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, int width,
 238           int height)
 239   {
 240     this(al, hiddenColumns, width, height, null);
 241   }
 242
 243   /**
 244    * Create alignment frame for al with hiddenColumns, a specific width and
 245    * height, and specific sequenceId
 246    *
 247    * @param al
 248    * @param hiddenColumns
 249    * @param width
 250    * @param height
 251    * @param sequenceSetId
 252    *          (may be null)
 253    */
 254   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 255           int height, String sequenceSetId)
 256   {
 257     this(al, hiddenColumns, width, height, sequenceSetId, null);
 258   }
 259
 260   /**
 261    * Create alignment frame for al with hiddenColumns, a specific width and
 262    * height, and specific sequenceId
 263    *
 264    * @param al
 265    * @param hiddenColumns
 266    * @param width
 267    * @param height
 268    * @param sequenceSetId
 269    *          (may be null)
 270    * @param viewId
 271    *          (may be null)
 272    */
 273   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 274           int height, String sequenceSetId, String viewId)
 275   {
 276     setSize(width, height);
 277
 278     if (al.getDataset() == null)
 279     {
 280       al.setDataset(null);
 281     }
 282
 283     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 284
 285     alignPanel = new AlignmentPanel(this, viewport);
 286
 287     addAlignmentPanel(alignPanel, true);
 288     init();
 289   }
 290
 291   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 292           HiddenColumns hiddenColumns, int width, int height)
 293   {
 294     setSize(width, height);
 295
 296     if (al.getDataset() == null)
 297     {
 298       al.setDataset(null);
 299     }
 300
 301     viewport = new AlignViewport(al, hiddenColumns);
 302
 303     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 304     {
 305       viewport.hideSequence(hiddenSeqs);
 306     }
 307     alignPanel = new AlignmentPanel(this, viewport);
 308     addAlignmentPanel(alignPanel, true);
 309     init();
 310   }
 311
 312   /**
 313    * Make a new AlignFrame from existing alignmentPanels
 314    *
 315    * @param ap
 316    *          AlignmentPanel
 317    * @param av
 318    *          AlignViewport
 319    */
 320   public AlignFrame(AlignmentPanel ap)
 321   {
 322     viewport = ap.av;
 323     alignPanel = ap;
 324     addAlignmentPanel(ap, false);
 325     init();
 326   }
 327
 328   /**
 329    * initalise the alignframe from the underlying viewport data and the
 330    * configurations
 331    */
 332   void init()
 333   {
 334     if (!Jalview.isHeadlessMode())
 335     {
 336       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 337     }
 338
 339     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
 514                         && evt.getKeyCode() <= KeyEvent.VK_9)
 515                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 516                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 517                 && Character.isDigit(evt.getKeyChar()))
 518         {
 519           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 520         }
 521
 522         switch (evt.getKeyCode())
 523         {
 524
 525         case 27: // escape key
 526           deselectAllSequenceMenuItem_actionPerformed(null);
 527
 528           break;
 529
 530         case KeyEvent.VK_DOWN:
 531           if (evt.isAltDown() || !viewport.cursorMode)
 532           {
 533             moveSelectedSequences(false);
 534           }
 535           if (viewport.cursorMode)
 536           {
 537             alignPanel.getSeqPanel().moveCursor(0, 1);
 538           }
 539           break;
 540
 541         case KeyEvent.VK_UP:
 542           if (evt.isAltDown() || !viewport.cursorMode)
 543           {
 544             moveSelectedSequences(true);
 545           }
 546           if (viewport.cursorMode)
 547           {
 548             alignPanel.getSeqPanel().moveCursor(0, -1);
 549           }
 550
 551           break;
 552
 553         case KeyEvent.VK_LEFT:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555           {
 556             slideSequences(false,
 557                     alignPanel.getSeqPanel().getKeyboardNo1());
 558           }
 559           else
 560           {
 561             alignPanel.getSeqPanel().moveCursor(-1, 0);
 562           }
 563
 564           break;
 565
 566         case KeyEvent.VK_RIGHT:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 570           }
 571           else
 572           {
 573             alignPanel.getSeqPanel().moveCursor(1, 0);
 574           }
 575           break;
 576
 577         case KeyEvent.VK_SPACE:
 578           if (viewport.cursorMode)
 579           {
 580             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 581                     || evt.isShiftDown() || evt.isAltDown());
 582           }
 583           break;
 584
 585         // case KeyEvent.VK_A:
 586         // if (viewport.cursorMode)
 587         // {
 588         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 589         // //System.out.println("A");
 590         // }
 591         // break;
 592         /*
 593          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 594          * System.out.println("closing bracket"); } break;
