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