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