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.ColourMenuHelper.ColourChangeListener;
  63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  64 import jalview.io.AlignmentProperties;
  65 import jalview.io.AnnotationFile;
  66 import jalview.io.BioJsHTMLOutput;
  67 import jalview.io.DataSourceType;
  68 import jalview.io.FileFormat;
  69 import jalview.io.FileFormatI;
  70 import jalview.io.FileLoader;
  71 import jalview.io.FormatAdapter;
  72 import jalview.io.HtmlSvgOutput;
  73 import jalview.io.IdentifyFile;
  74 import jalview.io.JPredFile;
  75 import jalview.io.JalviewFileChooser;
  76 import jalview.io.JalviewFileView;
  77 import jalview.io.JnetAnnotationMaker;
  78 import jalview.io.NewickFile;
  79 import jalview.io.TCoffeeScoreFile;
  80 import jalview.jbgui.GAlignFrame;
  81 import jalview.schemes.ColourSchemeI;
  82 import jalview.schemes.ColourSchemes;
  83 import jalview.schemes.ResidueColourScheme;
  84 import jalview.schemes.ResidueProperties;
  85 import jalview.schemes.TCoffeeColourScheme;
  86 import jalview.util.MessageManager;
  87 import jalview.viewmodel.AlignmentViewport;
  88 import jalview.ws.DBRefFetcher;
  89 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  90 import jalview.ws.jws1.Discoverer;
  91 import jalview.ws.jws2.Jws2Discoverer;
  92 import jalview.ws.jws2.jabaws2.Jws2Instance;
  93 import jalview.ws.seqfetcher.DbSourceProxy;
  94
  95 import java.awt.BorderLayout;
  96 import java.awt.Component;
  97 import java.awt.Rectangle;
  98 import java.awt.Toolkit;
  99 import java.awt.datatransfer.Clipboard;
 100 import java.awt.datatransfer.DataFlavor;
 101 import java.awt.datatransfer.StringSelection;
 102 import java.awt.datatransfer.Transferable;
 103 import java.awt.dnd.DnDConstants;
 104 import java.awt.dnd.DropTargetDragEvent;
 105 import java.awt.dnd.DropTargetDropEvent;
 106 import java.awt.dnd.DropTargetEvent;
 107 import java.awt.dnd.DropTargetListener;
 108 import java.awt.event.ActionEvent;
 109 import java.awt.event.ActionListener;
 110 import java.awt.event.FocusAdapter;
 111 import java.awt.event.FocusEvent;
 112 import java.awt.event.ItemEvent;
 113 import java.awt.event.ItemListener;
 114 import java.awt.event.KeyAdapter;
 115 import java.awt.event.KeyEvent;
 116 import java.awt.event.MouseEvent;
 117 import java.awt.print.PageFormat;
 118 import java.awt.print.PrinterJob;
 119 import java.beans.PropertyChangeEvent;
 120 import java.io.File;
 121 import java.net.URL;
 122 import java.util.ArrayList;
 123 import java.util.Arrays;
 124 import java.util.Deque;
 125 import java.util.Enumeration;
 126 import java.util.Hashtable;
 127 import java.util.List;
 128 import java.util.Vector;
 129
 130 import javax.swing.JCheckBoxMenuItem;
 131 import javax.swing.JEditorPane;
 132 import javax.swing.JInternalFrame;
 133 import javax.swing.JLayeredPane;
 134 import javax.swing.JMenu;
 135 import javax.swing.JMenuItem;
 136 import javax.swing.JScrollPane;
 137 import javax.swing.SwingUtilities;
 138
 139 /**
 140  * DOCUMENT ME!
 141  *
 142  * @author $author$
 143  * @version $Revision$
 144  */
 145 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 146         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 147 {
 148
 149   public static final int DEFAULT_WIDTH = 700;
 150
 151   public static final int DEFAULT_HEIGHT = 500;
 152
 153   /*
 154    * The currently displayed panel (selected tabbed view if more than one)
 155    */
 156   public AlignmentPanel alignPanel;
 157
 158   AlignViewport viewport;
 159
 160   public AlignViewControllerI avc;
 161
 162   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 163
 164   /**
 165    * Last format used to load or save alignments in this window
 166    */
 167   FileFormatI currentFileFormat = null;
 168
 169   /**
 170    * Current filename for this alignment
 171    */
 172   String fileName = null;
 173
 174   /**
 175    * Creates a new AlignFrame object with specific width and height.
 176    *
 177    * @param al
 178    * @param width
 179    * @param height
 180    */
 181   public AlignFrame(AlignmentI al, int width, int height)
 182   {
 183     this(al, null, width, height);
 184   }
 185
 186   /**
 187    * Creates a new AlignFrame object with specific width, height and
 188    * sequenceSetId
 189    *
 190    * @param al
 191    * @param width
 192    * @param height
 193    * @param sequenceSetId
 194    */
 195   public AlignFrame(AlignmentI al, int width, int height,
 196           String sequenceSetId)
 197   {
 198     this(al, null, width, height, sequenceSetId);
 199   }
 200
 201   /**
 202    * Creates a new AlignFrame object with specific width, height and
 203    * sequenceSetId
 204    *
 205    * @param al
 206    * @param width
 207    * @param height
 208    * @param sequenceSetId
 209    * @param viewId
 210    */
 211   public AlignFrame(AlignmentI al, int width, int height,
 212           String sequenceSetId, String viewId)
 213   {
 214     this(al, null, width, height, sequenceSetId, viewId);
 215   }
 216
 217   /**
 218    * new alignment window with hidden columns
 219    *
 220    * @param al
 221    *          AlignmentI
 222    * @param hiddenColumns
 223    *          ColumnSelection or null
 224    * @param width
 225    *          Width of alignment frame
 226    * @param height
 227    *          height of frame.
 228    */
 229   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 230           int width, int height)
 231   {
 232     this(al, hiddenColumns, width, height, null);
 233   }
 234
 235   /**
 236    * Create alignment frame for al with hiddenColumns, a specific width and
 237    * height, and specific sequenceId
 238    *
 239    * @param al
 240    * @param hiddenColumns
 241    * @param width
 242    * @param height
 243    * @param sequenceSetId
 244    *          (may be null)
 245    */
 246   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 247           int width, int height, String sequenceSetId)
 248   {
 249     this(al, hiddenColumns, width, height, sequenceSetId, null);
 250   }
 251
 252   /**
 253    * Create alignment frame for al with hiddenColumns, a specific width and
 254    * height, and specific sequenceId
 255    *
 256    * @param al
 257    * @param hiddenColumns
 258    * @param width
 259    * @param height
 260    * @param sequenceSetId
 261    *          (may be null)
 262    * @param viewId
 263    *          (may be null)
 264    */
 265   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 266           int width, int height, String sequenceSetId, String viewId)
 267   {
 268     setSize(width, height);
 269
 270     if (al.getDataset() == null)
 271     {
 272       al.setDataset(null);
 273     }
 274
 275     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 276
 277     alignPanel = new AlignmentPanel(this, viewport);
 278
 279     addAlignmentPanel(alignPanel, true);
 280     init();
 281   }
 282
 283   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 284           ColumnSelection hiddenColumns, int width, int height)
 285   {
 286     setSize(width, height);
 287
 288     if (al.getDataset() == null)
 289     {
 290       al.setDataset(null);
 291     }
 292
 293     viewport = new AlignViewport(al, hiddenColumns);
 294
 295     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 296     {
 297       viewport.hideSequence(hiddenSeqs);
 298     }
 299     alignPanel = new AlignmentPanel(this, viewport);
 300     addAlignmentPanel(alignPanel, true);
 301     init();
 302   }
 303
 304   /**
 305    * Make a new AlignFrame from existing alignmentPanels
 306    *
 307    * @param ap
 308    *          AlignmentPanel
 309    * @param av
 310    *          AlignViewport
 311    */
 312   public AlignFrame(AlignmentPanel ap)
 313   {
 314     viewport = ap.av;
 315     alignPanel = ap;
 316     addAlignmentPanel(ap, false);
 317     init();
 318   }
 319
 320   /**
 321    * initalise the alignframe from the underlying viewport data and the
 322    * configurations
 323    */
 324   void init()
 325   {
 326     if (!Jalview.isHeadlessMode())
 327     {
 328       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 329     }
 330
 331     avc = new jalview.controller.AlignViewController(this, viewport,
 332             alignPanel);
 333     if (viewport.getAlignmentConservationAnnotation() == null)
 334     {
 335       // BLOSUM62Colour.setEnabled(false);
 336       conservationMenuItem.setEnabled(false);
 337       modifyConservation.setEnabled(false);
 338       // PIDColour.setEnabled(false);
 339       // abovePIDThreshold.setEnabled(false);
 340       // modifyPID.setEnabled(false);
 341     }
 342
 343     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 344             "No sort");
 345
 346     if (sortby.equals("Id"))
 347     {
 348       sortIDMenuItem_actionPerformed(null);
 349     }
 350     else if (sortby.equals("Pairwise Identity"))
 351     {
 352       sortPairwiseMenuItem_actionPerformed(null);
 353     }
 354
 355     this.alignPanel.av
 356             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 357
 358     setMenusFromViewport(viewport);
 359     buildSortByAnnotationScoresMenu();
 360     buildTreeMenu();
 361     buildColourMenu();
 362
 363     if (Desktop.desktop != null)
 364     {
 365       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 366       addServiceListeners();
 367       setGUINucleotide();
 368     }
 369
 370     if (viewport.getWrapAlignment())
 371     {
 372       wrapMenuItem_actionPerformed(null);
 373     }
 374
 375     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 376     {
 377       this.overviewMenuItem_actionPerformed(null);
 378     }
 379
 380     addKeyListener();
 381
 382     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 383     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 384     final String menuLabel = MessageManager
 385             .getString("label.copy_format_from");
 386     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 387             new ViewSetProvider()
 388             {
 389
 390               @Override
 391               public AlignmentPanel[] getAllAlignmentPanels()
 392               {
 393                 origview.clear();
 394                 origview.add(alignPanel);
 395                 // make an array of all alignment panels except for this one
 396                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 397                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 398                 aps.remove(AlignFrame.this.alignPanel);
 399                 return aps.toArray(new AlignmentPanel[aps.size()]);
 400               }
 401             }, selviews, new ItemListener()
 402             {
 403
 404               @Override
 405               public void itemStateChanged(ItemEvent e)
 406               {
 407                 if (origview.size() > 0)
 408                 {
 409                   final AlignmentPanel ap = origview.get(0);
 410
 411                   /*
 412                    * Copy the ViewStyle of the selected panel to 'this one'.
 413                    * Don't change value of 'scaleProteinAsCdna' unless copying
 414                    * from a SplitFrame.
 415                    */
 416                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 417                           .getViewStyle();
 418                   boolean fromSplitFrame = selviews.get(0)
 419                           .getAlignViewport().getCodingComplement() != null;
 420                   if (!fromSplitFrame)
 421                   {
 422                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 423                             .getViewStyle().isScaleProteinAsCdna());
 424                   }
 425                   ap.getAlignViewport().setViewStyle(vs);
 426
 427                   /*
 428                    * Also rescale ViewStyle of SplitFrame complement if there is
 429                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 430                    * the whole ViewStyle (allow cDNA protein to have different
 431                    * fonts)
 432                    */
 433                   AlignViewportI complement = ap.getAlignViewport()
 434                           .getCodingComplement();
 435                   if (complement != null && vs.isScaleProteinAsCdna())
 436                   {
 437                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 438                     ((SplitFrame) af.getSplitViewContainer())
 439                             .adjustLayout();
 440                     af.setMenusForViewport();
 441                   }
 442
 443                   ap.updateLayout();
 444                   ap.setSelected(true);
 445                   ap.alignFrame.setMenusForViewport();
 446
 447                 }
 448               }
 449             });
 450     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 451             .indexOf("devel") > -1
 452             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 453                     .indexOf("test") > -1)
 454     {
 455       formatMenu.add(vsel);
 456     }
 457     addFocusListener(new FocusAdapter()
 458     {
 459       @Override
 460       public void focusGained(FocusEvent e)
 461       {
 462         Jalview.setCurrentAlignFrame(AlignFrame.this);
 463       }
 464     });
 465
 466   }
 467
 468   /**
 469    * Change the filename and format for the alignment, and enable the 'reload'
 470    * button functionality.
 471    *
 472    * @param file
 473    *          valid filename
 474    * @param format
 475    *          format of file
 476    */
 477   public void setFileName(String file, FileFormatI format)
 478   {
 479     fileName = file;
 480     setFileFormat(format);
 481     reload.setEnabled(true);
 482   }
 483
 484   /**
 485    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 486    * events
 487    */
 488   void addKeyListener()
 489   {
 490     addKeyListener(new KeyAdapter()
 491     {
 492       @Override
 493       public void keyPressed(KeyEvent evt)
 494       {
 495         if (viewport.cursorMode
 496                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 497                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 498                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 499                 && Character.isDigit(evt.getKeyChar()))
 500         {
 501           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 502         }
 503
 504         switch (evt.getKeyCode())
 505         {
 506
 507         case 27: // escape key
 508           deselectAllSequenceMenuItem_actionPerformed(null);
 509
 510           break;
 511
 512         case KeyEvent.VK_DOWN:
 513           if (evt.isAltDown() || !viewport.cursorMode)
 514           {
 515             moveSelectedSequences(false);
 516           }
 517           if (viewport.cursorMode)
 518           {
 519             alignPanel.getSeqPanel().moveCursor(0, 1);
 520           }
 521           break;
 522
 523         case KeyEvent.VK_UP:
 524           if (evt.isAltDown() || !viewport.cursorMode)
 525           {
 526             moveSelectedSequences(true);
 527           }
 528           if (viewport.cursorMode)
 529           {
 530             alignPanel.getSeqPanel().moveCursor(0, -1);
 531           }
 532
 533           break;
 534
 535         case KeyEvent.VK_LEFT:
 536           if (evt.isAltDown() || !viewport.cursorMode)
 537           {
 538             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 539           }
 540           else
 541           {
 542             alignPanel.getSeqPanel().moveCursor(-1, 0);
 543           }
 544
 545           break;
 546
 547         case KeyEvent.VK_RIGHT:
 548           if (evt.isAltDown() || !viewport.cursorMode)
 549           {
 550             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 551           }
 552           else
 553           {
 554             alignPanel.getSeqPanel().moveCursor(1, 0);
 555           }
 556           break;
 557
 558         case KeyEvent.VK_SPACE:
 559           if (viewport.cursorMode)
 560           {
 561             alignPanel.getSeqPanel().insertGapAtCursor(
 562                     evt.isControlDown() || evt.isShiftDown()
 563                             || evt.isAltDown());
 564           }
 565           break;
 566
 567         // case KeyEvent.VK_A:
 568         // if (viewport.cursorMode)
 569         // {
 570         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 571         // //System.out.println("A");
 572         // }
 573         // break;
 574         /*
 575          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 576          * System.out.println("closing bracket"); } break;
 577          */
 578         case KeyEvent.VK_DELETE:
 579         case KeyEvent.VK_BACK_SPACE:
 580           if (!viewport.cursorMode)
 581           {
 582             cut_actionPerformed(null);
 583           }
 584           else
 585           {
 586             alignPanel.getSeqPanel().deleteGapAtCursor(
 587                     evt.isControlDown() || evt.isShiftDown()
 588                             || evt.isAltDown());
 589           }
 590
 591           break;
 592
 593         case KeyEvent.VK_S:
 594           if (viewport.cursorMode)
 595           {
 596             alignPanel.getSeqPanel().setCursorRow();
 597           }
 598           break;
 599         case KeyEvent.VK_C:
 600           if (viewport.cursorMode && !evt.isControlDown())
 601           {
 602             alignPanel.getSeqPanel().setCursorColumn();
 603           }
 604           break;
 605         case KeyEvent.VK_P:
 606           if (viewport.cursorMode)
 607           {
 608             alignPanel.getSeqPanel().setCursorPosition();
 609           }
 610           break;
 611
 612         case KeyEvent.VK_ENTER:
 613         case KeyEvent.VK_COMMA:
 614           if (viewport.cursorMode)
 615           {
 616             alignPanel.getSeqPanel().setCursorRowAndColumn();
 617           }
 618           break;
 619
 620         case KeyEvent.VK_Q:
 621           if (viewport.cursorMode)
 622           {
 623             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 624           }
 625           break;
 626         case KeyEvent.VK_M:
 627           if (viewport.cursorMode)
 628           {
 629             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 630           }
 631           break;
 632
 633         case KeyEvent.VK_F2:
 634           viewport.cursorMode = !viewport.cursorMode;
 635           statusBar.setText(MessageManager.formatMessage(
 636                   "label.keyboard_editing_mode",
 637                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 641             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 642           }
 643           alignPanel.getSeqPanel().seqCanvas.repaint();
 644           break;
 645
 646         case KeyEvent.VK_F1:
 647           try
 648           {
 649             Help.showHelpWindow();
 650           } catch (Exception ex)
 651           {
 652             ex.printStackTrace();
 653           }
 654           break;
 655         case KeyEvent.VK_H:
 656         {
 657           boolean toggleSeqs = !evt.isControlDown();
 658           boolean toggleCols = !evt.isShiftDown();
 659           toggleHiddenRegions(toggleSeqs, toggleCols);
 660           break;
 661         }
 662         case KeyEvent.VK_B:
 663         {
 664           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 665           boolean modifyExisting = true; // always modify, don't clear
 666                                          // evt.isShiftDown();
 667           boolean invertHighlighted = evt.isAltDown();
 668           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 669                   toggleSel);
 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   public void setGUINucleotide()
 837   {
 838     AlignmentI al = getViewport().getAlignment();
 839     boolean nucleotide = al.isNucleotide();
 840
 841     showTranslation.setVisible(nucleotide);
 842     showReverse.setVisible(nucleotide);
 843     showReverseComplement.setVisible(nucleotide);
 844     conservationMenuItem.setEnabled(!nucleotide);
 845     modifyConservation.setEnabled(!nucleotide);
 846     showGroupConservation.setEnabled(!nucleotide);
 847
 848     showComplementMenuItem.setText(nucleotide ? MessageManager
 849             .getString("label.protein") : MessageManager
 850             .getString("label.nucleotide"));
 851   }
 852
 853   /**
 854    * set up menus for the current viewport. This may be called after any
 855    * operation that affects the data in the current view (selection changed,
 856    * etc) to update the menus to reflect the new state.
