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