 595          */
 596         case KeyEvent.VK_DELETE:
 597         case KeyEvent.VK_BACK_SPACE:
 598           if (!viewport.cursorMode)
 599           {
 600             cut_actionPerformed(null);
 601           }
 602           else
 603           {
 604             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 605                     || evt.isShiftDown() || 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
 653                   .formatMessage("label.keyboard_editing_mode", new String[]
 654                   { (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,
 709                     viewport.getAlignment().getSequences());
 710           }
 711           break;
 712
 713         case KeyEvent.VK_RIGHT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null,
 717                     viewport.getAlignment().getSequences());
 718           }
 719           break;
 720         }
 721       }
 722     });
 723   }
 724
 725   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 726   {
 727     ap.alignFrame = this;
 728     avc = new jalview.controller.AlignViewController(this, viewport,
 729             alignPanel);
 730
 731     alignPanels.add(ap);
 732
 733     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 734
 735     int aSize = alignPanels.size();
 736
 737     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 738
 739     if (aSize == 1 && ap.av.viewName == null)
 740     {
 741       this.getContentPane().add(ap, BorderLayout.CENTER);
 742     }
 743     else
 744     {
 745       if (aSize == 2)
 746       {
 747         setInitialTabVisible();
 748       }
 749
 750       expandViews.setEnabled(true);
 751       gatherViews.setEnabled(true);
 752       tabbedPane.addTab(ap.av.viewName, ap);
 753
 754       ap.setVisible(false);
 755     }
 756
 757     if (newPanel)
 758     {
 759       if (ap.av.isPadGaps())
 760       {
 761         ap.av.getAlignment().padGaps();
 762       }
 763       ap.av.updateConservation(ap);
 764       ap.av.updateConsensus(ap);
 765       ap.av.updateStrucConsensus(ap);
 766     }
 767   }
 768
 769   public void setInitialTabVisible()
 770   {
 771     expandViews.setEnabled(true);
 772     gatherViews.setEnabled(true);
 773     tabbedPane.setVisible(true);
 774     AlignmentPanel first = alignPanels.get(0);
 775     tabbedPane.addTab(first.av.viewName, first);
 776     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 777   }
 778
 779   public AlignViewport getViewport()
 780   {
 781     return viewport;
 782   }
 783
 784   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 785   private void addServiceListeners()
 786   {
 787     final java.beans.PropertyChangeListener thisListener;
 788     Desktop.instance.addJalviewPropertyChangeListener("services",
 789             thisListener = new java.beans.PropertyChangeListener()
 790             {
 791               @Override
 792               public void propertyChange(PropertyChangeEvent evt)
 793               {
 794                 // // System.out.println("Discoverer property change.");
 795                 // if (evt.getPropertyName().equals("services"))
 796                 {
 797                   SwingUtilities.invokeLater(new Runnable()
 798                   {
 799
 800                     @Override
 801                     public void run()
 802                     {
 803                       System.err.println(
 804                               "Rebuild WS Menu for service change");
 805                       BuildWebServiceMenu();
 806                     }
 807
 808                   });
 809                 }
 810               }
 811             });
 812     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 813     {
 814       @Override
 815       public void internalFrameClosed(
 816               javax.swing.event.InternalFrameEvent evt)
 817       {
 818         // System.out.println("deregistering discoverer listener");
 819         Desktop.instance.removeJalviewPropertyChangeListener("services",
 820                 thisListener);
 821         closeMenuItem_actionPerformed(true);
 822       };
 823     });
 824     // Finally, build the menu once to get current service state
 825     new Thread(new Runnable()
 826     {
 827       @Override
 828       public void run()
 829       {
 830         BuildWebServiceMenu();
 831       }
 832     }).start();
 833   }
 834
 835   /**
 836    * Configure menu items that vary according to whether the alignment is
 837    * nucleotide or protein
 838    */
 839   public void setGUINucleotide()
 840   {
 841     AlignmentI al = getViewport().getAlignment();
 842     boolean nucleotide = al.isNucleotide();
 843
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation
 849             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 850     showGroupConservation.setEnabled(!nucleotide);
 851
 852     showComplementMenuItem
 853             .setText(nucleotide ? MessageManager.getString("label.protein")
 854                     : MessageManager.getString("label.nucleotide"));
 855   }
 856
 857   /**
 858    * set up menus for the current viewport. This may be called after any
 859    * operation that affects the data in the current view (selection changed,
 860    * etc) to update the menus to reflect the new state.