 857    */
 858   @Override
 859   public void setMenusForViewport()
 860   {
 861     setMenusFromViewport(viewport);
 862   }
 863
 864   /**
 865    * Need to call this method when tabs are selected for multiple views, or when
 866    * loading from Jalview2XML.java
 867    *
 868    * @param av
 869    *          AlignViewport
 870    */
 871   void setMenusFromViewport(AlignViewport av)
 872   {
 873     padGapsMenuitem.setSelected(av.isPadGaps());
 874     colourTextMenuItem.setSelected(av.isShowColourText());
 875     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 876     conservationMenuItem.setSelected(av.getConservationSelected());
 877     seqLimits.setSelected(av.getShowJVSuffix());
 878     idRightAlign.setSelected(av.isRightAlignIds());
 879     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 880     renderGapsMenuItem.setSelected(av.isRenderGaps());
 881     wrapMenuItem.setSelected(av.getWrapAlignment());
 882     scaleAbove.setVisible(av.getWrapAlignment());
 883     scaleLeft.setVisible(av.getWrapAlignment());
 884     scaleRight.setVisible(av.getWrapAlignment());
 885     annotationPanelMenuItem.setState(av.isShowAnnotation());
 886     /*
 887      * Show/hide annotations only enabled if annotation panel is shown
 888      */
 889     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 890     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 891     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 892     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 893     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 894     viewTextMenuItem.setSelected(av.getShowText());
 895     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 896     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 897     showGroupConservation.setSelected(av.isShowGroupConservation());
 898     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 899     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 900     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 901
 902     ColourMenuHelper.setColourSelected(colourMenu,
 903             av.getGlobalColourScheme());
 904
 905     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 906     hiddenMarkers.setState(av.getShowHiddenMarkers());
 907     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 908     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 909     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 910     autoCalculate.setSelected(av.autoCalculateConsensus);
 911     sortByTree.setSelected(av.sortByTree);
 912     listenToViewSelections.setSelected(av.followSelection);
 913
 914     showProducts.setEnabled(canShowProducts());
 915     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 916
 917     updateEditMenuBar();
 918   }
 919
 920   /**
 921    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 922    *
 923    * @param b
 924    */
 925   public void setGroovyEnabled(boolean b)
 926   {
 927     runGroovy.setEnabled(b);
 928   }
 929
 930   private IProgressIndicator progressBar;
 931
 932   /*
 933    * (non-Javadoc)
 934    *
 935    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 936    */
 937   @Override
 938   public void setProgressBar(String message, long id)
 939   {
 940     progressBar.setProgressBar(message, id);
 941   }
 942
 943   @Override
 944   public void registerHandler(final long id,
 945           final IProgressIndicatorHandler handler)
 946   {
 947     progressBar.registerHandler(id, handler);
 948   }
 949
 950   /**
 951    *
 952    * @return true if any progress bars are still active
 953    */
 954   @Override
 955   public boolean operationInProgress()
 956   {
 957     return progressBar.operationInProgress();
 958   }
 959
 960   @Override
 961   public void setStatus(String text)
 962   {
 963     statusBar.setText(text);
 964   }
 965
 966   /*
 967    * Added so Castor Mapping file can obtain Jalview Version
 968    */
 969   public String getVersion()
 970   {
 971     return jalview.bin.Cache.getProperty("VERSION");
 972   }
 973
 974   public FeatureRenderer getFeatureRenderer()
 975   {
 976     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 977   }
 978
 979   @Override
 980   public void fetchSequence_actionPerformed(ActionEvent e)
 981   {
 982     new jalview.gui.SequenceFetcher(this);
 983   }
 984
 985   @Override
 986   public void addFromFile_actionPerformed(ActionEvent e)
 987   {
 988     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 989   }
 990
 991   @Override
 992   public void reload_actionPerformed(ActionEvent e)
 993   {
 994     if (fileName != null)
 995     {
 996       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 997       // originating file's format
 998       // TODO: work out how to recover feature settings for correct view(s) when
 999       // file is reloaded.
1000       if (FileFormat.Jalview.equals(currentFileFormat))
1001       {
1002         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1003         for (int i = 0; i < frames.length; i++)
1004         {
1005           if (frames[i] instanceof AlignFrame && frames[i] != this
1006                   && ((AlignFrame) frames[i]).fileName != null
1007                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1008           {
1009             try
1010             {
1011               frames[i].setSelected(true);
1012               Desktop.instance.closeAssociatedWindows();
1013             } catch (java.beans.PropertyVetoException ex)
1014             {
1015             }
1016           }
1017
1018         }
1019         Desktop.instance.closeAssociatedWindows();
1020
1021         FileLoader loader = new FileLoader();
1022         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1023                 : DataSourceType.FILE;
1024         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1025       }
1026       else
1027       {
1028         Rectangle bounds = this.getBounds();
1029
1030         FileLoader loader = new FileLoader();
1031         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1032                 : DataSourceType.FILE;
1033         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1034                 protocol, currentFileFormat);
1035
1036         newframe.setBounds(bounds);
1037         if (featureSettings != null && featureSettings.isShowing())
1038         {
1039           final Rectangle fspos = featureSettings.frame.getBounds();
1040           // TODO: need a 'show feature settings' function that takes bounds -
1041           // need to refactor Desktop.addFrame
1042           newframe.featureSettings_actionPerformed(null);
1043           final FeatureSettings nfs = newframe.featureSettings;
1044           SwingUtilities.invokeLater(new Runnable()
1045           {
1046             @Override
1047             public void run()
1048             {
1049               nfs.frame.setBounds(fspos);
1050             }
1051           });
1052           this.featureSettings.close();
1053           this.featureSettings = null;
1054         }
1055         this.closeMenuItem_actionPerformed(true);
1056       }
1057     }
1058   }
1059
1060   @Override
1061   public void addFromText_actionPerformed(ActionEvent e)
1062   {
1063     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1064             .getAlignPanel());
1065   }
1066
1067   @Override
1068   public void addFromURL_actionPerformed(ActionEvent e)
1069   {
1070     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1071   }
1072
1073   @Override
1074   public void save_actionPerformed(ActionEvent e)
1075   {
1076     if (fileName == null || (currentFileFormat == null)
1077             || fileName.startsWith("http"))
1078     {
1079       saveAs_actionPerformed(null);
1080     }
1081     else
1082     {
1083       saveAlignment(fileName, currentFileFormat);
1084     }
1085   }
1086
1087   /**
1088    * DOCUMENT ME!
1089    *
1090    * @param e
1091    *          DOCUMENT ME!
1092    */
1093   @Override
1094   public void saveAs_actionPerformed(ActionEvent e)
1095   {
1096     String format = currentFileFormat == null ? null : currentFileFormat
1097             .toString();
1098     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1099             Cache.getProperty("LAST_DIRECTORY"), format);
1100
1101     chooser.setFileView(new JalviewFileView());
1102     chooser.setDialogTitle(MessageManager
1103             .getString("label.save_alignment_to_file"));
1104     chooser.setToolTipText(MessageManager.getString("action.save"));
1105
1106     int value = chooser.showSaveDialog(this);
1107
1108     if (value == JalviewFileChooser.APPROVE_OPTION)
1109     {
1110       currentFileFormat = chooser.getSelectedFormat();
1111       while (currentFileFormat == null)
1112       {
1113         JvOptionPane
1114                 .showInternalMessageDialog(
1115                         Desktop.desktop,
1116                         MessageManager
1117                                 .getString("label.select_file_format_before_saving"),
1118                         MessageManager
1119                                 .getString("label.file_format_not_specified"),
1120                         JvOptionPane.WARNING_MESSAGE);
1121         currentFileFormat = chooser.getSelectedFormat();
1122         value = chooser.showSaveDialog(this);
1123         if (value != JalviewFileChooser.APPROVE_OPTION)
1124         {
1125           return;
1126         }
1127       }
1128
1129       fileName = chooser.getSelectedFile().getPath();
1130
1131       Cache.setProperty("DEFAULT_FILE_FORMAT",
1132               currentFileFormat.toString());
1133
1134       Cache.setProperty("LAST_DIRECTORY", fileName);
1135       saveAlignment(fileName, currentFileFormat);
1136     }
1137   }
1138
1139   public boolean saveAlignment(String file, FileFormatI format)
1140   {
1141     boolean success = true;
1142
1143     if (FileFormat.Jalview.equals(format))
1144     {
1145       String shortName = title;
1146
1147       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1148       {
1149         shortName = shortName.substring(shortName
1150                 .lastIndexOf(java.io.File.separatorChar) + 1);
1151       }
1152
1153       success = new Jalview2XML().saveAlignment(this, file, shortName);
1154
1155       statusBar.setText(MessageManager.formatMessage(
1156               "label.successfully_saved_to_file_in_format", new Object[] {
1157                   fileName, format }));
1158
1159     }
1160     else
1161     {
1162       // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1163       // {
1164       // warningMessage("Cannot save file " + fileName + " using format "
1165       // + format, "Alignment output format not supported");
1166       // if (!Jalview.isHeadlessMode())
1167       // {
1168       // saveAs_actionPerformed(null);
1169       // }
1170       // return false;
1171       // }
1172
1173       AlignmentExportData exportData = getAlignmentForExport(format,
1174               viewport, null);
1175       if (exportData.getSettings().isCancelled())
1176       {
1177         return false;
1178       }
1179       FormatAdapter f = new FormatAdapter(alignPanel,
1180               exportData.getSettings());
1181       String output = f.formatSequences(
1182               format,
1183               exportData.getAlignment(), // class cast exceptions will
1184               // occur in the distant future
1185               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1186               f.getCacheSuffixDefault(format),
1187               viewport.getColumnSelection());
1188
1189       if (output == null)
1190       {
1191         success = false;
1192       }
1193       else
1194       {
1195         try
1196         {
1197           java.io.PrintWriter out = new java.io.PrintWriter(
1198                   new java.io.FileWriter(file));
1199
1200           out.print(output);
1201           out.close();
1202           this.setTitle(file);
1203           statusBar.setText(MessageManager.formatMessage(
1204                   "label.successfully_saved_to_file_in_format",
1205                   new Object[] { fileName, format }));
1206         } catch (Exception ex)
1207         {
1208           success = false;
1209           ex.printStackTrace();
1210         }
1211       }
1212     }
1213
1214     if (!success)
1215     {
1216       JvOptionPane.showInternalMessageDialog(this, MessageManager
1217               .formatMessage("label.couldnt_save_file",
1218                       new Object[] { fileName }), MessageManager
1219               .getString("label.error_saving_file"),
1220               JvOptionPane.WARNING_MESSAGE);
1221     }
1222
1223     return success;
1224   }
1225
1226   private void warningMessage(String warning, String title)
1227   {
1228     if (new jalview.util.Platform().isHeadless())
1229     {
1230       System.err.println("Warning: " + title + "\nWarning: " + warning);
1231
1232     }
1233     else
1234     {
1235       JvOptionPane.showInternalMessageDialog(this, warning, title,
1236               JvOptionPane.WARNING_MESSAGE);
1237     }
1238     return;
1239   }
1240
1241   /**
1242    * DOCUMENT ME!
1243    *
1244    * @param e
1245    *          DOCUMENT ME!
1246    */
1247   @Override
1248   protected void outputText_actionPerformed(ActionEvent e)
1249   {
1250
1251     FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1252     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1253             viewport, null);
1254     if (exportData.getSettings().isCancelled())
1255     {
1256       return;
1257     }
1258     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1259     cap.setForInput(null);
1260     try
1261     {
1262       FileFormatI format = fileFormat;
1263       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1264               .formatSequences(format,
1265                       exportData.getAlignment(),
1266                       exportData.getOmitHidden(),
1267                       exportData.getStartEndPostions(),
1268                       viewport.getColumnSelection()));
1269       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1270               "label.alignment_output_command",
1271               new Object[] { e.getActionCommand() }), 600, 500);
1272     } catch (OutOfMemoryError oom)
1273     {
1274       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1275       cap.dispose();
1276     }
1277
1278   }
1279
1280   public static AlignmentExportData getAlignmentForExport(
1281           FileFormatI format, AlignViewportI viewport,
1282           AlignExportSettingI exportSettings)
1283   {
1284     AlignmentI alignmentToExport = null;
1285     AlignExportSettingI settings = exportSettings;
1286     String[] omitHidden = null;
1287
1288     HiddenSequences hiddenSeqs = viewport.getAlignment()
1289             .getHiddenSequences();
1290
1291     alignmentToExport = viewport.getAlignment();
1292
1293     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1294     if (settings == null)
1295     {
1296       settings = new AlignExportSettings(hasHiddenSeqs,
1297               viewport.hasHiddenColumns(), format);
1298     }
1299     // settings.isExportAnnotations();
1300
1301     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1302     {
1303       omitHidden = viewport.getViewAsString(false,
1304               settings.isExportHiddenSequences());
1305     }
1306
1307     int[] alignmentStartEnd = new int[2];
1308     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1309     {
1310       alignmentToExport = hiddenSeqs.getFullAlignment();
1311     }
1312     else
1313     {
1314       alignmentToExport = viewport.getAlignment();
1315     }
1316     alignmentStartEnd = alignmentToExport
1317             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1318                     .getHiddenColumns());
1319     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1320             omitHidden, alignmentStartEnd, settings);
1321     return ed;
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    *
1327    * @param e
1328    *          DOCUMENT ME!
1329    */
1330   @Override
1331   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1332   {
1333     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1334     htmlSVG.exportHTML(null);
1335   }
1336
1337   @Override
1338   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1339   {
1340     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1341     bjs.exportHTML(null);
1342   }
1343
1344   public void createImageMap(File file, String image)
1345   {
1346     alignPanel.makePNGImageMap(file, image);
1347   }
1348
1349   /**
1350    * DOCUMENT ME!
1351    *
1352    * @param e
1353    *          DOCUMENT ME!
1354    */
1355   @Override
1356   public void createPNG(File f)
1357   {
1358     alignPanel.makePNG(f);
1359   }
1360
1361   /**
1362    * DOCUMENT ME!
1363    *
1364    * @param e
1365    *          DOCUMENT ME!
1366    */
1367   @Override
1368   public void createEPS(File f)
1369   {
1370     alignPanel.makeEPS(f);
1371   }
1372
1373   @Override
1374   public void createSVG(File f)
1375   {
1376     alignPanel.makeSVG(f);
1377   }
1378
1379   @Override
1380   public void pageSetup_actionPerformed(ActionEvent e)
1381   {
1382     PrinterJob printJob = PrinterJob.getPrinterJob();
1383     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1384   }
1385
1386   /**
1387    * DOCUMENT ME!
1388    *
1389    * @param e
1390    *          DOCUMENT ME!
1391    */
1392   @Override
1393   public void printMenuItem_actionPerformed(ActionEvent e)
1394   {
1395     // Putting in a thread avoids Swing painting problems
1396     PrintThread thread = new PrintThread(alignPanel);
1397     thread.start();
1398   }
1399
1400   @Override
1401   public void exportFeatures_actionPerformed(ActionEvent e)
1402   {
1403     new AnnotationExporter().exportFeatures(alignPanel);
1404   }
1405
1406   @Override
1407   public void exportAnnotations_actionPerformed(ActionEvent e)
1408   {
1409     new AnnotationExporter().exportAnnotations(alignPanel);
1410   }
1411
1412   @Override
1413   public void associatedData_actionPerformed(ActionEvent e)
1414   {
1415     // Pick the tree file
1416     JalviewFileChooser chooser = new JalviewFileChooser(
1417             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1418     chooser.setFileView(new JalviewFileView());
1419     chooser.setDialogTitle(MessageManager
1420             .getString("label.load_jalview_annotations"));
1421     chooser.setToolTipText(MessageManager
1422             .getString("label.load_jalview_annotations"));
1423
1424     int value = chooser.showOpenDialog(null);
1425
1426     if (value == JalviewFileChooser.APPROVE_OPTION)
1427     {
1428       String choice = chooser.getSelectedFile().getPath();
1429       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1430       loadJalviewDataFile(choice, null, null, null);
1431     }
1432
1433   }
1434
1435   /**
1436    * Close the current view or all views in the alignment frame. If the frame
1437    * only contains one view then the alignment will be removed from memory.
1438    *
1439    * @param closeAllTabs
1440    */
1441   @Override
1442   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1443   {
1444     if (alignPanels != null && alignPanels.size() < 2)
1445     {
1446       closeAllTabs = true;
1447     }
1448
1449     try
1450     {
1451       if (alignPanels != null)
1452       {
1453         if (closeAllTabs)
1454         {
1455           if (this.isClosed())
1456           {
1457             // really close all the windows - otherwise wait till
1458             // setClosed(true) is called
1459             for (int i = 0; i < alignPanels.size(); i++)
1460             {
1461               AlignmentPanel ap = alignPanels.get(i);
1462               ap.closePanel();
1463             }
1464           }
1465         }
1466         else
1467         {
1468           closeView(alignPanel);
1469         }
1470       }
1471
1472       if (closeAllTabs)
1473       {
1474         /*
1475          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1476          * be called recursively, with the frame now in 'closed' state
1477          */
1478         this.setClosed(true);
1479       }
1480     } catch (Exception ex)
1481     {
1482       ex.printStackTrace();
1483     }
1484   }
1485
1486   /**
1487    * Close the specified panel and close up tabs appropriately.
1488    *
1489    * @param panelToClose
1490    */
1491   public void closeView(AlignmentPanel panelToClose)
1492   {
1493     int index = tabbedPane.getSelectedIndex();
1494     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1495     alignPanels.remove(panelToClose);
1496     panelToClose.closePanel();
1497     panelToClose = null;
1498
1499     tabbedPane.removeTabAt(closedindex);
1500     tabbedPane.validate();
1501
1502     if (index > closedindex || index == tabbedPane.getTabCount())
1503     {
1504       // modify currently selected tab index if necessary.
1505       index--;
1506     }
1507
1508     this.tabSelectionChanged(index);
1509   }
1510
1511   /**
1512    * DOCUMENT ME!
1513    */
1514   void updateEditMenuBar()
1515   {
1516
1517     if (viewport.getHistoryList().size() > 0)
1518     {
1519       undoMenuItem.setEnabled(true);
1520       CommandI command = viewport.getHistoryList().peek();
1521       undoMenuItem.setText(MessageManager.formatMessage(
1522               "label.undo_command",
1523               new Object[] { command.getDescription() }));
1524     }
1525     else
1526     {
1527       undoMenuItem.setEnabled(false);
1528       undoMenuItem.setText(MessageManager.getString("action.undo"));
1529     }
1530
1531     if (viewport.getRedoList().size() > 0)
1532     {
1533       redoMenuItem.setEnabled(true);
1534
1535       CommandI command = viewport.getRedoList().peek();
1536       redoMenuItem.setText(MessageManager.formatMessage(
1537               "label.redo_command",
1538               new Object[] { command.getDescription() }));
1539     }
1540     else
1541     {
1542       redoMenuItem.setEnabled(false);
1543       redoMenuItem.setText(MessageManager.getString("action.redo"));
1544     }
1545   }
1546
1547   @Override
1548   public void addHistoryItem(CommandI command)
1549   {
1550     if (command.getSize() > 0)
1551     {
1552       viewport.addToHistoryList(command);
1553       viewport.clearRedoList();
1554       updateEditMenuBar();
1555       viewport.updateHiddenColumns();
1556       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1557       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1558       // viewport.getColumnSelection()
1559       // .getHiddenColumns().size() > 0);
1560     }
1561   }
1562
1563   /**
1564    *
1565    * @return alignment objects for all views
1566    */
1567   AlignmentI[] getViewAlignments()
1568   {
1569     if (alignPanels != null)
1570     {
1571       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1572       int i = 0;
1573       for (AlignmentPanel ap : alignPanels)
1574       {
1575         als[i++] = ap.av.getAlignment();
1576       }
1577       return als;
1578     }
1579     if (viewport != null)
1580     {
1581       return new AlignmentI[] { viewport.getAlignment() };
1582     }
1583     return null;
1584   }
1585
1586   /**
1587    * DOCUMENT ME!
