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