 861    */
 862   @Override
 863   public void setMenusForViewport()
 864   {
 865     setMenusFromViewport(viewport);
 866   }
 867
 868   /**
 869    * Need to call this method when tabs are selected for multiple views, or when
 870    * loading from Jalview2XML.java
 871    *
 872    * @param av
 873    *          AlignViewport
 874    */
 875   void setMenusFromViewport(AlignViewport av)
 876   {
 877     padGapsMenuitem.setSelected(av.isPadGaps());
 878     colourTextMenuItem.setSelected(av.isShowColourText());
 879     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 880     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 881     conservationMenuItem.setSelected(av.getConservationSelected());
 882     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 883     seqLimits.setSelected(av.getShowJVSuffix());
 884     idRightAlign.setSelected(av.isRightAlignIds());
 885     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 886     renderGapsMenuItem.setSelected(av.isRenderGaps());
 887     wrapMenuItem.setSelected(av.getWrapAlignment());
 888     scaleAbove.setVisible(av.getWrapAlignment());
 889     scaleLeft.setVisible(av.getWrapAlignment());
 890     scaleRight.setVisible(av.getWrapAlignment());
 891     annotationPanelMenuItem.setState(av.isShowAnnotation());
 892     /*
 893      * Show/hide annotations only enabled if annotation panel is shown
 894      */
 895     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 900     viewTextMenuItem.setSelected(av.getShowText());
 901     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 902     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 903     showGroupConservation.setSelected(av.isShowGroupConservation());
 904     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 905     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 906     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 907
 908     ColourMenuHelper.setColourSelected(colourMenu,
 909             av.getGlobalColourScheme());
 910
 911     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 912     hiddenMarkers.setState(av.getShowHiddenMarkers());
 913     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 914     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 915     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 916     autoCalculate.setSelected(av.autoCalculateConsensus);
 917     sortByTree.setSelected(av.sortByTree);
 918     listenToViewSelections.setSelected(av.followSelection);
 919
 920     showProducts.setEnabled(canShowProducts());
 921     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 922
 923     updateEditMenuBar();
 924   }
 925
 926   /**
 927    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 928    *
 929    * @param b
 930    */
 931   public void setGroovyEnabled(boolean b)
 932   {
 933     runGroovy.setEnabled(b);
 934   }
 935
 936   private IProgressIndicator progressBar;
 937
 938   /*
 939    * (non-Javadoc)
 940    *
 941    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 942    */
 943   @Override
 944   public void setProgressBar(String message, long id)
 945   {
 946     progressBar.setProgressBar(message, id);
 947   }
 948
 949   @Override
 950   public void registerHandler(final long id,
 951           final IProgressIndicatorHandler handler)
 952   {
 953     progressBar.registerHandler(id, handler);
 954   }
 955
 956   /**
 957    *
 958    * @return true if any progress bars are still active
 959    */
 960   @Override
 961   public boolean operationInProgress()
 962   {
 963     return progressBar.operationInProgress();
 964   }
 965
 966   @Override
 967   public void setStatus(String text)
 968   {
 969     statusBar.setText(text);
 970   }
 971
 972   /*
 973    * Added so Castor Mapping file can obtain Jalview Version
 974    */
 975   public String getVersion()
 976   {
 977     return jalview.bin.Cache.getProperty("VERSION");
 978   }
 979
 980   public FeatureRenderer getFeatureRenderer()
 981   {
 982     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 983   }
 984
 985   @Override
 986   public void fetchSequence_actionPerformed(ActionEvent e)
 987   {
 988     new jalview.gui.SequenceFetcher(this);
 989   }
 990
 991   @Override
 992   public void addFromFile_actionPerformed(ActionEvent e)
 993   {
 994     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 995   }
 996
 997   @Override
 998   public void reload_actionPerformed(ActionEvent e)
 999   {
1000     if (fileName != null)
1001     {
1002       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003       // originating file's format
1004       // TODO: work out how to recover feature settings for correct view(s) when
1005       // file is reloaded.