1588    *
1589    * @param e
1590    *          DOCUMENT ME!
1591    */
1592   @Override
1593   protected void undoMenuItem_actionPerformed(ActionEvent e)
1594   {
1595     if (viewport.getHistoryList().isEmpty())
1596     {
1597       return;
1598     }
1599     CommandI command = viewport.getHistoryList().pop();
1600     viewport.addToRedoList(command);
1601     command.undoCommand(getViewAlignments());
1602
1603     AlignmentViewport originalSource = getOriginatingSource(command);
1604     updateEditMenuBar();
1605
1606     if (originalSource != null)
1607     {
1608       if (originalSource != viewport)
1609       {
1610         Cache.log
1611                 .warn("Implementation worry: mismatch of viewport origin for undo");
1612       }
1613       originalSource.updateHiddenColumns();
1614       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1615       // null
1616       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1617       // viewport.getColumnSelection()
1618       // .getHiddenColumns().size() > 0);
1619       originalSource.firePropertyChange("alignment", null, originalSource
1620               .getAlignment().getSequences());
1621     }
1622   }
1623
1624   /**
1625    * DOCUMENT ME!
1626    *
1627    * @param e
1628    *          DOCUMENT ME!
1629    */
1630   @Override
1631   protected void redoMenuItem_actionPerformed(ActionEvent e)
1632   {
1633     if (viewport.getRedoList().size() < 1)
1634     {
1635       return;
1636     }
1637
1638     CommandI command = viewport.getRedoList().pop();
1639     viewport.addToHistoryList(command);
1640     command.doCommand(getViewAlignments());
1641
1642     AlignmentViewport originalSource = getOriginatingSource(command);
1643     updateEditMenuBar();
1644
1645     if (originalSource != null)
1646     {
1647
1648       if (originalSource != viewport)
1649       {
1650         Cache.log
1651                 .warn("Implementation worry: mismatch of viewport origin for redo");
1652       }
1653       originalSource.updateHiddenColumns();
1654       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655       // null
1656       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657       // viewport.getColumnSelection()
1658       // .getHiddenColumns().size() > 0);
1659       originalSource.firePropertyChange("alignment", null, originalSource
1660               .getAlignment().getSequences());
1661     }
1662   }
1663
1664   AlignmentViewport getOriginatingSource(CommandI command)
1665   {
1666     AlignmentViewport originalSource = null;
1667     // For sequence removal and addition, we need to fire
1668     // the property change event FROM the viewport where the
1669     // original alignment was altered
1670     AlignmentI al = null;
1671     if (command instanceof EditCommand)
1672     {
1673       EditCommand editCommand = (EditCommand) command;
1674       al = editCommand.getAlignment();
1675       List<Component> comps = PaintRefresher.components.get(viewport
1676               .getSequenceSetId());
1677
1678       for (Component comp : comps)
1679       {
1680         if (comp instanceof AlignmentPanel)
1681         {
1682           if (al == ((AlignmentPanel) comp).av.getAlignment())
1683           {
1684             originalSource = ((AlignmentPanel) comp).av;
1685             break;
1686           }
1687         }
1688       }
1689     }
1690
1691     if (originalSource == null)
1692     {
1693       // The original view is closed, we must validate
1694       // the current view against the closed view first
1695       if (al != null)
1696       {
1697         PaintRefresher.validateSequences(al, viewport.getAlignment());
1698       }
1699
1700       originalSource = viewport;
1701     }
1702
1703     return originalSource;
1704   }
1705
1706   /**
1707    * DOCUMENT ME!
1708    *
1709    * @param up
1710    *          DOCUMENT ME!
1711    */
1712   public void moveSelectedSequences(boolean up)
1713   {
1714     SequenceGroup sg = viewport.getSelectionGroup();
1715
1716     if (sg == null)
1717     {
1718       return;
1719     }
1720     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1721             viewport.getHiddenRepSequences(), up);
1722     alignPanel.paintAlignment(true);
1723   }
1724
1725   synchronized void slideSequences(boolean right, int size)
1726   {
1727     List<SequenceI> sg = new ArrayList<SequenceI>();
1728     if (viewport.cursorMode)
1729     {
1730       sg.add(viewport.getAlignment().getSequenceAt(
1731               alignPanel.getSeqPanel().seqCanvas.cursorY));
1732     }
1733     else if (viewport.getSelectionGroup() != null
1734             && viewport.getSelectionGroup().getSize() != viewport
1735                     .getAlignment().getHeight())
1736     {
1737       sg = viewport.getSelectionGroup().getSequences(
1738               viewport.getHiddenRepSequences());
1739     }
1740
1741     if (sg.size() < 1)
1742     {
1743       return;
1744     }
1745
1746     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1747
1748     for (SequenceI seq : viewport.getAlignment().getSequences())
1749     {
1750       if (!sg.contains(seq))
1751       {
1752         invertGroup.add(seq);
1753       }
1754     }
1755
1756     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1757
1758     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1759     for (int i = 0; i < invertGroup.size(); i++)
1760     {
1761       seqs2[i] = invertGroup.get(i);
1762     }
1763
1764     SlideSequencesCommand ssc;
1765     if (right)
1766     {
1767       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1768               size, viewport.getGapCharacter());
1769     }
1770     else
1771     {
1772       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1773               size, viewport.getGapCharacter());
1774     }
1775
1776     int groupAdjustment = 0;
1777     if (ssc.getGapsInsertedBegin() && right)
1778     {
1779       if (viewport.cursorMode)
1780       {
1781         alignPanel.getSeqPanel().moveCursor(size, 0);
1782       }
1783       else
1784       {
1785         groupAdjustment = size;
1786       }
1787     }
1788     else if (!ssc.getGapsInsertedBegin() && !right)
1789     {
1790       if (viewport.cursorMode)
1791       {
1792         alignPanel.getSeqPanel().moveCursor(-size, 0);
1793       }
1794       else
1795       {
1796         groupAdjustment = -size;
1797       }
1798     }
1799
1800     if (groupAdjustment != 0)
1801     {
1802       viewport.getSelectionGroup().setStartRes(
1803               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804       viewport.getSelectionGroup().setEndRes(
1805               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1806     }
1807
1808     /*
1809      * just extend the last slide command if compatible; but not if in
1810      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1811      */
1812     boolean appendHistoryItem = false;
1813     Deque<CommandI> historyList = viewport.getHistoryList();
1814     boolean inSplitFrame = getSplitViewContainer() != null;
1815     if (!inSplitFrame && historyList != null && historyList.size() > 0
1816             && historyList.peek() instanceof SlideSequencesCommand)
1817     {
1818       appendHistoryItem = ssc
1819               .appendSlideCommand((SlideSequencesCommand) historyList
1820                       .peek());
1821     }
1822
1823     if (!appendHistoryItem)
1824     {
1825       addHistoryItem(ssc);
1826     }
1827
1828     repaint();
1829   }
1830
1831   /**
1832    * DOCUMENT ME!
1833    *
1834    * @param e
1835    *          DOCUMENT ME!
1836    */
1837   @Override
1838   protected void copy_actionPerformed(ActionEvent e)
1839   {
1840     System.gc();
1841     if (viewport.getSelectionGroup() == null)
1842     {
1843       return;
1844     }
1845     // TODO: preserve the ordering of displayed alignment annotation in any
1846     // internal paste (particularly sequence associated annotation)
1847     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1848     String[] omitHidden = null;
1849
1850     if (viewport.hasHiddenColumns())
1851     {
1852       omitHidden = viewport.getViewAsString(true);
1853     }
1854
1855     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1856             seqs,
1857             omitHidden, null);
1858
1859     StringSelection ss = new StringSelection(output);
1860
1861     try
1862     {
1863       jalview.gui.Desktop.internalCopy = true;
1864       // Its really worth setting the clipboard contents
1865       // to empty before setting the large StringSelection!!
1866       Toolkit.getDefaultToolkit().getSystemClipboard()
1867               .setContents(new StringSelection(""), null);
1868
1869       Toolkit.getDefaultToolkit().getSystemClipboard()
1870               .setContents(ss, Desktop.instance);
1871     } catch (OutOfMemoryError er)
1872     {
1873       new OOMWarning("copying region", er);
1874       return;
1875     }
1876
1877     ArrayList<int[]> hiddenColumns = null;
1878     if (viewport.hasHiddenColumns())
1879     {
1880       hiddenColumns = new ArrayList<int[]>();
1881       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1882               .getSelectionGroup().getEndRes();
1883       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1884       {
1885         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1886         {
1887           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1888               region[1] - hiddenOffset });
1889         }
1890       }
1891     }
1892
1893     Desktop.jalviewClipboard = new Object[] { seqs,
1894         viewport.getAlignment().getDataset(), hiddenColumns };
1895     statusBar.setText(MessageManager.formatMessage(
1896             "label.copied_sequences_to_clipboard", new Object[] { Integer
1897                     .valueOf(seqs.length).toString() }));
1898   }
1899
1900   /**
1901    * DOCUMENT ME!
1902    *
1903    * @param e
1904    *          DOCUMENT ME!
1905    */
1906   @Override
1907   protected void pasteNew_actionPerformed(ActionEvent e)
1908   {
1909     paste(true);
1910   }
1911
1912   /**
1913    * DOCUMENT ME!
1914    *
1915    * @param e
1916    *          DOCUMENT ME!
1917    */
1918   @Override
1919   protected void pasteThis_actionPerformed(ActionEvent e)
1920   {
1921     paste(false);
1922   }
1923
1924   /**
1925    * Paste contents of Jalview clipboard
1926    *
1927    * @param newAlignment
1928    *          true to paste to a new alignment, otherwise add to this.
1929    */
1930   void paste(boolean newAlignment)
1931   {
1932     boolean externalPaste = true;
1933     try
1934     {
1935       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1936       Transferable contents = c.getContents(this);
1937
1938       if (contents == null)
1939       {
1940         return;
1941       }
1942
1943       String str;
1944       FileFormatI format;
1945       try
1946       {
1947         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1948         if (str.length() < 1)
1949         {
1950           return;
1951         }
1952
1953         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1954
1955       } catch (OutOfMemoryError er)
1956       {
1957         new OOMWarning("Out of memory pasting sequences!!", er);
1958         return;
1959       }
1960
1961       SequenceI[] sequences;
1962       boolean annotationAdded = false;
1963       AlignmentI alignment = null;
1964
1965       if (Desktop.jalviewClipboard != null)
1966       {
1967         // The clipboard was filled from within Jalview, we must use the
1968         // sequences
1969         // And dataset from the copied alignment
1970         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1971         // be doubly sure that we create *new* sequence objects.
1972         sequences = new SequenceI[newseq.length];
1973         for (int i = 0; i < newseq.length; i++)
1974         {
1975           sequences[i] = new Sequence(newseq[i]);
1976         }
1977         alignment = new Alignment(sequences);
1978         externalPaste = false;
1979       }
1980       else
1981       {
1982         // parse the clipboard as an alignment.
1983         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1984                 format);
1985         sequences = alignment.getSequencesArray();
1986       }
1987
1988       int alwidth = 0;
1989       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1990       int fgroup = -1;
1991
1992       if (newAlignment)
1993       {
1994
1995         if (Desktop.jalviewClipboard != null)
1996         {
1997           // dataset is inherited
1998           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1999         }
2000         else
2001         {
2002           // new dataset is constructed
2003           alignment.setDataset(null);
2004         }
2005         alwidth = alignment.getWidth() + 1;
2006       }
2007       else
2008       {
2009         AlignmentI pastedal = alignment; // preserve pasted alignment object
2010         // Add pasted sequences and dataset into existing alignment.
2011         alignment = viewport.getAlignment();
2012         alwidth = alignment.getWidth() + 1;
2013         // decide if we need to import sequences from an existing dataset
2014         boolean importDs = Desktop.jalviewClipboard != null
2015                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2016         // importDs==true instructs us to copy over new dataset sequences from
2017         // an existing alignment
2018         Vector newDs = (importDs) ? new Vector() : null; // used to create
2019         // minimum dataset set
2020
2021         for (int i = 0; i < sequences.length; i++)
2022         {
2023           if (importDs)
2024           {
2025             newDs.addElement(null);
2026           }
2027           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2028           // paste
2029           if (importDs && ds != null)
2030           {
2031             if (!newDs.contains(ds))
2032             {
2033               newDs.setElementAt(ds, i);
2034               ds = new Sequence(ds);
2035               // update with new dataset sequence
2036               sequences[i].setDatasetSequence(ds);
2037             }
2038             else
2039             {
2040               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2041             }
2042           }
2043           else
2044           {
2045             // copy and derive new dataset sequence
2046             sequences[i] = sequences[i].deriveSequence();
2047             alignment.getDataset().addSequence(
2048                     sequences[i].getDatasetSequence());
2049             // TODO: avoid creation of duplicate dataset sequences with a
2050             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2051           }
2052           alignment.addSequence(sequences[i]); // merges dataset
2053         }
2054         if (newDs != null)
2055         {
2056           newDs.clear(); // tidy up
2057         }
2058         if (alignment.getAlignmentAnnotation() != null)
2059         {
2060           for (AlignmentAnnotation alan : alignment
2061                   .getAlignmentAnnotation())
2062           {
2063             if (alan.graphGroup > fgroup)
2064             {
2065               fgroup = alan.graphGroup;
2066             }
2067           }
2068         }
2069         if (pastedal.getAlignmentAnnotation() != null)
2070         {
2071           // Add any annotation attached to alignment.
2072           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2073           for (int i = 0; i < alann.length; i++)
2074           {
2075             annotationAdded = true;
2076             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2077             {
2078               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2079               if (newann.graphGroup > -1)
2080               {
2081                 if (newGraphGroups.size() <= newann.graphGroup
2082                         || newGraphGroups.get(newann.graphGroup) == null)
2083                 {
2084                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2085                   {
2086                     newGraphGroups.add(q, null);
2087                   }
2088                   newGraphGroups.set(newann.graphGroup, new Integer(
2089                           ++fgroup));
2090                 }
2091                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2092                         .intValue();
2093               }
2094
2095               newann.padAnnotation(alwidth);
2096               alignment.addAnnotation(newann);
2097             }
2098           }
2099         }
2100       }
2101       if (!newAlignment)
2102       {
2103         // /////
2104         // ADD HISTORY ITEM
2105         //
2106         addHistoryItem(new EditCommand(
2107                 MessageManager.getString("label.add_sequences"),
2108                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2109       }
2110       // Add any annotations attached to sequences
2111       for (int i = 0; i < sequences.length; i++)
2112       {
2113         if (sequences[i].getAnnotation() != null)
2114         {
2115           AlignmentAnnotation newann;
2116           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2117           {
2118             annotationAdded = true;
2119             newann = sequences[i].getAnnotation()[a];
2120             newann.adjustForAlignment();
2121             newann.padAnnotation(alwidth);
2122             if (newann.graphGroup > -1)
2123             {
2124               if (newann.graphGroup > -1)
2125               {
2126                 if (newGraphGroups.size() <= newann.graphGroup
2127                         || newGraphGroups.get(newann.graphGroup) == null)
2128                 {
2129                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2130                   {
2131                     newGraphGroups.add(q, null);
2132                   }
2133                   newGraphGroups.set(newann.graphGroup, new Integer(
2134                           ++fgroup));
2135                 }
2136                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2137                         .intValue();
2138               }
2139             }
2140             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2141             // was
2142             // duplicated
2143             // earlier
2144             alignment
2145                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2146           }
2147         }
2148       }
2149       if (!newAlignment)
2150       {
2151
2152         // propagate alignment changed.
2153         viewport.setEndSeq(alignment.getHeight());
2154         if (annotationAdded)
2155         {
2156           // Duplicate sequence annotation in all views.
2157           AlignmentI[] alview = this.getViewAlignments();
2158           for (int i = 0; i < sequences.length; i++)
2159           {
2160             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2161             if (sann == null)
2162             {
2163               continue;
2164             }
2165             for (int avnum = 0; avnum < alview.length; avnum++)
2166             {
2167               if (alview[avnum] != alignment)
2168               {
2169                 // duplicate in a view other than the one with input focus
2170                 int avwidth = alview[avnum].getWidth() + 1;
2171                 // this relies on sann being preserved after we
2172                 // modify the sequence's annotation array for each duplication
2173                 for (int a = 0; a < sann.length; a++)
2174                 {
2175                   AlignmentAnnotation newann = new AlignmentAnnotation(
2176                           sann[a]);
2177                   sequences[i].addAlignmentAnnotation(newann);
2178                   newann.padAnnotation(avwidth);
2179                   alview[avnum].addAnnotation(newann); // annotation was
2180                   // duplicated earlier
2181                   // TODO JAL-1145 graphGroups are not updated for sequence
2182                   // annotation added to several views. This may cause
2183                   // strangeness
2184                   alview[avnum].setAnnotationIndex(newann, a);
2185                 }
2186               }
2187             }
2188           }
2189           buildSortByAnnotationScoresMenu();
2190         }
2191         viewport.firePropertyChange("alignment", null,
2192                 alignment.getSequences());
2193         if (alignPanels != null)
2194         {
2195           for (AlignmentPanel ap : alignPanels)
2196           {
2197             ap.validateAnnotationDimensions(false);
2198           }
2199         }
2200         else
2201         {
2202           alignPanel.validateAnnotationDimensions(false);
2203         }
2204
2205       }
2206       else
2207       {
2208         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2209                 DEFAULT_HEIGHT);
2210         String newtitle = new String("Copied sequences");
2211
2212         if (Desktop.jalviewClipboard != null
2213                 && Desktop.jalviewClipboard[2] != null)
2214         {
2215           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2216           for (int[] region : hc)
2217           {
2218             af.viewport.hideColumns(region[0], region[1]);
2219           }
2220         }
2221
2222         // >>>This is a fix for the moment, until a better solution is
2223         // found!!<<<
2224         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2225                 .transferSettings(
2226                         alignPanel.getSeqPanel().seqCanvas
2227                                 .getFeatureRenderer());
2228
2229         // TODO: maintain provenance of an alignment, rather than just make the
2230         // title a concatenation of operations.
