src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  63 import jalview.io.AlignmentProperties;
  64 import jalview.io.AnnotationFile;
  65 import jalview.io.BioJsHTMLOutput;
  66 import jalview.io.DataSourceType;
  67 import jalview.io.FileFormat;
  68 import jalview.io.FileFormatI;
  69 import jalview.io.FileLoader;
  70 import jalview.io.FormatAdapter;
  71 import jalview.io.HtmlSvgOutput;
  72 import jalview.io.IdentifyFile;
  73 import jalview.io.JPredFile;
  74 import jalview.io.JalviewFileChooser;
  75 import jalview.io.JalviewFileView;
  76 import jalview.io.JnetAnnotationMaker;
  77 import jalview.io.NewickFile;
  78 import jalview.io.TCoffeeScoreFile;
  79 import jalview.jbgui.GAlignFrame;
  80 import jalview.schemes.Blosum62ColourScheme;
  81 import jalview.schemes.BuriedColourScheme;
  82 import jalview.schemes.ClustalxColourScheme;
  83 import jalview.schemes.ColourSchemeI;
  84 import jalview.schemes.ColourSchemeProperty;
  85 import jalview.schemes.HelixColourScheme;
  86 import jalview.schemes.HydrophobicColourScheme;
  87 import jalview.schemes.NucleotideColourScheme;
  88 import jalview.schemes.PIDColourScheme;
  89 import jalview.schemes.PurinePyrimidineColourScheme;
  90 import jalview.schemes.RNAHelicesColour;
  91 import jalview.schemes.RNAHelicesColourChooser;
  92 import jalview.schemes.ResidueColourScheme;
  93 import jalview.schemes.ResidueProperties;
  94 import jalview.schemes.StrandColourScheme;
  95 import jalview.schemes.TCoffeeColourScheme;
  96 import jalview.schemes.TaylorColourScheme;
  97 import jalview.schemes.TurnColourScheme;
  98 import jalview.schemes.UserColourScheme;
  99 import jalview.schemes.ZappoColourScheme;
 100 import jalview.util.MessageManager;
 101 import jalview.viewmodel.AlignmentViewport;
 102 import jalview.ws.DBRefFetcher;
 103 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 104 import jalview.ws.jws1.Discoverer;
 105 import jalview.ws.jws2.Jws2Discoverer;
 106 import jalview.ws.jws2.jabaws2.Jws2Instance;
 107 import jalview.ws.seqfetcher.DbSourceProxy;
 108
 109 import java.awt.BorderLayout;
 110 import java.awt.Component;
 111 import java.awt.Rectangle;
 112 import java.awt.Toolkit;
 113 import java.awt.datatransfer.Clipboard;
 114 import java.awt.datatransfer.DataFlavor;
 115 import java.awt.datatransfer.StringSelection;
 116 import java.awt.datatransfer.Transferable;
 117 import java.awt.dnd.DnDConstants;
 118 import java.awt.dnd.DropTargetDragEvent;
 119 import java.awt.dnd.DropTargetDropEvent;
 120 import java.awt.dnd.DropTargetEvent;
 121 import java.awt.dnd.DropTargetListener;
 122 import java.awt.event.ActionEvent;
 123 import java.awt.event.ActionListener;
 124 import java.awt.event.FocusAdapter;
 125 import java.awt.event.FocusEvent;
 126 import java.awt.event.ItemEvent;
 127 import java.awt.event.ItemListener;
 128 import java.awt.event.KeyAdapter;
 129 import java.awt.event.KeyEvent;
 130 import java.awt.event.MouseEvent;
 131 import java.awt.print.PageFormat;
 132 import java.awt.print.PrinterJob;
 133 import java.beans.PropertyChangeEvent;
 134 import java.io.File;
 135 import java.net.URL;
 136 import java.util.ArrayList;
 137 import java.util.Arrays;
 138 import java.util.Deque;
 139 import java.util.Enumeration;
 140 import java.util.Hashtable;
 141 import java.util.List;
 142 import java.util.Vector;
 143
 144 import javax.swing.JCheckBoxMenuItem;
 145 import javax.swing.JEditorPane;
 146 import javax.swing.JInternalFrame;
 147 import javax.swing.JLayeredPane;
 148 import javax.swing.JMenu;
 149 import javax.swing.JMenuItem;
 150 import javax.swing.JScrollPane;
 151 import javax.swing.SwingUtilities;
 152
 153 /**
 154  * DOCUMENT ME!
 155  *
 156  * @author $author$
 157  * @version $Revision$
 158  */
 159 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 160         IProgressIndicator, AlignViewControllerGuiI
 161 {
 162
 163   public static final int DEFAULT_WIDTH = 700;
 164
 165   public static final int DEFAULT_HEIGHT = 500;
 166
 167   /*
 168    * The currently displayed panel (selected tabbed view if more than one)
 169    */
 170   public AlignmentPanel alignPanel;
 171
 172   AlignViewport viewport;
 173
 174   public AlignViewControllerI avc;
 175
 176   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 177
 178   /**
 179    * Last format used to load or save alignments in this window
 180    */
 181   FileFormatI currentFileFormat = null;
 182
 183   /**
 184    * Current filename for this alignment
 185    */
 186   String fileName = null;
 187
 188   /**
 189    * Creates a new AlignFrame object with specific width and height.
 190    *
 191    * @param al
 192    * @param width
 193    * @param height
 194    */
 195   public AlignFrame(AlignmentI al, int width, int height)
 196   {
 197     this(al, null, width, height);
 198   }
 199
 200   /**
 201    * Creates a new AlignFrame object with specific width, height and
 202    * sequenceSetId
 203    *
 204    * @param al
 205    * @param width
 206    * @param height
 207    * @param sequenceSetId
 208    */
 209   public AlignFrame(AlignmentI al, int width, int height,
 210           String sequenceSetId)
 211   {
 212     this(al, null, width, height, sequenceSetId);
 213   }
 214
 215   /**
 216    * Creates a new AlignFrame object with specific width, height and
 217    * sequenceSetId
 218    *
 219    * @param al
 220    * @param width
 221    * @param height
 222    * @param sequenceSetId
 223    * @param viewId
 224    */
 225   public AlignFrame(AlignmentI al, int width, int height,
 226           String sequenceSetId, String viewId)
 227   {
 228     this(al, null, width, height, sequenceSetId, viewId);
 229   }
 230
 231   /**
 232    * new alignment window with hidden columns
 233    *
 234    * @param al
 235    *          AlignmentI
 236    * @param hiddenColumns
 237    *          ColumnSelection or null
 238    * @param width
 239    *          Width of alignment frame
 240    * @param height
 241    *          height of frame.
 242    */
 243   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 244           int width, int height)
 245   {
 246     this(al, hiddenColumns, width, height, null);
 247   }
 248
 249   /**
 250    * Create alignment frame for al with hiddenColumns, a specific width and
 251    * height, and specific sequenceId
 252    *
 253    * @param al
 254    * @param hiddenColumns
 255    * @param width
 256    * @param height
 257    * @param sequenceSetId
 258    *          (may be null)
 259    */
 260   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 261           int width, int height, String sequenceSetId)
 262   {
 263     this(al, hiddenColumns, width, height, sequenceSetId, null);
 264   }
 265
 266   /**
 267    * Create alignment frame for al with hiddenColumns, a specific width and
 268    * height, and specific sequenceId
 269    *
 270    * @param al
 271    * @param hiddenColumns
 272    * @param width
 273    * @param height
 274    * @param sequenceSetId
 275    *          (may be null)
 276    * @param viewId
 277    *          (may be null)
 278    */
 279   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 280           int width, int height, String sequenceSetId, String viewId)
 281   {
 282     setSize(width, height);
 283
 284     if (al.getDataset() == null)
 285     {
 286       al.setDataset(null);
 287     }
 288
 289     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 290
 291     alignPanel = new AlignmentPanel(this, viewport);
 292
 293     addAlignmentPanel(alignPanel, true);
 294     init();
 295   }
 296
 297   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 298           ColumnSelection hiddenColumns, int width, int height)
 299   {
 300     setSize(width, height);
 301
 302     if (al.getDataset() == null)
 303     {
 304       al.setDataset(null);
 305     }
 306
 307     viewport = new AlignViewport(al, hiddenColumns);
 308
 309     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 310     {
 311       viewport.hideSequence(hiddenSeqs);
 312     }
 313     alignPanel = new AlignmentPanel(this, viewport);
 314     addAlignmentPanel(alignPanel, true);
 315     init();
 316   }
 317
 318   /**
 319    * Make a new AlignFrame from existing alignmentPanels
 320    *
 321    * @param ap
 322    *          AlignmentPanel
 323    * @param av
 324    *          AlignViewport
 325    */
 326   public AlignFrame(AlignmentPanel ap)
 327   {
 328     viewport = ap.av;
 329     alignPanel = ap;
 330     addAlignmentPanel(ap, false);
 331     init();
 332   }
 333
 334   /**
 335    * initalise the alignframe from the underlying viewport data and the
 336    * configurations
 337    */
 338   void init()
 339   {
 340     if (!Jalview.isHeadlessMode())
 341     {
 342       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 343     }
 344
 345     avc = new jalview.controller.AlignViewController(this, viewport,
 346             alignPanel);
 347     if (viewport.getAlignmentConservationAnnotation() == null)
 348     {
 349       BLOSUM62Colour.setEnabled(false);
 350       conservationMenuItem.setEnabled(false);
 351       modifyConservation.setEnabled(false);
 352       // PIDColour.setEnabled(false);
 353       // abovePIDThreshold.setEnabled(false);
 354       // modifyPID.setEnabled(false);
 355     }
 356
 357     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 358             "No sort");
 359
 360     if (sortby.equals("Id"))
 361     {
 362       sortIDMenuItem_actionPerformed(null);
 363     }
 364     else if (sortby.equals("Pairwise Identity"))
 365     {
 366       sortPairwiseMenuItem_actionPerformed(null);
 367     }
 368
 369     if (Desktop.desktop != null)
 370     {
 371       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 372       addServiceListeners();
 373       setGUINucleotide(viewport.getAlignment().isNucleotide());
 374     }
 375
 376     this.alignPanel.av
 377             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 378
 379     setMenusFromViewport(viewport);
 380     buildSortByAnnotationScoresMenu();
 381     buildTreeMenu();
 382
 383     if (viewport.getWrapAlignment())
 384     {
 385       wrapMenuItem_actionPerformed(null);
 386     }
 387
 388     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 389     {
 390       this.overviewMenuItem_actionPerformed(null);
 391     }
 392
 393     addKeyListener();
 394
 395     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 396     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 397     final String menuLabel = MessageManager
 398             .getString("label.copy_format_from");
 399     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 400             new ViewSetProvider()
 401             {
 402
 403               @Override
 404               public AlignmentPanel[] getAllAlignmentPanels()
 405               {
 406                 origview.clear();
 407                 origview.add(alignPanel);
 408                 // make an array of all alignment panels except for this one
 409                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 410                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 411                 aps.remove(AlignFrame.this.alignPanel);
 412                 return aps.toArray(new AlignmentPanel[aps.size()]);
 413               }
 414             }, selviews, new ItemListener()
 415             {
 416
 417               @Override
 418               public void itemStateChanged(ItemEvent e)
 419               {
 420                 if (origview.size() > 0)
 421                 {
 422                   final AlignmentPanel ap = origview.get(0);
 423
 424                   /*
 425                    * Copy the ViewStyle of the selected panel to 'this one'.
 426                    * Don't change value of 'scaleProteinAsCdna' unless copying
 427                    * from a SplitFrame.
 428                    */
 429                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 430                           .getViewStyle();
 431                   boolean fromSplitFrame = selviews.get(0)
 432                           .getAlignViewport().getCodingComplement() != null;
 433                   if (!fromSplitFrame)
 434                   {
 435                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 436                             .getViewStyle().isScaleProteinAsCdna());
 437                   }
 438                   ap.getAlignViewport().setViewStyle(vs);
 439
 440                   /*
 441                    * Also rescale ViewStyle of SplitFrame complement if there is
 442                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 443                    * the whole ViewStyle (allow cDNA protein to have different
 444                    * fonts)
 445                    */
 446                   AlignViewportI complement = ap.getAlignViewport()
 447                           .getCodingComplement();
 448                   if (complement != null && vs.isScaleProteinAsCdna())
 449                   {
 450                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 451                     ((SplitFrame) af.getSplitViewContainer())
 452                             .adjustLayout();
 453                     af.setMenusForViewport();
 454                   }
 455
 456                   ap.updateLayout();
 457                   ap.setSelected(true);
 458                   ap.alignFrame.setMenusForViewport();
 459
 460                 }
 461               }
 462             });
 463     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 464             .indexOf("devel") > -1
 465             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 466                     .indexOf("test") > -1)
 467     {
 468       formatMenu.add(vsel);
 469     }
 470     addFocusListener(new FocusAdapter()
 471     {
 472       @Override
 473       public void focusGained(FocusEvent e)
 474       {
 475         Jalview.setCurrentAlignFrame(AlignFrame.this);
 476       }
 477     });
 478
 479   }
 480
 481   /**
 482    * Change the filename and format for the alignment, and enable the 'reload'
 483    * button functionality.
 484    *
 485    * @param file
 486    *          valid filename
 487    * @param format
 488    *          format of file
 489    */
 490   public void setFileName(String file, FileFormatI format)
 491   {
 492     fileName = file;
 493     setFileFormat(format);
 494     reload.setEnabled(true);
 495   }
 496
 497   /**
 498    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 499    * events
 500    */
 501   void addKeyListener()
 502   {
 503     addKeyListener(new KeyAdapter()
 504     {
 505       @Override
 506       public void keyPressed(KeyEvent evt)
 507       {
 508         if (viewport.cursorMode
 509                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 510                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 511                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 512                 && Character.isDigit(evt.getKeyChar()))
 513         {
 514           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 515         }
 516
 517         switch (evt.getKeyCode())
 518         {
 519
 520         case 27: // escape key
 521           deselectAllSequenceMenuItem_actionPerformed(null);
 522
 523           break;
 524
 525         case KeyEvent.VK_DOWN:
 526           if (evt.isAltDown() || !viewport.cursorMode)
 527           {
 528             moveSelectedSequences(false);
 529           }
 530           if (viewport.cursorMode)
 531           {
 532             alignPanel.getSeqPanel().moveCursor(0, 1);
 533           }
 534           break;
 535
 536         case KeyEvent.VK_UP:
 537           if (evt.isAltDown() || !viewport.cursorMode)
 538           {
 539             moveSelectedSequences(true);
 540           }
 541           if (viewport.cursorMode)
 542           {
 543             alignPanel.getSeqPanel().moveCursor(0, -1);
 544           }
 545
 546           break;
 547
 548         case KeyEvent.VK_LEFT:
 549           if (evt.isAltDown() || !viewport.cursorMode)
 550           {
 551             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 552           }
 553           else
 554           {
 555             alignPanel.getSeqPanel().moveCursor(-1, 0);
 556           }
 557
 558           break;
 559
 560         case KeyEvent.VK_RIGHT:
 561           if (evt.isAltDown() || !viewport.cursorMode)
 562           {
 563             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 564           }
 565           else
 566           {
 567             alignPanel.getSeqPanel().moveCursor(1, 0);
 568           }
 569           break;
 570
 571         case KeyEvent.VK_SPACE:
 572           if (viewport.cursorMode)
 573           {
 574             alignPanel.getSeqPanel().insertGapAtCursor(
 575                     evt.isControlDown() || evt.isShiftDown()
 576                             || evt.isAltDown());
 577           }
 578           break;
 579
 580         // case KeyEvent.VK_A:
 581         // if (viewport.cursorMode)
 582         // {
 583         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 584         // //System.out.println("A");
 585         // }
 586         // break;
 587         /*
 588          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 589          * System.out.println("closing bracket"); } break;
 590          */
 591         case KeyEvent.VK_DELETE:
 592         case KeyEvent.VK_BACK_SPACE:
 593           if (!viewport.cursorMode)
 594           {
 595             cut_actionPerformed(null);
 596           }
 597           else
 598           {
 599             alignPanel.getSeqPanel().deleteGapAtCursor(
 600                     evt.isControlDown() || evt.isShiftDown()
 601                             || evt.isAltDown());
 602           }
 603
 604           break;
 605
 606         case KeyEvent.VK_S:
 607           if (viewport.cursorMode)
 608           {
 609             alignPanel.getSeqPanel().setCursorRow();
 610           }
 611           break;
 612         case KeyEvent.VK_C:
 613           if (viewport.cursorMode && !evt.isControlDown())
 614           {
 615             alignPanel.getSeqPanel().setCursorColumn();
 616           }
 617           break;
 618         case KeyEvent.VK_P:
 619           if (viewport.cursorMode)
 620           {
 621             alignPanel.getSeqPanel().setCursorPosition();
 622           }
 623           break;
 624
 625         case KeyEvent.VK_ENTER:
 626         case KeyEvent.VK_COMMA:
 627           if (viewport.cursorMode)
 628           {
 629             alignPanel.getSeqPanel().setCursorRowAndColumn();
 630           }
 631           break;
 632
 633         case KeyEvent.VK_Q:
 634           if (viewport.cursorMode)
 635           {
 636             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 637           }
 638           break;
 639         case KeyEvent.VK_M:
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 643           }
 644           break;
 645
 646         case KeyEvent.VK_F2:
 647           viewport.cursorMode = !viewport.cursorMode;
 648           statusBar.setText(MessageManager.formatMessage(
 649                   "label.keyboard_editing_mode",
 650                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 651           if (viewport.cursorMode)
 652           {
 653             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 654             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 655           }
 656           alignPanel.getSeqPanel().seqCanvas.repaint();
 657           break;
 658
 659         case KeyEvent.VK_F1:
 660           try
 661           {
 662             Help.showHelpWindow();
 663           } catch (Exception ex)
 664           {
 665             ex.printStackTrace();
 666           }
 667           break;
 668         case KeyEvent.VK_H:
 669         {
 670           boolean toggleSeqs = !evt.isControlDown();
 671           boolean toggleCols = !evt.isShiftDown();
 672           toggleHiddenRegions(toggleSeqs, toggleCols);
 673           break;
 674         }
 675         case KeyEvent.VK_B:
 676         {
 677           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 678           boolean modifyExisting = true; // always modify, don't clear
 679                                          // evt.isShiftDown();
 680           boolean invertHighlighted = evt.isAltDown();
 681           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 682                   toggleSel);
 683           break;
 684         }
 685         case KeyEvent.VK_PAGE_UP:
 686           if (viewport.getWrapAlignment())
 687           {
 688             alignPanel.scrollUp(true);
 689           }
 690           else
 691           {
 692             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 693                     - viewport.endSeq + viewport.startSeq);
 694           }
 695           break;
 696         case KeyEvent.VK_PAGE_DOWN:
 697           if (viewport.getWrapAlignment())
 698           {
 699             alignPanel.scrollUp(false);
 700           }
 701           else
 702           {
 703             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 704                     + viewport.endSeq - viewport.startSeq);
 705           }
 706           break;
 707         }
 708       }
 709
 710       @Override
 711       public void keyReleased(KeyEvent evt)
 712       {
 713         switch (evt.getKeyCode())
 714         {
 715         case KeyEvent.VK_LEFT:
 716           if (evt.isAltDown() || !viewport.cursorMode)
 717           {
 718             viewport.firePropertyChange("alignment", null, viewport
 719                     .getAlignment().getSequences());
 720           }
 721           break;
 722
 723         case KeyEvent.VK_RIGHT:
 724           if (evt.isAltDown() || !viewport.cursorMode)
 725           {
 726             viewport.firePropertyChange("alignment", null, viewport
 727                     .getAlignment().getSequences());
 728           }
 729           break;
 730         }
 731       }
 732     });
 733   }
 734
 735   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 736   {
 737     ap.alignFrame = this;
 738     avc = new jalview.controller.AlignViewController(this, viewport,
 739             alignPanel);
 740
 741     alignPanels.add(ap);
 742
 743     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 744
 745     int aSize = alignPanels.size();
 746
 747     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 748
 749     if (aSize == 1 && ap.av.viewName == null)
 750     {
 751       this.getContentPane().add(ap, BorderLayout.CENTER);
 752     }
 753     else
 754     {
 755       if (aSize == 2)
 756       {
 757         setInitialTabVisible();
 758       }
 759
 760       expandViews.setEnabled(true);
 761       gatherViews.setEnabled(true);
 762       tabbedPane.addTab(ap.av.viewName, ap);
 763
 764       ap.setVisible(false);
 765     }
 766
 767     if (newPanel)
 768     {
 769       if (ap.av.isPadGaps())
 770       {
 771         ap.av.getAlignment().padGaps();
 772       }
 773       ap.av.updateConservation(ap);
 774       ap.av.updateConsensus(ap);
 775       ap.av.updateStrucConsensus(ap);
 776     }
 777   }
 778
 779   public void setInitialTabVisible()
 780   {
 781     expandViews.setEnabled(true);
 782     gatherViews.setEnabled(true);
 783     tabbedPane.setVisible(true);
 784     AlignmentPanel first = alignPanels.get(0);
 785     tabbedPane.addTab(first.av.viewName, first);
 786     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 787   }
 788
 789   public AlignViewport getViewport()
 790   {
 791     return viewport;
 792   }
 793
 794   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 795   private void addServiceListeners()
 796   {
 797     final java.beans.PropertyChangeListener thisListener;
 798     Desktop.instance.addJalviewPropertyChangeListener("services",
 799             thisListener = new java.beans.PropertyChangeListener()
 800             {
 801               @Override
 802               public void propertyChange(PropertyChangeEvent evt)
 803               {
 804                 // // System.out.println("Discoverer property change.");
 805                 // if (evt.getPropertyName().equals("services"))
 806                 {
 807                   SwingUtilities.invokeLater(new Runnable()
 808                   {
 809
 810                     @Override
 811                     public void run()
 812                     {
 813                       System.err
 814                               .println("Rebuild WS Menu for service change");
 815                       BuildWebServiceMenu();
 816                     }
 817
 818                   });
 819                 }
 820               }
 821             });
 822     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 823     {
 824       @Override
 825       public void internalFrameClosed(
 826               javax.swing.event.InternalFrameEvent evt)
 827       {
 828         // System.out.println("deregistering discoverer listener");
 829         Desktop.instance.removeJalviewPropertyChangeListener("services",
 830                 thisListener);
 831         closeMenuItem_actionPerformed(true);
 832       };
 833     });
 834     // Finally, build the menu once to get current service state
 835     new Thread(new Runnable()
 836     {
 837       @Override
 838       public void run()
 839       {
 840         BuildWebServiceMenu();
 841       }
 842     }).start();
 843   }
 844
 845   /**
 846    * Configure menu items that vary according to whether the alignment is
 847    * nucleotide or protein
 848    *
 849    * @param nucleotide
 850    */
 851   public void setGUINucleotide(boolean nucleotide)
 852   {
 853     showTranslation.setVisible(nucleotide);
 854     showReverse.setVisible(nucleotide);
 855     showReverseComplement.setVisible(nucleotide);
 856     conservationMenuItem.setEnabled(!nucleotide);
 857     modifyConservation.setEnabled(!nucleotide);
 858     showGroupConservation.setEnabled(!nucleotide);
 859
 860     /*
 861      * enable / disable colour schemes
 862      * - the old, simple way (based on the nucleotide flag), or
 863      * - the new, generic way (interrogate the colour scheme)
 864      */
 865     AlignmentI al = getViewport().getAlignment();
 866     clustalColour.setEnabled(!nucleotide);
 867     zappoColour.setEnabled(!nucleotide);
 868     taylorColour.setEnabled(!nucleotide);
 869     hydrophobicityColour.setEnabled(!nucleotide);
 870     helixColour.setEnabled(!nucleotide);
 871     strandColour.setEnabled(!nucleotide);
 872     turnColour.setEnabled(!nucleotide);
 873     // buriedColour.setEnabled(!nucleotide);
 874     // TODO make isApplicableTo static in ColourSchemeI in Java 8
 875     buriedColour.setEnabled(new BuriedColourScheme().isApplicableTo(al));
 876     rnahelicesColour.setEnabled(nucleotide);
 877     nucleotideColour.setEnabled(nucleotide);
 878     // purinePyrimidineColour.setEnabled(nucleotide);
 879     purinePyrimidineColour.setEnabled(new PurinePyrimidineColourScheme()
 880             .isApplicableTo(al));
 881     tcoffeeColour
 882             .setEnabled(new TCoffeeColourScheme(al).isApplicableTo(al));
 883     RNAInteractionColour.setEnabled(nucleotide);
 884     showComplementMenuItem.setText(nucleotide ? MessageManager
 885             .getString("label.protein") : MessageManager
 886             .getString("label.nucleotide"));
 887
 888     String selectedColourScheme = Cache.getDefault(
 889             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 890                     : Preferences.DEFAULT_COLOUR_PROT,
 891             ResidueColourScheme.NONE);
 892     setColourSelected(selectedColourScheme);
 893   }
 894
 895   /**
 896    * set up menus for the current viewport. This may be called after any
 897    * operation that affects the data in the current view (selection changed,
 898    * etc) to update the menus to reflect the new state.
