
5947   {
5948     PrinterJob printJob = PrinterJob.getPrinterJob();
5949
5950     if (pf != null)
5951     {
5952       printJob.setPrintable(ap, pf);
5953     }
5954     else
5955     {
5956       printJob.setPrintable(ap);
5957     }
5958
5959     if (printJob.printDialog())
5960     {
5961       try
5962       {
5963         printJob.print();
5964       } catch (Exception PrintException)
5965       {
5966         PrintException.printStackTrace();
5967       }
5968     }
5969   }
5970 }