2231         if (!externalPaste)
2232         {
2233           if (title.startsWith("Copied sequences"))
2234           {
2235             newtitle = title;
2236           }
2237           else
2238           {
2239             newtitle = newtitle.concat("- from " + title);
2240           }
2241         }
2242         else
2243         {
2244           newtitle = new String("Pasted sequences");
2245         }
2246
2247         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2248                 DEFAULT_HEIGHT);
2249
2250       }
2251
2252     } catch (Exception ex)
2253     {
2254       ex.printStackTrace();
2255       System.out.println("Exception whilst pasting: " + ex);
2256       // could be anything being pasted in here
2257     }
2258
2259   }
2260
2261   @Override
2262   protected void expand_newalign(ActionEvent e)
2263   {
2264     try
2265     {
2266       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2267               .getAlignment(), -1);
2268       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2269               DEFAULT_HEIGHT);
2270       String newtitle = new String("Flanking alignment");
2271
2272       if (Desktop.jalviewClipboard != null
2273               && Desktop.jalviewClipboard[2] != null)
2274       {
2275         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2276         for (int region[] : hc)
2277         {
2278           af.viewport.hideColumns(region[0], region[1]);
2279         }
2280       }
2281
2282       // >>>This is a fix for the moment, until a better solution is
2283       // found!!<<<
2284       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2285               .transferSettings(
2286                       alignPanel.getSeqPanel().seqCanvas
2287                               .getFeatureRenderer());
2288
2289       // TODO: maintain provenance of an alignment, rather than just make the
2290       // title a concatenation of operations.
2291       {
2292         if (title.startsWith("Copied sequences"))
2293         {
2294           newtitle = title;
2295         }
2296         else
2297         {
2298           newtitle = newtitle.concat("- from " + title);
2299         }
2300       }
2301
2302       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2303
2304     } catch (Exception ex)
2305     {
2306       ex.printStackTrace();
2307       System.out.println("Exception whilst pasting: " + ex);
2308       // could be anything being pasted in here
2309     } catch (OutOfMemoryError oom)
2310     {
2311       new OOMWarning("Viewing flanking region of alignment", oom);
2312     }
2313   }
2314
2315   /**
2316    * DOCUMENT ME!
2317    *
2318    * @param e
2319    *          DOCUMENT ME!
2320    */
2321   @Override
2322   protected void cut_actionPerformed(ActionEvent e)
2323   {
2324     copy_actionPerformed(null);
2325     delete_actionPerformed(null);
2326   }
2327
2328   /**
2329    * DOCUMENT ME!
2330    *
2331    * @param e
2332    *          DOCUMENT ME!
2333    */
2334   @Override
2335   protected void delete_actionPerformed(ActionEvent evt)
2336   {
2337
2338     SequenceGroup sg = viewport.getSelectionGroup();
2339     if (sg == null)
2340     {
2341       return;
2342     }
2343
2344     /*
2345      * If the cut affects all sequences, warn, remove highlighted columns
2346      */
2347     if (sg.getSize() == viewport.getAlignment().getHeight())
2348     {
2349       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2350               .getAlignment().getWidth()) ? true : false;
2351       if (isEntireAlignWidth)
2352       {
2353         int confirm = JvOptionPane.showConfirmDialog(this,
2354                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2355                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2356                 JvOptionPane.OK_CANCEL_OPTION);
2357
2358         if (confirm == JvOptionPane.CANCEL_OPTION
2359                 || confirm == JvOptionPane.CLOSED_OPTION)
2360         {
2361           return;
2362         }
2363       }
2364       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2365               sg.getEndRes() + 1);
2366     }
2367     SequenceI[] cut = sg.getSequences()
2368             .toArray(new SequenceI[sg.getSize()]);
2369
2370     addHistoryItem(new EditCommand(
2371             MessageManager.getString("label.cut_sequences"), Action.CUT,
2372             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2373             viewport.getAlignment()));
2374
2375     viewport.setSelectionGroup(null);
2376     viewport.sendSelection();
2377     viewport.getAlignment().deleteGroup(sg);
2378
2379     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2380             .getSequences());
2381     if (viewport.getAlignment().getHeight() < 1)
2382     {
2383       try
2384       {
2385         this.setClosed(true);
2386       } catch (Exception ex)
2387       {
2388       }
2389     }
2390   }
2391
2392   /**
2393    * DOCUMENT ME!
2394    *
2395    * @param e
2396    *          DOCUMENT ME!
2397    */
2398   @Override
2399   protected void deleteGroups_actionPerformed(ActionEvent e)
2400   {
2401     if (avc.deleteGroups())
2402     {
2403       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2404       alignPanel.updateAnnotation();
2405       alignPanel.paintAlignment(true);
2406     }
2407   }
2408
2409   /**
2410    * DOCUMENT ME!
2411    *
2412    * @param e
2413    *          DOCUMENT ME!
2414    */
2415   @Override
2416   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2417   {
2418     SequenceGroup sg = new SequenceGroup();
2419
2420     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2421     {
2422       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2423     }
2424
2425     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2426     viewport.setSelectionGroup(sg);
2427     viewport.sendSelection();
2428     // JAL-2034 - should delegate to
2429     // alignPanel to decide if overview needs
2430     // updating.
2431     alignPanel.paintAlignment(false);
2432     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2433   }
2434
2435   /**
2436    * DOCUMENT ME!
2437    *
2438    * @param e
2439    *          DOCUMENT ME!
2440    */
2441   @Override
2442   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2443   {
2444     if (viewport.cursorMode)
2445     {
2446       alignPanel.getSeqPanel().keyboardNo1 = null;
2447       alignPanel.getSeqPanel().keyboardNo2 = null;
2448     }
2449     viewport.setSelectionGroup(null);
2450     viewport.getColumnSelection().clear();
2451     viewport.setSelectionGroup(null);
2452     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2453     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2454     // JAL-2034 - should delegate to
2455     // alignPanel to decide if overview needs
2456     // updating.
2457     alignPanel.paintAlignment(false);
2458     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2459     viewport.sendSelection();
2460   }
2461
2462   /**
2463    * DOCUMENT ME!
2464    *
2465    * @param e
2466    *          DOCUMENT ME!
2467    */
2468   @Override
2469   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2470   {
2471     SequenceGroup sg = viewport.getSelectionGroup();
2472
2473     if (sg == null)
2474     {
2475       selectAllSequenceMenuItem_actionPerformed(null);
2476
2477       return;
2478     }
2479
2480     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2481     {
2482       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2483     }
2484     // JAL-2034 - should delegate to
2485     // alignPanel to decide if overview needs
2486     // updating.
2487
2488     alignPanel.paintAlignment(true);
2489     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490     viewport.sendSelection();
2491   }
2492
2493   @Override
2494   public void invertColSel_actionPerformed(ActionEvent e)
2495   {
2496     viewport.invertColumnSelection();
2497     alignPanel.paintAlignment(true);
2498     viewport.sendSelection();
2499   }
2500
2501   /**
2502    * DOCUMENT ME!
2503    *
2504    * @param e
2505    *          DOCUMENT ME!
2506    */
2507   @Override
2508   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2509   {
2510     trimAlignment(true);
2511   }
2512
2513   /**
2514    * DOCUMENT ME!
2515    *
2516    * @param e
2517    *          DOCUMENT ME!
2518    */
2519   @Override
2520   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2521   {
2522     trimAlignment(false);
2523   }
2524
2525   void trimAlignment(boolean trimLeft)
2526   {
2527     ColumnSelection colSel = viewport.getColumnSelection();
2528     int column;
2529
2530     if (!colSel.isEmpty())
2531     {
2532       if (trimLeft)
2533       {
2534         column = colSel.getMin();
2535       }
2536       else
2537       {
2538         column = colSel.getMax();
2539       }
2540
2541       SequenceI[] seqs;
2542       if (viewport.getSelectionGroup() != null)
2543       {
2544         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2545                 viewport.getHiddenRepSequences());
2546       }
2547       else
2548       {
2549         seqs = viewport.getAlignment().getSequencesArray();
2550       }
2551
2552       TrimRegionCommand trimRegion;
2553       if (trimLeft)
2554       {
2555         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2556                 column, viewport.getAlignment());
2557         viewport.setStartRes(0);
2558       }
2559       else
2560       {
2561         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2562                 column, viewport.getAlignment());
2563       }
2564
2565       statusBar.setText(MessageManager.formatMessage(
2566               "label.removed_columns",
2567               new String[] { Integer.valueOf(trimRegion.getSize())
2568                       .toString() }));
2569
2570       addHistoryItem(trimRegion);
2571
2572       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2573       {
2574         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2575                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2576         {
2577           viewport.getAlignment().deleteGroup(sg);
2578         }
2579       }
2580
2581       viewport.firePropertyChange("alignment", null, viewport
2582               .getAlignment().getSequences());
2583     }
2584   }
2585
2586   /**
2587    * DOCUMENT ME!
2588    *
2589    * @param e
2590    *          DOCUMENT ME!
2591    */
2592   @Override
2593   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2594   {
2595     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2596
2597     SequenceI[] seqs;
2598     if (viewport.getSelectionGroup() != null)
2599     {
2600       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2601               viewport.getHiddenRepSequences());
2602       start = viewport.getSelectionGroup().getStartRes();
2603       end = viewport.getSelectionGroup().getEndRes();
2604     }
2605     else
2606     {
2607       seqs = viewport.getAlignment().getSequencesArray();
2608     }
2609
2610     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2611             "Remove Gapped Columns", seqs, start, end,
2612             viewport.getAlignment());
2613
2614     addHistoryItem(removeGapCols);
2615
2616     statusBar.setText(MessageManager.formatMessage(
2617             "label.removed_empty_columns",
2618             new Object[] { Integer.valueOf(removeGapCols.getSize())
2619                     .toString() }));
2620
2621     // This is to maintain viewport position on first residue
2622     // of first sequence
2623     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2624     int startRes = seq.findPosition(viewport.startRes);
2625     // ShiftList shifts;
2626     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2627     // edit.alColumnChanges=shifts.getInverse();
2628     // if (viewport.hasHiddenColumns)
2629     // viewport.getColumnSelection().compensateForEdits(shifts);
2630     viewport.setStartRes(seq.findIndex(startRes) - 1);
2631     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2632             .getSequences());
2633
2634   }
2635
2636   /**
2637    * DOCUMENT ME!
2638    *
2639    * @param e
2640    *          DOCUMENT ME!
2641    */
2642   @Override
2643   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2644   {
2645     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2646
2647     SequenceI[] seqs;
2648     if (viewport.getSelectionGroup() != null)
2649     {
2650       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2651               viewport.getHiddenRepSequences());
2652       start = viewport.getSelectionGroup().getStartRes();
2653       end = viewport.getSelectionGroup().getEndRes();
2654     }
2655     else
2656     {
2657       seqs = viewport.getAlignment().getSequencesArray();
2658     }
2659
2660     // This is to maintain viewport position on first residue
2661     // of first sequence
2662     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2663     int startRes = seq.findPosition(viewport.startRes);
2664
2665     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2666             viewport.getAlignment()));
2667
2668     viewport.setStartRes(seq.findIndex(startRes) - 1);
2669
2670     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2671             .getSequences());
2672
2673   }
2674
2675   /**
2676    * DOCUMENT ME!
2677    *
2678    * @param e
2679    *          DOCUMENT ME!
2680    */
2681   @Override
2682   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2683   {
2684     viewport.setPadGaps(padGapsMenuitem.isSelected());
2685     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2686             .getSequences());
2687   }
2688
2689   /**
2690    * DOCUMENT ME!
2691    *
2692    * @param e
2693    *          DOCUMENT ME!
2694    */
2695   @Override
2696   public void findMenuItem_actionPerformed(ActionEvent e)
2697   {
2698     new Finder();
2699   }
2700
2701   /**
2702    * Create a new view of the current alignment.
2703    */
2704   @Override
2705   public void newView_actionPerformed(ActionEvent e)
2706   {
2707     newView(null, true);
2708   }
2709
2710   /**
2711    * Creates and shows a new view of the current alignment.
2712    *
2713    * @param viewTitle
2714    *          title of newly created view; if null, one will be generated
2715    * @param copyAnnotation
2716    *          if true then duplicate all annnotation, groups and settings
2717    * @return new alignment panel, already displayed.
2718    */
2719   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2720   {
2721     /*
2722      * Create a new AlignmentPanel (with its own, new Viewport)
2723      */
2724     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2725             true);
2726     if (!copyAnnotation)
2727     {
2728       /*
2729        * remove all groups and annotation except for the automatic stuff
2730        */
2731       newap.av.getAlignment().deleteAllGroups();
2732       newap.av.getAlignment().deleteAllAnnotations(false);
2733     }
2734
2735     newap.av.setGatherViewsHere(false);
2736
2737     if (viewport.viewName == null)
2738     {
2739       viewport.viewName = MessageManager
2740               .getString("label.view_name_original");
2741     }
2742
2743     /*
2744      * Views share the same edits undo and redo stacks
2745      */
2746     newap.av.setHistoryList(viewport.getHistoryList());
2747     newap.av.setRedoList(viewport.getRedoList());
2748
2749     /*
2750      * Views share the same mappings; need to deregister any new mappings
2751      * created by copyAlignPanel, and register the new reference to the shared
2752      * mappings
2753      */
2754     newap.av.replaceMappings(viewport.getAlignment());
2755
2756     newap.av.viewName = getNewViewName(viewTitle);
2757
2758     addAlignmentPanel(newap, true);
2759     newap.alignmentChanged();
2760
2761     if (alignPanels.size() == 2)
2762     {
2763       viewport.setGatherViewsHere(true);
2764     }
2765     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2766     return newap;
2767   }
2768
2769   /**
2770    * Make a new name for the view, ensuring it is unique within the current
2771    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2772    * these now use viewId. Unique view names are still desirable for usability.)
2773    *
2774    * @param viewTitle
2775    * @return
2776    */
2777   protected String getNewViewName(String viewTitle)
2778   {
2779     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2780     boolean addFirstIndex = false;
2781     if (viewTitle == null || viewTitle.trim().length() == 0)
2782     {
2783       viewTitle = MessageManager.getString("action.view");
2784       addFirstIndex = true;
2785     }
2786     else
2787     {
2788       index = 1;// we count from 1 if given a specific name
2789     }
2790     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2791
2792     List<Component> comps = PaintRefresher.components.get(viewport
2793             .getSequenceSetId());
2794
2795     List<String> existingNames = getExistingViewNames(comps);
2796
2797     while (existingNames.contains(newViewName))
2798     {
2799       newViewName = viewTitle + " " + (++index);
2800     }
2801     return newViewName;
2802   }
2803
2804   /**
2805    * Returns a list of distinct view names found in the given list of
2806    * components. View names are held on the viewport of an AlignmentPanel.
2807    *
2808    * @param comps
2809    * @return
2810    */
2811   protected List<String> getExistingViewNames(List<Component> comps)
2812   {
2813     List<String> existingNames = new ArrayList<String>();
2814     for (Component comp : comps)
2815     {
2816       if (comp instanceof AlignmentPanel)
2817       {
2818         AlignmentPanel ap = (AlignmentPanel) comp;
2819         if (!existingNames.contains(ap.av.viewName))
2820         {
2821           existingNames.add(ap.av.viewName);
2822         }
2823       }
2824     }
2825     return existingNames;
2826   }
2827
2828   /**
2829    * Explode tabbed views into separate windows.
2830    */
2831   @Override
2832   public void expandViews_actionPerformed(ActionEvent e)
2833   {
2834     Desktop.explodeViews(this);
2835   }
2836
2837   /**
2838    * Gather views in separate windows back into a tabbed presentation.
2839    */
2840   @Override
2841   public void gatherViews_actionPerformed(ActionEvent e)
2842   {
2843     Desktop.instance.gatherViews(this);
2844   }
2845
2846   /**
2847    * DOCUMENT ME!
2848    *
2849    * @param e
2850    *          DOCUMENT ME!
2851    */
2852   @Override
2853   public void font_actionPerformed(ActionEvent e)
2854   {
2855     new FontChooser(alignPanel);
2856   }
2857
2858   /**
2859    * DOCUMENT ME!
2860    *
2861    * @param e
2862    *          DOCUMENT ME!
2863    */
2864   @Override
2865   protected void seqLimit_actionPerformed(ActionEvent e)
2866   {
2867     viewport.setShowJVSuffix(seqLimits.isSelected());
2868
2869     alignPanel.getIdPanel().getIdCanvas()
2870             .setPreferredSize(alignPanel.calculateIdWidth());
2871     alignPanel.paintAlignment(true);
2872   }
2873
2874   @Override
2875   public void idRightAlign_actionPerformed(ActionEvent e)
2876   {
2877     viewport.setRightAlignIds(idRightAlign.isSelected());
2878     alignPanel.paintAlignment(true);
2879   }
2880
2881   @Override
2882   public void centreColumnLabels_actionPerformed(ActionEvent e)
2883   {
2884     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2885     alignPanel.paintAlignment(true);
2886   }
2887
2888   /*
2889    * (non-Javadoc)
2890    *
2891    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2892    */
2893   @Override
2894   protected void followHighlight_actionPerformed()
2895   {
2896     /*
2897      * Set the 'follow' flag on the Viewport (and scroll to position if now
2898      * true).
2899      */
2900     final boolean state = this.followHighlightMenuItem.getState();
2901     viewport.setFollowHighlight(state);
2902     if (state)
2903     {
2904       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2905     }
2906   }
2907
2908   /**
2909    * DOCUMENT ME!
2910    *
2911    * @param e
2912    *          DOCUMENT ME!
2913    */
2914   @Override
2915   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2916   {
2917     viewport.setColourText(colourTextMenuItem.isSelected());
2918     alignPanel.paintAlignment(true);
2919   }
2920
2921   /**
2922    * DOCUMENT ME!
2923    *
2924    * @param e
2925    *          DOCUMENT ME!
2926    */
2927   @Override
2928   public void wrapMenuItem_actionPerformed(ActionEvent e)
2929   {
2930     scaleAbove.setVisible(wrapMenuItem.isSelected());
2931     scaleLeft.setVisible(wrapMenuItem.isSelected());
2932     scaleRight.setVisible(wrapMenuItem.isSelected());
2933     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2934     alignPanel.updateLayout();
2935   }
2936
2937   @Override
2938   public void showAllSeqs_actionPerformed(ActionEvent e)
2939   {
2940     viewport.showAllHiddenSeqs();
2941   }
2942
2943   @Override
2944   public void showAllColumns_actionPerformed(ActionEvent e)
2945   {
2946     viewport.showAllHiddenColumns();
2947     repaint();
2948     viewport.sendSelection();
2949   }
2950
2951   @Override
2952   public void hideSelSequences_actionPerformed(ActionEvent e)
2953   {
2954     viewport.hideAllSelectedSeqs();
2955     // alignPanel.paintAlignment(true);
2956   }
2957
2958   /**
2959    * called by key handler and the hide all/show all menu items
2960    *
2961    * @param toggleSeqs
2962    * @param toggleCols
2963    */
2964   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2965   {
2966
2967     boolean hide = false;
2968     SequenceGroup sg = viewport.getSelectionGroup();
2969     if (!toggleSeqs && !toggleCols)
2970     {
2971       // Hide everything by the current selection - this is a hack - we do the
2972       // invert and then hide
2973       // first check that there will be visible columns after the invert.
2974       if (viewport.hasSelectedColumns()
2975               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2976                       .getEndRes()))
2977       {
2978         // now invert the sequence set, if required - empty selection implies
2979         // that no hiding is required.