 899    */
 900   @Override
 901   public void setMenusForViewport()
 902   {
 903     setMenusFromViewport(viewport);
 904   }
 905
 906   /**
 907    * Need to call this method when tabs are selected for multiple views, or when
 908    * loading from Jalview2XML.java
 909    *
 910    * @param av
 911    *          AlignViewport
 912    */
 913   void setMenusFromViewport(AlignViewport av)
 914   {
 915     padGapsMenuitem.setSelected(av.isPadGaps());
 916     colourTextMenuItem.setSelected(av.isShowColourText());
 917     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 918     conservationMenuItem.setSelected(av.getConservationSelected());
 919     seqLimits.setSelected(av.getShowJVSuffix());
 920     idRightAlign.setSelected(av.isRightAlignIds());
 921     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 922     renderGapsMenuItem.setSelected(av.isRenderGaps());
 923     wrapMenuItem.setSelected(av.getWrapAlignment());
 924     scaleAbove.setVisible(av.getWrapAlignment());
 925     scaleLeft.setVisible(av.getWrapAlignment());
 926     scaleRight.setVisible(av.getWrapAlignment());
 927     annotationPanelMenuItem.setState(av.isShowAnnotation());
 928     /*
 929      * Show/hide annotations only enabled if annotation panel is shown
 930      */
 931     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 932     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 933     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 934     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 935     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 936     viewTextMenuItem.setSelected(av.getShowText());
 937     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 938     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 939     showGroupConservation.setSelected(av.isShowGroupConservation());
 940     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 941     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 942     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 943
 944     setColourSelected(ColourSchemeProperty.getColourName(av
 945             .getGlobalColourScheme()));
 946
 947     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 948     hiddenMarkers.setState(av.getShowHiddenMarkers());
 949     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 950     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 951     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 952     autoCalculate.setSelected(av.autoCalculateConsensus);
 953     sortByTree.setSelected(av.sortByTree);
 954     listenToViewSelections.setSelected(av.followSelection);
 955     // rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 956     rnahelicesColour.setEnabled(new RNAHelicesColour(av.getAlignment())
 957             .isApplicableTo(av.getAlignment()));
 958     rnahelicesColour
 959             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 960
 961     showProducts.setEnabled(canShowProducts());
 962     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 963
 964     updateEditMenuBar();
 965   }
 966
 967   /**
 968    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 969    *
 970    * @param b
 971    */
 972   public void setGroovyEnabled(boolean b)
 973   {
 974     runGroovy.setEnabled(b);
 975   }
 976
 977   private IProgressIndicator progressBar;
 978
 979   /*
 980    * (non-Javadoc)
 981    *
 982    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 983    */
 984   @Override
 985   public void setProgressBar(String message, long id)
 986   {
 987     progressBar.setProgressBar(message, id);
 988   }
 989
 990   @Override
 991   public void registerHandler(final long id,
 992           final IProgressIndicatorHandler handler)
 993   {
 994     progressBar.registerHandler(id, handler);
 995   }
 996
 997   /**
 998    *
 999    * @return true if any progress bars are still active
1000    */
1001   @Override
1002   public boolean operationInProgress()
1003   {
1004     return progressBar.operationInProgress();
1005   }
1006
1007   @Override
1008   public void setStatus(String text)
1009   {
1010     statusBar.setText(text);
1011   }
1012
1013   /*
1014    * Added so Castor Mapping file can obtain Jalview Version
1015    */
1016   public String getVersion()
1017   {
1018     return jalview.bin.Cache.getProperty("VERSION");
1019   }
1020
1021   public FeatureRenderer getFeatureRenderer()
1022   {
1023     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1024   }
1025
1026   @Override
1027   public void fetchSequence_actionPerformed(ActionEvent e)
1028   {
1029     new jalview.gui.SequenceFetcher(this);
1030   }
1031
1032   @Override
1033   public void addFromFile_actionPerformed(ActionEvent e)
1034   {
1035     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1036   }
1037
1038   @Override
1039   public void reload_actionPerformed(ActionEvent e)
1040   {
1041     if (fileName != null)
1042     {
1043       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1044       // originating file's format
1045       // TODO: work out how to recover feature settings for correct view(s) when
1046       // file is reloaded.
1047       if (FileFormat.Jalview.equals(currentFileFormat))
1048       {
1049         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1050         for (int i = 0; i < frames.length; i++)
1051         {
1052           if (frames[i] instanceof AlignFrame && frames[i] != this
1053                   && ((AlignFrame) frames[i]).fileName != null
1054                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1055           {
1056             try
1057             {
1058               frames[i].setSelected(true);
1059               Desktop.instance.closeAssociatedWindows();
1060             } catch (java.beans.PropertyVetoException ex)
1061             {
1062             }
1063           }
1064
1065         }
1066         Desktop.instance.closeAssociatedWindows();
1067
1068         FileLoader loader = new FileLoader();
1069         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1070                 : DataSourceType.FILE;
1071         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1072       }
1073       else
1074       {
1075         Rectangle bounds = this.getBounds();
1076
1077         FileLoader loader = new FileLoader();
1078         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1079                 : DataSourceType.FILE;
1080         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1081                 protocol, currentFileFormat);
1082
1083         newframe.setBounds(bounds);
1084         if (featureSettings != null && featureSettings.isShowing())
1085         {
1086           final Rectangle fspos = featureSettings.frame.getBounds();
1087           // TODO: need a 'show feature settings' function that takes bounds -
1088           // need to refactor Desktop.addFrame
1089           newframe.featureSettings_actionPerformed(null);
1090           final FeatureSettings nfs = newframe.featureSettings;
1091           SwingUtilities.invokeLater(new Runnable()
1092           {
1093             @Override
1094             public void run()
1095             {
1096               nfs.frame.setBounds(fspos);
1097             }
1098           });
1099           this.featureSettings.close();
1100           this.featureSettings = null;
1101         }
1102         this.closeMenuItem_actionPerformed(true);
1103       }
1104     }
1105   }
1106
1107   @Override
1108   public void addFromText_actionPerformed(ActionEvent e)
1109   {
1110     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1111             .getAlignPanel());
1112   }
1113
1114   @Override
1115   public void addFromURL_actionPerformed(ActionEvent e)
1116   {
1117     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1118   }
1119
1120   @Override
1121   public void save_actionPerformed(ActionEvent e)
1122   {
1123     if (fileName == null || (currentFileFormat == null)
1124             || fileName.startsWith("http"))
1125     {
1126       saveAs_actionPerformed(null);
1127     }
1128     else
1129     {
1130       saveAlignment(fileName, currentFileFormat);
1131     }
1132   }
1133
1134   /**
1135    * DOCUMENT ME!
1136    *
1137    * @param e
1138    *          DOCUMENT ME!
1139    */
1140   @Override
1141   public void saveAs_actionPerformed(ActionEvent e)
1142   {
1143     String format = currentFileFormat == null ? null : currentFileFormat
1144             .toString();
1145     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1146             Cache.getProperty("LAST_DIRECTORY"), format);
1147
1148     chooser.setFileView(new JalviewFileView());
1149     chooser.setDialogTitle(MessageManager
1150             .getString("label.save_alignment_to_file"));
1151     chooser.setToolTipText(MessageManager.getString("action.save"));
1152
1153     int value = chooser.showSaveDialog(this);
1154
1155     if (value == JalviewFileChooser.APPROVE_OPTION)
1156     {
1157       currentFileFormat = chooser.getSelectedFormat();
1158       while (currentFileFormat == null)
1159       {
1160         JvOptionPane
1161                 .showInternalMessageDialog(
1162                         Desktop.desktop,
1163                         MessageManager
1164                                 .getString("label.select_file_format_before_saving"),
1165                         MessageManager
1166                                 .getString("label.file_format_not_specified"),
1167                         JvOptionPane.WARNING_MESSAGE);
1168         currentFileFormat = chooser.getSelectedFormat();
1169         value = chooser.showSaveDialog(this);
1170         if (value != JalviewFileChooser.APPROVE_OPTION)
1171         {
1172           return;
1173         }
1174       }
1175
1176       fileName = chooser.getSelectedFile().getPath();
1177
1178       Cache.setProperty("DEFAULT_FILE_FORMAT",
1179               currentFileFormat.toString());
1180
1181       Cache.setProperty("LAST_DIRECTORY", fileName);
1182       saveAlignment(fileName, currentFileFormat);
1183     }
1184   }
1185
1186   public boolean saveAlignment(String file, FileFormatI format)
1187   {
1188     boolean success = true;
1189
1190     if (FileFormat.Jalview.equals(format))
1191     {
1192       String shortName = title;
1193
1194       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1195       {
1196         shortName = shortName.substring(shortName
1197                 .lastIndexOf(java.io.File.separatorChar) + 1);
1198       }
1199
1200       success = new Jalview2XML().saveAlignment(this, file, shortName);
1201
1202       statusBar.setText(MessageManager.formatMessage(
1203               "label.successfully_saved_to_file_in_format", new Object[] {
1204                   fileName, format }));
1205
1206     }
1207     else
1208     {
1209       // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1210       // {
1211       // warningMessage("Cannot save file " + fileName + " using format "
1212       // + format, "Alignment output format not supported");
1213       // if (!Jalview.isHeadlessMode())
1214       // {
1215       // saveAs_actionPerformed(null);
1216       // }
1217       // return false;
1218       // }
1219
1220       AlignmentExportData exportData = getAlignmentForExport(format,
1221               viewport, null);
1222       if (exportData.getSettings().isCancelled())
1223       {
1224         return false;
1225       }
1226       FormatAdapter f = new FormatAdapter(alignPanel,
1227               exportData.getSettings());
1228       String output = f.formatSequences(
1229               format,
1230               exportData.getAlignment(), // class cast exceptions will
1231               // occur in the distant future
1232               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1233               f.getCacheSuffixDefault(format),
1234               viewport.getColumnSelection());
1235
1236       if (output == null)
1237       {
1238         success = false;
1239       }
1240       else
1241       {
1242         try
1243         {
1244           java.io.PrintWriter out = new java.io.PrintWriter(
1245                   new java.io.FileWriter(file));
1246
1247           out.print(output);
1248           out.close();
1249           this.setTitle(file);
1250           statusBar.setText(MessageManager.formatMessage(
1251                   "label.successfully_saved_to_file_in_format",
1252                   new Object[] { fileName, format }));
1253         } catch (Exception ex)
1254         {
1255           success = false;
1256           ex.printStackTrace();
1257         }
1258       }
1259     }
1260
1261     if (!success)
1262     {
1263       JvOptionPane.showInternalMessageDialog(this, MessageManager
1264               .formatMessage("label.couldnt_save_file",
1265                       new Object[] { fileName }), MessageManager
1266               .getString("label.error_saving_file"),
1267               JvOptionPane.WARNING_MESSAGE);
1268     }
1269
1270     return success;
1271   }
1272
1273   private void warningMessage(String warning, String title)
1274   {
1275     if (new jalview.util.Platform().isHeadless())
1276     {
1277       System.err.println("Warning: " + title + "\nWarning: " + warning);
1278
1279     }
1280     else
1281     {
1282       JvOptionPane.showInternalMessageDialog(this, warning, title,
1283               JvOptionPane.WARNING_MESSAGE);
1284     }
1285     return;
1286   }
1287
1288   /**
1289    * DOCUMENT ME!
1290    *
1291    * @param e
1292    *          DOCUMENT ME!
1293    */
1294   @Override
1295   protected void outputText_actionPerformed(ActionEvent e)
1296   {
1297
1298     FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1299     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1300             viewport, null);
1301     if (exportData.getSettings().isCancelled())
1302     {
1303       return;
1304     }
1305     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1306     cap.setForInput(null);
1307     try
1308     {
1309       FileFormatI format = fileFormat;
1310       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1311               .formatSequences(format,
1312                       exportData.getAlignment(),
1313                       exportData.getOmitHidden(),
1314                       exportData.getStartEndPostions(),
1315                       viewport.getColumnSelection()));
1316       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1317               "label.alignment_output_command",
1318               new Object[] { e.getActionCommand() }), 600, 500);
1319     } catch (OutOfMemoryError oom)
1320     {
1321       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1322       cap.dispose();
1323     }
1324
1325   }
1326
1327   public static AlignmentExportData getAlignmentForExport(
1328           FileFormatI format, AlignViewportI viewport,
1329           AlignExportSettingI exportSettings)
1330   {
1331     AlignmentI alignmentToExport = null;
1332     AlignExportSettingI settings = exportSettings;
1333     String[] omitHidden = null;
1334
1335     HiddenSequences hiddenSeqs = viewport.getAlignment()
1336             .getHiddenSequences();
1337
1338     alignmentToExport = viewport.getAlignment();
1339
1340     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1341     if (settings == null)
1342     {
1343       settings = new AlignExportSettings(hasHiddenSeqs,
1344               viewport.hasHiddenColumns(), format);
1345     }
1346     // settings.isExportAnnotations();
1347
1348     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1349     {
1350       omitHidden = viewport.getViewAsString(false,
1351               settings.isExportHiddenSequences());
1352     }
1353
1354     int[] alignmentStartEnd = new int[2];
1355     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1356     {
1357       alignmentToExport = hiddenSeqs.getFullAlignment();
1358     }
1359     else
1360     {
1361       alignmentToExport = viewport.getAlignment();
1362     }
1363     alignmentStartEnd = alignmentToExport
1364             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1365                     .getHiddenColumns());
1366     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1367             omitHidden, alignmentStartEnd, settings);
1368     return ed;
1369   }
1370
1371   /**
1372    * DOCUMENT ME!
1373    *
1374    * @param e
1375    *          DOCUMENT ME!
1376    */
1377   @Override
1378   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1379   {
1380     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1381     htmlSVG.exportHTML(null);
1382   }
1383
1384   @Override
1385   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1386   {
1387     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1388     bjs.exportHTML(null);
1389   }
1390
1391   public void createImageMap(File file, String image)
1392   {
1393     alignPanel.makePNGImageMap(file, image);
1394   }
1395
1396   /**
1397    * DOCUMENT ME!
1398    *
1399    * @param e
1400    *          DOCUMENT ME!
1401    */
1402   @Override
1403   public void createPNG(File f)
1404   {
1405     alignPanel.makePNG(f);
1406   }
1407
1408   /**
1409    * DOCUMENT ME!
1410    *
1411    * @param e
1412    *          DOCUMENT ME!
1413    */
1414   @Override
1415   public void createEPS(File f)
1416   {
1417     alignPanel.makeEPS(f);
1418   }
1419
1420   @Override
1421   public void createSVG(File f)
1422   {
1423     alignPanel.makeSVG(f);
1424   }
1425
1426   @Override
1427   public void pageSetup_actionPerformed(ActionEvent e)
1428   {
1429     PrinterJob printJob = PrinterJob.getPrinterJob();
1430     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1431   }
1432
1433   /**
1434    * DOCUMENT ME!
1435    *
1436    * @param e
1437    *          DOCUMENT ME!