1006       if (FileFormat.Jalview.equals(currentFileFormat))
1007       {
1008         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009         for (int i = 0; i < frames.length; i++)
1010         {
1011           if (frames[i] instanceof AlignFrame && frames[i] != this
1012                   && ((AlignFrame) frames[i]).fileName != null
1013                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014           {
1015             try
1016             {
1017               frames[i].setSelected(true);
1018               Desktop.instance.closeAssociatedWindows();
1019             } catch (java.beans.PropertyVetoException ex)
1020             {
1021             }
1022           }
1023
1024         }
1025         Desktop.instance.closeAssociatedWindows();
1026
1027         FileLoader loader = new FileLoader();
1028         DataSourceType protocol = fileName.startsWith("http:")
1029                 ? DataSourceType.URL
1030                 : DataSourceType.FILE;
1031         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1032       }
1033       else
1034       {
1035         Rectangle bounds = this.getBounds();
1036
1037         FileLoader loader = new FileLoader();
1038         DataSourceType protocol = fileName.startsWith("http:")
1039                 ? DataSourceType.URL
1040                 : DataSourceType.FILE;
1041         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042                 protocol, currentFileFormat);
1043
1044         newframe.setBounds(bounds);
1045         if (featureSettings != null && featureSettings.isShowing())
1046         {
1047           final Rectangle fspos = featureSettings.frame.getBounds();
1048           // TODO: need a 'show feature settings' function that takes bounds -
1049           // need to refactor Desktop.addFrame
1050           newframe.featureSettings_actionPerformed(null);
1051           final FeatureSettings nfs = newframe.featureSettings;
1052           SwingUtilities.invokeLater(new Runnable()
1053           {
1054             @Override
1055             public void run()
1056             {
1057               nfs.frame.setBounds(fspos);
1058             }
1059           });
1060           this.featureSettings.close();
1061           this.featureSettings = null;
1062         }
1063         this.closeMenuItem_actionPerformed(true);
1064       }
1065     }
1066   }
1067
1068   @Override
1069   public void addFromText_actionPerformed(ActionEvent e)
1070   {
1071     Desktop.instance
1072             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1073   }
1074
1075   @Override
1076   public void addFromURL_actionPerformed(ActionEvent e)
1077   {
1078     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1079   }
1080
1081   @Override
1082   public void save_actionPerformed(ActionEvent e)
1083   {
1084     if (fileName == null || (currentFileFormat == null)
1085             || fileName.startsWith("http"))
1086     {
1087       saveAs_actionPerformed(null);
1088     }
1089     else
1090     {
1091       saveAlignment(fileName, currentFileFormat);
1092     }
1093   }
1094
1095   /**
1096    * DOCUMENT ME!
1097    *
1098    * @param e
1099    *          DOCUMENT ME!