2980         if (sg != null)
2981         {
2982           invertSequenceMenuItem_actionPerformed(null);
2983           sg = viewport.getSelectionGroup();
2984           toggleSeqs = true;
2985
2986         }
2987         viewport.expandColSelection(sg, true);
2988         // finally invert the column selection and get the new sequence
2989         // selection.
2990         invertColSel_actionPerformed(null);
2991         toggleCols = true;
2992       }
2993     }
2994
2995     if (toggleSeqs)
2996     {
2997       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2998       {
2999         hideSelSequences_actionPerformed(null);
3000         hide = true;
3001       }
3002       else if (!(toggleCols && viewport.hasSelectedColumns()))
3003       {
3004         showAllSeqs_actionPerformed(null);
3005       }
3006     }
3007
3008     if (toggleCols)
3009     {
3010       if (viewport.hasSelectedColumns())
3011       {
3012         hideSelColumns_actionPerformed(null);
3013         if (!toggleSeqs)
3014         {
3015           viewport.setSelectionGroup(sg);
3016         }
3017       }
3018       else if (!hide)
3019       {
3020         showAllColumns_actionPerformed(null);
3021       }
3022     }
3023   }
3024
3025   /*
3026    * (non-Javadoc)
3027    *
3028    * @see
3029    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3030    * event.ActionEvent)
3031    */
3032   @Override
3033   public void hideAllButSelection_actionPerformed(ActionEvent e)
3034   {
3035     toggleHiddenRegions(false, false);
3036     viewport.sendSelection();
3037   }
3038
3039   /*
3040    * (non-Javadoc)
3041    *
3042    * @see
3043    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3044    * .ActionEvent)
3045    */
3046   @Override
3047   public void hideAllSelection_actionPerformed(ActionEvent e)
3048   {
3049     SequenceGroup sg = viewport.getSelectionGroup();
3050     viewport.expandColSelection(sg, false);
3051     viewport.hideAllSelectedSeqs();
3052     viewport.hideSelectedColumns();
3053     alignPanel.paintAlignment(true);
3054     viewport.sendSelection();
3055   }
3056
3057   /*
3058    * (non-Javadoc)
3059    *
3060    * @see
3061    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3062    * ActionEvent)
3063    */
3064   @Override
3065   public void showAllhidden_actionPerformed(ActionEvent e)
3066   {
3067     viewport.showAllHiddenColumns();
3068     viewport.showAllHiddenSeqs();
3069     alignPanel.paintAlignment(true);
3070     viewport.sendSelection();
3071   }
3072
3073   @Override
3074   public void hideSelColumns_actionPerformed(ActionEvent e)
3075   {
3076     viewport.hideSelectedColumns();
3077     alignPanel.paintAlignment(true);
3078     viewport.sendSelection();
3079   }
3080
3081   @Override
3082   public void hiddenMarkers_actionPerformed(ActionEvent e)
3083   {
3084     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3085     repaint();
3086   }
3087
3088   /**
3089    * DOCUMENT ME!
3090    *
3091    * @param e
3092    *          DOCUMENT ME!
3093    */
3094   @Override
3095   protected void scaleAbove_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3098     alignPanel.paintAlignment(true);
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   protected void scaleLeft_actionPerformed(ActionEvent e)
3109   {
3110     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3111     alignPanel.paintAlignment(true);
3112   }
3113
3114   /**
3115    * DOCUMENT ME!
3116    *
3117    * @param e
3118    *          DOCUMENT ME!
3119    */
3120   @Override
3121   protected void scaleRight_actionPerformed(ActionEvent e)
3122   {
3123     viewport.setScaleRightWrapped(scaleRight.isSelected());
3124     alignPanel.paintAlignment(true);
3125   }
3126
3127   /**
3128    * DOCUMENT ME!
3129    *
3130    * @param e
3131    *          DOCUMENT ME!
3132    */
3133   @Override
3134   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3135   {
3136     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3137     alignPanel.paintAlignment(true);
3138   }
3139
3140   /**
3141    * DOCUMENT ME!
3142    *
3143    * @param e
3144    *          DOCUMENT ME!
3145    */
3146   @Override
3147   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3148   {
3149     viewport.setShowText(viewTextMenuItem.isSelected());
3150     alignPanel.paintAlignment(true);
3151   }
3152
3153   /**
3154    * DOCUMENT ME!
3155    *
3156    * @param e
3157    *          DOCUMENT ME!
3158    */
3159   @Override
3160   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3161   {
3162     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3163     alignPanel.paintAlignment(true);
3164   }
3165
3166   public FeatureSettings featureSettings;
3167
3168   @Override
3169   public FeatureSettingsControllerI getFeatureSettingsUI()
3170   {
3171     return featureSettings;
3172   }
3173
3174   @Override
3175   public void featureSettings_actionPerformed(ActionEvent e)
3176   {
3177     if (featureSettings != null)
3178     {
3179       featureSettings.close();
3180       featureSettings = null;
3181     }
3182     if (!showSeqFeatures.isSelected())
3183     {
3184       // make sure features are actually displayed
3185       showSeqFeatures.setSelected(true);
3186       showSeqFeatures_actionPerformed(null);
3187     }
3188     featureSettings = new FeatureSettings(this);
3189   }
3190
3191   /**
3192    * Set or clear 'Show Sequence Features'
3193    *
3194    * @param evt
3195    *          DOCUMENT ME!
3196    */
3197   @Override
3198   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3199   {
3200     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3201     alignPanel.paintAlignment(true);
3202     if (alignPanel.getOverviewPanel() != null)
3203     {
3204       alignPanel.getOverviewPanel().updateOverviewImage();
3205     }
3206   }
3207
3208   /**
3209    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3210    * the annotations panel as a whole.
3211    *
3212    * The options to show/hide all annotations should be enabled when the panel
3213    * is shown, and disabled when the panel is hidden.
3214    *
3215    * @param e
3216    */
3217   @Override
3218   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3219   {
3220     final boolean setVisible = annotationPanelMenuItem.isSelected();
3221     viewport.setShowAnnotation(setVisible);
3222     this.showAllSeqAnnotations.setEnabled(setVisible);
3223     this.hideAllSeqAnnotations.setEnabled(setVisible);
3224     this.showAllAlAnnotations.setEnabled(setVisible);
3225     this.hideAllAlAnnotations.setEnabled(setVisible);
3226     alignPanel.updateLayout();
3227   }
3228
3229   @Override
3230   public void alignmentProperties()
3231   {
3232     JEditorPane editPane = new JEditorPane("text/html", "");
3233     editPane.setEditable(false);
3234     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3235             .formatAsHtml();
3236     editPane.setText(MessageManager.formatMessage("label.html_content",
3237             new Object[] { contents.toString() }));
3238     JInternalFrame frame = new JInternalFrame();
3239     frame.getContentPane().add(new JScrollPane(editPane));
3240
3241     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3242             "label.alignment_properties", new Object[] { getTitle() }),
3243             500, 400);
3244   }
3245
3246   /**
3247    * DOCUMENT ME!
3248    *
3249    * @param e
3250    *          DOCUMENT ME!
3251    */
3252   @Override
3253   public void overviewMenuItem_actionPerformed(ActionEvent e)
3254   {
3255     if (alignPanel.overviewPanel != null)
3256     {
3257       return;
3258     }
3259
3260     JInternalFrame frame = new JInternalFrame();
3261     OverviewPanel overview = new OverviewPanel(alignPanel);
3262     frame.setContentPane(overview);
3263     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3264             "label.overview_params", new Object[] { this.getTitle() }),
3265             frame.getWidth(), frame.getHeight());
3266     frame.pack();
3267     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3268     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3269     {
3270       @Override
3271       public void internalFrameClosed(
3272               javax.swing.event.InternalFrameEvent evt)
3273       {
3274         alignPanel.setOverviewPanel(null);
3275       };
3276     });
3277
3278     alignPanel.setOverviewPanel(overview);
3279   }
3280
3281   @Override
3282   public void textColour_actionPerformed()
3283   {
3284     new TextColourChooser().chooseColour(alignPanel, null);
3285   }
3286
3287   /*
3288    * public void covariationColour_actionPerformed() {
3289    * changeColour(new
3290    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3291    * ()[0])); }
3292    */
3293   @Override
3294   public void annotationColour_actionPerformed()
3295   {
3296     new AnnotationColourChooser(viewport, alignPanel);
3297   }
3298
3299   @Override
3300   public void annotationColumn_actionPerformed(ActionEvent e)
3301   {
3302     new AnnotationColumnChooser(viewport, alignPanel);
3303   }
3304
3305   /**
3306    * Action on the user checking or unchecking the option to apply the selected
3307    * colour scheme to all groups. If unchecked, groups may have their own
3308    * independent colour schemes.
3309    *
3310    */
3311   @Override
3312   protected void applyToAllGroups_actionPerformed()
3313   {
3314     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3315   }
3316
3317   /**
3318    * Action on user selecting a colour from the colour menu
3319    *
3320    * @param name
3321    *          the name (not the menu item label!) of the colour scheme
3322    */
3323   @Override
3324   public void changeColour_actionPerformed(String name)
3325   {
3326     /*
3327      * 'User Defined' opens a panel to configure or load a
3328      * user-defined colour scheme
3329      */
3330     if (ResidueColourScheme.USER_DEFINED.equals(name))
3331     {
3332       new UserDefinedColours(alignPanel, null);
3333       return;
3334     }
3335
3336     /*
3337      * otherwise set the chosen colour scheme (or null for 'None')
3338      */
3339     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3340             viewport.getAlignment(), viewport.getHiddenRepSequences());
3341     changeColour(cs);
3342   }
3343
3344   /**
3345    * Actions on setting or changing the alignment colour scheme
3346    *
3347    * @param cs
3348    */
3349   @Override
3350   public void changeColour(ColourSchemeI cs)
3351   {
3352     // TODO: pull up to controller method
3353     if (cs != null)
3354     {
3355       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3356       // Make sure viewport is up to date w.r.t. any sliders
3357       if (viewport.getAbovePIDThreshold())
3358       {
3359         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3360                 "Background");
3361         viewport.setThreshold(threshold);
3362       }
3363
3364       if (viewport.getConservationSelected())
3365       {
3366         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3367                 cs, "Background"));
3368       }
3369     }
3370
3371     viewport.setGlobalColourScheme(cs);
3372
3373     alignPanel.paintAlignment(true);
3374   }
3375
3376   /**
3377    * DOCUMENT ME!
3378    *
3379    * @param e
3380    *          DOCUMENT ME!
3381    */
3382   @Override
3383   protected void modifyPID_actionPerformed()
3384   {
3385     if (viewport.getAbovePIDThreshold()
3386             && viewport.getGlobalColourScheme() != null)
3387     {
3388       SliderPanel.setPIDSliderSource(alignPanel,
3389               viewport.getGlobalColourScheme(), "Background");
3390       SliderPanel.showPIDSlider();
3391     }
3392   }
3393
3394   /**
3395    * DOCUMENT ME!
3396    *
3397    * @param e
3398    *          DOCUMENT ME!
3399    */
3400   @Override
3401   protected void modifyConservation_actionPerformed()
3402   {
3403     if (viewport.getConservationSelected()
3404             && viewport.getGlobalColourScheme() != null)
3405     {
3406       SliderPanel.setConservationSlider(alignPanel,
3407               viewport.getGlobalColourScheme(), "Background");
3408       SliderPanel.showConservationSlider();
3409     }
3410   }
3411
3412   /**
3413    * DOCUMENT ME!
3414    *
3415    * @param e
3416    *          DOCUMENT ME!
3417    */
3418   @Override
3419   protected void conservationMenuItem_actionPerformed()
3420   {
3421     viewport.setConservationSelected(conservationMenuItem.isSelected());
3422
3423     viewport.setAbovePIDThreshold(false);
3424     abovePIDThreshold.setSelected(false);
3425
3426     changeColour(viewport.getGlobalColourScheme());
3427
3428     modifyConservation_actionPerformed();
3429   }
3430
3431   /**
3432    * DOCUMENT ME!
3433    *
3434    * @param e
3435    *          DOCUMENT ME!
3436    */
3437   @Override
3438   public void abovePIDThreshold_actionPerformed()
3439   {
3440     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3441
3442     conservationMenuItem.setSelected(false);
3443     viewport.setConservationSelected(false);
3444
3445     changeColour(viewport.getGlobalColourScheme());
3446
3447     modifyPID_actionPerformed();
3448   }
3449
3450   /**
3451    * DOCUMENT ME!
3452    *
3453    * @param e
3454    *          DOCUMENT ME!
3455    */
3456   @Override
3457   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3458   {
3459     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3460     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3461             .getAlignment().getSequenceAt(0), null);
3462     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3463             viewport.getAlignment()));
3464     alignPanel.paintAlignment(true);
3465   }
3466
3467   /**
3468    * DOCUMENT ME!
3469    *
3470    * @param e
3471    *          DOCUMENT ME!
3472    */
3473   @Override
3474   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3475   {
3476     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3477     AlignmentSorter.sortByID(viewport.getAlignment());
3478     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3479             viewport.getAlignment()));
3480     alignPanel.paintAlignment(true);
3481   }
3482
3483   /**
3484    * DOCUMENT ME!
3485    *
3486    * @param e
3487    *          DOCUMENT ME!
3488    */
3489   @Override
3490   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3491   {
3492     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3493     AlignmentSorter.sortByLength(viewport.getAlignment());
3494     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3495             viewport.getAlignment()));
3496     alignPanel.paintAlignment(true);
3497   }
3498
3499   /**
3500    * DOCUMENT ME!
3501    *
3502    * @param e
3503    *          DOCUMENT ME!
3504    */
3505   @Override
3506   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3507   {
3508     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3509     AlignmentSorter.sortByGroup(viewport.getAlignment());
3510     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3511             viewport.getAlignment()));
3512
3513     alignPanel.paintAlignment(true);
3514   }
3515
3516   /**
3517    * DOCUMENT ME!
3518    *
3519    * @param e
3520    *          DOCUMENT ME!
3521    */
3522   @Override
3523   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3524   {
3525     new RedundancyPanel(alignPanel, this);
3526   }
3527
3528   /**
3529    * DOCUMENT ME!
3530    *
3531    * @param e
3532    *          DOCUMENT ME!
3533    */
3534   @Override
3535   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3536   {
3537     if ((viewport.getSelectionGroup() == null)
3538             || (viewport.getSelectionGroup().getSize() < 2))
3539     {
3540       JvOptionPane.showInternalMessageDialog(this, MessageManager
3541               .getString("label.you_must_select_least_two_sequences"),
3542               MessageManager.getString("label.invalid_selection"),
3543               JvOptionPane.WARNING_MESSAGE);
3544     }
3545     else
3546     {
3547       JInternalFrame frame = new JInternalFrame();
3548       frame.setContentPane(new PairwiseAlignPanel(viewport));
3549       Desktop.addInternalFrame(frame,
3550               MessageManager.getString("action.pairwise_alignment"), 600,
3551               500);
3552     }
3553   }
3554
3555   /**
3556    * DOCUMENT ME!
3557    *
3558    * @param e
3559    *          DOCUMENT ME!
3560    */
3561   @Override
3562   public void PCAMenuItem_actionPerformed(ActionEvent e)
3563   {
3564     if (((viewport.getSelectionGroup() != null)
3565             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3566             .getSelectionGroup().getSize() > 0))
3567             || (viewport.getAlignment().getHeight() < 4))
3568     {
3569       JvOptionPane
3570               .showInternalMessageDialog(
3571                       this,
3572                       MessageManager
3573                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3574                       MessageManager
3575                               .getString("label.sequence_selection_insufficient"),
3576                       JvOptionPane.WARNING_MESSAGE);
3577
3578       return;
3579     }
3580
3581     new PCAPanel(alignPanel);
3582   }
3583
3584   @Override
3585   public void autoCalculate_actionPerformed(ActionEvent e)
3586   {
3587     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3588     if (viewport.autoCalculateConsensus)
3589     {
3590       viewport.firePropertyChange("alignment", null, viewport
3591               .getAlignment().getSequences());
3592     }
3593   }
3594
3595   @Override
3596   public void sortByTreeOption_actionPerformed(ActionEvent e)
3597   {
3598     viewport.sortByTree = sortByTree.isSelected();
3599   }
3600
3601   @Override
3602   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3603   {
3604     viewport.followSelection = listenToViewSelections.isSelected();
3605   }
3606
3607   /**
3608    * DOCUMENT ME!
3609    *
3610    * @param e
3611    *          DOCUMENT ME!
3612    */
3613   @Override
3614   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3615   {
3616     newTreePanel("AV", "PID", "Average distance tree using PID");
3617   }
3618
3619   /**
3620    * DOCUMENT ME!
3621    *
3622    * @param e
3623    *          DOCUMENT ME!
3624    */
3625   @Override
3626   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3627   {
3628     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3629   }
3630
3631   /**
3632    * DOCUMENT ME!
3633    *
3634    * @param e
3635    *          DOCUMENT ME!
3636    */
3637   @Override
3638   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3639   {
3640     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3641   }
3642
3643   /**
3644    * DOCUMENT ME!
3645    *
3646    * @param e
3647    *          DOCUMENT ME!
3648    */
3649   @Override
3650   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3651   {
3652     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3653   }
3654
3655   /**
3656    * DOCUMENT ME!
3657    *
3658    * @param type
3659    *          DOCUMENT ME!
3660    * @param pwType
3661    *          DOCUMENT ME!
3662    * @param title
3663    *          DOCUMENT ME!
3664    */
3665   void newTreePanel(String type, String pwType, String title)
3666   {
3667     TreePanel tp;
3668
3669     if (viewport.getSelectionGroup() != null
3670             && viewport.getSelectionGroup().getSize() > 0)
3671     {
3672       if (viewport.getSelectionGroup().getSize() < 3)
3673       {
3674         JvOptionPane
3675                 .showMessageDialog(
3676                         Desktop.desktop,
3677                         MessageManager
3678                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3679                         MessageManager
3680                                 .getString("label.not_enough_sequences"),
3681                         JvOptionPane.WARNING_MESSAGE);
3682         return;
3683       }
3684
3685       SequenceGroup sg = viewport.getSelectionGroup();
3686
3687       /* Decide if the selection is a column region */
3688       for (SequenceI _s : sg.getSequences())
3689       {
3690         if (_s.getLength() < sg.getEndRes())
3691         {
3692           JvOptionPane
3693                   .showMessageDialog(
3694                           Desktop.desktop,
3695                           MessageManager
3696                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3697                           MessageManager
3698                                   .getString("label.sequences_selection_not_aligned"),
3699                           JvOptionPane.WARNING_MESSAGE);
3700
3701           return;
3702         }
3703       }
3704
3705       title = title + " on region";
3706       tp = new TreePanel(alignPanel, type, pwType);
3707     }
3708     else
3709     {
3710       // are the visible sequences aligned?