1438    */
1439   @Override
1440   public void printMenuItem_actionPerformed(ActionEvent e)
1441   {
1442     // Putting in a thread avoids Swing painting problems
1443     PrintThread thread = new PrintThread(alignPanel);
1444     thread.start();
1445   }
1446
1447   @Override
1448   public void exportFeatures_actionPerformed(ActionEvent e)
1449   {
1450     new AnnotationExporter().exportFeatures(alignPanel);
1451   }
1452
1453   @Override
1454   public void exportAnnotations_actionPerformed(ActionEvent e)
1455   {
1456     new AnnotationExporter().exportAnnotations(alignPanel);
1457   }
1458
1459   @Override
1460   public void associatedData_actionPerformed(ActionEvent e)
1461   {
1462     // Pick the tree file
1463     JalviewFileChooser chooser = new JalviewFileChooser(
1464             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1465     chooser.setFileView(new JalviewFileView());
1466     chooser.setDialogTitle(MessageManager
1467             .getString("label.load_jalview_annotations"));
1468     chooser.setToolTipText(MessageManager
1469             .getString("label.load_jalview_annotations"));
1470
1471     int value = chooser.showOpenDialog(null);
1472
1473     if (value == JalviewFileChooser.APPROVE_OPTION)
1474     {
1475       String choice = chooser.getSelectedFile().getPath();
1476       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1477       loadJalviewDataFile(choice, null, null, null);
1478     }
1479
1480   }
1481
1482   /**
1483    * Close the current view or all views in the alignment frame. If the frame
1484    * only contains one view then the alignment will be removed from memory.
1485    *
1486    * @param closeAllTabs
1487    */
1488   @Override
1489   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1490   {
1491     if (alignPanels != null && alignPanels.size() < 2)
1492     {
1493       closeAllTabs = true;
1494     }
1495
1496     try
1497     {
1498       if (alignPanels != null)
1499       {
1500         if (closeAllTabs)
1501         {
1502           if (this.isClosed())
1503           {
1504             // really close all the windows - otherwise wait till
1505             // setClosed(true) is called
1506             for (int i = 0; i < alignPanels.size(); i++)
1507             {
1508               AlignmentPanel ap = alignPanels.get(i);
1509               ap.closePanel();
1510             }
1511           }
1512         }
1513         else
1514         {
1515           closeView(alignPanel);
1516         }
1517       }
1518
1519       if (closeAllTabs)
1520       {
1521         /*
1522          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1523          * be called recursively, with the frame now in 'closed' state
1524          */
1525         this.setClosed(true);
1526       }
1527     } catch (Exception ex)
1528     {
1529       ex.printStackTrace();
1530     }
1531   }
1532
1533   /**
1534    * Close the specified panel and close up tabs appropriately.
1535    *
1536    * @param panelToClose
1537    */
1538   public void closeView(AlignmentPanel panelToClose)
1539   {
1540     int index = tabbedPane.getSelectedIndex();
1541     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1542     alignPanels.remove(panelToClose);
1543     panelToClose.closePanel();
1544     panelToClose = null;
1545
1546     tabbedPane.removeTabAt(closedindex);
1547     tabbedPane.validate();
1548
1549     if (index > closedindex || index == tabbedPane.getTabCount())
1550     {
1551       // modify currently selected tab index if necessary.
1552       index--;
1553     }
1554
1555     this.tabSelectionChanged(index);
1556   }
1557
1558   /**
1559    * DOCUMENT ME!
1560    */
1561   void updateEditMenuBar()
1562   {
1563
1564     if (viewport.getHistoryList().size() > 0)
1565     {
1566       undoMenuItem.setEnabled(true);
1567       CommandI command = viewport.getHistoryList().peek();
1568       undoMenuItem.setText(MessageManager.formatMessage(
1569               "label.undo_command",
1570               new Object[] { command.getDescription() }));
1571     }
1572     else
1573     {
1574       undoMenuItem.setEnabled(false);
1575       undoMenuItem.setText(MessageManager.getString("action.undo"));
1576     }
1577
1578     if (viewport.getRedoList().size() > 0)
1579     {
1580       redoMenuItem.setEnabled(true);
1581
1582       CommandI command = viewport.getRedoList().peek();
1583       redoMenuItem.setText(MessageManager.formatMessage(
1584               "label.redo_command",
1585               new Object[] { command.getDescription() }));
1586     }
1587     else
1588     {
1589       redoMenuItem.setEnabled(false);
1590       redoMenuItem.setText(MessageManager.getString("action.redo"));
1591     }
1592   }
1593
1594   @Override
1595   public void addHistoryItem(CommandI command)
1596   {
1597     if (command.getSize() > 0)
1598     {
1599       viewport.addToHistoryList(command);
1600       viewport.clearRedoList();
1601       updateEditMenuBar();
1602       viewport.updateHiddenColumns();
1603       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1604       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1605       // viewport.getColumnSelection()
1606       // .getHiddenColumns().size() > 0);
1607     }
1608   }
1609
1610   /**
1611    *
1612    * @return alignment objects for all views
1613    */
1614   AlignmentI[] getViewAlignments()
1615   {
1616     if (alignPanels != null)
1617     {
1618       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1619       int i = 0;
1620       for (AlignmentPanel ap : alignPanels)
1621       {
1622         als[i++] = ap.av.getAlignment();
1623       }
1624       return als;
1625     }
1626     if (viewport != null)
1627     {
1628       return new AlignmentI[] { viewport.getAlignment() };
1629     }
1630     return null;
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   @Override
1640   protected void undoMenuItem_actionPerformed(ActionEvent e)
1641   {
1642     if (viewport.getHistoryList().isEmpty())
1643     {
1644       return;
1645     }
1646     CommandI command = viewport.getHistoryList().pop();
1647     viewport.addToRedoList(command);
1648     command.undoCommand(getViewAlignments());
1649
1650     AlignmentViewport originalSource = getOriginatingSource(command);
1651     updateEditMenuBar();
1652
1653     if (originalSource != null)
1654     {
1655       if (originalSource != viewport)
1656       {
1657         Cache.log
1658                 .warn("Implementation worry: mismatch of viewport origin for undo");
1659       }
1660       originalSource.updateHiddenColumns();
1661       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1662       // null
1663       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1664       // viewport.getColumnSelection()
1665       // .getHiddenColumns().size() > 0);
1666       originalSource.firePropertyChange("alignment", null, originalSource
1667               .getAlignment().getSequences());
1668     }
1669   }
1670
1671   /**
1672    * DOCUMENT ME!
1673    *
1674    * @param e
1675    *          DOCUMENT ME!
1676    */
1677   @Override
1678   protected void redoMenuItem_actionPerformed(ActionEvent e)
1679   {
1680     if (viewport.getRedoList().size() < 1)
1681     {
1682       return;
1683     }
1684
1685     CommandI command = viewport.getRedoList().pop();
1686     viewport.addToHistoryList(command);
1687     command.doCommand(getViewAlignments());
1688
1689     AlignmentViewport originalSource = getOriginatingSource(command);
1690     updateEditMenuBar();
1691
1692     if (originalSource != null)
1693     {
1694
1695       if (originalSource != viewport)
1696       {
1697         Cache.log
1698                 .warn("Implementation worry: mismatch of viewport origin for redo");
1699       }
1700       originalSource.updateHiddenColumns();
1701       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1702       // null
1703       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1704       // viewport.getColumnSelection()
1705       // .getHiddenColumns().size() > 0);
1706       originalSource.firePropertyChange("alignment", null, originalSource
1707               .getAlignment().getSequences());
1708     }
1709   }
1710
1711   AlignmentViewport getOriginatingSource(CommandI command)
1712   {
1713     AlignmentViewport originalSource = null;
1714     // For sequence removal and addition, we need to fire
1715     // the property change event FROM the viewport where the
1716     // original alignment was altered
1717     AlignmentI al = null;
1718     if (command instanceof EditCommand)
1719     {
1720       EditCommand editCommand = (EditCommand) command;
1721       al = editCommand.getAlignment();
1722       List<Component> comps = PaintRefresher.components.get(viewport
1723               .getSequenceSetId());
1724
1725       for (Component comp : comps)
1726       {
1727         if (comp instanceof AlignmentPanel)
1728         {
1729           if (al == ((AlignmentPanel) comp).av.getAlignment())
1730           {
1731             originalSource = ((AlignmentPanel) comp).av;
1732             break;
1733           }
1734         }
1735       }
1736     }
1737
1738     if (originalSource == null)
1739     {
1740       // The original view is closed, we must validate
1741       // the current view against the closed view first
1742       if (al != null)
1743       {
1744         PaintRefresher.validateSequences(al, viewport.getAlignment());
1745       }
1746
1747       originalSource = viewport;
1748     }
1749
1750     return originalSource;
1751   }
1752
1753   /**
1754    * DOCUMENT ME!
1755    *
1756    * @param up
1757    *          DOCUMENT ME!
1758    */
1759   public void moveSelectedSequences(boolean up)
1760   {
1761     SequenceGroup sg = viewport.getSelectionGroup();
1762
1763     if (sg == null)
1764     {
1765       return;
1766     }
1767     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1768             viewport.getHiddenRepSequences(), up);
1769     alignPanel.paintAlignment(true);
1770   }
1771
1772   synchronized void slideSequences(boolean right, int size)
1773   {
1774     List<SequenceI> sg = new ArrayList<SequenceI>();
1775     if (viewport.cursorMode)
1776     {
1777       sg.add(viewport.getAlignment().getSequenceAt(
1778               alignPanel.getSeqPanel().seqCanvas.cursorY));
1779     }
1780     else if (viewport.getSelectionGroup() != null
1781             && viewport.getSelectionGroup().getSize() != viewport
1782                     .getAlignment().getHeight())
1783     {
1784       sg = viewport.getSelectionGroup().getSequences(
1785               viewport.getHiddenRepSequences());
1786     }
1787
1788     if (sg.size() < 1)
1789     {
1790       return;
1791     }
1792
1793     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1794
1795     for (SequenceI seq : viewport.getAlignment().getSequences())
1796     {
1797       if (!sg.contains(seq))
1798       {
1799         invertGroup.add(seq);
1800       }
1801     }
1802
1803     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1804
1805     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1806     for (int i = 0; i < invertGroup.size(); i++)
1807     {
1808       seqs2[i] = invertGroup.get(i);
1809     }
1810
1811     SlideSequencesCommand ssc;
1812     if (right)
1813     {
1814       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1815               size, viewport.getGapCharacter());
1816     }
1817     else
1818     {
1819       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1820               size, viewport.getGapCharacter());
1821     }
1822
1823     int groupAdjustment = 0;
1824     if (ssc.getGapsInsertedBegin() && right)
1825     {
1826       if (viewport.cursorMode)
1827       {
1828         alignPanel.getSeqPanel().moveCursor(size, 0);
1829       }
1830       else
1831       {
1832         groupAdjustment = size;
1833       }
1834     }
1835     else if (!ssc.getGapsInsertedBegin() && !right)
1836     {
1837       if (viewport.cursorMode)
1838       {
1839         alignPanel.getSeqPanel().moveCursor(-size, 0);
1840       }
1841       else
1842       {
1843         groupAdjustment = -size;
1844       }
1845     }
1846
1847     if (groupAdjustment != 0)
1848     {
1849       viewport.getSelectionGroup().setStartRes(
1850               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1851       viewport.getSelectionGroup().setEndRes(
1852               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1853     }
1854
1855     /*
1856      * just extend the last slide command if compatible; but not if in
1857      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1858      */
1859     boolean appendHistoryItem = false;
1860     Deque<CommandI> historyList = viewport.getHistoryList();
1861     boolean inSplitFrame = getSplitViewContainer() != null;
1862     if (!inSplitFrame && historyList != null && historyList.size() > 0
1863             && historyList.peek() instanceof SlideSequencesCommand)
1864     {
1865       appendHistoryItem = ssc
1866               .appendSlideCommand((SlideSequencesCommand) historyList
1867                       .peek());
1868     }
1869
1870     if (!appendHistoryItem)
1871     {
1872       addHistoryItem(ssc);
1873     }
1874
1875     repaint();
1876   }
1877
1878   /**
1879    * DOCUMENT ME!
1880    *
1881    * @param e
1882    *          DOCUMENT ME!
1883    */
1884   @Override
1885   protected void copy_actionPerformed(ActionEvent e)
1886   {
1887     System.gc();
1888     if (viewport.getSelectionGroup() == null)
1889     {
1890       return;
1891     }
1892     // TODO: preserve the ordering of displayed alignment annotation in any
1893     // internal paste (particularly sequence associated annotation)
1894     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1895     String[] omitHidden = null;
1896
1897     if (viewport.hasHiddenColumns())
1898     {
1899       omitHidden = viewport.getViewAsString(true);
1900     }
1901
1902     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1903             seqs,
1904             omitHidden, null);
1905
1906     StringSelection ss = new StringSelection(output);
1907
1908     try
1909     {
1910       jalview.gui.Desktop.internalCopy = true;
1911       // Its really worth setting the clipboard contents
1912       // to empty before setting the large StringSelection!!
1913       Toolkit.getDefaultToolkit().getSystemClipboard()
1914               .setContents(new StringSelection(""), null);
1915
1916       Toolkit.getDefaultToolkit().getSystemClipboard()
1917               .setContents(ss, Desktop.instance);
1918     } catch (OutOfMemoryError er)
1919     {
1920       new OOMWarning("copying region", er);
1921       return;
1922     }
1923
1924     ArrayList<int[]> hiddenColumns = null;
1925     if (viewport.hasHiddenColumns())
1926     {
1927       hiddenColumns = new ArrayList<int[]>();
1928       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1929               .getSelectionGroup().getEndRes();
1930       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1931       {
1932         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1933         {
1934           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1935               region[1] - hiddenOffset });
1936         }
1937       }
1938     }
1939
1940     Desktop.jalviewClipboard = new Object[] { seqs,
1941         viewport.getAlignment().getDataset(), hiddenColumns };
1942     statusBar.setText(MessageManager.formatMessage(
1943             "label.copied_sequences_to_clipboard", new Object[] { Integer
1944                     .valueOf(seqs.length).toString() }));
1945   }
1946
1947   /**
1948    * DOCUMENT ME!
1949    *
1950    * @param e
1951    *          DOCUMENT ME!
1952    */
1953   @Override
1954   protected void pasteNew_actionPerformed(ActionEvent e)
1955   {
1956     paste(true);
1957   }
1958
1959   /**
1960    * DOCUMENT ME!
1961    *
1962    * @param e
1963    *          DOCUMENT ME!
1964    */
1965   @Override
1966   protected void pasteThis_actionPerformed(ActionEvent e)
1967   {
1968     paste(false);
1969   }
1970
1971   /**
1972    * Paste contents of Jalview clipboard
1973    *
1974    * @param newAlignment
1975    *          true to paste to a new alignment, otherwise add to this.
1976    */
1977   void paste(boolean newAlignment)
1978   {
1979     boolean externalPaste = true;
1980     try
1981     {
1982       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1983       Transferable contents = c.getContents(this);
1984
1985       if (contents == null)
1986       {
1987         return;
1988       }
1989
1990       String str;
1991       FileFormatI format;
1992       try
1993       {
1994         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1995         if (str.length() < 1)
1996         {
1997           return;
1998         }
1999
2000         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2001
2002       } catch (OutOfMemoryError er)
2003       {
2004         new OOMWarning("Out of memory pasting sequences!!", er);
2005         return;
2006       }
2007
2008       SequenceI[] sequences;
2009       boolean annotationAdded = false;
2010       AlignmentI alignment = null;
2011
2012       if (Desktop.jalviewClipboard != null)
2013       {
2014         // The clipboard was filled from within Jalview, we must use the
2015         // sequences
2016         // And dataset from the copied alignment
2017         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2018         // be doubly sure that we create *new* sequence objects.
2019         sequences = new SequenceI[newseq.length];
2020         for (int i = 0; i < newseq.length; i++)
2021         {
2022           sequences[i] = new Sequence(newseq[i]);
2023         }
2024         alignment = new Alignment(sequences);
2025         externalPaste = false;
2026       }
2027       else
2028       {
2029         // parse the clipboard as an alignment.
2030         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2031                 format);
2032         sequences = alignment.getSequencesArray();
2033       }
2034
2035       int alwidth = 0;
2036       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2037       int fgroup = -1;
2038
2039       if (newAlignment)
2040       {
2041
2042         if (Desktop.jalviewClipboard != null)
2043         {
2044           // dataset is inherited
2045           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2046         }
2047         else
2048         {
2049           // new dataset is constructed
2050           alignment.setDataset(null);
2051         }
2052         alwidth = alignment.getWidth() + 1;
2053       }
2054       else
2055       {
2056         AlignmentI pastedal = alignment; // preserve pasted alignment object
2057         // Add pasted sequences and dataset into existing alignment.
2058         alignment = viewport.getAlignment();
2059         alwidth = alignment.getWidth() + 1;
2060         // decide if we need to import sequences from an existing dataset
2061         boolean importDs = Desktop.jalviewClipboard != null
2062                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2063         // importDs==true instructs us to copy over new dataset sequences from
2064         // an existing alignment
2065         Vector newDs = (importDs) ? new Vector() : null; // used to create
2066         // minimum dataset set
2067
2068         for (int i = 0; i < sequences.length; i++)
2069         {
2070           if (importDs)
2071           {
2072             newDs.addElement(null);
2073           }
2074           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2075           // paste
2076           if (importDs && ds != null)
2077           {
2078             if (!newDs.contains(ds))
2079             {
2080               newDs.setElementAt(ds, i);
2081               ds = new Sequence(ds);
2082               // update with new dataset sequence
2083               sequences[i].setDatasetSequence(ds);
2084             }
2085             else
2086             {
2087               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2088             }
2089           }
2090           else
2091           {
2092             // copy and derive new dataset sequence
2093             sequences[i] = sequences[i].deriveSequence();
2094             alignment.getDataset().addSequence(
2095                     sequences[i].getDatasetSequence());
2096             // TODO: avoid creation of duplicate dataset sequences with a
2097             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2098           }
2099           alignment.addSequence(sequences[i]); // merges dataset
2100         }
2101         if (newDs != null)
2102         {
2103           newDs.clear(); // tidy up
2104         }
2105         if (alignment.getAlignmentAnnotation() != null)
2106         {
2107           for (AlignmentAnnotation alan : alignment
2108                   .getAlignmentAnnotation())
2109           {
2110             if (alan.graphGroup > fgroup)
2111             {
2112               fgroup = alan.graphGroup;
2113             }
2114           }
2115         }
2116         if (pastedal.getAlignmentAnnotation() != null)
2117         {
2118           // Add any annotation attached to alignment.
2119           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2120           for (int i = 0; i < alann.length; i++)
2121           {
2122             annotationAdded = true;
2123             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2124             {
2125               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2126               if (newann.graphGroup > -1)
2127               {
2128                 if (newGraphGroups.size() <= newann.graphGroup
2129                         || newGraphGroups.get(newann.graphGroup) == null)
2130                 {
2131                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2132                   {
2133                     newGraphGroups.add(q, null);
2134                   }
2135                   newGraphGroups.set(newann.graphGroup, new Integer(
2136                           ++fgroup));
2137                 }
2138                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2139                         .intValue();
2140               }
2141
2142               newann.padAnnotation(alwidth);
2143               alignment.addAnnotation(newann);
2144             }
2145           }
2146         }
2147       }
2148       if (!newAlignment)
2149       {
2150         // /////
2151         // ADD HISTORY ITEM
2152         //
2153         addHistoryItem(new EditCommand(
2154                 MessageManager.getString("label.add_sequences"),
2155                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2156       }
2157       // Add any annotations attached to sequences
2158       for (int i = 0; i < sequences.length; i++)
2159       {
2160         if (sequences[i].getAnnotation() != null)
2161         {
2162           AlignmentAnnotation newann;
2163           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2164           {
2165             annotationAdded = true;
2166             newann = sequences[i].getAnnotation()[a];
2167             newann.adjustForAlignment();
2168             newann.padAnnotation(alwidth);
2169             if (newann.graphGroup > -1)
2170             {
2171               if (newann.graphGroup > -1)
2172               {
2173                 if (newGraphGroups.size() <= newann.graphGroup
2174                         || newGraphGroups.get(newann.graphGroup) == null)
2175                 {
2176                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2177                   {
2178                     newGraphGroups.add(q, null);
2179                   }
2180                   newGraphGroups.set(newann.graphGroup, new Integer(
2181                           ++fgroup));
2182                 }
2183                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2184                         .intValue();
2185               }
2186             }
2187             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2188             // was
2189             // duplicated
2190             // earlier
2191             alignment
2192                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2193           }
2194         }
2195       }
2196       if (!newAlignment)
2197       {
2198
2199         // propagate alignment changed.