1100    */
1101   @Override
1102   public void saveAs_actionPerformed(ActionEvent e)
1103   {
1104     String format = currentFileFormat == null ? null
1105             : currentFileFormat.getName();
1106     JalviewFileChooser chooser = JalviewFileChooser
1107             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1108
1109     chooser.setFileView(new JalviewFileView());
1110     chooser.setDialogTitle(
1111             MessageManager.getString("label.save_alignment_to_file"));
1112     chooser.setToolTipText(MessageManager.getString("action.save"));
1113
1114     int value = chooser.showSaveDialog(this);
1115
1116     if (value == JalviewFileChooser.APPROVE_OPTION)
1117     {
1118       currentFileFormat = chooser.getSelectedFormat();
1119       while (currentFileFormat == null)
1120       {
1121         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1122                 MessageManager.getString(
1123                         "label.select_file_format_before_saving"),
1124                 MessageManager.getString("label.file_format_not_specified"),
1125                 JvOptionPane.WARNING_MESSAGE);
1126         currentFileFormat = chooser.getSelectedFormat();
1127         value = chooser.showSaveDialog(this);
1128         if (value != JalviewFileChooser.APPROVE_OPTION)
1129         {
1130           return;
1131         }
1132       }
1133
1134       fileName = chooser.getSelectedFile().getPath();
1135
1136       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1137
1138       Cache.setProperty("LAST_DIRECTORY", fileName);
1139       saveAlignment(fileName, currentFileFormat);
1140     }
1141   }
1142
1143   public boolean saveAlignment(String file, FileFormatI format)
1144   {
1145     boolean success = true;
1146
1147     if (FileFormat.Jalview.equals(format))
1148     {
1149       String shortName = title;
1150
1151       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1152       {
1153         shortName = shortName.substring(
1154                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1155       }
1156
1157       success = new Jalview2XML().saveAlignment(this, file, shortName);
1158
1159       statusBar.setText(MessageManager.formatMessage(
1160               "label.successfully_saved_to_file_in_format", new Object[]
1161               { fileName, format }));
1162
1163     }
1164     else
1165     {
1166       AlignmentExportData exportData = getAlignmentForExport(format,
1167               viewport, null);
1168       if (exportData.getSettings().isCancelled())
1169       {
1170         return false;
1171       }
1172       FormatAdapter f = new FormatAdapter(alignPanel,
1173               exportData.getSettings());
1174       String output = f.formatSequences(format, exportData.getAlignment(), // class
1175                                                                            // cast
1176                                                                            // exceptions
1177                                                                            // will
1178               // occur in the distant future
1179               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180               f.getCacheSuffixDefault(format),
1181               viewport.getAlignment().getHiddenColumns());
1182
1183       if (output == null)
1184       {
1185         success = false;
1186       }
1187       else
1188       {
1189         try
1190         {
1191           PrintWriter out = new PrintWriter(new FileWriter(file));
1192
1193           out.print(output);
1194           out.close();
1195           this.setTitle(file);
1196           statusBar.setText(MessageManager.formatMessage(
1197                   "label.successfully_saved_to_file_in_format", new Object[]
1198                   { fileName, format.getName() }));
1199         } catch (Exception ex)
1200         {
1201           success = false;
1202           ex.printStackTrace();
1203         }
1204       }
1205     }
1206
1207     if (!success)
1208     {
1209       JvOptionPane.showInternalMessageDialog(this, MessageManager
1210               .formatMessage("label.couldnt_save_file", new Object[]
1211               { fileName }),
1212               MessageManager.getString("label.error_saving_file"),
1213               JvOptionPane.WARNING_MESSAGE);
1214     }
1215
1216     return success;
1217   }
1218
1219   private void warningMessage(String warning, String title)
1220   {
1221     if (new jalview.util.Platform().isHeadless())
1222     {
1223       System.err.println("Warning: " + title + "\nWarning: " + warning);
1224
1225     }
1226     else
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, warning, title,
1229               JvOptionPane.WARNING_MESSAGE);
1230     }
1231     return;
1232   }
1233
1234   /**
1235    * DOCUMENT ME!
1236    *
1237    * @param e
1238    *          DOCUMENT ME!