3711       if (!viewport.getAlignment().isAligned(false))
3712       {
3713         JvOptionPane
3714                 .showMessageDialog(
3715                         Desktop.desktop,
3716                         MessageManager
3717                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3718                         MessageManager
3719                                 .getString("label.sequences_not_aligned"),
3720                         JvOptionPane.WARNING_MESSAGE);
3721
3722         return;
3723       }
3724
3725       if (viewport.getAlignment().getHeight() < 2)
3726       {
3727         return;
3728       }
3729
3730       tp = new TreePanel(alignPanel, type, pwType);
3731     }
3732
3733     title += " from ";
3734
3735     if (viewport.viewName != null)
3736     {
3737       title += viewport.viewName + " of ";
3738     }
3739
3740     title += this.title;
3741
3742     Desktop.addInternalFrame(tp, title, 600, 500);
3743   }
3744
3745   /**
3746    * DOCUMENT ME!
3747    *
3748    * @param title
3749    *          DOCUMENT ME!
3750    * @param order
3751    *          DOCUMENT ME!
3752    */
3753   public void addSortByOrderMenuItem(String title,
3754           final AlignmentOrder order)
3755   {
3756     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3757             "action.by_title_param", new Object[] { title }));
3758     sort.add(item);
3759     item.addActionListener(new java.awt.event.ActionListener()
3760     {
3761       @Override
3762       public void actionPerformed(ActionEvent e)
3763       {
3764         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3765
3766         // TODO: JBPNote - have to map order entries to curent SequenceI
3767         // pointers
3768         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3769
3770         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3771                 .getAlignment()));
3772
3773         alignPanel.paintAlignment(true);
3774       }
3775     });
3776   }
3777
3778   /**
3779    * Add a new sort by annotation score menu item
3780    *
3781    * @param sort
3782    *          the menu to add the option to
3783    * @param scoreLabel
3784    *          the label used to retrieve scores for each sequence on the
3785    *          alignment
3786    */
3787   public void addSortByAnnotScoreMenuItem(JMenu sort,
3788           final String scoreLabel)
3789   {
3790     final JMenuItem item = new JMenuItem(scoreLabel);
3791     sort.add(item);
3792     item.addActionListener(new java.awt.event.ActionListener()
3793     {
3794       @Override
3795       public void actionPerformed(ActionEvent e)
3796       {
3797         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3798         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3799                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3800         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3801                 viewport.getAlignment()));
3802         alignPanel.paintAlignment(true);
3803       }
3804     });
3805   }
3806
3807   /**
3808    * last hash for alignment's annotation array - used to minimise cost of
3809    * rebuild.
3810    */
3811   protected int _annotationScoreVectorHash;
3812
3813   /**
3814    * search the alignment and rebuild the sort by annotation score submenu the
3815    * last alignment annotation vector hash is stored to minimize cost of
3816    * rebuilding in subsequence calls.
3817    *
3818    */
3819   @Override
3820   public void buildSortByAnnotationScoresMenu()
3821   {
3822     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3823     {
3824       return;
3825     }
3826
3827     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3828     {
3829       sortByAnnotScore.removeAll();
3830       // almost certainly a quicker way to do this - but we keep it simple
3831       Hashtable scoreSorts = new Hashtable();
3832       AlignmentAnnotation aann[];
3833       for (SequenceI sqa : viewport.getAlignment().getSequences())
3834       {
3835         aann = sqa.getAnnotation();
3836         for (int i = 0; aann != null && i < aann.length; i++)
3837         {
3838           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3839           {
3840             scoreSorts.put(aann[i].label, aann[i].label);
3841           }
3842         }
3843       }
3844       Enumeration labels = scoreSorts.keys();
3845       while (labels.hasMoreElements())
3846       {
3847         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3848                 (String) labels.nextElement());
3849       }
3850       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3851       scoreSorts.clear();
3852
3853       _annotationScoreVectorHash = viewport.getAlignment()
3854               .getAlignmentAnnotation().hashCode();
3855     }
3856   }
3857
3858   /**
3859    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3860    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3861    * call. Listeners are added to remove the menu item when the treePanel is
3862    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3863    * modified.
3864    *
3865    * @param treePanel
3866    *          Displayed tree window.
3867    * @param title
3868    *          SortBy menu item title.
3869    */
3870   @Override
3871   public void buildTreeMenu()
3872   {
3873     calculateTree.removeAll();
3874     // build the calculate menu
3875
3876     for (final String type : new String[] { "NJ", "AV" })
3877     {
3878       String treecalcnm = MessageManager.getString("label.tree_calc_"
3879               + type.toLowerCase());
3880       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3881       {
3882         JMenuItem tm = new JMenuItem();
3883         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3884         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3885                 || sm.isProtein() == !viewport.getAlignment()
3886                         .isNucleotide())
3887         {
3888           String smn = MessageManager.getStringOrReturn(
3889                   "label.score_model_", sm.getName());
3890           final String title = MessageManager.formatMessage(
3891                   "label.treecalc_title", treecalcnm, smn);
3892           tm.setText(title);//
3893           tm.addActionListener(new java.awt.event.ActionListener()
3894           {
3895             @Override
3896             public void actionPerformed(ActionEvent e)
3897             {
3898               newTreePanel(type, pwtype, title);
3899             }
3900           });
3901           calculateTree.add(tm);
3902         }
3903
3904       }
3905     }
3906     sortByTreeMenu.removeAll();
3907
3908     List<Component> comps = PaintRefresher.components.get(viewport
3909             .getSequenceSetId());
3910     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3911     for (Component comp : comps)
3912     {
3913       if (comp instanceof TreePanel)
3914       {
3915         treePanels.add((TreePanel) comp);
3916       }
3917     }
3918
3919     if (treePanels.size() < 1)
3920     {
3921       sortByTreeMenu.setVisible(false);
3922       return;
3923     }
3924
3925     sortByTreeMenu.setVisible(true);
3926
3927     for (final TreePanel tp : treePanels)
3928     {
3929       final JMenuItem item = new JMenuItem(tp.getTitle());
3930       item.addActionListener(new java.awt.event.ActionListener()
3931       {
3932         @Override
3933         public void actionPerformed(ActionEvent e)
3934         {
3935           tp.sortByTree_actionPerformed();
3936           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3937
3938         }
3939       });
3940
3941       sortByTreeMenu.add(item);
3942     }
3943   }
3944
3945   public boolean sortBy(AlignmentOrder alorder, String undoname)
3946   {
3947     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3948     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3949     if (undoname != null)
3950     {
3951       addHistoryItem(new OrderCommand(undoname, oldOrder,
3952               viewport.getAlignment()));
3953     }
3954     alignPanel.paintAlignment(true);
3955     return true;
3956   }
3957
3958   /**
3959    * Work out whether the whole set of sequences or just the selected set will
3960    * be submitted for multiple alignment.
3961    *
3962    */
3963   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3964   {
3965     // Now, check we have enough sequences
3966     AlignmentView msa = null;
3967
3968     if ((viewport.getSelectionGroup() != null)
3969             && (viewport.getSelectionGroup().getSize() > 1))
3970     {
3971       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3972       // some common interface!
3973       /*
3974        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3975        * SequenceI[sz = seqs.getSize(false)];
3976        *
3977        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3978        * seqs.getSequenceAt(i); }
3979        */
3980       msa = viewport.getAlignmentView(true);
3981     }
3982     else if (viewport.getSelectionGroup() != null
3983             && viewport.getSelectionGroup().getSize() == 1)
3984     {
3985       int option = JvOptionPane.showConfirmDialog(this,
3986               MessageManager.getString("warn.oneseq_msainput_selection"),
3987               MessageManager.getString("label.invalid_selection"),
3988               JvOptionPane.OK_CANCEL_OPTION);
3989       if (option == JvOptionPane.OK_OPTION)
3990       {
3991         msa = viewport.getAlignmentView(false);
3992       }
3993     }
3994     else
3995     {
3996       msa = viewport.getAlignmentView(false);
3997     }
3998     return msa;
3999   }
4000
4001   /**
4002    * Decides what is submitted to a secondary structure prediction service: the
4003    * first sequence in the alignment, or in the current selection, or, if the
4004    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4005    * region or the whole alignment. (where the first sequence in the set is the
4006    * one that the prediction will be for).
4007    */
4008   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4009   {
4010     AlignmentView seqs = null;
4011
4012     if ((viewport.getSelectionGroup() != null)
4013             && (viewport.getSelectionGroup().getSize() > 0))
4014     {
4015       seqs = viewport.getAlignmentView(true);
4016     }
4017     else
4018     {
4019       seqs = viewport.getAlignmentView(false);
4020     }
4021     // limit sequences - JBPNote in future - could spawn multiple prediction
4022     // jobs
4023     // TODO: viewport.getAlignment().isAligned is a global state - the local
4024     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4025     if (!viewport.getAlignment().isAligned(false))
4026     {
4027       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4028       // TODO: if seqs.getSequences().length>1 then should really have warned
4029       // user!
4030
4031     }
4032     return seqs;
4033   }
4034
4035   /**
4036    * DOCUMENT ME!
4037    *
4038    * @param e
4039    *          DOCUMENT ME!
4040    */
4041   @Override
4042   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4043   {
4044     // Pick the tree file
4045     JalviewFileChooser chooser = new JalviewFileChooser(
4046             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4047     chooser.setFileView(new JalviewFileView());
4048     chooser.setDialogTitle(MessageManager
4049             .getString("label.select_newick_like_tree_file"));
4050     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4051
4052     int value = chooser.showOpenDialog(null);
4053
4054     if (value == JalviewFileChooser.APPROVE_OPTION)
4055     {
4056       String choice = chooser.getSelectedFile().getPath();
4057       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4058       jalview.io.NewickFile fin = null;
4059       try
4060       {
4061         fin = new NewickFile(choice, DataSourceType.FILE);
4062         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4063       } catch (Exception ex)
4064       {
4065         JvOptionPane
4066                 .showMessageDialog(
4067                         Desktop.desktop,
4068                         ex.getMessage(),
4069                         MessageManager
4070                                 .getString("label.problem_reading_tree_file"),
4071                         JvOptionPane.WARNING_MESSAGE);
4072         ex.printStackTrace();
4073       }
4074       if (fin != null && fin.hasWarningMessage())
4075       {
4076         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4077                 .getWarningMessage(), MessageManager
4078                 .getString("label.possible_problem_with_tree_file"),
4079                 JvOptionPane.WARNING_MESSAGE);
4080       }
4081     }
4082   }
4083
4084   public TreePanel ShowNewickTree(NewickFile nf, String title)
4085   {
4086     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4087   }
4088
4089   public TreePanel ShowNewickTree(NewickFile nf, String title,
4090           AlignmentView input)
4091   {
4092     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4093   }
4094
4095   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4096           int h, int x, int y)
4097   {
4098     return ShowNewickTree(nf, title, null, w, h, x, y);
4099   }
4100
4101   /**
4102    * Add a treeviewer for the tree extracted from a newick file object to the
4103    * current alignment view
4104    *
4105    * @param nf
4106    *          the tree
4107    * @param title
4108    *          tree viewer title
4109    * @param input
4110    *          Associated alignment input data (or null)
4111    * @param w
4112    *          width
4113    * @param h
4114    *          height
4115    * @param x
4116    *          position
4117    * @param y
4118    *          position
4119    * @return TreePanel handle
4120    */
4121   public TreePanel ShowNewickTree(NewickFile nf, String title,
4122           AlignmentView input, int w, int h, int x, int y)
4123   {
4124     TreePanel tp = null;
4125
4126     try
4127     {
4128       nf.parse();
4129
4130       if (nf.getTree() != null)
4131       {
4132         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4133
4134         tp.setSize(w, h);
4135
4136         if (x > 0 && y > 0)
4137         {
4138           tp.setLocation(x, y);
4139         }
4140
4141         Desktop.addInternalFrame(tp, title, w, h);
4142       }
4143     } catch (Exception ex)
4144     {
4145       ex.printStackTrace();
4146     }
4147
4148     return tp;
4149   }
4150
4151   private boolean buildingMenu = false;
4152
4153   /**
4154    * Generates menu items and listener event actions for web service clients
4155    *
4156    */
4157   public void BuildWebServiceMenu()
4158   {
4159     while (buildingMenu)
4160     {
4161       try
4162       {
4163         System.err.println("Waiting for building menu to finish.");
4164         Thread.sleep(10);
4165       } catch (Exception e)
4166       {
4167       }
4168     }
4169     final AlignFrame me = this;
4170     buildingMenu = true;
4171     new Thread(new Runnable()
4172     {
4173       @Override
4174       public void run()
4175       {
4176         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4177         try
4178         {
4179           // System.err.println("Building ws menu again "
4180           // + Thread.currentThread());
4181           // TODO: add support for context dependent disabling of services based
4182           // on
4183           // alignment and current selection
4184           // TODO: add additional serviceHandle parameter to specify abstract
4185           // handler
4186           // class independently of AbstractName
4187           // TODO: add in rediscovery GUI function to restart discoverer
4188           // TODO: group services by location as well as function and/or
4189           // introduce
4190           // object broker mechanism.
4191           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4192           final IProgressIndicator af = me;
4193
4194           /*
4195            * do not i18n these strings - they are hard-coded in class
4196            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4197            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4198            */
4199           final JMenu msawsmenu = new JMenu("Alignment");
4200           final JMenu secstrmenu = new JMenu(
4201                   "Secondary Structure Prediction");
4202           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4203           final JMenu analymenu = new JMenu("Analysis");
4204           final JMenu dismenu = new JMenu("Protein Disorder");
4205           // JAL-940 - only show secondary structure prediction services from
4206           // the legacy server
4207           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4208               // &&
4209           Discoverer.services != null && (Discoverer.services.size() > 0))
4210           {
4211             // TODO: refactor to allow list of AbstractName/Handler bindings to
4212             // be
4213             // stored or retrieved from elsewhere
4214             // No MSAWS used any more:
4215             // Vector msaws = null; // (Vector)
4216             // Discoverer.services.get("MsaWS");
4217             Vector secstrpr = (Vector) Discoverer.services
4218                     .get("SecStrPred");
4219             if (secstrpr != null)
4220             {
4221               // Add any secondary structure prediction services
4222               for (int i = 0, j = secstrpr.size(); i < j; i++)
4223               {
4224                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4225                         .get(i);
4226                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4227                         .getServiceClient(sh);
4228                 int p = secstrmenu.getItemCount();
4229                 impl.attachWSMenuEntry(secstrmenu, me);
4230                 int q = secstrmenu.getItemCount();
4231                 for (int litm = p; litm < q; litm++)
4232                 {
4233                   legacyItems.add(secstrmenu.getItem(litm));
4234                 }
4235               }
4236             }
4237           }
4238
4239           // Add all submenus in the order they should appear on the web
4240           // services menu
4241           wsmenu.add(msawsmenu);
4242           wsmenu.add(secstrmenu);
4243           wsmenu.add(dismenu);
4244           wsmenu.add(analymenu);
4245           // No search services yet
4246           // wsmenu.add(seqsrchmenu);
4247
4248           javax.swing.SwingUtilities.invokeLater(new Runnable()
4249           {
4250             @Override
4251             public void run()
4252             {
4253               try
4254               {
4255                 webService.removeAll();
4256                 // first, add discovered services onto the webservices menu
4257                 if (wsmenu.size() > 0)
4258                 {
4259                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4260                   {
4261                     webService.add(wsmenu.get(i));
4262                   }
4263                 }
4264                 else
4265                 {
4266                   webService.add(me.webServiceNoServices);
4267                 }
4268                 // TODO: move into separate menu builder class.
4269                 boolean new_sspred = false;
4270                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4271                 {
4272                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4273                   if (jws2servs != null)
4274                   {
4275                     if (jws2servs.hasServices())
4276                     {
4277                       jws2servs.attachWSMenuEntry(webService, me);
4278                       for (Jws2Instance sv : jws2servs.getServices())
4279                       {
4280                         if (sv.description.toLowerCase().contains("jpred"))
4281                         {
4282                           for (JMenuItem jmi : legacyItems)
4283                           {
4284                             jmi.setVisible(false);
4285                           }
4286                         }
4287                       }
4288
4289                     }
4290                     if (jws2servs.isRunning())
4291                     {
4292                       JMenuItem tm = new JMenuItem(
4293                               "Still discovering JABA Services");
4294                       tm.setEnabled(false);
4295                       webService.add(tm);
4296                     }
4297                   }
4298                 }
4299                 build_urlServiceMenu(me.webService);
4300                 build_fetchdbmenu(webService);
4301                 for (JMenu item : wsmenu)
4302                 {
4303                   if (item.getItemCount() == 0)
4304                   {
4305                     item.setEnabled(false);
4306                   }
4307                   else
4308                   {
4309                     item.setEnabled(true);
4310                   }
4311                 }
4312               } catch (Exception e)
4313               {
4314                 Cache.log
4315                         .debug("Exception during web service menu building process.",
4316                                 e);
4317               }
4318             }
4319           });
4320         } catch (Exception e)
4321         {
4322         }
4323         buildingMenu = false;
4324       }
4325     }).start();
4326
4327   }
4328
4329   /**
4330    * construct any groupURL type service menu entries.
4331    *
4332    * @param webService
4333    */
4334   private void build_urlServiceMenu(JMenu webService)
4335   {
4336     // TODO: remove this code when 2.7 is released
4337     // DEBUG - alignmentView
4338     /*
4339      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4340      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4341      *
4342      * @Override public void actionPerformed(ActionEvent e) {
4343      * jalview.datamodel.AlignmentView
4344      * .testSelectionViews(af.viewport.getAlignment(),
4345      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4346      *
4347      * }); webService.add(testAlView);
4348      */
4349     // TODO: refactor to RestClient discoverer and merge menu entries for
4350     // rest-style services with other types of analysis/calculation service
4351     // SHmmr test client - still being implemented.
4352     // DEBUG - alignmentView
4353
4354     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4355             .getRestClients())
4356     {
4357       client.attachWSMenuEntry(
4358               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4359               this);
4360     }
4361   }
4362
4363   /**
4364    * Searches the alignment sequences for xRefs and builds the Show
4365    * Cross-References menu (formerly called Show Products), with database
4366    * sources for which cross-references are found (protein sources for a
4367    * nucleotide alignment and vice versa)
4368    *
4369    * @return true if Show Cross-references menu should be enabled
4370    */
4371   public boolean canShowProducts()
4372   {
4373     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4374     AlignmentI dataset = viewport.getAlignment().getDataset();
4375
4376     showProducts.removeAll();
4377     final boolean dna = viewport.getAlignment().isNucleotide();
4378
4379     if (seqs == null || seqs.length == 0)
4380     {
4381       // nothing to see here.