2200         viewport.setEndSeq(alignment.getHeight());
2201         if (annotationAdded)
2202         {
2203           // Duplicate sequence annotation in all views.
2204           AlignmentI[] alview = this.getViewAlignments();
2205           for (int i = 0; i < sequences.length; i++)
2206           {
2207             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2208             if (sann == null)
2209             {
2210               continue;
2211             }
2212             for (int avnum = 0; avnum < alview.length; avnum++)
2213             {
2214               if (alview[avnum] != alignment)
2215               {
2216                 // duplicate in a view other than the one with input focus
2217                 int avwidth = alview[avnum].getWidth() + 1;
2218                 // this relies on sann being preserved after we
2219                 // modify the sequence's annotation array for each duplication
2220                 for (int a = 0; a < sann.length; a++)
2221                 {
2222                   AlignmentAnnotation newann = new AlignmentAnnotation(
2223                           sann[a]);
2224                   sequences[i].addAlignmentAnnotation(newann);
2225                   newann.padAnnotation(avwidth);
2226                   alview[avnum].addAnnotation(newann); // annotation was
2227                   // duplicated earlier
2228                   // TODO JAL-1145 graphGroups are not updated for sequence
2229                   // annotation added to several views. This may cause
2230                   // strangeness
2231                   alview[avnum].setAnnotationIndex(newann, a);
2232                 }
2233               }
2234             }
2235           }
2236           buildSortByAnnotationScoresMenu();
2237         }
2238         viewport.firePropertyChange("alignment", null,
2239                 alignment.getSequences());
2240         if (alignPanels != null)
2241         {
2242           for (AlignmentPanel ap : alignPanels)
2243           {
2244             ap.validateAnnotationDimensions(false);
2245           }
2246         }
2247         else
2248         {
2249           alignPanel.validateAnnotationDimensions(false);
2250         }
2251
2252       }
2253       else
2254       {
2255         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2256                 DEFAULT_HEIGHT);
2257         String newtitle = new String("Copied sequences");
2258
2259         if (Desktop.jalviewClipboard != null
2260                 && Desktop.jalviewClipboard[2] != null)
2261         {
2262           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2263           for (int[] region : hc)
2264           {
2265             af.viewport.hideColumns(region[0], region[1]);
2266           }
2267         }
2268
2269         // >>>This is a fix for the moment, until a better solution is
2270         // found!!<<<
2271         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2272                 .transferSettings(
2273                         alignPanel.getSeqPanel().seqCanvas
2274                                 .getFeatureRenderer());
2275
2276         // TODO: maintain provenance of an alignment, rather than just make the
2277         // title a concatenation of operations.
2278         if (!externalPaste)
2279         {
2280           if (title.startsWith("Copied sequences"))
2281           {
2282             newtitle = title;
2283           }
2284           else
2285           {
2286             newtitle = newtitle.concat("- from " + title);
2287           }
2288         }
2289         else
2290         {
2291           newtitle = new String("Pasted sequences");
2292         }
2293
2294         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2295                 DEFAULT_HEIGHT);
2296
2297       }
2298
2299     } catch (Exception ex)
2300     {
2301       ex.printStackTrace();
2302       System.out.println("Exception whilst pasting: " + ex);
2303       // could be anything being pasted in here
2304     }
2305
2306   }
2307
2308   @Override
2309   protected void expand_newalign(ActionEvent e)
2310   {
2311     try
2312     {
2313       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2314               .getAlignment(), -1);
2315       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2316               DEFAULT_HEIGHT);
2317       String newtitle = new String("Flanking alignment");
2318
2319       if (Desktop.jalviewClipboard != null
2320               && Desktop.jalviewClipboard[2] != null)
2321       {
2322         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2323         for (int region[] : hc)
2324         {
2325           af.viewport.hideColumns(region[0], region[1]);
2326         }
2327       }
2328
2329       // >>>This is a fix for the moment, until a better solution is
2330       // found!!<<<
2331       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2332               .transferSettings(
2333                       alignPanel.getSeqPanel().seqCanvas
2334                               .getFeatureRenderer());
2335
2336       // TODO: maintain provenance of an alignment, rather than just make the
2337       // title a concatenation of operations.
2338       {
2339         if (title.startsWith("Copied sequences"))
2340         {
2341           newtitle = title;
2342         }
2343         else
2344         {
2345           newtitle = newtitle.concat("- from " + title);
2346         }
2347       }
2348
2349       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2350
2351     } catch (Exception ex)
2352     {
2353       ex.printStackTrace();
2354       System.out.println("Exception whilst pasting: " + ex);
2355       // could be anything being pasted in here
2356     } catch (OutOfMemoryError oom)
2357     {
2358       new OOMWarning("Viewing flanking region of alignment", oom);
2359     }
2360   }
2361
2362   /**
2363    * DOCUMENT ME!
2364    *
2365    * @param e
2366    *          DOCUMENT ME!
2367    */
2368   @Override
2369   protected void cut_actionPerformed(ActionEvent e)
2370   {
2371     copy_actionPerformed(null);
2372     delete_actionPerformed(null);
2373   }
2374
2375   /**
2376    * DOCUMENT ME!
2377    *
2378    * @param e
2379    *          DOCUMENT ME!
2380    */
2381   @Override
2382   protected void delete_actionPerformed(ActionEvent evt)
2383   {
2384
2385     SequenceGroup sg = viewport.getSelectionGroup();
2386     if (sg == null)
2387     {
2388       return;
2389     }
2390
2391     /*
2392      * If the cut affects all sequences, warn, remove highlighted columns
2393      */
2394     if (sg.getSize() == viewport.getAlignment().getHeight())
2395     {
2396       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2397               .getAlignment().getWidth()) ? true : false;
2398       if (isEntireAlignWidth)
2399       {
2400         int confirm = JvOptionPane.showConfirmDialog(this,
2401                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2402                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2403                 JvOptionPane.OK_CANCEL_OPTION);
2404
2405         if (confirm == JvOptionPane.CANCEL_OPTION
2406                 || confirm == JvOptionPane.CLOSED_OPTION)
2407         {
2408           return;
2409         }
2410       }
2411       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2412               sg.getEndRes() + 1);
2413     }
2414     SequenceI[] cut = sg.getSequences()
2415             .toArray(new SequenceI[sg.getSize()]);
2416
2417     addHistoryItem(new EditCommand(
2418             MessageManager.getString("label.cut_sequences"), Action.CUT,
2419             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2420             viewport.getAlignment()));
2421
2422     viewport.setSelectionGroup(null);
2423     viewport.sendSelection();
2424     viewport.getAlignment().deleteGroup(sg);
2425
2426     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2427             .getSequences());
2428     if (viewport.getAlignment().getHeight() < 1)
2429     {
2430       try
2431       {
2432         this.setClosed(true);
2433       } catch (Exception ex)
2434       {
2435       }
2436     }
2437   }
2438
2439   /**
2440    * DOCUMENT ME!
2441    *
2442    * @param e
2443    *          DOCUMENT ME!
2444    */
2445   @Override
2446   protected void deleteGroups_actionPerformed(ActionEvent e)
2447   {
2448     if (avc.deleteGroups())
2449     {
2450       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2451       alignPanel.updateAnnotation();
2452       alignPanel.paintAlignment(true);
2453     }
2454   }
2455
2456   /**
2457    * DOCUMENT ME!
2458    *
2459    * @param e
2460    *          DOCUMENT ME!
2461    */
2462   @Override
2463   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2464   {
2465     SequenceGroup sg = new SequenceGroup();
2466
2467     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2468     {
2469       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2470     }
2471
2472     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2473     viewport.setSelectionGroup(sg);
2474     viewport.sendSelection();
2475     // JAL-2034 - should delegate to
2476     // alignPanel to decide if overview needs
2477     // updating.
2478     alignPanel.paintAlignment(false);
2479     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480   }
2481
2482   /**
2483    * DOCUMENT ME!
2484    *
2485    * @param e
2486    *          DOCUMENT ME!
2487    */
2488   @Override
2489   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2490   {
2491     if (viewport.cursorMode)
2492     {
2493       alignPanel.getSeqPanel().keyboardNo1 = null;
2494       alignPanel.getSeqPanel().keyboardNo2 = null;
2495     }
2496     viewport.setSelectionGroup(null);
2497     viewport.getColumnSelection().clear();
2498     viewport.setSelectionGroup(null);
2499     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2500     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2501     // JAL-2034 - should delegate to
2502     // alignPanel to decide if overview needs
2503     // updating.
2504     alignPanel.paintAlignment(false);
2505     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2506     viewport.sendSelection();
2507   }
2508
2509   /**
2510    * DOCUMENT ME!
2511    *
2512    * @param e
2513    *          DOCUMENT ME!
2514    */
2515   @Override
2516   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2517   {
2518     SequenceGroup sg = viewport.getSelectionGroup();
2519
2520     if (sg == null)
2521     {
2522       selectAllSequenceMenuItem_actionPerformed(null);
2523
2524       return;
2525     }
2526
2527     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2528     {
2529       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2530     }
2531     // JAL-2034 - should delegate to
2532     // alignPanel to decide if overview needs
2533     // updating.
2534
2535     alignPanel.paintAlignment(true);
2536     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2537     viewport.sendSelection();
2538   }
2539
2540   @Override
2541   public void invertColSel_actionPerformed(ActionEvent e)
2542   {
2543     viewport.invertColumnSelection();
2544     alignPanel.paintAlignment(true);
2545     viewport.sendSelection();
2546   }
2547
2548   /**
2549    * DOCUMENT ME!
2550    *
2551    * @param e
2552    *          DOCUMENT ME!
2553    */
2554   @Override
2555   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2556   {
2557     trimAlignment(true);
2558   }
2559
2560   /**
2561    * DOCUMENT ME!
2562    *
2563    * @param e
2564    *          DOCUMENT ME!
2565    */
2566   @Override
2567   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2568   {
2569     trimAlignment(false);
2570   }
2571
2572   void trimAlignment(boolean trimLeft)
2573   {
2574     ColumnSelection colSel = viewport.getColumnSelection();
2575     int column;
2576
2577     if (!colSel.isEmpty())
2578     {
2579       if (trimLeft)
2580       {
2581         column = colSel.getMin();
2582       }
2583       else
2584       {
2585         column = colSel.getMax();
2586       }
2587
2588       SequenceI[] seqs;
2589       if (viewport.getSelectionGroup() != null)
2590       {
2591         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2592                 viewport.getHiddenRepSequences());
2593       }
2594       else
2595       {
2596         seqs = viewport.getAlignment().getSequencesArray();
2597       }
2598
2599       TrimRegionCommand trimRegion;
2600       if (trimLeft)
2601       {
2602         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2603                 column, viewport.getAlignment());
2604         viewport.setStartRes(0);
2605       }
2606       else
2607       {
2608         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2609                 column, viewport.getAlignment());
2610       }
2611
2612       statusBar.setText(MessageManager.formatMessage(
2613               "label.removed_columns",
2614               new String[] { Integer.valueOf(trimRegion.getSize())
2615                       .toString() }));
2616
2617       addHistoryItem(trimRegion);
2618
2619       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2620       {
2621         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2622                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2623         {
2624           viewport.getAlignment().deleteGroup(sg);
2625         }
2626       }
2627
2628       viewport.firePropertyChange("alignment", null, viewport
2629               .getAlignment().getSequences());
2630     }
2631   }
2632
2633   /**
2634    * DOCUMENT ME!
2635    *
2636    * @param e
2637    *          DOCUMENT ME!
2638    */
2639   @Override
2640   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2641   {
2642     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2643
2644     SequenceI[] seqs;
2645     if (viewport.getSelectionGroup() != null)
2646     {
2647       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2648               viewport.getHiddenRepSequences());
2649       start = viewport.getSelectionGroup().getStartRes();
2650       end = viewport.getSelectionGroup().getEndRes();
2651     }
2652     else
2653     {
2654       seqs = viewport.getAlignment().getSequencesArray();
2655     }
2656
2657     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2658             "Remove Gapped Columns", seqs, start, end,
2659             viewport.getAlignment());
2660
2661     addHistoryItem(removeGapCols);
2662
2663     statusBar.setText(MessageManager.formatMessage(
2664             "label.removed_empty_columns",
2665             new Object[] { Integer.valueOf(removeGapCols.getSize())
2666                     .toString() }));
2667
2668     // This is to maintain viewport position on first residue
2669     // of first sequence
2670     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2671     int startRes = seq.findPosition(viewport.startRes);
2672     // ShiftList shifts;
2673     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2674     // edit.alColumnChanges=shifts.getInverse();
2675     // if (viewport.hasHiddenColumns)
2676     // viewport.getColumnSelection().compensateForEdits(shifts);
2677     viewport.setStartRes(seq.findIndex(startRes) - 1);
2678     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2679             .getSequences());
2680
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e
2687    *          DOCUMENT ME!
2688    */
2689   @Override
2690   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2691   {
2692     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2693
2694     SequenceI[] seqs;
2695     if (viewport.getSelectionGroup() != null)
2696     {
2697       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2698               viewport.getHiddenRepSequences());
2699       start = viewport.getSelectionGroup().getStartRes();
2700       end = viewport.getSelectionGroup().getEndRes();
2701     }
2702     else
2703     {
2704       seqs = viewport.getAlignment().getSequencesArray();
2705     }
2706
2707     // This is to maintain viewport position on first residue
2708     // of first sequence
2709     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2710     int startRes = seq.findPosition(viewport.startRes);
2711
2712     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2713             viewport.getAlignment()));
2714
2715     viewport.setStartRes(seq.findIndex(startRes) - 1);
2716
2717     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2718             .getSequences());
2719
2720   }
2721
2722   /**
2723    * DOCUMENT ME!
2724    *
2725    * @param e
2726    *          DOCUMENT ME!
2727    */
2728   @Override
2729   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2730   {
2731     viewport.setPadGaps(padGapsMenuitem.isSelected());
2732     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2733             .getSequences());
2734   }
2735
2736   /**
2737    * DOCUMENT ME!
2738    *
2739    * @param e
2740    *          DOCUMENT ME!
2741    */
2742   @Override
2743   public void findMenuItem_actionPerformed(ActionEvent e)
2744   {
2745     new Finder();
2746   }
2747
2748   /**
2749    * Create a new view of the current alignment.
2750    */
2751   @Override
2752   public void newView_actionPerformed(ActionEvent e)
2753   {
2754     newView(null, true);
2755   }
2756
2757   /**
2758    * Creates and shows a new view of the current alignment.
2759    *
2760    * @param viewTitle
2761    *          title of newly created view; if null, one will be generated
2762    * @param copyAnnotation
2763    *          if true then duplicate all annnotation, groups and settings
2764    * @return new alignment panel, already displayed.
2765    */
2766   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2767   {
2768     /*
2769      * Create a new AlignmentPanel (with its own, new Viewport)
2770      */
2771     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2772             true);
2773     if (!copyAnnotation)
2774     {
2775       /*
2776        * remove all groups and annotation except for the automatic stuff
2777        */
2778       newap.av.getAlignment().deleteAllGroups();
2779       newap.av.getAlignment().deleteAllAnnotations(false);
2780     }
2781
2782     newap.av.setGatherViewsHere(false);
2783
2784     if (viewport.viewName == null)
2785     {
2786       viewport.viewName = MessageManager
2787               .getString("label.view_name_original");
2788     }
2789
2790     /*
2791      * Views share the same edits undo and redo stacks
2792      */
2793     newap.av.setHistoryList(viewport.getHistoryList());
2794     newap.av.setRedoList(viewport.getRedoList());
2795
2796     /*
2797      * Views share the same mappings; need to deregister any new mappings
2798      * created by copyAlignPanel, and register the new reference to the shared
2799      * mappings
2800      */
2801     newap.av.replaceMappings(viewport.getAlignment());
2802
2803     newap.av.viewName = getNewViewName(viewTitle);
2804
2805     addAlignmentPanel(newap, true);
2806     newap.alignmentChanged();
2807
2808     if (alignPanels.size() == 2)
2809     {
2810       viewport.setGatherViewsHere(true);
2811     }
2812     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2813     return newap;
2814   }
2815
2816   /**
2817    * Make a new name for the view, ensuring it is unique within the current
2818    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2819    * these now use viewId. Unique view names are still desirable for usability.)
2820    *
2821    * @param viewTitle
2822    * @return
2823    */
2824   protected String getNewViewName(String viewTitle)
2825   {
2826     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2827     boolean addFirstIndex = false;
2828     if (viewTitle == null || viewTitle.trim().length() == 0)
2829     {
2830       viewTitle = MessageManager.getString("action.view");
2831       addFirstIndex = true;
2832     }
2833     else
2834     {
2835       index = 1;// we count from 1 if given a specific name
2836     }
2837     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2838
2839     List<Component> comps = PaintRefresher.components.get(viewport
2840             .getSequenceSetId());
2841
2842     List<String> existingNames = getExistingViewNames(comps);
2843
2844     while (existingNames.contains(newViewName))
2845     {
2846       newViewName = viewTitle + " " + (++index);
2847     }
2848     return newViewName;
2849   }
2850
2851   /**
2852    * Returns a list of distinct view names found in the given list of
2853    * components. View names are held on the viewport of an AlignmentPanel.
2854    *
2855    * @param comps
2856    * @return
2857    */
2858   protected List<String> getExistingViewNames(List<Component> comps)
2859   {
2860     List<String> existingNames = new ArrayList<String>();
2861     for (Component comp : comps)
2862     {
2863       if (comp instanceof AlignmentPanel)
2864       {
2865         AlignmentPanel ap = (AlignmentPanel) comp;
2866         if (!existingNames.contains(ap.av.viewName))
2867         {
2868           existingNames.add(ap.av.viewName);
2869         }
2870       }
2871     }
2872     return existingNames;
2873   }
2874
2875   /**
2876    * Explode tabbed views into separate windows.
2877    */
2878   @Override
2879   public void expandViews_actionPerformed(ActionEvent e)
2880   {
2881     Desktop.explodeViews(this);
2882   }
2883
2884   /**
2885    * Gather views in separate windows back into a tabbed presentation.
2886    */
2887   @Override
2888   public void gatherViews_actionPerformed(ActionEvent e)
2889   {
2890     Desktop.instance.gatherViews(this);
2891   }
2892
2893   /**
2894    * DOCUMENT ME!
2895    *
2896    * @param e
2897    *          DOCUMENT ME!
2898    */
2899   @Override
2900   public void font_actionPerformed(ActionEvent e)
2901   {
2902     new FontChooser(alignPanel);
2903   }
2904
2905   /**
2906    * DOCUMENT ME!
2907    *
2908    * @param e
2909    *          DOCUMENT ME!
2910    */
2911   @Override
2912   protected void seqLimit_actionPerformed(ActionEvent e)
2913   {
2914     viewport.setShowJVSuffix(seqLimits.isSelected());
2915
2916     alignPanel.getIdPanel().getIdCanvas()
2917             .setPreferredSize(alignPanel.calculateIdWidth());
2918     alignPanel.paintAlignment(true);
2919   }
2920
2921   @Override
2922   public void idRightAlign_actionPerformed(ActionEvent e)
2923   {
2924     viewport.setRightAlignIds(idRightAlign.isSelected());
2925     alignPanel.paintAlignment(true);
2926   }
2927
2928   @Override
2929   public void centreColumnLabels_actionPerformed(ActionEvent e)
2930   {
2931     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2932     alignPanel.paintAlignment(true);
2933   }
2934
2935   /*
2936    * (non-Javadoc)
2937    *
2938    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2939    */
2940   @Override
2941   protected void followHighlight_actionPerformed()
2942   {
2943     /*
2944      * Set the 'follow' flag on the Viewport (and scroll to position if now
2945      * true).
2946      */
2947     final boolean state = this.followHighlightMenuItem.getState();
2948     viewport.setFollowHighlight(state);
2949     if (state)
2950     {
2951       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2952     }
2953   }
2954
2955   /**
2956    * DOCUMENT ME!