1239    */
1240   @Override
1241   protected void outputText_actionPerformed(ActionEvent e)
1242   {
1243     FileFormatI fileFormat = FileFormats.getInstance()
1244             .forName(e.getActionCommand());
1245     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1246             viewport, null);
1247     if (exportData.getSettings().isCancelled())
1248     {
1249       return;
1250     }
1251     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252     cap.setForInput(null);
1253     try
1254     {
1255       FileFormatI format = fileFormat;
1256       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257               .formatSequences(format, exportData.getAlignment(),
1258                       exportData.getOmitHidden(),
1259                       exportData.getStartEndPostions(),
1260                       viewport.getAlignment().getHiddenColumns()));
1261       Desktop.addInternalFrame(cap, MessageManager
1262               .formatMessage("label.alignment_output_command", new Object[]
1263               { e.getActionCommand() }), 600, 500);
1264     } catch (OutOfMemoryError oom)
1265     {
1266       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1267               oom);
1268       cap.dispose();
1269     }
1270
1271   }
1272
1273   public static AlignmentExportData getAlignmentForExport(
1274           FileFormatI format, AlignViewportI viewport,
1275           AlignExportSettingI exportSettings)
1276   {
1277     AlignmentI alignmentToExport = null;
1278     AlignExportSettingI settings = exportSettings;
1279     String[] omitHidden = null;
1280
1281     HiddenSequences hiddenSeqs = viewport.getAlignment()
1282             .getHiddenSequences();
1283
1284     alignmentToExport = viewport.getAlignment();
1285
1286     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287     if (settings == null)
1288     {
1289       settings = new AlignExportSettings(hasHiddenSeqs,
1290               viewport.hasHiddenColumns(), format);
1291     }
1292     // settings.isExportAnnotations();
1293
1294     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1295     {
1296       omitHidden = viewport.getViewAsString(false,
1297               settings.isExportHiddenSequences());
1298     }
1299
1300     int[] alignmentStartEnd = new int[2];
1301     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1302     {
1303       alignmentToExport = hiddenSeqs.getFullAlignment();
1304     }
1305     else
1306     {
1307       alignmentToExport = viewport.getAlignment();
1308     }
1309     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1310             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1311     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1312             omitHidden, alignmentStartEnd, settings);
1313     return ed;
1314   }
1315
1316   /**
1317    * DOCUMENT ME!
1318    *
1319    * @param e
1320    *          DOCUMENT ME!
1321    */
1322   @Override
1323   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1324   {
1325     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1326     htmlSVG.exportHTML(null);
1327   }
1328
1329   @Override
1330   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1331   {
1332     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1333     bjs.exportHTML(null);
1334   }
1335
1336   public void createImageMap(File file, String image)
1337   {
1338     alignPanel.makePNGImageMap(file, image);
1339   }
1340
1341   /**
1342    * DOCUMENT ME!
1343    *
1344    * @param e
1345    *          DOCUMENT ME!
1346    */
1347   @Override
1348   public void createPNG(File f)
1349   {
1350     alignPanel.makePNG(f);
1351   }
1352
1353   /**
1354    * DOCUMENT ME!
1355    *
1356    * @param e
1357    *          DOCUMENT ME!
1358    */
1359   @Override
1360   public void createEPS(File f)
1361   {
1362     alignPanel.makeEPS(f);
1363   }
1364
1365   @Override
1366   public void createSVG(File f)
1367   {
1368     alignPanel.makeSVG(f);
1369   }
1370
1371   @Override
1372   public void pageSetup_actionPerformed(ActionEvent e)
1373   {
1374     PrinterJob printJob = PrinterJob.getPrinterJob();
1375     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1376   }
1377
1378   /**
1379    * DOCUMENT ME!
1380    *
1381    * @param e
1382    *          DOCUMENT ME!