4382       return false;
4383     }
4384
4385     boolean showp = false;
4386     try
4387     {
4388       List<String> ptypes = new CrossRef(seqs, dataset)
4389               .findXrefSourcesForSequences(dna);
4390
4391       for (final String source : ptypes)
4392       {
4393         showp = true;
4394         final AlignFrame af = this;
4395         JMenuItem xtype = new JMenuItem(source);
4396         xtype.addActionListener(new ActionListener()
4397         {
4398           @Override
4399           public void actionPerformed(ActionEvent e)
4400           {
4401             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4402           }
4403         });
4404         showProducts.add(xtype);
4405       }
4406       showProducts.setVisible(showp);
4407       showProducts.setEnabled(showp);
4408     } catch (Exception e)
4409     {
4410       Cache.log
4411               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4412                       e);
4413       return false;
4414     }
4415     return showp;
4416   }
4417
4418   /**
4419    * Finds and displays cross-references for the selected sequences (protein
4420    * products for nucleotide sequences, dna coding sequences for peptides).
4421    *
4422    * @param sel
4423    *          the sequences to show cross-references for
4424    * @param dna
4425    *          true if from a nucleotide alignment (so showing proteins)
4426    * @param source
4427    *          the database to show cross-references for
4428    */
4429   protected void showProductsFor(final SequenceI[] sel,
4430           final boolean _odna, final String source)
4431   {
4432     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4433             .start();
4434   }
4435
4436   /**
4437    * Construct and display a new frame containing the translation of this
4438    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4439    */
4440   @Override
4441   public void showTranslation_actionPerformed(ActionEvent e)
4442   {
4443     AlignmentI al = null;
4444     try
4445     {
4446       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4447
4448       al = dna.translateCdna();
4449     } catch (Exception ex)
4450     {
4451       jalview.bin.Cache.log.error(
4452               "Exception during translation. Please report this !", ex);
4453       final String msg = MessageManager
4454               .getString("label.error_when_translating_sequences_submit_bug_report");
4455       final String errorTitle = MessageManager
4456               .getString("label.implementation_error")
4457               + MessageManager.getString("label.translation_failed");
4458       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4459               JvOptionPane.ERROR_MESSAGE);
4460       return;
4461     }
4462     if (al == null || al.getHeight() == 0)
4463     {
4464       final String msg = MessageManager
4465               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4466       final String errorTitle = MessageManager
4467               .getString("label.translation_failed");
4468       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4469               JvOptionPane.WARNING_MESSAGE);
4470     }
4471     else
4472     {
4473       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4474       af.setFileFormat(this.currentFileFormat);
4475       final String newTitle = MessageManager.formatMessage(
4476               "label.translation_of_params",
4477               new Object[] { this.getTitle() });
4478       af.setTitle(newTitle);
4479       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4480       {
4481         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4482         viewport.openSplitFrame(af, new Alignment(seqs));
4483       }
4484       else
4485       {
4486         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4487                 DEFAULT_HEIGHT);
4488       }
4489     }
4490   }
4491
4492   /**
4493    * Set the file format
4494    *
4495    * @param format
4496    */
4497   public void setFileFormat(FileFormatI format)
4498   {
4499     this.currentFileFormat = format;
4500   }
4501
4502   /**
4503    * Try to load a features file onto the alignment.
4504    *
4505    * @param file
4506    *          contents or path to retrieve file
4507    * @param sourceType
4508    *          access mode of file (see jalview.io.AlignFile)
4509    * @return true if features file was parsed correctly.
4510    */
4511   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4512   {
4513     return avc.parseFeaturesFile(file, sourceType,
4514             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4515
4516   }
4517
4518   @Override
4519   public void refreshFeatureUI(boolean enableIfNecessary)
4520   {
4521     // note - currently this is only still here rather than in the controller
4522     // because of the featureSettings hard reference that is yet to be
4523     // abstracted
4524     if (enableIfNecessary)
4525     {
4526       viewport.setShowSequenceFeatures(true);
4527       showSeqFeatures.setSelected(true);
4528     }
4529
4530   }
4531
4532   @Override
4533   public void dragEnter(DropTargetDragEvent evt)
4534   {
4535   }
4536
4537   @Override
4538   public void dragExit(DropTargetEvent evt)
4539   {
4540   }
4541
4542   @Override
4543   public void dragOver(DropTargetDragEvent evt)
4544   {
4545   }
4546
4547   @Override
4548   public void dropActionChanged(DropTargetDragEvent evt)
4549   {
4550   }
4551
4552   @Override
4553   public void drop(DropTargetDropEvent evt)
4554   {
4555     // JAL-1552 - acceptDrop required before getTransferable call for
4556     // Java's Transferable for native dnd
4557     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4558     Transferable t = evt.getTransferable();
4559     List<String> files = new ArrayList<String>();
4560     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4561
4562     try
4563     {
4564       Desktop.transferFromDropTarget(files, protocols, evt, t);
4565     } catch (Exception e)
4566     {
4567       e.printStackTrace();
4568     }
4569     if (files != null)
4570     {
4571       try
4572       {
4573         // check to see if any of these files have names matching sequences in
4574         // the alignment
4575         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4576                 .getAlignment().getSequencesArray());
4577         /**
4578          * Object[] { String,SequenceI}
4579          */
4580         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4581         ArrayList<String> filesnotmatched = new ArrayList<String>();
4582         for (int i = 0; i < files.size(); i++)
4583         {
4584           String file = files.get(i).toString();
4585           String pdbfn = "";
4586           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4587           if (protocol == DataSourceType.FILE)
4588           {
4589             File fl = new File(file);
4590             pdbfn = fl.getName();
4591           }
4592           else if (protocol == DataSourceType.URL)
4593           {
4594             URL url = new URL(file);
4595             pdbfn = url.getFile();
4596           }
4597           if (pdbfn.length() > 0)
4598           {
4599             // attempt to find a match in the alignment
4600             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4601             int l = 0, c = pdbfn.indexOf(".");
4602             while (mtch == null && c != -1)
4603             {
4604               do
4605               {
4606                 l = c;
4607               } while ((c = pdbfn.indexOf(".", l)) > l);
4608               if (l > -1)
4609               {
4610                 pdbfn = pdbfn.substring(0, l);
4611               }
4612               mtch = idm.findAllIdMatches(pdbfn);
4613             }
4614             if (mtch != null)
4615             {
4616               FileFormatI type = null;
4617               try
4618               {
4619                 type = new IdentifyFile().identify(file, protocol);
4620               } catch (Exception ex)
4621               {
4622                 type = null;
4623               }
4624               if (type != null && type.isStructureFile())
4625               {
4626                 filesmatched.add(new Object[] { file, protocol, mtch });
4627                 continue;
4628               }
4629             }
4630             // File wasn't named like one of the sequences or wasn't a PDB file.
4631             filesnotmatched.add(file);
4632           }
4633         }
4634         int assocfiles = 0;
4635         if (filesmatched.size() > 0)
4636         {
4637           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4638                   || JvOptionPane
4639                           .showConfirmDialog(
4640                                   this,
4641                                   MessageManager
4642                                           .formatMessage(
4643                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4644                                                   new Object[] { Integer
4645                                                           .valueOf(
4646                                                                   filesmatched
4647                                                                           .size())
4648                                                           .toString() }),
4649                                   MessageManager
4650                                           .getString("label.automatically_associate_structure_files_by_name"),
4651                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4652
4653           {
4654             for (Object[] fm : filesmatched)
4655             {
4656               // try and associate
4657               // TODO: may want to set a standard ID naming formalism for
4658               // associating PDB files which have no IDs.
4659               for (SequenceI toassoc : (SequenceI[]) fm[2])
4660               {
4661                 PDBEntry pe = new AssociatePdbFileWithSeq()
4662                         .associatePdbWithSeq((String) fm[0],
4663                                 (DataSourceType) fm[1], toassoc, false,
4664                                 Desktop.instance);
4665                 if (pe != null)
4666                 {
4667                   System.err.println("Associated file : "
4668                           + ((String) fm[0]) + " with "
4669                           + toassoc.getDisplayId(true));
4670                   assocfiles++;
4671                 }
4672               }
4673               alignPanel.paintAlignment(true);
4674             }
4675           }
4676         }
4677         if (filesnotmatched.size() > 0)
4678         {
4679           if (assocfiles > 0
4680                   && (Cache.getDefault(
4681                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4682                           .showConfirmDialog(
4683                                   this,
4684                                   "<html>"
4685                                           + MessageManager
4686                                                   .formatMessage(
4687                                                           "label.ignore_unmatched_dropped_files_info",
4688                                                           new Object[] { Integer
4689                                                                   .valueOf(
4690                                                                           filesnotmatched
4691                                                                                   .size())
4692                                                                   .toString() })
4693                                           + "</html>",
4694                                   MessageManager
4695                                           .getString("label.ignore_unmatched_dropped_files"),
4696                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4697           {
4698             return;
4699           }
4700           for (String fn : filesnotmatched)
4701           {
4702             loadJalviewDataFile(fn, null, null, null);
4703           }
4704
4705         }
4706       } catch (Exception ex)
4707       {
4708         ex.printStackTrace();
4709       }
4710     }
4711   }
4712
4713   /**
4714    * Attempt to load a "dropped" file or URL string: First by testing whether
4715    * it's an Annotation file, then a JNet file, and finally a features file. If
4716    * all are false then the user may have dropped an alignment file onto this
4717    * AlignFrame.
4718    *
4719    * @param file
4720    *          either a filename or a URL string.
4721    */
4722   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4723           FileFormatI format, SequenceI assocSeq)
4724   {
4725     try
4726     {
4727       if (sourceType == null)
4728       {
4729         sourceType = FormatAdapter.checkProtocol(file);
4730       }
4731       // if the file isn't identified, or not positively identified as some
4732       // other filetype (PFAM is default unidentified alignment file type) then
4733       // try to parse as annotation.
4734       boolean isAnnotation = (format == null || FileFormat.Pfam
4735               .equals(format)) ? new AnnotationFile()
4736               .annotateAlignmentView(viewport, file, sourceType) : false;
4737
4738       if (!isAnnotation)
4739       {
4740         // first see if its a T-COFFEE score file
4741         TCoffeeScoreFile tcf = null;
4742         try
4743         {
4744           tcf = new TCoffeeScoreFile(file, sourceType);
4745           if (tcf.isValid())
4746           {
4747             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4748             {
4749               buildColourMenu();
4750               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4751               isAnnotation = true;
4752               statusBar
4753                       .setText(MessageManager
4754                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4755             }
4756             else
4757             {
4758               // some problem - if no warning its probable that the ID matching
4759               // process didn't work
4760               JvOptionPane
4761                       .showMessageDialog(
4762                               Desktop.desktop,
4763                               tcf.getWarningMessage() == null ? MessageManager
4764                                       .getString("label.check_file_matches_sequence_ids_alignment")
4765                                       : tcf.getWarningMessage(),
4766                               MessageManager
4767                                       .getString("label.problem_reading_tcoffee_score_file"),
4768                               JvOptionPane.WARNING_MESSAGE);
4769             }
4770           }
4771           else
4772           {
4773             tcf = null;
4774           }
4775         } catch (Exception x)
4776         {
4777           Cache.log
4778                   .debug("Exception when processing data source as T-COFFEE score file",
4779                           x);
4780           tcf = null;
4781         }
4782         if (tcf == null)
4783         {
4784           // try to see if its a JNet 'concise' style annotation file *before*
4785           // we
4786           // try to parse it as a features file
4787           if (format == null)
4788           {
4789             format = new IdentifyFile().identify(file, sourceType);
4790           }
4791           if (FileFormat.Jnet.equals(format))
4792           {
4793             JPredFile predictions = new JPredFile(
4794                     file, sourceType);
4795             new JnetAnnotationMaker();
4796             JnetAnnotationMaker.add_annotation(predictions,
4797                     viewport.getAlignment(), 0, false);
4798             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4799             viewport.getAlignment().setSeqrep(repseq);
4800             ColumnSelection cs = new ColumnSelection();
4801             cs.hideInsertionsFor(repseq);
4802             viewport.setColumnSelection(cs);
4803             isAnnotation = true;
4804           }
4805           // else if (IdentifyFile.FeaturesFile.equals(format))
4806           else if (FileFormat.Features.equals(format))
4807           {
4808             if (parseFeaturesFile(file, sourceType))
4809             {
4810               alignPanel.paintAlignment(true);
4811             }
4812           }
4813           else
4814           {
4815             new FileLoader().LoadFile(viewport, file, sourceType, format);
4816           }
4817         }
4818       }
4819       if (isAnnotation)
4820       {
4821
4822         alignPanel.adjustAnnotationHeight();
4823         viewport.updateSequenceIdColours();
4824         buildSortByAnnotationScoresMenu();
4825         alignPanel.paintAlignment(true);
4826       }
4827     } catch (Exception ex)
4828     {
4829       ex.printStackTrace();
4830     } catch (OutOfMemoryError oom)
4831     {
4832       try
4833       {
4834         System.gc();
4835       } catch (Exception x)
4836       {
4837       }
4838       new OOMWarning(
4839               "loading data "
4840                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4841                               : "using " + sourceType + " from " + file)
4842                               : ".")
4843                       + (format != null ? "(parsing as '" + format
4844                               + "' file)" : ""), oom, Desktop.desktop);
4845     }
4846   }
4847
4848   /**
4849    * Method invoked by the ChangeListener on the tabbed pane, in other words
4850    * when a different tabbed pane is selected by the user or programmatically.
4851    */
4852   @Override
4853   public void tabSelectionChanged(int index)
4854   {
4855     if (index > -1)
4856     {
4857       alignPanel = alignPanels.get(index);
4858       viewport = alignPanel.av;
4859       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4860       setMenusFromViewport(viewport);
4861     }
4862
4863     /*
4864      * If there is a frame linked to this one in a SplitPane, switch it to the
4865      * same view tab index. No infinite recursion of calls should happen, since
4866      * tabSelectionChanged() should not get invoked on setting the selected
4867      * index to an unchanged value. Guard against setting an invalid index
4868      * before the new view peer tab has been created.
4869      */
4870     final AlignViewportI peer = viewport.getCodingComplement();
4871     if (peer != null)
4872     {
4873       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4874       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4875       {
4876         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4877       }
4878     }
4879   }
4880
4881   /**
4882    * On right mouse click on view tab, prompt for and set new view name.
4883    */
4884   @Override
4885   public void tabbedPane_mousePressed(MouseEvent e)
4886   {
4887     if (e.isPopupTrigger())
4888     {
4889       String msg = MessageManager.getString("label.enter_view_name");
4890       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4891               JvOptionPane.QUESTION_MESSAGE);
4892
4893       if (reply != null)
4894       {
4895         viewport.viewName = reply;
4896         // TODO warn if reply is in getExistingViewNames()?
4897         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4898       }
4899     }
4900   }
4901
4902   public AlignViewport getCurrentView()
4903   {
4904     return viewport;
4905   }
4906
4907   /**
4908    * Open the dialog for regex description parsing.
4909    */
4910   @Override
4911   protected void extractScores_actionPerformed(ActionEvent e)
4912   {
4913     ParseProperties pp = new jalview.analysis.ParseProperties(
4914             viewport.getAlignment());
4915     // TODO: verify regex and introduce GUI dialog for version 2.5
4916     // if (pp.getScoresFromDescription("col", "score column ",
4917     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4918     // true)>0)
4919     if (pp.getScoresFromDescription("description column",
4920             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4921     {
4922       buildSortByAnnotationScoresMenu();
4923     }
4924   }
4925
4926   /*
4927    * (non-Javadoc)
4928    *
4929    * @see
4930    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4931    * )
4932    */
4933   @Override
4934   protected void showDbRefs_actionPerformed(ActionEvent e)
4935   {
4936     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4937   }
4938
4939   /*
4940    * (non-Javadoc)
4941    *
4942    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4943    * ActionEvent)
4944    */
4945   @Override
4946   protected void showNpFeats_actionPerformed(ActionEvent e)
4947   {
4948     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4949   }
4950
4951   /**
4952    * find the viewport amongst the tabs in this alignment frame and close that
4953    * tab
4954    *
4955    * @param av
4956    */
4957   public boolean closeView(AlignViewportI av)
4958   {
4959     if (viewport == av)
4960     {
4961       this.closeMenuItem_actionPerformed(false);
4962       return true;
4963     }
4964     Component[] comp = tabbedPane.getComponents();
4965     for (int i = 0; comp != null && i < comp.length; i++)
4966     {
4967       if (comp[i] instanceof AlignmentPanel)
4968       {
4969         if (((AlignmentPanel) comp[i]).av == av)
4970         {
4971           // close the view.
4972           closeView((AlignmentPanel) comp[i]);
4973           return true;
4974         }
4975       }
4976     }
4977     return false;
4978   }
4979
4980   protected void build_fetchdbmenu(JMenu webService)
4981   {
4982     // Temporary hack - DBRef Fetcher always top level ws entry.