2957    *
2958    * @param e
2959    *          DOCUMENT ME!
2960    */
2961   @Override
2962   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2963   {
2964     viewport.setColourText(colourTextMenuItem.isSelected());
2965     alignPanel.paintAlignment(true);
2966   }
2967
2968   /**
2969    * DOCUMENT ME!
2970    *
2971    * @param e
2972    *          DOCUMENT ME!
2973    */
2974   @Override
2975   public void wrapMenuItem_actionPerformed(ActionEvent e)
2976   {
2977     scaleAbove.setVisible(wrapMenuItem.isSelected());
2978     scaleLeft.setVisible(wrapMenuItem.isSelected());
2979     scaleRight.setVisible(wrapMenuItem.isSelected());
2980     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2981     alignPanel.updateLayout();
2982   }
2983
2984   @Override
2985   public void showAllSeqs_actionPerformed(ActionEvent e)
2986   {
2987     viewport.showAllHiddenSeqs();
2988   }
2989
2990   @Override
2991   public void showAllColumns_actionPerformed(ActionEvent e)
2992   {
2993     viewport.showAllHiddenColumns();
2994     repaint();
2995     viewport.sendSelection();
2996   }
2997
2998   @Override
2999   public void hideSelSequences_actionPerformed(ActionEvent e)
3000   {
3001     viewport.hideAllSelectedSeqs();
3002     // alignPanel.paintAlignment(true);
3003   }
3004
3005   /**
3006    * called by key handler and the hide all/show all menu items
3007    *
3008    * @param toggleSeqs
3009    * @param toggleCols
3010    */
3011   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3012   {
3013
3014     boolean hide = false;
3015     SequenceGroup sg = viewport.getSelectionGroup();
3016     if (!toggleSeqs && !toggleCols)
3017     {
3018       // Hide everything by the current selection - this is a hack - we do the
3019       // invert and then hide
3020       // first check that there will be visible columns after the invert.
3021       if (viewport.hasSelectedColumns()
3022               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3023                       .getEndRes()))
3024       {
3025         // now invert the sequence set, if required - empty selection implies
3026         // that no hiding is required.
3027         if (sg != null)
3028         {
3029           invertSequenceMenuItem_actionPerformed(null);
3030           sg = viewport.getSelectionGroup();
3031           toggleSeqs = true;
3032
3033         }
3034         viewport.expandColSelection(sg, true);
3035         // finally invert the column selection and get the new sequence
3036         // selection.
3037         invertColSel_actionPerformed(null);
3038         toggleCols = true;
3039       }
3040     }
3041
3042     if (toggleSeqs)
3043     {
3044       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3045       {
3046         hideSelSequences_actionPerformed(null);
3047         hide = true;
3048       }
3049       else if (!(toggleCols && viewport.hasSelectedColumns()))
3050       {
3051         showAllSeqs_actionPerformed(null);
3052       }
3053     }
3054
3055     if (toggleCols)
3056     {
3057       if (viewport.hasSelectedColumns())
3058       {
3059         hideSelColumns_actionPerformed(null);
3060         if (!toggleSeqs)
3061         {
3062           viewport.setSelectionGroup(sg);
3063         }
3064       }
3065       else if (!hide)
3066       {
3067         showAllColumns_actionPerformed(null);
3068       }
3069     }
3070   }
3071
3072   /*
3073    * (non-Javadoc)
3074    *
3075    * @see
3076    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3077    * event.ActionEvent)
3078    */
3079   @Override
3080   public void hideAllButSelection_actionPerformed(ActionEvent e)
3081   {
3082     toggleHiddenRegions(false, false);
3083     viewport.sendSelection();
3084   }
3085
3086   /*
3087    * (non-Javadoc)
3088    *
3089    * @see
3090    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3091    * .ActionEvent)
3092    */
3093   @Override
3094   public void hideAllSelection_actionPerformed(ActionEvent e)
3095   {
3096     SequenceGroup sg = viewport.getSelectionGroup();
3097     viewport.expandColSelection(sg, false);
3098     viewport.hideAllSelectedSeqs();
3099     viewport.hideSelectedColumns();
3100     alignPanel.paintAlignment(true);
3101     viewport.sendSelection();
3102   }
3103
3104   /*
3105    * (non-Javadoc)
3106    *
3107    * @see
3108    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3109    * ActionEvent)
3110    */
3111   @Override
3112   public void showAllhidden_actionPerformed(ActionEvent e)
3113   {
3114     viewport.showAllHiddenColumns();
3115     viewport.showAllHiddenSeqs();
3116     alignPanel.paintAlignment(true);
3117     viewport.sendSelection();
3118   }
3119
3120   @Override
3121   public void hideSelColumns_actionPerformed(ActionEvent e)
3122   {
3123     viewport.hideSelectedColumns();
3124     alignPanel.paintAlignment(true);
3125     viewport.sendSelection();
3126   }
3127
3128   @Override
3129   public void hiddenMarkers_actionPerformed(ActionEvent e)
3130   {
3131     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3132     repaint();
3133   }
3134
3135   /**
3136    * DOCUMENT ME!
3137    *
3138    * @param e
3139    *          DOCUMENT ME!
3140    */
3141   @Override
3142   protected void scaleAbove_actionPerformed(ActionEvent e)
3143   {
3144     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3145     alignPanel.paintAlignment(true);
3146   }
3147
3148   /**
3149    * DOCUMENT ME!
3150    *
3151    * @param e
3152    *          DOCUMENT ME!
3153    */
3154   @Override
3155   protected void scaleLeft_actionPerformed(ActionEvent e)
3156   {
3157     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3158     alignPanel.paintAlignment(true);
3159   }
3160
3161   /**
3162    * DOCUMENT ME!
3163    *
3164    * @param e
3165    *          DOCUMENT ME!
3166    */
3167   @Override
3168   protected void scaleRight_actionPerformed(ActionEvent e)
3169   {
3170     viewport.setScaleRightWrapped(scaleRight.isSelected());
3171     alignPanel.paintAlignment(true);
3172   }
3173
3174   /**
3175    * DOCUMENT ME!
3176    *
3177    * @param e
3178    *          DOCUMENT ME!
3179    */
3180   @Override
3181   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3182   {
3183     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3184     alignPanel.paintAlignment(true);
3185   }
3186
3187   /**
3188    * DOCUMENT ME!
3189    *
3190    * @param e
3191    *          DOCUMENT ME!
3192    */
3193   @Override
3194   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3195   {
3196     viewport.setShowText(viewTextMenuItem.isSelected());
3197     alignPanel.paintAlignment(true);
3198   }
3199
3200   /**
3201    * DOCUMENT ME!
3202    *
3203    * @param e
3204    *          DOCUMENT ME!
3205    */
3206   @Override
3207   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3208   {
3209     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3210     alignPanel.paintAlignment(true);
3211   }
3212
3213   public FeatureSettings featureSettings;
3214
3215   @Override
3216   public FeatureSettingsControllerI getFeatureSettingsUI()
3217   {
3218     return featureSettings;
3219   }
3220
3221   @Override
3222   public void featureSettings_actionPerformed(ActionEvent e)
3223   {
3224     if (featureSettings != null)
3225     {
3226       featureSettings.close();
3227       featureSettings = null;
3228     }
3229     if (!showSeqFeatures.isSelected())
3230     {
3231       // make sure features are actually displayed
3232       showSeqFeatures.setSelected(true);
3233       showSeqFeatures_actionPerformed(null);
3234     }
3235     featureSettings = new FeatureSettings(this);
3236   }
3237
3238   /**
3239    * Set or clear 'Show Sequence Features'
3240    *
3241    * @param evt
3242    *          DOCUMENT ME!
3243    */
3244   @Override
3245   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3246   {
3247     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3248     alignPanel.paintAlignment(true);
3249     if (alignPanel.getOverviewPanel() != null)
3250     {
3251       alignPanel.getOverviewPanel().updateOverviewImage();
3252     }
3253   }
3254
3255   /**
3256    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3257    * the annotations panel as a whole.
3258    *
3259    * The options to show/hide all annotations should be enabled when the panel
3260    * is shown, and disabled when the panel is hidden.
3261    *
3262    * @param e
3263    */
3264   @Override
3265   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3266   {
3267     final boolean setVisible = annotationPanelMenuItem.isSelected();
3268     viewport.setShowAnnotation(setVisible);
3269     this.showAllSeqAnnotations.setEnabled(setVisible);
3270     this.hideAllSeqAnnotations.setEnabled(setVisible);
3271     this.showAllAlAnnotations.setEnabled(setVisible);
3272     this.hideAllAlAnnotations.setEnabled(setVisible);
3273     alignPanel.updateLayout();
3274   }
3275
3276   @Override
3277   public void alignmentProperties()
3278   {
3279     JEditorPane editPane = new JEditorPane("text/html", "");
3280     editPane.setEditable(false);
3281     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3282             .formatAsHtml();
3283     editPane.setText(MessageManager.formatMessage("label.html_content",
3284             new Object[] { contents.toString() }));
3285     JInternalFrame frame = new JInternalFrame();
3286     frame.getContentPane().add(new JScrollPane(editPane));
3287
3288     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3289             "label.alignment_properties", new Object[] { getTitle() }),
3290             500, 400);
3291   }
3292
3293   /**
3294    * DOCUMENT ME!
3295    *
3296    * @param e
3297    *          DOCUMENT ME!
3298    */
3299   @Override
3300   public void overviewMenuItem_actionPerformed(ActionEvent e)
3301   {
3302     if (alignPanel.overviewPanel != null)
3303     {
3304       return;
3305     }
3306
3307     JInternalFrame frame = new JInternalFrame();
3308     OverviewPanel overview = new OverviewPanel(alignPanel);
3309     frame.setContentPane(overview);
3310     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3311             "label.overview_params", new Object[] { this.getTitle() }),
3312             frame.getWidth(), frame.getHeight());
3313     frame.pack();
3314     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3315     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3316     {
3317       @Override
3318       public void internalFrameClosed(
3319               javax.swing.event.InternalFrameEvent evt)
3320       {
3321         alignPanel.setOverviewPanel(null);
3322       };
3323     });
3324
3325     alignPanel.setOverviewPanel(overview);
3326   }
3327
3328   @Override
3329   public void textColour_actionPerformed()
3330   {
3331     new TextColourChooser().chooseColour(alignPanel, null);
3332   }
3333
3334   /**
3335    * DOCUMENT ME!
3336    *
3337    * @param e
3338    *          DOCUMENT ME!
3339    */
3340   @Override
3341   protected void noColourmenuItem_actionPerformed()
3342   {
3343     changeColour(null);
3344   }
3345
3346   /**
3347    * DOCUMENT ME!
3348    *
3349    * @param e
3350    *          DOCUMENT ME!
3351    */
3352   @Override
3353   public void clustalColour_actionPerformed()
3354   {
3355     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3356             viewport.getHiddenRepSequences()));
3357   }
3358
3359   /**
3360    * DOCUMENT ME!
3361    *
3362    * @param e
3363    *          DOCUMENT ME!
3364    */
3365   @Override
3366   public void zappoColour_actionPerformed()
3367   {
3368     changeColour(new ZappoColourScheme());
3369   }
3370
3371   /**
3372    * DOCUMENT ME!
3373    *
3374    * @param e
3375    *          DOCUMENT ME!
3376    */
3377   @Override
3378   public void taylorColour_actionPerformed()
3379   {
3380     changeColour(new TaylorColourScheme());
3381   }
3382
3383   /**
3384    * DOCUMENT ME!
3385    *
3386    * @param e
3387    *          DOCUMENT ME!
3388    */
3389   @Override
3390   public void hydrophobicityColour_actionPerformed()
3391   {
3392     changeColour(new HydrophobicColourScheme());
3393   }
3394
3395   /**
3396    * DOCUMENT ME!
3397    *
3398    * @param e
3399    *          DOCUMENT ME!
3400    */
3401   @Override
3402   public void helixColour_actionPerformed()
3403   {
3404     changeColour(new HelixColourScheme());
3405   }
3406
3407   /**
3408    * DOCUMENT ME!
3409    *
3410    * @param e
3411    *          DOCUMENT ME!
3412    */
3413   @Override
3414   public void strandColour_actionPerformed()
3415   {
3416     changeColour(new StrandColourScheme());
3417   }
3418
3419   /**
3420    * DOCUMENT ME!
3421    *
3422    * @param e
3423    *          DOCUMENT ME!
3424    */
3425   @Override
3426   public void turnColour_actionPerformed()
3427   {
3428     changeColour(new TurnColourScheme());
3429   }
3430
3431   /**
3432    * DOCUMENT ME!
3433    *
3434    * @param e
3435    *          DOCUMENT ME!
3436    */
3437   @Override
3438   public void buriedColour_actionPerformed()
3439   {
3440     changeColour(new BuriedColourScheme());
3441   }
3442
3443   /**
3444    * DOCUMENT ME!
3445    *
3446    * @param e
3447    *          DOCUMENT ME!
3448    */
3449   @Override
3450   public void nucleotideColour_actionPerformed()
3451   {
3452     changeColour(new NucleotideColourScheme());
3453   }
3454
3455   @Override
3456   public void purinePyrimidineColour_actionPerformed()
3457   {
3458     changeColour(new PurinePyrimidineColourScheme());
3459   }
3460
3461   /*
3462    * public void covariationColour_actionPerformed() {
3463    * changeColour(new
3464    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3465    * ()[0])); }
3466    */
3467   @Override
3468   public void annotationColour_actionPerformed()
3469   {
3470     new AnnotationColourChooser(viewport, alignPanel);
3471   }
3472
3473   @Override
3474   public void annotationColumn_actionPerformed(ActionEvent e)
3475   {
3476     new AnnotationColumnChooser(viewport, alignPanel);
3477   }
3478
3479   @Override
3480   public void rnahelicesColour_actionPerformed()
3481   {
3482     new RNAHelicesColourChooser(viewport, alignPanel);
3483   }
3484
3485   /**
3486    * DOCUMENT ME!
3487    *
3488    */
3489   @Override
3490   protected void applyToAllGroups_actionPerformed()
3491   {
3492     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param cs
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   public void changeColour(ColourSchemeI cs)
3503   {
3504     // TODO: pull up to controller method
3505
3506     if (cs != null)
3507     {
3508       // Make sure viewport is up to date w.r.t. any sliders
3509       if (viewport.getAbovePIDThreshold())
3510       {
3511         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3512                 "Background");
3513         viewport.setThreshold(threshold);
3514       }
3515
3516       if (viewport.getConservationSelected())
3517       {
3518         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3519                 cs, "Background"));
3520       }
3521       if (cs instanceof TCoffeeColourScheme)
3522       {
3523         tcoffeeColour.setEnabled(true);
3524         tcoffeeColour.setSelected(true);
3525       }
3526     }
3527
3528     viewport.setGlobalColourScheme(cs);
3529
3530     alignPanel.paintAlignment(true);
3531   }
3532
3533   /**
3534    * DOCUMENT ME!
3535    *
3536    * @param e
3537    *          DOCUMENT ME!
3538    */
3539   @Override
3540   protected void modifyPID_actionPerformed()
3541   {
3542     if (viewport.getAbovePIDThreshold()
3543             && viewport.getGlobalColourScheme() != null)
3544     {
3545       SliderPanel.setPIDSliderSource(alignPanel,
3546               viewport.getGlobalColourScheme(), "Background");
3547       SliderPanel.showPIDSlider();
3548     }
3549   }
3550
3551   /**
3552    * DOCUMENT ME!
3553    *
3554    * @param e
3555    *          DOCUMENT ME!
3556    */
3557   @Override
3558   protected void modifyConservation_actionPerformed()
3559   {
3560     if (viewport.getConservationSelected()
3561             && viewport.getGlobalColourScheme() != null)
3562     {
3563       SliderPanel.setConservationSlider(alignPanel,
3564               viewport.getGlobalColourScheme(), "Background");
3565       SliderPanel.showConservationSlider();
3566     }
3567   }
3568
3569   /**
3570    * DOCUMENT ME!
3571    *
3572    * @param e
3573    *          DOCUMENT ME!
3574    */
3575   @Override
3576   protected void conservationMenuItem_actionPerformed()
3577   {
3578     viewport.setConservationSelected(conservationMenuItem.isSelected());
3579
3580     viewport.setAbovePIDThreshold(false);
3581     abovePIDThreshold.setSelected(false);
3582
3583     changeColour(viewport.getGlobalColourScheme());
3584
3585     modifyConservation_actionPerformed();
3586   }
3587
3588   /**
3589    * DOCUMENT ME!
3590    *
3591    * @param e
3592    *          DOCUMENT ME!
3593    */
3594   @Override
3595   public void abovePIDThreshold_actionPerformed()
3596   {
3597     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3598
3599     conservationMenuItem.setSelected(false);
3600     viewport.setConservationSelected(false);
3601
3602     changeColour(viewport.getGlobalColourScheme());
3603
3604     modifyPID_actionPerformed();
3605   }
3606
3607   /**
3608    * DOCUMENT ME!
3609    *
3610    * @param e
3611    *          DOCUMENT ME!
3612    */
3613   @Override
3614   public void userDefinedColour_actionPerformed(ActionEvent e)
3615   {
3616     if (e.getActionCommand().equals(
3617             MessageManager.getString("action.user_defined")))
3618     {
3619       new UserDefinedColours(alignPanel, null);
3620     }
3621     else
3622     {
3623       UserColourScheme udc = UserDefinedColours
3624               .getUserColourSchemes().get(e.getActionCommand());
3625
3626       changeColour(udc);
3627     }
3628   }
3629
3630   /**
3631    * DOCUMENT ME!
3632    *
3633    * @param e
3634    *          DOCUMENT ME!
3635    */
3636   @Override
3637   public void PIDColour_actionPerformed()
3638   {
3639     changeColour(new PIDColourScheme());
3640   }
3641
3642   /**
3643    * DOCUMENT ME!
3644    *
3645    * @param e
3646    *          DOCUMENT ME!
3647    */
3648   @Override
3649   public void BLOSUM62Colour_actionPerformed()
3650   {
3651     changeColour(new Blosum62ColourScheme());
3652   }
3653
3654   /**
3655    * DOCUMENT ME!
3656    *
3657    * @param e
3658    *          DOCUMENT ME!
3659    */
3660   @Override
3661   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3662   {
3663     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3664     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3665             .getAlignment().getSequenceAt(0), null);
3666     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3667             viewport.getAlignment()));
3668     alignPanel.paintAlignment(true);
3669   }
3670
3671   /**
3672    * DOCUMENT ME!
3673    *
3674    * @param e
3675    *          DOCUMENT ME!
3676    */
3677   @Override
3678   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3679   {
3680     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3681     AlignmentSorter.sortByID(viewport.getAlignment());
3682     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3683             viewport.getAlignment()));
3684     alignPanel.paintAlignment(true);
3685   }
3686
3687   /**
3688    * DOCUMENT ME!
3689    *
3690    * @param e
3691    *          DOCUMENT ME!
3692    */
3693   @Override
3694   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3695   {
3696     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3697     AlignmentSorter.sortByLength(viewport.getAlignment());
3698     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3699             viewport.getAlignment()));
3700     alignPanel.paintAlignment(true);
3701   }
3702
3703   /**
3704    * DOCUMENT ME!
3705    *
3706    * @param e
3707    *          DOCUMENT ME!
3708    */
3709   @Override
3710   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3711   {
3712     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3713     AlignmentSorter.sortByGroup(viewport.getAlignment());
3714     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3715             viewport.getAlignment()));
3716
3717     alignPanel.paintAlignment(true);
3718   }
3719
3720   /**
3721    * DOCUMENT ME!
3722    *
3723    * @param e
3724    *          DOCUMENT ME!
3725    */
3726   @Override
3727   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3728   {
3729     new RedundancyPanel(alignPanel, this);
3730   }
3731
3732   /**
3733    * DOCUMENT ME!
3734    *
3735    * @param e
3736    *          DOCUMENT ME!
