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