4983     // TODO We probably want to store a sequence database checklist in
4984     // preferences and have checkboxes.. rather than individual sources selected
4985     // here
4986     final JMenu rfetch = new JMenu(
4987             MessageManager.getString("action.fetch_db_references"));
4988     rfetch.setToolTipText(MessageManager
4989             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4990     webService.add(rfetch);
4991
4992     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4993             MessageManager.getString("option.trim_retrieved_seqs"));
4994     trimrs.setToolTipText(MessageManager
4995             .getString("label.trim_retrieved_sequences"));
4996     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4997     trimrs.addActionListener(new ActionListener()
4998     {
4999       @Override
5000       public void actionPerformed(ActionEvent e)
5001       {
5002         trimrs.setSelected(trimrs.isSelected());
5003         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5004                 Boolean.valueOf(trimrs.isSelected()).toString());
5005       };
5006     });
5007     rfetch.add(trimrs);
5008     JMenuItem fetchr = new JMenuItem(
5009             MessageManager.getString("label.standard_databases"));
5010     fetchr.setToolTipText(MessageManager
5011             .getString("label.fetch_embl_uniprot"));
5012     fetchr.addActionListener(new ActionListener()
5013     {
5014
5015       @Override
5016       public void actionPerformed(ActionEvent e)
5017       {
5018         new Thread(new Runnable()
5019         {
5020           @Override
5021           public void run()
5022           {
5023             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5024                     .getAlignment().isNucleotide();
5025             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5026                     .getSequenceSelection(), alignPanel.alignFrame, null,
5027                     alignPanel.alignFrame.featureSettings, isNucleotide);
5028             dbRefFetcher.addListener(new FetchFinishedListenerI()
5029             {
5030               @Override
5031               public void finished()
5032               {
5033                 AlignFrame.this.setMenusForViewport();
5034               }
5035             });
5036             dbRefFetcher.fetchDBRefs(false);
5037           }
5038         }).start();
5039
5040       }
5041
5042     });
5043     rfetch.add(fetchr);
5044     final AlignFrame me = this;
5045     new Thread(new Runnable()
5046     {
5047       @Override
5048       public void run()
5049       {
5050         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5051                 .getSequenceFetcherSingleton(me);
5052         javax.swing.SwingUtilities.invokeLater(new Runnable()
5053         {
5054           @Override
5055           public void run()
5056           {
5057             String[] dbclasses = sf.getOrderedSupportedSources();
5058             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5059             // jalview.util.QuickSort.sort(otherdb, otherdb);
5060             List<DbSourceProxy> otherdb;
5061             JMenu dfetch = new JMenu();
5062             JMenu ifetch = new JMenu();
5063             JMenuItem fetchr = null;
5064             int comp = 0, icomp = 0, mcomp = 15;
5065             String mname = null;
5066             int dbi = 0;
5067             for (String dbclass : dbclasses)
5068             {
5069               otherdb = sf.getSourceProxy(dbclass);
5070               // add a single entry for this class, or submenu allowing 'fetch
5071               // all' or pick one
5072               if (otherdb == null || otherdb.size() < 1)
5073               {
5074                 continue;
5075               }
5076               // List<DbSourceProxy> dbs=otherdb;
5077               // otherdb=new ArrayList<DbSourceProxy>();
5078               // for (DbSourceProxy db:dbs)
5079               // {
5080               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5081               // }
5082               if (mname == null)
5083               {
5084                 mname = "From " + dbclass;
5085               }
5086               if (otherdb.size() == 1)
5087               {
5088                 final DbSourceProxy[] dassource = otherdb
5089                         .toArray(new DbSourceProxy[0]);
5090                 DbSourceProxy src = otherdb.get(0);
5091                 fetchr = new JMenuItem(src.getDbSource());
5092                 fetchr.addActionListener(new ActionListener()
5093                 {
5094
5095                   @Override
5096                   public void actionPerformed(ActionEvent e)
5097                   {
5098                     new Thread(new Runnable()
5099                     {
5100
5101                       @Override
5102                       public void run()
5103                       {
5104                         boolean isNucleotide = alignPanel.alignFrame
5105                                 .getViewport().getAlignment()
5106                                 .isNucleotide();
5107                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5108                                 alignPanel.av.getSequenceSelection(),
5109                                 alignPanel.alignFrame, dassource,
5110                                 alignPanel.alignFrame.featureSettings,
5111                                 isNucleotide);
5112                         dbRefFetcher
5113                                 .addListener(new FetchFinishedListenerI()
5114                                 {
5115                                   @Override
5116                                   public void finished()
5117                                   {
5118                                     AlignFrame.this.setMenusForViewport();
5119                                   }
5120                                 });
5121                         dbRefFetcher.fetchDBRefs(false);
5122                       }
5123                     }).start();
5124                   }
5125
5126                 });
5127                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5128                         MessageManager.formatMessage(
5129                                 "label.fetch_retrieve_from",
5130                                 new Object[] { src.getDbName() })));
5131                 dfetch.add(fetchr);
5132                 comp++;
5133               }
5134               else
5135               {
5136                 final DbSourceProxy[] dassource = otherdb
5137                         .toArray(new DbSourceProxy[0]);
5138                 // fetch all entry
5139                 DbSourceProxy src = otherdb.get(0);
5140                 fetchr = new JMenuItem(MessageManager.formatMessage(
5141                         "label.fetch_all_param",
5142                         new Object[] { src.getDbSource() }));
5143                 fetchr.addActionListener(new ActionListener()
5144                 {
5145                   @Override
5146                   public void actionPerformed(ActionEvent e)
5147                   {
5148                     new Thread(new Runnable()
5149                     {
5150
5151                       @Override
5152                       public void run()
5153                       {
5154                         boolean isNucleotide = alignPanel.alignFrame
5155                                 .getViewport().getAlignment()
5156                                 .isNucleotide();
5157                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5158                                 alignPanel.av.getSequenceSelection(),
5159                                 alignPanel.alignFrame, dassource,
5160                                 alignPanel.alignFrame.featureSettings,
5161                                 isNucleotide);
5162                         dbRefFetcher
5163                                 .addListener(new FetchFinishedListenerI()
5164                                 {
5165                                   @Override
5166                                   public void finished()
5167                                   {
5168                                     AlignFrame.this.setMenusForViewport();
5169                                   }
5170                                 });
5171                         dbRefFetcher.fetchDBRefs(false);
5172                       }
5173                     }).start();
5174                   }
5175                 });
5176
5177                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5178                         MessageManager.formatMessage(
5179                                 "label.fetch_retrieve_from_all_sources",
5180                                 new Object[] {
5181                                     Integer.valueOf(otherdb.size())
5182                                             .toString(), src.getDbSource(),
5183                                     src.getDbName() })));
5184                 dfetch.add(fetchr);
5185                 comp++;
5186                 // and then build the rest of the individual menus
5187                 ifetch = new JMenu(MessageManager.formatMessage(
5188                         "label.source_from_db_source",
5189                         new Object[] { src.getDbSource() }));
5190                 icomp = 0;
5191                 String imname = null;
5192                 int i = 0;
5193                 for (DbSourceProxy sproxy : otherdb)
5194                 {
5195                   String dbname = sproxy.getDbName();
5196                   String sname = dbname.length() > 5 ? dbname.substring(0,
5197                           5) + "..." : dbname;
5198                   String msname = dbname.length() > 10 ? dbname.substring(
5199                           0, 10) + "..." : dbname;
5200                   if (imname == null)
5201                   {
5202                     imname = MessageManager.formatMessage(
5203                             "label.from_msname", new Object[] { sname });
5204                   }
5205                   fetchr = new JMenuItem(msname);
5206                   final DbSourceProxy[] dassrc = { sproxy };
5207                   fetchr.addActionListener(new ActionListener()
5208                   {
5209
5210                     @Override
5211                     public void actionPerformed(ActionEvent e)
5212                     {
5213                       new Thread(new Runnable()
5214                       {
5215
5216                         @Override
5217                         public void run()
5218                         {
5219                           boolean isNucleotide = alignPanel.alignFrame
5220                                   .getViewport().getAlignment()
5221                                   .isNucleotide();
5222                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5223                                   alignPanel.av.getSequenceSelection(),
5224                                   alignPanel.alignFrame, dassrc,
5225                                   alignPanel.alignFrame.featureSettings,
5226                                   isNucleotide);
5227                           dbRefFetcher
5228                                   .addListener(new FetchFinishedListenerI()
5229                                   {
5230                                     @Override
5231                                     public void finished()
5232                                     {
5233                                       AlignFrame.this.setMenusForViewport();
5234                                     }
5235                                   });
5236                           dbRefFetcher.fetchDBRefs(false);
5237                         }
5238                       }).start();
5239                     }
5240
5241                   });
5242                   fetchr.setToolTipText("<html>"
5243                           + MessageManager.formatMessage(
5244                                   "label.fetch_retrieve_from", new Object[]
5245                                   { dbname }));
5246                   ifetch.add(fetchr);
5247                   ++i;
5248                   if (++icomp >= mcomp || i == (otherdb.size()))
5249                   {
5250                     ifetch.setText(MessageManager.formatMessage(
5251                             "label.source_to_target", imname, sname));
5252                     dfetch.add(ifetch);
5253                     ifetch = new JMenu();
5254                     imname = null;
5255                     icomp = 0;
5256                     comp++;
5257                   }
5258                 }
5259               }
5260               ++dbi;
5261               if (comp >= mcomp || dbi >= (dbclasses.length))
5262               {
5263                 dfetch.setText(MessageManager.formatMessage(
5264                         "label.source_to_target", mname, dbclass));
5265                 rfetch.add(dfetch);
5266                 dfetch = new JMenu();
5267                 mname = null;
5268                 comp = 0;
5269               }
5270             }
5271           }
5272         });
5273       }
5274     }).start();
5275
5276   }
5277
5278   /**
5279    * Left justify the whole alignment.
5280    */
5281   @Override
5282   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5283   {
5284     AlignmentI al = viewport.getAlignment();
5285     al.justify(false);
5286     viewport.firePropertyChange("alignment", null, al);
5287   }
5288
5289   /**
5290    * Right justify the whole alignment.
5291    */
5292   @Override
5293   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5294   {
5295     AlignmentI al = viewport.getAlignment();
5296     al.justify(true);
5297     viewport.firePropertyChange("alignment", null, al);
5298   }
5299
5300   @Override
5301   public void setShowSeqFeatures(boolean b)
5302   {
5303     showSeqFeatures.setSelected(b);
5304     viewport.setShowSequenceFeatures(b);
5305   }
5306
5307   /*
5308    * (non-Javadoc)
5309    *
5310    * @see
5311    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5312    * awt.event.ActionEvent)
5313    */
5314   @Override
5315   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5316   {
5317     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5318     alignPanel.paintAlignment(true);
5319   }
5320
5321   /*
5322    * (non-Javadoc)
5323    *
5324    * @see
5325    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5326    * .ActionEvent)
5327    */
5328   @Override
5329   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5330   {
5331     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5332     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5333
5334   }
5335
5336   /*
5337    * (non-Javadoc)
5338    *
5339    * @see
5340    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5341    * .event.ActionEvent)
5342    */
5343   @Override
5344   protected void showGroupConservation_actionPerformed(ActionEvent e)
5345   {
5346     viewport.setShowGroupConservation(showGroupConservation.getState());
5347     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5348   }
5349
5350   /*
5351    * (non-Javadoc)
5352    *
5353    * @see
5354    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5355    * .event.ActionEvent)
5356    */
5357   @Override
5358   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5359   {
5360     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5361     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5362   }
5363
5364   /*
5365    * (non-Javadoc)
5366    *
5367    * @see
5368    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5369    * .event.ActionEvent)
5370    */
5371   @Override
5372   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5373   {
5374     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5375     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5376   }
5377
5378   @Override
5379   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5380   {
5381     showSequenceLogo.setState(true);
5382     viewport.setShowSequenceLogo(true);
5383     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5384     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5385   }
5386
5387   @Override
5388   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5389   {
5390     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5391   }
5392
5393   /*
5394    * (non-Javadoc)
5395    *
5396    * @see
5397    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5398    * .event.ActionEvent)
5399    */
5400   @Override
5401   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5402   {
5403     if (avc.makeGroupsFromSelection())
5404     {
5405       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5406       alignPanel.updateAnnotation();
5407       alignPanel.paintAlignment(true);
5408     }
5409   }
5410
5411   public void clearAlignmentSeqRep()
5412   {
5413     // TODO refactor alignmentseqrep to controller
5414     if (viewport.getAlignment().hasSeqrep())
5415     {
5416       viewport.getAlignment().setSeqrep(null);
5417       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5418       alignPanel.updateAnnotation();
5419       alignPanel.paintAlignment(true);
5420     }
5421   }
5422
5423   @Override
5424   protected void createGroup_actionPerformed(ActionEvent e)
5425   {
5426     if (avc.createGroup())
5427     {
5428       alignPanel.alignmentChanged();
5429     }
5430   }
5431
5432   @Override
5433   protected void unGroup_actionPerformed(ActionEvent e)
5434   {
5435     if (avc.unGroup())
5436     {
5437       alignPanel.alignmentChanged();
5438     }
5439   }
5440
5441   /**
5442    * make the given alignmentPanel the currently selected tab
5443    *
5444    * @param alignmentPanel
5445    */
5446   public void setDisplayedView(AlignmentPanel alignmentPanel)
5447   {
5448     if (!viewport.getSequenceSetId().equals(
5449             alignmentPanel.av.getSequenceSetId()))
5450     {
5451       throw new Error(
5452               MessageManager
5453                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5454     }
5455     if (tabbedPane != null
5456             && tabbedPane.getTabCount() > 0
5457             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5458                     .getSelectedIndex())
5459     {
5460       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5461     }
5462   }
5463
5464   /**
5465    * Action on selection of menu options to Show or Hide annotations.
5466    *
5467    * @param visible
5468    * @param forSequences
5469    *          update sequence-related annotations
5470    * @param forAlignment
5471    *          update non-sequence-related annotations
5472    */
5473   @Override
5474   protected void setAnnotationsVisibility(boolean visible,
5475           boolean forSequences, boolean forAlignment)
5476   {
5477     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5478             .getAlignmentAnnotation();
5479     if (anns == null)
5480     {
5481       return;
5482     }
5483     for (AlignmentAnnotation aa : anns)
5484     {
5485       /*
5486        * don't display non-positional annotations on an alignment
5487        */
5488       if (aa.annotations == null)
5489       {
5490         continue;
5491       }
5492       boolean apply = (aa.sequenceRef == null && forAlignment)
5493               || (aa.sequenceRef != null && forSequences);
5494       if (apply)
5495       {
5496         aa.visible = visible;
5497       }
5498     }
5499     alignPanel.validateAnnotationDimensions(true);
5500     alignPanel.alignmentChanged();
5501   }
5502
5503   /**
5504    * Store selected annotation sort order for the view and repaint.
5505    */
5506   @Override
5507   protected void sortAnnotations_actionPerformed()
5508   {
5509     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5510     this.alignPanel.av
5511             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5512     alignPanel.paintAlignment(true);
5513   }
5514
5515   /**
5516    *
5517    * @return alignment panels in this alignment frame
5518    */
5519   public List<? extends AlignmentViewPanel> getAlignPanels()
5520   {
5521     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5522   }
5523
5524   /**
5525    * Open a new alignment window, with the cDNA associated with this (protein)
5526    * alignment, aligned as is the protein.
5527    */
5528   protected void viewAsCdna_actionPerformed()
5529   {
5530     // TODO no longer a menu action - refactor as required
5531     final AlignmentI alignment = getViewport().getAlignment();
5532     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5533     if (mappings == null)
5534     {
5535       return;
5536     }
5537     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5538     for (SequenceI aaSeq : alignment.getSequences())
5539     {
5540       for (AlignedCodonFrame acf : mappings)
5541       {
5542         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5543         if (dnaSeq != null)
5544         {
5545           /*
5546            * There is a cDNA mapping for this protein sequence - add to new
5547            * alignment. It will share the same dataset sequence as other mapped
5548            * cDNA (no new mappings need to be created).
5549            */
5550           final Sequence newSeq = new Sequence(dnaSeq);
5551           newSeq.setDatasetSequence(dnaSeq);
5552           cdnaSeqs.add(newSeq);
5553         }
5554       }
5555     }
5556     if (cdnaSeqs.size() == 0)
5557     {
5558       // show a warning dialog no mapped cDNA
5559       return;
5560     }
5561     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5562             .size()]));
5563     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5564             AlignFrame.DEFAULT_HEIGHT);
5565     cdna.alignAs(alignment);
5566     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5567             + this.title;
5568     Desktop.addInternalFrame(alignFrame, newtitle,
5569             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5570   }
5571
5572   /**
5573    * Set visibility of dna/protein complement view (available when shown in a
5574    * split frame).
5575    *
5576    * @param show
5577    */
5578   @Override
5579   protected void showComplement_actionPerformed(boolean show)
5580   {
5581     SplitContainerI sf = getSplitViewContainer();
5582     if (sf != null)
5583     {
5584       sf.setComplementVisible(this, show);
5585     }
5586   }
5587
5588   /**
5589    * Generate the reverse (optionally complemented) of the selected sequences,
5590    * and add them to the alignment
5591    */
5592   @Override
5593   protected void showReverse_actionPerformed(boolean complement)
5594   {
5595     AlignmentI al = null;
5596     try
5597     {
5598       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5599       al = dna.reverseCdna(complement);
5600       viewport.addAlignment(al, "");
5601       addHistoryItem(new EditCommand(
5602               MessageManager.getString("label.add_sequences"),
5603               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5604               viewport.getAlignment()));
5605     } catch (Exception ex)
5606     {
5607       System.err.println(ex.getMessage());
5608       return;
5609     }
5610   }
5611
5612   /**
5613    * Try to run a script in the Groovy console, having first ensured that this
5614    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5615    * be targeted at this alignment.
5616    */
5617   @Override
5618   protected void runGroovy_actionPerformed()
5619   {
5620     Jalview.setCurrentAlignFrame(this);
5621     groovy.ui.Console console = Desktop.getGroovyConsole();
5622     if (console != null)
5623     {
5624       try
5625       {
5626         console.runScript();
5627       } catch (Exception ex)
5628       {
5629         System.err.println((ex.toString()));
5630         JvOptionPane
5631                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5632                         .getString("label.couldnt_run_groovy_script"),
5633                         MessageManager
5634                                 .getString("label.groovy_support_failed"),
5635                         JvOptionPane.ERROR_MESSAGE);
5636       }
5637     }
5638     else
5639     {
5640       System.err.println("Can't run Groovy script as console not found");
5641     }
5642   }
5643
5644   /**
5645    * Hides columns containing (or not containing) a specified feature, provided
5646    * that would not leave all columns hidden
5647    *
5648    * @param featureType
5649    * @param columnsContaining
5650    * @return
5651    */
5652   public boolean hideFeatureColumns(String featureType,
5653           boolean columnsContaining)
5654   {
5655     boolean notForHiding = avc.markColumnsContainingFeatures(
5656             columnsContaining, false, false, featureType);
5657     if (notForHiding)
5658     {
5659       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5660               false, featureType))
5661       {
5662         getViewport().hideSelectedColumns();
5663         return true;
5664       }
5665     }
5666     return false;
5667   }
5668
5669   @Override
5670   protected void selectHighlightedColumns_actionPerformed(
5671           ActionEvent actionEvent)
5672   {
5673     // include key modifier check in case user selects from menu
5674     avc.markHighlightedColumns(
5675             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5676             true,
5677             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5678   }
5679
5680   /**
5681    * Rebuilds the Colour menu, including any user-defined colours which have
5682    * been loaded either on startup or during the session
5683    */
5684   public void buildColourMenu()
5685   {
5686     colourMenu.removeAll();
5687
5688     colourMenu.add(applyToAllGroups);
5689     colourMenu.add(textColour);
5690     colourMenu.addSeparator();
5691
5692     ColourMenuHelper.addMenuItems(colourMenu, this,
5693             viewport.getAlignment(), false);
5694
5695     colourMenu.addSeparator();
5696     colourMenu.add(conservationMenuItem);
5697     colourMenu.add(modifyConservation);
5698     colourMenu.add(abovePIDThreshold);
5699     colourMenu.add(modifyPID);
5700     colourMenu.add(annotationColour);
5701
5702     /*
5703      * select the default colour for the alignment (this may be
5704      * overridden later)
5705      */
5706     boolean nucleotide = viewport.getAlignment().isNucleotide();
5707     String defaultColourScheme = Cache.getDefault(
5708             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
5709                     : Preferences.DEFAULT_COLOUR_PROT,
5710             ResidueColourScheme.NONE);
5711
5712     ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
5713   }
5714 }
5715
5716 class PrintThread extends Thread
5717 {
5718   AlignmentPanel ap;
5719
5720   public PrintThread(AlignmentPanel ap)
5721   {
5722     this.ap = ap;
5723   }
5724
5725   static PageFormat pf;
5726
5727   @Override
5728   public void run()
5729   {
5730     PrinterJob printJob = PrinterJob.getPrinterJob();
5731
5732     if (pf != null)
5733     {
5734       printJob.setPrintable(ap, pf);
5735     }
5736     else
5737     {
5738       printJob.setPrintable(ap);
5739     }
5740
5741     if (printJob.printDialog())
5742     {
5743       try
5744       {
5745         printJob.print();
5746       } catch (Exception PrintException)
5747       {
5748         PrintException.printStackTrace();
5749       }
5750     }
5751   }
5752 }