3737    */
3738   @Override
3739   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3740   {
3741     if ((viewport.getSelectionGroup() == null)
3742             || (viewport.getSelectionGroup().getSize() < 2))
3743     {
3744       JvOptionPane.showInternalMessageDialog(this, MessageManager
3745               .getString("label.you_must_select_least_two_sequences"),
3746               MessageManager.getString("label.invalid_selection"),
3747               JvOptionPane.WARNING_MESSAGE);
3748     }
3749     else
3750     {
3751       JInternalFrame frame = new JInternalFrame();
3752       frame.setContentPane(new PairwiseAlignPanel(viewport));
3753       Desktop.addInternalFrame(frame,
3754               MessageManager.getString("action.pairwise_alignment"), 600,
3755               500);
3756     }
3757   }
3758
3759   /**
3760    * DOCUMENT ME!
3761    *
3762    * @param e
3763    *          DOCUMENT ME!
3764    */
3765   @Override
3766   public void PCAMenuItem_actionPerformed(ActionEvent e)
3767   {
3768     if (((viewport.getSelectionGroup() != null)
3769             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3770             .getSelectionGroup().getSize() > 0))
3771             || (viewport.getAlignment().getHeight() < 4))
3772     {
3773       JvOptionPane
3774               .showInternalMessageDialog(
3775                       this,
3776                       MessageManager
3777                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3778                       MessageManager
3779                               .getString("label.sequence_selection_insufficient"),
3780                       JvOptionPane.WARNING_MESSAGE);
3781
3782       return;
3783     }
3784
3785     new PCAPanel(alignPanel);
3786   }
3787
3788   @Override
3789   public void autoCalculate_actionPerformed(ActionEvent e)
3790   {
3791     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3792     if (viewport.autoCalculateConsensus)
3793     {
3794       viewport.firePropertyChange("alignment", null, viewport
3795               .getAlignment().getSequences());
3796     }
3797   }
3798
3799   @Override
3800   public void sortByTreeOption_actionPerformed(ActionEvent e)
3801   {
3802     viewport.sortByTree = sortByTree.isSelected();
3803   }
3804
3805   @Override
3806   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3807   {
3808     viewport.followSelection = listenToViewSelections.isSelected();
3809   }
3810
3811   /**
3812    * DOCUMENT ME!
3813    *
3814    * @param e
3815    *          DOCUMENT ME!
3816    */
3817   @Override
3818   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3819   {
3820     newTreePanel("AV", "PID", "Average distance tree using PID");
3821   }
3822
3823   /**
3824    * DOCUMENT ME!
3825    *
3826    * @param e
3827    *          DOCUMENT ME!
3828    */
3829   @Override
3830   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3831   {
3832     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3833   }
3834
3835   /**
3836    * DOCUMENT ME!
3837    *
3838    * @param e
3839    *          DOCUMENT ME!
3840    */
3841   @Override
3842   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3843   {
3844     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3845   }
3846
3847   /**
3848    * DOCUMENT ME!
3849    *
3850    * @param e
3851    *          DOCUMENT ME!
3852    */
3853   @Override
3854   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3855   {
3856     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3857   }
3858
3859   /**
3860    * DOCUMENT ME!
3861    *
3862    * @param type
3863    *          DOCUMENT ME!
3864    * @param pwType
3865    *          DOCUMENT ME!
3866    * @param title
3867    *          DOCUMENT ME!
3868    */
3869   void newTreePanel(String type, String pwType, String title)
3870   {
3871     TreePanel tp;
3872
3873     if (viewport.getSelectionGroup() != null
3874             && viewport.getSelectionGroup().getSize() > 0)
3875     {
3876       if (viewport.getSelectionGroup().getSize() < 3)
3877       {
3878         JvOptionPane
3879                 .showMessageDialog(
3880                         Desktop.desktop,
3881                         MessageManager
3882                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3883                         MessageManager
3884                                 .getString("label.not_enough_sequences"),
3885                         JvOptionPane.WARNING_MESSAGE);
3886         return;
3887       }
3888
3889       SequenceGroup sg = viewport.getSelectionGroup();
3890
3891       /* Decide if the selection is a column region */
3892       for (SequenceI _s : sg.getSequences())
3893       {
3894         if (_s.getLength() < sg.getEndRes())
3895         {
3896           JvOptionPane
3897                   .showMessageDialog(
3898                           Desktop.desktop,
3899                           MessageManager
3900                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3901                           MessageManager
3902                                   .getString("label.sequences_selection_not_aligned"),
3903                           JvOptionPane.WARNING_MESSAGE);
3904
3905           return;
3906         }
3907       }
3908
3909       title = title + " on region";
3910       tp = new TreePanel(alignPanel, type, pwType);
3911     }
3912     else
3913     {
3914       // are the visible sequences aligned?
3915       if (!viewport.getAlignment().isAligned(false))
3916       {
3917         JvOptionPane
3918                 .showMessageDialog(
3919                         Desktop.desktop,
3920                         MessageManager
3921                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3922                         MessageManager
3923                                 .getString("label.sequences_not_aligned"),
3924                         JvOptionPane.WARNING_MESSAGE);
3925
3926         return;
3927       }
3928
3929       if (viewport.getAlignment().getHeight() < 2)
3930       {
3931         return;
3932       }
3933
3934       tp = new TreePanel(alignPanel, type, pwType);
3935     }
3936
3937     title += " from ";
3938
3939     if (viewport.viewName != null)
3940     {
3941       title += viewport.viewName + " of ";
3942     }
3943
3944     title += this.title;
3945
3946     Desktop.addInternalFrame(tp, title, 600, 500);
3947   }
3948
3949   /**
3950    * DOCUMENT ME!
3951    *
3952    * @param title
3953    *          DOCUMENT ME!
3954    * @param order
3955    *          DOCUMENT ME!
3956    */
3957   public void addSortByOrderMenuItem(String title,
3958           final AlignmentOrder order)
3959   {
3960     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3961             "action.by_title_param", new Object[] { title }));
3962     sort.add(item);
3963     item.addActionListener(new java.awt.event.ActionListener()
3964     {
3965       @Override
3966       public void actionPerformed(ActionEvent e)
3967       {
3968         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3969
3970         // TODO: JBPNote - have to map order entries to curent SequenceI
3971         // pointers
3972         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3973
3974         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3975                 .getAlignment()));
3976
3977         alignPanel.paintAlignment(true);
3978       }
3979     });
3980   }
3981
3982   /**
3983    * Add a new sort by annotation score menu item
3984    *
3985    * @param sort
3986    *          the menu to add the option to
3987    * @param scoreLabel
3988    *          the label used to retrieve scores for each sequence on the
3989    *          alignment
3990    */
3991   public void addSortByAnnotScoreMenuItem(JMenu sort,
3992           final String scoreLabel)
3993   {
3994     final JMenuItem item = new JMenuItem(scoreLabel);
3995     sort.add(item);
3996     item.addActionListener(new java.awt.event.ActionListener()
3997     {
3998       @Override
3999       public void actionPerformed(ActionEvent e)
4000       {
4001         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4002         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4003                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4004         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4005                 viewport.getAlignment()));
4006         alignPanel.paintAlignment(true);
4007       }
4008     });
4009   }
4010
4011   /**
4012    * last hash for alignment's annotation array - used to minimise cost of
4013    * rebuild.
4014    */
4015   protected int _annotationScoreVectorHash;
4016
4017   /**
4018    * search the alignment and rebuild the sort by annotation score submenu the
4019    * last alignment annotation vector hash is stored to minimize cost of
4020    * rebuilding in subsequence calls.
4021    *
4022    */
4023   @Override
4024   public void buildSortByAnnotationScoresMenu()
4025   {
4026     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4027     {
4028       return;
4029     }
4030
4031     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4032     {
4033       sortByAnnotScore.removeAll();
4034       // almost certainly a quicker way to do this - but we keep it simple
4035       Hashtable scoreSorts = new Hashtable();
4036       AlignmentAnnotation aann[];
4037       for (SequenceI sqa : viewport.getAlignment().getSequences())
4038       {
4039         aann = sqa.getAnnotation();
4040         for (int i = 0; aann != null && i < aann.length; i++)
4041         {
4042           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4043           {
4044             scoreSorts.put(aann[i].label, aann[i].label);
4045           }
4046         }
4047       }
4048       Enumeration labels = scoreSorts.keys();
4049       while (labels.hasMoreElements())
4050       {
4051         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4052                 (String) labels.nextElement());
4053       }
4054       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4055       scoreSorts.clear();
4056
4057       _annotationScoreVectorHash = viewport.getAlignment()
4058               .getAlignmentAnnotation().hashCode();
4059     }
4060   }
4061
4062   /**
4063    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4064    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4065    * call. Listeners are added to remove the menu item when the treePanel is
4066    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4067    * modified.
4068    *
4069    * @param treePanel
4070    *          Displayed tree window.
4071    * @param title
4072    *          SortBy menu item title.
4073    */
4074   @Override
4075   public void buildTreeMenu()
4076   {
4077     calculateTree.removeAll();
4078     // build the calculate menu
4079
4080     for (final String type : new String[] { "NJ", "AV" })
4081     {
4082       String treecalcnm = MessageManager.getString("label.tree_calc_"
4083               + type.toLowerCase());
4084       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4085       {
4086         JMenuItem tm = new JMenuItem();
4087         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4088         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4089                 || sm.isProtein() == !viewport.getAlignment()
4090                         .isNucleotide())
4091         {
4092           String smn = MessageManager.getStringOrReturn(
4093                   "label.score_model_", sm.getName());
4094           final String title = MessageManager.formatMessage(
4095                   "label.treecalc_title", treecalcnm, smn);
4096           tm.setText(title);//
4097           tm.addActionListener(new java.awt.event.ActionListener()
4098           {
4099             @Override
4100             public void actionPerformed(ActionEvent e)
4101             {
4102               newTreePanel(type, pwtype, title);
4103             }
4104           });
4105           calculateTree.add(tm);
4106         }
4107
4108       }
4109     }
4110     sortByTreeMenu.removeAll();
4111
4112     List<Component> comps = PaintRefresher.components.get(viewport
4113             .getSequenceSetId());
4114     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4115     for (Component comp : comps)
4116     {
4117       if (comp instanceof TreePanel)
4118       {
4119         treePanels.add((TreePanel) comp);
4120       }
4121     }
4122
4123     if (treePanels.size() < 1)
4124     {
4125       sortByTreeMenu.setVisible(false);
4126       return;
4127     }
4128
4129     sortByTreeMenu.setVisible(true);
4130
4131     for (final TreePanel tp : treePanels)
4132     {
4133       final JMenuItem item = new JMenuItem(tp.getTitle());
4134       item.addActionListener(new java.awt.event.ActionListener()
4135       {
4136         @Override
4137         public void actionPerformed(ActionEvent e)
4138         {
4139           tp.sortByTree_actionPerformed();
4140           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4141
4142         }
4143       });
4144
4145       sortByTreeMenu.add(item);
4146     }
4147   }
4148
4149   public boolean sortBy(AlignmentOrder alorder, String undoname)
4150   {
4151     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4152     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4153     if (undoname != null)
4154     {
4155       addHistoryItem(new OrderCommand(undoname, oldOrder,
4156               viewport.getAlignment()));
4157     }
4158     alignPanel.paintAlignment(true);
4159     return true;
4160   }
4161
4162   /**
4163    * Work out whether the whole set of sequences or just the selected set will
4164    * be submitted for multiple alignment.
4165    *
4166    */
4167   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4168   {
4169     // Now, check we have enough sequences
4170     AlignmentView msa = null;
4171
4172     if ((viewport.getSelectionGroup() != null)
4173             && (viewport.getSelectionGroup().getSize() > 1))
4174     {
4175       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4176       // some common interface!
4177       /*
4178        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4179        * SequenceI[sz = seqs.getSize(false)];
4180        *
4181        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4182        * seqs.getSequenceAt(i); }
4183        */
4184       msa = viewport.getAlignmentView(true);
4185     }
4186     else if (viewport.getSelectionGroup() != null
4187             && viewport.getSelectionGroup().getSize() == 1)
4188     {
4189       int option = JvOptionPane.showConfirmDialog(this,
4190               MessageManager.getString("warn.oneseq_msainput_selection"),
4191               MessageManager.getString("label.invalid_selection"),
4192               JvOptionPane.OK_CANCEL_OPTION);
4193       if (option == JvOptionPane.OK_OPTION)
4194       {
4195         msa = viewport.getAlignmentView(false);
4196       }
4197     }
4198     else
4199     {
4200       msa = viewport.getAlignmentView(false);
4201     }
4202     return msa;
4203   }
4204
4205   /**
4206    * Decides what is submitted to a secondary structure prediction service: the
4207    * first sequence in the alignment, or in the current selection, or, if the
4208    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4209    * region or the whole alignment. (where the first sequence in the set is the
4210    * one that the prediction will be for).
4211    */
4212   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4213   {
4214     AlignmentView seqs = null;
4215
4216     if ((viewport.getSelectionGroup() != null)
4217             && (viewport.getSelectionGroup().getSize() > 0))
4218     {
4219       seqs = viewport.getAlignmentView(true);
4220     }
4221     else
4222     {
4223       seqs = viewport.getAlignmentView(false);
4224     }
4225     // limit sequences - JBPNote in future - could spawn multiple prediction
4226     // jobs
4227     // TODO: viewport.getAlignment().isAligned is a global state - the local
4228     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4229     if (!viewport.getAlignment().isAligned(false))
4230     {
4231       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4232       // TODO: if seqs.getSequences().length>1 then should really have warned
4233       // user!
4234
4235     }
4236     return seqs;
4237   }
4238
4239   /**
4240    * DOCUMENT ME!
4241    *
4242    * @param e
4243    *          DOCUMENT ME!
4244    */
4245   @Override
4246   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4247   {
4248     // Pick the tree file
4249     JalviewFileChooser chooser = new JalviewFileChooser(
4250             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4251     chooser.setFileView(new JalviewFileView());
4252     chooser.setDialogTitle(MessageManager
4253             .getString("label.select_newick_like_tree_file"));
4254     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4255
4256     int value = chooser.showOpenDialog(null);
4257
4258     if (value == JalviewFileChooser.APPROVE_OPTION)
4259     {
4260       String choice = chooser.getSelectedFile().getPath();
4261       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4262       jalview.io.NewickFile fin = null;
4263       try
4264       {
4265         fin = new NewickFile(choice, DataSourceType.FILE);
4266         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4267       } catch (Exception ex)
4268       {
4269         JvOptionPane
4270                 .showMessageDialog(
4271                         Desktop.desktop,
4272                         ex.getMessage(),
4273                         MessageManager
4274                                 .getString("label.problem_reading_tree_file"),
4275                         JvOptionPane.WARNING_MESSAGE);
4276         ex.printStackTrace();
4277       }
4278       if (fin != null && fin.hasWarningMessage())
4279       {
4280         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4281                 .getWarningMessage(), MessageManager
4282                 .getString("label.possible_problem_with_tree_file"),
4283                 JvOptionPane.WARNING_MESSAGE);
4284       }
4285     }
4286   }
4287
4288   @Override
4289   protected void tcoffeeColorScheme_actionPerformed()
4290   {
4291     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4292   }
4293
4294   public TreePanel ShowNewickTree(NewickFile nf, String title)
4295   {
4296     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4297   }
4298
4299   public TreePanel ShowNewickTree(NewickFile nf, String title,
4300           AlignmentView input)
4301   {
4302     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4303   }
4304
4305   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4306           int h, int x, int y)
4307   {
4308     return ShowNewickTree(nf, title, null, w, h, x, y);
4309   }
4310
4311   /**
4312    * Add a treeviewer for the tree extracted from a newick file object to the
4313    * current alignment view
4314    *
4315    * @param nf
4316    *          the tree
4317    * @param title
4318    *          tree viewer title
4319    * @param input
4320    *          Associated alignment input data (or null)
4321    * @param w
4322    *          width
4323    * @param h
4324    *          height
4325    * @param x
4326    *          position
4327    * @param y
4328    *          position
4329    * @return TreePanel handle
4330    */
4331   public TreePanel ShowNewickTree(NewickFile nf, String title,
4332           AlignmentView input, int w, int h, int x, int y)
4333   {
4334     TreePanel tp = null;
4335
4336     try
4337     {
4338       nf.parse();
4339
4340       if (nf.getTree() != null)
4341       {
4342         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4343
4344         tp.setSize(w, h);
4345
4346         if (x > 0 && y > 0)
4347         {
4348           tp.setLocation(x, y);
4349         }
4350
4351         Desktop.addInternalFrame(tp, title, w, h);
4352       }
4353     } catch (Exception ex)
4354     {
4355       ex.printStackTrace();
4356     }
4357
4358     return tp;
4359   }
4360
4361   private boolean buildingMenu = false;
4362
4363   /**
4364    * Generates menu items and listener event actions for web service clients
4365    *
4366    */
4367   public void BuildWebServiceMenu()
4368   {
4369     while (buildingMenu)
4370     {
4371       try
4372       {
4373         System.err.println("Waiting for building menu to finish.");
4374         Thread.sleep(10);
4375       } catch (Exception e)
4376       {
4377       }
4378     }
4379     final AlignFrame me = this;
4380     buildingMenu = true;
4381     new Thread(new Runnable()
4382     {
4383       @Override
4384       public void run()
4385       {
4386         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4387         try
4388         {
4389           // System.err.println("Building ws menu again "
4390           // + Thread.currentThread());
4391           // TODO: add support for context dependent disabling of services based
4392           // on
4393           // alignment and current selection
4394           // TODO: add additional serviceHandle parameter to specify abstract
4395           // handler
4396           // class independently of AbstractName
4397           // TODO: add in rediscovery GUI function to restart discoverer
4398           // TODO: group services by location as well as function and/or
4399           // introduce
4400           // object broker mechanism.
4401           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4402           final IProgressIndicator af = me;
4403
4404           /*
4405            * do not i18n these strings - they are hard-coded in class
4406            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4407            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4408            */
4409           final JMenu msawsmenu = new JMenu("Alignment");
4410           final JMenu secstrmenu = new JMenu(
4411                   "Secondary Structure Prediction");
4412           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4413           final JMenu analymenu = new JMenu("Analysis");
4414           final JMenu dismenu = new JMenu("Protein Disorder");
4415           // JAL-940 - only show secondary structure prediction services from
4416           // the legacy server
4417           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4418               // &&
4419           Discoverer.services != null && (Discoverer.services.size() > 0))
4420           {
4421             // TODO: refactor to allow list of AbstractName/Handler bindings to
4422             // be
4423             // stored or retrieved from elsewhere
4424             // No MSAWS used any more:
4425             // Vector msaws = null; // (Vector)
4426             // Discoverer.services.get("MsaWS");
4427             Vector secstrpr = (Vector) Discoverer.services
4428                     .get("SecStrPred");
4429             if (secstrpr != null)
4430             {
4431               // Add any secondary structure prediction services
4432               for (int i = 0, j = secstrpr.size(); i < j; i++)
4433               {
4434                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4435                         .get(i);
4436                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4437                         .getServiceClient(sh);
4438                 int p = secstrmenu.getItemCount();
4439                 impl.attachWSMenuEntry(secstrmenu, me);
4440                 int q = secstrmenu.getItemCount();
4441                 for (int litm = p; litm < q; litm++)
4442                 {
4443                   legacyItems.add(secstrmenu.getItem(litm));
4444                 }
4445               }
4446             }
4447           }
4448
4449           // Add all submenus in the order they should appear on the web
4450           // services menu
4451           wsmenu.add(msawsmenu);
4452           wsmenu.add(secstrmenu);
4453           wsmenu.add(dismenu);
4454           wsmenu.add(analymenu);
4455           // No search services yet
4456           // wsmenu.add(seqsrchmenu);
4457
4458           javax.swing.SwingUtilities.invokeLater(new Runnable()
4459           {
4460             @Override
4461             public void run()
4462             {
4463               try
4464               {
4465                 webService.removeAll();
4466                 // first, add discovered services onto the webservices menu
4467                 if (wsmenu.size() > 0)
4468                 {
4469                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4470                   {
4471                     webService.add(wsmenu.get(i));
4472                   }
4473                 }
4474                 else
4475                 {
4476                   webService.add(me.webServiceNoServices);
4477                 }
4478                 // TODO: move into separate menu builder class.
