src/jalview/gui/AlignFrame.java

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