4479                 boolean new_sspred = false;
4480                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4481                 {
4482                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4483                   if (jws2servs != null)
4484                   {
4485                     if (jws2servs.hasServices())
4486                     {
4487                       jws2servs.attachWSMenuEntry(webService, me);
4488                       for (Jws2Instance sv : jws2servs.getServices())
4489                       {
4490                         if (sv.description.toLowerCase().contains("jpred"))
4491                         {
4492                           for (JMenuItem jmi : legacyItems)
4493                           {
4494                             jmi.setVisible(false);
4495                           }
4496                         }
4497                       }
4498
4499                     }
4500                     if (jws2servs.isRunning())
4501                     {
4502                       JMenuItem tm = new JMenuItem(
4503                               "Still discovering JABA Services");
4504                       tm.setEnabled(false);
4505                       webService.add(tm);
4506                     }
4507                   }
4508                 }
4509                 build_urlServiceMenu(me.webService);
4510                 build_fetchdbmenu(webService);
4511                 for (JMenu item : wsmenu)
4512                 {
4513                   if (item.getItemCount() == 0)
4514                   {
4515                     item.setEnabled(false);
4516                   }
4517                   else
4518                   {
4519                     item.setEnabled(true);
4520                   }
4521                 }
4522               } catch (Exception e)
4523               {
4524                 Cache.log
4525                         .debug("Exception during web service menu building process.",
4526                                 e);
4527               }
4528             }
4529           });
4530         } catch (Exception e)
4531         {
4532         }
4533         buildingMenu = false;
4534       }
4535     }).start();
4536
4537   }
4538
4539   /**
4540    * construct any groupURL type service menu entries.
4541    *
4542    * @param webService
4543    */
4544   private void build_urlServiceMenu(JMenu webService)
4545   {
4546     // TODO: remove this code when 2.7 is released
4547     // DEBUG - alignmentView
4548     /*
4549      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4550      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4551      *
4552      * @Override public void actionPerformed(ActionEvent e) {
4553      * jalview.datamodel.AlignmentView
4554      * .testSelectionViews(af.viewport.getAlignment(),
4555      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4556      *
4557      * }); webService.add(testAlView);
4558      */
4559     // TODO: refactor to RestClient discoverer and merge menu entries for
4560     // rest-style services with other types of analysis/calculation service
4561     // SHmmr test client - still being implemented.
4562     // DEBUG - alignmentView
4563
4564     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4565             .getRestClients())
4566     {
4567       client.attachWSMenuEntry(
4568               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4569               this);
4570     }
4571   }
4572
4573   /**
4574    * Searches the alignment sequences for xRefs and builds the Show
4575    * Cross-References menu (formerly called Show Products), with database
4576    * sources for which cross-references are found (protein sources for a
4577    * nucleotide alignment and vice versa)
4578    *
4579    * @return true if Show Cross-references menu should be enabled
4580    */
4581   public boolean canShowProducts()
4582   {
4583     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4584     AlignmentI dataset = viewport.getAlignment().getDataset();
4585
4586     showProducts.removeAll();
4587     final boolean dna = viewport.getAlignment().isNucleotide();
4588
4589     if (seqs == null || seqs.length == 0)
4590     {
4591       // nothing to see here.
4592       return false;
4593     }
4594
4595     boolean showp = false;
4596     try
4597     {
4598       List<String> ptypes = new CrossRef(seqs, dataset)
4599               .findXrefSourcesForSequences(dna);
4600
4601       for (final String source : ptypes)
4602       {
4603         showp = true;
4604         final AlignFrame af = this;
4605         JMenuItem xtype = new JMenuItem(source);
4606         xtype.addActionListener(new ActionListener()
4607         {
4608           @Override
4609           public void actionPerformed(ActionEvent e)
4610           {
4611             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4612           }
4613         });
4614         showProducts.add(xtype);
4615       }
4616       showProducts.setVisible(showp);
4617       showProducts.setEnabled(showp);
4618     } catch (Exception e)
4619     {
4620       Cache.log
4621               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4622                       e);
4623       return false;
4624     }
4625     return showp;
4626   }
4627
4628   /**
4629    * Finds and displays cross-references for the selected sequences (protein
4630    * products for nucleotide sequences, dna coding sequences for peptides).
4631    *
4632    * @param sel
4633    *          the sequences to show cross-references for
4634    * @param dna
4635    *          true if from a nucleotide alignment (so showing proteins)
4636    * @param source
4637    *          the database to show cross-references for
4638    */
4639   protected void showProductsFor(final SequenceI[] sel,
4640           final boolean _odna, final String source)
4641   {
4642     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4643             .start();
4644   }
4645
4646   /**
4647    * Construct and display a new frame containing the translation of this
4648    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4649    */
4650   @Override
4651   public void showTranslation_actionPerformed(ActionEvent e)
4652   {
4653     AlignmentI al = null;
4654     try
4655     {
4656       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4657
4658       al = dna.translateCdna();
4659     } catch (Exception ex)
4660     {
4661       jalview.bin.Cache.log.error(
4662               "Exception during translation. Please report this !", ex);
4663       final String msg = MessageManager
4664               .getString("label.error_when_translating_sequences_submit_bug_report");
4665       final String errorTitle = MessageManager
4666               .getString("label.implementation_error")
4667               + MessageManager.getString("label.translation_failed");
4668       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4669               JvOptionPane.ERROR_MESSAGE);
4670       return;
4671     }
4672     if (al == null || al.getHeight() == 0)
4673     {
4674       final String msg = MessageManager
4675               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4676       final String errorTitle = MessageManager
4677               .getString("label.translation_failed");
4678       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4679               JvOptionPane.WARNING_MESSAGE);
4680     }
4681     else
4682     {
4683       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4684       af.setFileFormat(this.currentFileFormat);
4685       final String newTitle = MessageManager.formatMessage(
4686               "label.translation_of_params",
4687               new Object[] { this.getTitle() });
4688       af.setTitle(newTitle);
4689       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4690       {
4691         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4692         viewport.openSplitFrame(af, new Alignment(seqs));
4693       }
4694       else
4695       {
4696         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4697                 DEFAULT_HEIGHT);
4698       }
4699     }
4700   }
4701
4702   /**
4703    * Set the file format
4704    *
4705    * @param format
4706    */
4707   public void setFileFormat(FileFormatI format)
4708   {
4709     this.currentFileFormat = format;
4710   }
4711
4712   /**
4713    * Try to load a features file onto the alignment.
4714    *
4715    * @param file
4716    *          contents or path to retrieve file
4717    * @param sourceType
4718    *          access mode of file (see jalview.io.AlignFile)
4719    * @return true if features file was parsed correctly.
4720    */
4721   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4722   {
4723     return avc.parseFeaturesFile(file, sourceType,
4724             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4725
4726   }
4727
4728   @Override
4729   public void refreshFeatureUI(boolean enableIfNecessary)
4730   {
4731     // note - currently this is only still here rather than in the controller
4732     // because of the featureSettings hard reference that is yet to be
4733     // abstracted
4734     if (enableIfNecessary)
4735     {
4736       viewport.setShowSequenceFeatures(true);
4737       showSeqFeatures.setSelected(true);
4738     }
4739
4740   }
4741
4742   @Override
4743   public void dragEnter(DropTargetDragEvent evt)
4744   {
4745   }
4746
4747   @Override
4748   public void dragExit(DropTargetEvent evt)
4749   {
4750   }
4751
4752   @Override
4753   public void dragOver(DropTargetDragEvent evt)
4754   {
4755   }
4756
4757   @Override
4758   public void dropActionChanged(DropTargetDragEvent evt)
4759   {
4760   }
4761
4762   @Override
4763   public void drop(DropTargetDropEvent evt)
4764   {
4765     // JAL-1552 - acceptDrop required before getTransferable call for
4766     // Java's Transferable for native dnd
4767     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4768     Transferable t = evt.getTransferable();
4769     List<String> files = new ArrayList<String>();
4770     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4771
4772     try
4773     {
4774       Desktop.transferFromDropTarget(files, protocols, evt, t);
4775     } catch (Exception e)
4776     {
4777       e.printStackTrace();
4778     }
4779     if (files != null)
4780     {
4781       try
4782       {
4783         // check to see if any of these files have names matching sequences in
4784         // the alignment
4785         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4786                 .getAlignment().getSequencesArray());
4787         /**
4788          * Object[] { String,SequenceI}
4789          */
4790         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4791         ArrayList<String> filesnotmatched = new ArrayList<String>();
4792         for (int i = 0; i < files.size(); i++)
4793         {
4794           String file = files.get(i).toString();
4795           String pdbfn = "";
4796           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4797           if (protocol == DataSourceType.FILE)
4798           {
4799             File fl = new File(file);
4800             pdbfn = fl.getName();
4801           }
4802           else if (protocol == DataSourceType.URL)
4803           {
4804             URL url = new URL(file);
4805             pdbfn = url.getFile();
4806           }
4807           if (pdbfn.length() > 0)
4808           {
4809             // attempt to find a match in the alignment
4810             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4811             int l = 0, c = pdbfn.indexOf(".");
4812             while (mtch == null && c != -1)
4813             {
4814               do
4815               {
4816                 l = c;
4817               } while ((c = pdbfn.indexOf(".", l)) > l);
4818               if (l > -1)
4819               {
4820                 pdbfn = pdbfn.substring(0, l);
4821               }
4822               mtch = idm.findAllIdMatches(pdbfn);
4823             }
4824             if (mtch != null)
4825             {
4826               FileFormatI type = null;
4827               try
4828               {
4829                 type = new IdentifyFile().identify(file, protocol);
4830               } catch (Exception ex)
4831               {
4832                 type = null;
4833               }
4834               if (type != null && type.isStructureFile())
4835               {
4836                 filesmatched.add(new Object[] { file, protocol, mtch });
4837                 continue;
4838               }
4839             }
4840             // File wasn't named like one of the sequences or wasn't a PDB file.
4841             filesnotmatched.add(file);
4842           }
4843         }
4844         int assocfiles = 0;
4845         if (filesmatched.size() > 0)
4846         {
4847           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4848                   || JvOptionPane
4849                           .showConfirmDialog(
4850                                   this,
4851                                   MessageManager
4852                                           .formatMessage(
4853                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4854                                                   new Object[] { Integer
4855                                                           .valueOf(
4856                                                                   filesmatched
4857                                                                           .size())
4858                                                           .toString() }),
4859                                   MessageManager
4860                                           .getString("label.automatically_associate_structure_files_by_name"),
4861                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4862
4863           {
4864             for (Object[] fm : filesmatched)
4865             {
4866               // try and associate
4867               // TODO: may want to set a standard ID naming formalism for
4868               // associating PDB files which have no IDs.
4869               for (SequenceI toassoc : (SequenceI[]) fm[2])
4870               {
4871                 PDBEntry pe = new AssociatePdbFileWithSeq()
4872                         .associatePdbWithSeq((String) fm[0],
4873                                 (DataSourceType) fm[1], toassoc, false,
4874                                 Desktop.instance);
4875                 if (pe != null)
4876                 {
4877                   System.err.println("Associated file : "
4878                           + ((String) fm[0]) + " with "
4879                           + toassoc.getDisplayId(true));
4880                   assocfiles++;
4881                 }
4882               }
4883               alignPanel.paintAlignment(true);
4884             }
4885           }
4886         }
4887         if (filesnotmatched.size() > 0)
4888         {
4889           if (assocfiles > 0
4890                   && (Cache.getDefault(
4891                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4892                           .showConfirmDialog(
4893                                   this,
4894                                   "<html>"
4895                                           + MessageManager
4896                                                   .formatMessage(
4897                                                           "label.ignore_unmatched_dropped_files_info",
4898                                                           new Object[] { Integer
4899                                                                   .valueOf(
4900                                                                           filesnotmatched
4901                                                                                   .size())
4902                                                                   .toString() })
4903                                           + "</html>",
4904                                   MessageManager
4905                                           .getString("label.ignore_unmatched_dropped_files"),
4906                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4907           {
4908             return;
4909           }
4910           for (String fn : filesnotmatched)
4911           {
4912             loadJalviewDataFile(fn, null, null, null);
4913           }
4914
4915         }
4916       } catch (Exception ex)
4917       {
4918         ex.printStackTrace();
4919       }
4920     }
4921   }
4922
4923   /**
4924    * Attempt to load a "dropped" file or URL string: First by testing whether
4925    * it's an Annotation file, then a JNet file, and finally a features file. If
4926    * all are false then the user may have dropped an alignment file onto this
4927    * AlignFrame.
4928    *
4929    * @param file
4930    *          either a filename or a URL string.
4931    */
4932   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4933           FileFormatI format, SequenceI assocSeq)
4934   {
4935     try
4936     {
4937       if (sourceType == null)
4938       {
4939         sourceType = FormatAdapter.checkProtocol(file);
4940       }
4941       // if the file isn't identified, or not positively identified as some
4942       // other filetype (PFAM is default unidentified alignment file type) then
4943       // try to parse as annotation.
4944       boolean isAnnotation = (format == null || FileFormat.Pfam
4945               .equals(format)) ? new AnnotationFile()
4946               .annotateAlignmentView(viewport, file, sourceType) : false;
4947
4948       if (!isAnnotation)
4949       {
4950         // first see if its a T-COFFEE score file
4951         TCoffeeScoreFile tcf = null;
4952         try
4953         {
4954           tcf = new TCoffeeScoreFile(file, sourceType);
4955           if (tcf.isValid())
4956           {
4957             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4958             {
4959               tcoffeeColour.setEnabled(true);
4960               tcoffeeColour.setSelected(true);
4961               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4962               isAnnotation = true;
4963               statusBar
4964                       .setText(MessageManager
4965                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4966             }
4967             else
4968             {
4969               // some problem - if no warning its probable that the ID matching
4970               // process didn't work
4971               JvOptionPane
4972                       .showMessageDialog(
4973                               Desktop.desktop,
4974                               tcf.getWarningMessage() == null ? MessageManager
4975                                       .getString("label.check_file_matches_sequence_ids_alignment")
4976                                       : tcf.getWarningMessage(),
4977                               MessageManager
4978                                       .getString("label.problem_reading_tcoffee_score_file"),
4979                               JvOptionPane.WARNING_MESSAGE);
4980             }
4981           }
4982           else
4983           {
4984             tcf = null;
4985           }
4986         } catch (Exception x)
4987         {
4988           Cache.log
4989                   .debug("Exception when processing data source as T-COFFEE score file",
4990                           x);
4991           tcf = null;
4992         }
4993         if (tcf == null)
4994         {
4995           // try to see if its a JNet 'concise' style annotation file *before*
4996           // we
4997           // try to parse it as a features file
4998           if (format == null)
4999           {
5000             format = new IdentifyFile().identify(file, sourceType);
5001           }
5002           if (FileFormat.Jnet.equals(format))
5003           {
5004             JPredFile predictions = new JPredFile(
5005                     file, sourceType);
5006             new JnetAnnotationMaker();
5007             JnetAnnotationMaker.add_annotation(predictions,
5008                     viewport.getAlignment(), 0, false);
5009             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5010             viewport.getAlignment().setSeqrep(repseq);
5011             ColumnSelection cs = new ColumnSelection();
5012             cs.hideInsertionsFor(repseq);
5013             viewport.setColumnSelection(cs);
5014             isAnnotation = true;
5015           }
5016           // else if (IdentifyFile.FeaturesFile.equals(format))
5017           else if (FileFormat.Features.equals(format))
5018           {
5019             if (parseFeaturesFile(file, sourceType))
5020             {
5021               alignPanel.paintAlignment(true);
5022             }
5023           }
5024           else
5025           {
5026             new FileLoader().LoadFile(viewport, file, sourceType, format);
5027           }
5028         }
5029       }
5030       if (isAnnotation)
5031       {
5032
5033         alignPanel.adjustAnnotationHeight();
5034         viewport.updateSequenceIdColours();
5035         buildSortByAnnotationScoresMenu();
5036         alignPanel.paintAlignment(true);
5037       }
5038     } catch (Exception ex)
5039     {
5040       ex.printStackTrace();
5041     } catch (OutOfMemoryError oom)
5042     {
5043       try
5044       {
5045         System.gc();
5046       } catch (Exception x)
5047       {
5048       }
5049       new OOMWarning(
5050               "loading data "
5051                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5052                               : "using " + sourceType + " from " + file)
5053                               : ".")
5054                       + (format != null ? "(parsing as '" + format
5055                               + "' file)" : ""), oom, Desktop.desktop);
5056     }
5057   }
5058
5059   /**
5060    * Method invoked by the ChangeListener on the tabbed pane, in other words
5061    * when a different tabbed pane is selected by the user or programmatically.
5062    */
5063   @Override
5064   public void tabSelectionChanged(int index)
5065   {
5066     if (index > -1)
5067     {
5068       alignPanel = alignPanels.get(index);
5069       viewport = alignPanel.av;
5070       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5071       setMenusFromViewport(viewport);
5072     }
5073
5074     /*
5075      * If there is a frame linked to this one in a SplitPane, switch it to the
5076      * same view tab index. No infinite recursion of calls should happen, since
5077      * tabSelectionChanged() should not get invoked on setting the selected
5078      * index to an unchanged value. Guard against setting an invalid index
5079      * before the new view peer tab has been created.
5080      */
5081     final AlignViewportI peer = viewport.getCodingComplement();
5082     if (peer != null)
5083     {
5084       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5085       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5086       {
5087         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5088       }
5089     }
5090   }
5091
5092   /**
5093    * On right mouse click on view tab, prompt for and set new view name.
5094    */
5095   @Override
5096   public void tabbedPane_mousePressed(MouseEvent e)
5097   {
5098     if (e.isPopupTrigger())
5099     {
5100       String msg = MessageManager.getString("label.enter_view_name");
5101       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5102               JvOptionPane.QUESTION_MESSAGE);
5103
5104       if (reply != null)
5105       {
5106         viewport.viewName = reply;
5107         // TODO warn if reply is in getExistingViewNames()?
5108         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5109       }
5110     }
5111   }
5112
5113   public AlignViewport getCurrentView()
5114   {
5115     return viewport;
5116   }
5117
5118   /**
5119    * Open the dialog for regex description parsing.
5120    */
5121   @Override
5122   protected void extractScores_actionPerformed(ActionEvent e)
5123   {
5124     ParseProperties pp = new jalview.analysis.ParseProperties(
5125             viewport.getAlignment());
5126     // TODO: verify regex and introduce GUI dialog for version 2.5
5127     // if (pp.getScoresFromDescription("col", "score column ",
5128     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5129     // true)>0)
5130     if (pp.getScoresFromDescription("description column",
5131             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5132     {
5133       buildSortByAnnotationScoresMenu();
5134     }
5135   }
5136
5137   /*
5138    * (non-Javadoc)
5139    *
5140    * @see
5141    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5142    * )
5143    */
5144   @Override
5145   protected void showDbRefs_actionPerformed(ActionEvent e)
5146   {
5147     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5148   }
5149
5150   /*
5151    * (non-Javadoc)
5152    *
5153    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5154    * ActionEvent)
5155    */
5156   @Override
5157   protected void showNpFeats_actionPerformed(ActionEvent e)
5158   {
5159     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5160   }
5161
5162   /**
5163    * find the viewport amongst the tabs in this alignment frame and close that
5164    * tab
5165    *
5166    * @param av
5167    */
5168   public boolean closeView(AlignViewportI av)
5169   {
5170     if (viewport == av)
5171     {
5172       this.closeMenuItem_actionPerformed(false);
5173       return true;
5174     }
5175     Component[] comp = tabbedPane.getComponents();
5176     for (int i = 0; comp != null && i < comp.length; i++)
5177     {
5178       if (comp[i] instanceof AlignmentPanel)
5179       {
5180         if (((AlignmentPanel) comp[i]).av == av)
5181         {
5182           // close the view.
5183           closeView((AlignmentPanel) comp[i]);
5184           return true;
5185         }
5186       }
5187     }
5188     return false;
5189   }
5190
5191   protected void build_fetchdbmenu(JMenu webService)
5192   {
5193     // Temporary hack - DBRef Fetcher always top level ws entry.
5194     // TODO We probably want to store a sequence database checklist in
5195     // preferences and have checkboxes.. rather than individual sources selected
5196     // here
5197     final JMenu rfetch = new JMenu(
5198             MessageManager.getString("action.fetch_db_references"));
5199     rfetch.setToolTipText(MessageManager
5200             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5201     webService.add(rfetch);
5202
5203     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5204             MessageManager.getString("option.trim_retrieved_seqs"));
5205     trimrs.setToolTipText(MessageManager
5206             .getString("label.trim_retrieved_sequences"));
5207     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5208     trimrs.addActionListener(new ActionListener()
5209     {
5210       @Override
5211       public void actionPerformed(ActionEvent e)
5212       {
5213         trimrs.setSelected(trimrs.isSelected());
5214         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5215                 Boolean.valueOf(trimrs.isSelected()).toString());
5216       };
5217     });
5218     rfetch.add(trimrs);
5219     JMenuItem fetchr = new JMenuItem(
5220             MessageManager.getString("label.standard_databases"));
5221     fetchr.setToolTipText(MessageManager
5222             .getString("label.fetch_embl_uniprot"));
5223     fetchr.addActionListener(new ActionListener()
5224     {
5225
5226       @Override
5227       public void actionPerformed(ActionEvent e)
5228       {
5229         new Thread(new Runnable()
5230         {
5231           @Override
5232           public void run()
5233           {
5234             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5235                     .getAlignment().isNucleotide();
5236             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5237                     .getSequenceSelection(), alignPanel.alignFrame, null,
5238                     alignPanel.alignFrame.featureSettings, isNucleotide);
5239             dbRefFetcher.addListener(new FetchFinishedListenerI()
5240             {
5241               @Override
5242               public void finished()
5243               {
5244                 AlignFrame.this.setMenusForViewport();
5245               }
5246             });
5247             dbRefFetcher.fetchDBRefs(false);
5248           }
5249         }).start();
5250
5251       }
5252
5253     });
5254     rfetch.add(fetchr);
5255     final AlignFrame me = this;
5256     new Thread(new Runnable()
5257     {
5258       @Override
5259       public void run()
5260       {
5261         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5262                 .getSequenceFetcherSingleton(me);
5263         javax.swing.SwingUtilities.invokeLater(new Runnable()
5264         {
5265           @Override
5266           public void run()
5267           {
5268             String[] dbclasses = sf.getOrderedSupportedSources();
5269             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5270             // jalview.util.QuickSort.sort(otherdb, otherdb);
5271             List<DbSourceProxy> otherdb;
5272             JMenu dfetch = new JMenu();
5273             JMenu ifetch = new JMenu();
5274             JMenuItem fetchr = null;
5275             int comp = 0, icomp = 0, mcomp = 15;
5276             String mname = null;
5277             int dbi = 0;
5278             for (String dbclass : dbclasses)
5279             {
5280               otherdb = sf.getSourceProxy(dbclass);
5281               // add a single entry for this class, or submenu allowing 'fetch
5282               // all' or pick one
5283               if (otherdb == null || otherdb.size() < 1)
5284               {
5285                 continue;
5286               }
5287               // List<DbSourceProxy> dbs=otherdb;
5288               // otherdb=new ArrayList<DbSourceProxy>();
5289               // for (DbSourceProxy db:dbs)
5290               // {
5291               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5292               // }
5293               if (mname == null)
5294               {
5295                 mname = "From " + dbclass;
5296               }
5297               if (otherdb.size() == 1)
5298               {
5299                 final DbSourceProxy[] dassource = otherdb
5300                         .toArray(new DbSourceProxy[0]);
5301                 DbSourceProxy src = otherdb.get(0);
5302                 fetchr = new JMenuItem(src.getDbSource());
5303                 fetchr.addActionListener(new ActionListener()
5304                 {
5305
5306                   @Override
5307                   public void actionPerformed(ActionEvent e)
5308                   {
5309                     new Thread(new Runnable()
5310                     {
5311
5312                       @Override
5313                       public void run()
5314                       {
5315                         boolean isNucleotide = alignPanel.alignFrame
5316                                 .getViewport().getAlignment()
5317                                 .isNucleotide();
5318                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5319                                 alignPanel.av.getSequenceSelection(),
5320                                 alignPanel.alignFrame, dassource,
5321                                 alignPanel.alignFrame.featureSettings,
5322                                 isNucleotide);
5323                         dbRefFetcher
5324                                 .addListener(new FetchFinishedListenerI()
5325                                 {
5326                                   @Override
5327                                   public void finished()
5328                                   {
5329                                     AlignFrame.this.setMenusForViewport();
5330                                   }
5331                                 });
5332                         dbRefFetcher.fetchDBRefs(false);
5333                       }
5334                     }).start();
5335                   }
5336
5337                 });
5338                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5339                         MessageManager.formatMessage(
5340                                 "label.fetch_retrieve_from",
5341                                 new Object[] { src.getDbName() })));
5342                 dfetch.add(fetchr);
5343                 comp++;
5344               }
5345               else
5346               {
5347                 final DbSourceProxy[] dassource = otherdb
5348                         .toArray(new DbSourceProxy[0]);
5349                 // fetch all entry
5350                 DbSourceProxy src = otherdb.get(0);
5351                 fetchr = new JMenuItem(MessageManager.formatMessage(
5352                         "label.fetch_all_param",
5353                         new Object[] { src.getDbSource() }));
5354                 fetchr.addActionListener(new ActionListener()
5355                 {
5356                   @Override
5357                   public void actionPerformed(ActionEvent e)
5358                   {
5359                     new Thread(new Runnable()
5360                     {
5361
5362                       @Override
5363                       public void run()
5364                       {
5365                         boolean isNucleotide = alignPanel.alignFrame
5366                                 .getViewport().getAlignment()
5367                                 .isNucleotide();
5368                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5369                                 alignPanel.av.getSequenceSelection(),
5370                                 alignPanel.alignFrame, dassource,
5371                                 alignPanel.alignFrame.featureSettings,
5372                                 isNucleotide);
5373                         dbRefFetcher
5374                                 .addListener(new FetchFinishedListenerI()
5375                                 {
5376                                   @Override
5377                                   public void finished()
5378                                   {
5379                                     AlignFrame.this.setMenusForViewport();
5380                                   }
5381                                 });
5382                         dbRefFetcher.fetchDBRefs(false);
5383                       }
5384                     }).start();
5385                   }
5386                 });
5387
5388                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5389                         MessageManager.formatMessage(
5390                                 "label.fetch_retrieve_from_all_sources",
5391                                 new Object[] {
5392                                     Integer.valueOf(otherdb.size())
5393                                             .toString(), src.getDbSource(),
5394                                     src.getDbName() })));
5395                 dfetch.add(fetchr);
5396                 comp++;
5397                 // and then build the rest of the individual menus
5398                 ifetch = new JMenu(MessageManager.formatMessage(
5399                         "label.source_from_db_source",
5400                         new Object[] { src.getDbSource() }));
5401                 icomp = 0;
5402                 String imname = null;
5403                 int i = 0;
5404                 for (DbSourceProxy sproxy : otherdb)
5405                 {
5406                   String dbname = sproxy.getDbName();
5407                   String sname = dbname.length() > 5 ? dbname.substring(0,
5408                           5) + "..." : dbname;
5409                   String msname = dbname.length() > 10 ? dbname.substring(
5410                           0, 10) + "..." : dbname;
5411                   if (imname == null)
5412                   {
5413                     imname = MessageManager.formatMessage(
5414                             "label.from_msname", new Object[] { sname });
5415                   }
5416                   fetchr = new JMenuItem(msname);
5417                   final DbSourceProxy[] dassrc = { sproxy };
5418                   fetchr.addActionListener(new ActionListener()
5419                   {
5420
5421                     @Override
5422                     public void actionPerformed(ActionEvent e)
5423                     {
5424                       new Thread(new Runnable()
5425                       {
5426
5427                         @Override
5428                         public void run()
5429                         {
5430                           boolean isNucleotide = alignPanel.alignFrame
5431                                   .getViewport().getAlignment()
5432                                   .isNucleotide();
5433                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5434                                   alignPanel.av.getSequenceSelection(),
5435                                   alignPanel.alignFrame, dassrc,
5436                                   alignPanel.alignFrame.featureSettings,
5437                                   isNucleotide);
5438                           dbRefFetcher
5439                                   .addListener(new FetchFinishedListenerI()
5440                                   {
5441                                     @Override
5442                                     public void finished()
5443                                     {
5444                                       AlignFrame.this.setMenusForViewport();
5445                                     }
5446                                   });
5447                           dbRefFetcher.fetchDBRefs(false);
5448                         }
5449                       }).start();
5450                     }
5451
5452                   });
5453                   fetchr.setToolTipText("<html>"
5454                           + MessageManager.formatMessage(
5455                                   "label.fetch_retrieve_from", new Object[]
5456                                   { dbname }));
5457                   ifetch.add(fetchr);
5458                   ++i;
5459                   if (++icomp >= mcomp || i == (otherdb.size()))
5460                   {
5461                     ifetch.setText(MessageManager.formatMessage(
5462                             "label.source_to_target", imname, sname));
5463                     dfetch.add(ifetch);
5464                     ifetch = new JMenu();
5465                     imname = null;
5466                     icomp = 0;
5467                     comp++;
5468                   }
5469                 }
5470               }
5471               ++dbi;
5472               if (comp >= mcomp || dbi >= (dbclasses.length))
5473               {
5474                 dfetch.setText(MessageManager.formatMessage(
5475                         "label.source_to_target", mname, dbclass));
5476                 rfetch.add(dfetch);
5477                 dfetch = new JMenu();
5478                 mname = null;
5479                 comp = 0;
5480               }
5481             }
5482           }
5483         });
5484       }
5485     }).start();
5486
5487   }
5488
5489   /**
5490    * Left justify the whole alignment.
5491    */
5492   @Override
5493   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5494   {
5495     AlignmentI al = viewport.getAlignment();
5496     al.justify(false);
5497     viewport.firePropertyChange("alignment", null, al);
5498   }
5499
5500   /**
5501    * Right justify the whole alignment.
5502    */
5503   @Override
5504   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5505   {
5506     AlignmentI al = viewport.getAlignment();
5507     al.justify(true);
5508     viewport.firePropertyChange("alignment", null, al);
5509   }
5510
5511   @Override
5512   public void setShowSeqFeatures(boolean b)
5513   {
5514     showSeqFeatures.setSelected(b);
5515     viewport.setShowSequenceFeatures(b);
5516   }
5517
5518   /*
5519    * (non-Javadoc)
5520    *
5521    * @see
5522    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5523    * awt.event.ActionEvent)
5524    */
5525   @Override
5526   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5527   {
5528     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5529     alignPanel.paintAlignment(true);
5530   }
5531
5532   /*
5533    * (non-Javadoc)
5534    *
5535    * @see
5536    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5537    * .ActionEvent)
5538    */
5539   @Override
5540   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5541   {
5542     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5543     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5544
5545   }
5546
5547   /*
5548    * (non-Javadoc)
5549    *
5550    * @see
5551    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5552    * .event.ActionEvent)
5553    */
5554   @Override
5555   protected void showGroupConservation_actionPerformed(ActionEvent e)
5556   {
5557     viewport.setShowGroupConservation(showGroupConservation.getState());
5558     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5559   }
5560
5561   /*
5562    * (non-Javadoc)
5563    *
5564    * @see
5565    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5566    * .event.ActionEvent)
5567    */
5568   @Override
5569   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5570   {
5571     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5572     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5573   }
5574
5575   /*
5576    * (non-Javadoc)
5577    *
5578    * @see
5579    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5580    * .event.ActionEvent)
5581    */
5582   @Override
5583   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5584   {
5585     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5586     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5587   }
5588
5589   @Override
5590   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5591   {
5592     showSequenceLogo.setState(true);
5593     viewport.setShowSequenceLogo(true);
5594     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5595     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5596   }
5597
5598   @Override
5599   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5600   {
5601     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5602   }
5603
5604   /*
5605    * (non-Javadoc)
5606    *
5607    * @see
5608    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5609    * .event.ActionEvent)
5610    */
5611   @Override
5612   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5613   {
5614     if (avc.makeGroupsFromSelection())
5615     {
5616       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5617       alignPanel.updateAnnotation();
5618       alignPanel.paintAlignment(true);
5619     }
5620   }
5621
5622   public void clearAlignmentSeqRep()
5623   {
5624     // TODO refactor alignmentseqrep to controller
5625     if (viewport.getAlignment().hasSeqrep())
5626     {
5627       viewport.getAlignment().setSeqrep(null);
5628       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5629       alignPanel.updateAnnotation();
5630       alignPanel.paintAlignment(true);
5631     }
5632   }
5633
5634   @Override
5635   protected void createGroup_actionPerformed(ActionEvent e)
5636   {
5637     if (avc.createGroup())
5638     {
5639       alignPanel.alignmentChanged();
5640     }
5641   }
5642
5643   @Override
5644   protected void unGroup_actionPerformed(ActionEvent e)
5645   {
5646     if (avc.unGroup())
5647     {
5648       alignPanel.alignmentChanged();
5649     }
5650   }
5651
5652   /**
5653    * make the given alignmentPanel the currently selected tab
5654    *
5655    * @param alignmentPanel
5656    */
5657   public void setDisplayedView(AlignmentPanel alignmentPanel)
5658   {
5659     if (!viewport.getSequenceSetId().equals(
5660             alignmentPanel.av.getSequenceSetId()))
5661     {
5662       throw new Error(
5663               MessageManager
5664                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5665     }
5666     if (tabbedPane != null
5667             && tabbedPane.getTabCount() > 0
5668             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5669                     .getSelectedIndex())
5670     {
5671       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5672     }
5673   }
5674
5675   /**
5676    * Action on selection of menu options to Show or Hide annotations.
5677    *
5678    * @param visible
5679    * @param forSequences
5680    *          update sequence-related annotations
5681    * @param forAlignment
5682    *          update non-sequence-related annotations
5683    */
5684   @Override
5685   protected void setAnnotationsVisibility(boolean visible,
5686           boolean forSequences, boolean forAlignment)
5687   {
5688     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5689             .getAlignmentAnnotation();
5690     if (anns == null)
5691     {
5692       return;
5693     }
5694     for (AlignmentAnnotation aa : anns)
5695     {
5696       /*
5697        * don't display non-positional annotations on an alignment
5698        */
5699       if (aa.annotations == null)
5700       {
5701         continue;
5702       }
5703       boolean apply = (aa.sequenceRef == null && forAlignment)
5704               || (aa.sequenceRef != null && forSequences);
5705       if (apply)
5706       {
5707         aa.visible = visible;
5708       }
5709     }
5710     alignPanel.validateAnnotationDimensions(true);
5711     alignPanel.alignmentChanged();
5712   }
5713
5714   /**
5715    * Store selected annotation sort order for the view and repaint.
5716    */
5717   @Override
5718   protected void sortAnnotations_actionPerformed()
5719   {
5720     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5721     this.alignPanel.av
5722             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5723     alignPanel.paintAlignment(true);
5724   }
5725
5726   /**
5727    *
5728    * @return alignment panels in this alignment frame
5729    */
5730   public List<? extends AlignmentViewPanel> getAlignPanels()
5731   {
5732     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5733   }
5734
5735   /**
5736    * Open a new alignment window, with the cDNA associated with this (protein)
5737    * alignment, aligned as is the protein.
5738    */
5739   protected void viewAsCdna_actionPerformed()
5740   {
5741     // TODO no longer a menu action - refactor as required
5742     final AlignmentI alignment = getViewport().getAlignment();
5743     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5744     if (mappings == null)
5745     {
5746       return;
5747     }
5748     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5749     for (SequenceI aaSeq : alignment.getSequences())
5750     {
5751       for (AlignedCodonFrame acf : mappings)
5752       {
5753         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5754         if (dnaSeq != null)
5755         {
5756           /*
5757            * There is a cDNA mapping for this protein sequence - add to new
5758            * alignment. It will share the same dataset sequence as other mapped
5759            * cDNA (no new mappings need to be created).
5760            */
5761           final Sequence newSeq = new Sequence(dnaSeq);
5762           newSeq.setDatasetSequence(dnaSeq);
5763           cdnaSeqs.add(newSeq);
5764         }
5765       }
5766     }
5767     if (cdnaSeqs.size() == 0)
5768     {
5769       // show a warning dialog no mapped cDNA
5770       return;
5771     }
5772     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5773             .size()]));
5774     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5775             AlignFrame.DEFAULT_HEIGHT);
5776     cdna.alignAs(alignment);
5777     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5778             + this.title;
5779     Desktop.addInternalFrame(alignFrame, newtitle,
5780             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5781   }
5782
5783   /**
5784    * Set visibility of dna/protein complement view (available when shown in a
5785    * split frame).
5786    *
5787    * @param show
5788    */
5789   @Override
5790   protected void showComplement_actionPerformed(boolean show)
5791   {
5792     SplitContainerI sf = getSplitViewContainer();
5793     if (sf != null)
5794     {
5795       sf.setComplementVisible(this, show);
5796     }
5797   }
5798
5799   /**
5800    * Generate the reverse (optionally complemented) of the selected sequences,
5801    * and add them to the alignment
5802    */
5803   @Override
5804   protected void showReverse_actionPerformed(boolean complement)
5805   {
5806     AlignmentI al = null;
5807     try
5808     {
5809       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5810       al = dna.reverseCdna(complement);
5811       viewport.addAlignment(al, "");
5812       addHistoryItem(new EditCommand(
5813               MessageManager.getString("label.add_sequences"),
5814               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5815               viewport.getAlignment()));
5816     } catch (Exception ex)
5817     {
5818       System.err.println(ex.getMessage());
5819       return;
5820     }
5821   }
5822
5823   /**
5824    * Try to run a script in the Groovy console, having first ensured that this
5825    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5826    * be targeted at this alignment.
5827    */
5828   @Override
5829   protected void runGroovy_actionPerformed()
5830   {
5831     Jalview.setCurrentAlignFrame(this);
5832     groovy.ui.Console console = Desktop.getGroovyConsole();
5833     if (console != null)
5834     {
5835       try
5836       {
5837         console.runScript();
5838       } catch (Exception ex)
5839       {
5840         System.err.println((ex.toString()));
5841         JvOptionPane
5842                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5843                         .getString("label.couldnt_run_groovy_script"),
5844                         MessageManager
5845                                 .getString("label.groovy_support_failed"),
5846                         JvOptionPane.ERROR_MESSAGE);
5847       }
5848     }
5849     else
5850     {
5851       System.err.println("Can't run Groovy script as console not found");
5852     }
5853   }
5854
5855   /**
5856    * Hides columns containing (or not containing) a specified feature, provided
5857    * that would not leave all columns hidden
5858    *
5859    * @param featureType
5860    * @param columnsContaining
5861    * @return
5862    */
5863   public boolean hideFeatureColumns(String featureType,
5864           boolean columnsContaining)
5865   {
5866     boolean notForHiding = avc.markColumnsContainingFeatures(
5867             columnsContaining, false, false, featureType);
5868     if (notForHiding)
5869     {
5870       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5871               false, featureType))
5872       {
5873         getViewport().hideSelectedColumns();
5874         return true;
5875       }
5876     }
5877     return false;
5878   }
5879
5880   @Override
5881   protected void selectHighlightedColumns_actionPerformed(
5882           ActionEvent actionEvent)
5883   {
5884     // include key modifier check in case user selects from menu
5885     avc.markHighlightedColumns(
5886             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5887             true,
5888             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5889   }
5890 }
5891
5892 class PrintThread extends Thread
5893 {
5894   AlignmentPanel ap;
5895
5896   public PrintThread(AlignmentPanel ap)
5897   {
5898     this.ap = ap;
5899   }
5900
5901   static PageFormat pf;
5902
5903   @Override
5904   public void run()
5905   {
5906     PrinterJob printJob = PrinterJob.getPrinterJob();
5907
5908     if (pf != null)
5909     {
5910       printJob.setPrintable(ap, pf);
5911     }
5912     else
5913     {
5914       printJob.setPrintable(ap);
5915     }
5916
5917     if (printJob.printDialog())
5918     {
5919       try
5920       {
5921         printJob.print();
5922       } catch (Exception PrintException)
5923       {
5924         PrintException.printStackTrace();
5925       }
5926     }
5927   }
5928 }