1383    */
1384   @Override
1385   public void printMenuItem_actionPerformed(ActionEvent e)
1386   {
1387     // Putting in a thread avoids Swing painting problems
1388     PrintThread thread = new PrintThread(alignPanel);
1389     thread.start();
1390   }
1391
1392   @Override
1393   public void exportFeatures_actionPerformed(ActionEvent e)
1394   {
1395     new AnnotationExporter().exportFeatures(alignPanel);
1396   }
1397
1398   @Override
1399   public void exportAnnotations_actionPerformed(ActionEvent e)
1400   {
1401     new AnnotationExporter().exportAnnotations(alignPanel);
1402   }
1403
1404   @Override
1405   public void associatedData_actionPerformed(ActionEvent e)
1406   {
1407     // Pick the tree file
1408     JalviewFileChooser chooser = new JalviewFileChooser(
1409             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1410     chooser.setFileView(new JalviewFileView());
1411     chooser.setDialogTitle(
1412             MessageManager.getString("label.load_jalview_annotations"));
1413     chooser.setToolTipText(
1414             MessageManager.getString("label.load_jalview_annotations"));
1415
1416     int value = chooser.showOpenDialog(null);
1417
1418     if (value == JalviewFileChooser.APPROVE_OPTION)
1419     {
1420       String choice = chooser.getSelectedFile().getPath();
1421       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1422       loadJalviewDataFile(choice, null, null, null);
1423     }
1424
1425   }
1426
1427   /**
1428    * Close the current view or all views in the alignment frame. If the frame
1429    * only contains one view then the alignment will be removed from memory.
1430    *
1431    * @param closeAllTabs
1432    */
1433   @Override
1434   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1435   {
1436     if (alignPanels != null && alignPanels.size() < 2)
1437     {
1438       closeAllTabs = true;
1439     }
1440
1441     try
1442     {
1443       if (alignPanels != null)
1444       {
1445         if (closeAllTabs)
1446         {
1447           if (this.isClosed())
1448           {
1449             // really close all the windows - otherwise wait till
1450             // setClosed(true) is called
1451             for (int i = 0; i < alignPanels.size(); i++)
1452             {
1453               AlignmentPanel ap = alignPanels.get(i);
1454               ap.closePanel();
1455             }
1456           }
1457         }
1458         else
1459         {
1460           closeView(alignPanel);
1461         }
1462       }
1463
1464       if (closeAllTabs)
1465       {
1466         /*
1467          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1468          * be called recursively, with the frame now in 'closed' state
1469          */
1470         this.setClosed(true);
1471       }
1472     } catch (Exception ex)
1473     {
1474       ex.printStackTrace();
1475     }
1476   }
1477
1478   /**
1479    * Close the specified panel and close up tabs appropriately.
1480    *
1481    * @param panelToClose
1482    */
1483   public void closeView(AlignmentPanel panelToClose)
1484   {
1485     int index = tabbedPane.getSelectedIndex();
1486     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1487     alignPanels.remove(panelToClose);
1488     panelToClose.closePanel();
1489     panelToClose = null;
1490
1491     tabbedPane.removeTabAt(closedindex);
1492     tabbedPane.validate();
1493
1494     if (index > closedindex || index == tabbedPane.getTabCount())
1495     {
1496       // modify currently selected tab index if necessary.
1497       index--;
1498     }
1499
1500     this.tabSelectionChanged(index);
1501   }
1502
1503   /**
1504    * DOCUMENT ME!
1505    */
1506   void updateEditMenuBar()
1507   {
1508
1509     if (viewport.getHistoryList().size() > 0)
1510     {
1511       undoMenuItem.setEnabled(true);
1512       CommandI command = viewport.getHistoryList().peek();
1513       undoMenuItem.setText(MessageManager
1514               .formatMessage("label.undo_command", new Object[]
1515               { command.getDescription() }));
1516     }
1517     else
1518     {
1519       undoMenuItem.setEnabled(false);
1520       undoMenuItem.setText(MessageManager.getString("action.undo"));
1521     }
1522
1523     if (viewport.getRedoList().size() > 0)
1524     {
1525       redoMenuItem.setEnabled(true);
1526
1527       CommandI command = viewport.getRedoList().peek();
1528       redoMenuItem.setText(MessageManager
1529               .formatMessage("label.redo_command", new Object[]
1530               { command.getDescription() }));
1531     }
1532     else
1533     {
1534       redoMenuItem.setEnabled(false);
1535       redoMenuItem.setText(MessageManager.getString("action.redo"));
1536     }
1537   }
1538
1539   @Override
1540   public void addHistoryItem(CommandI command)
1541   {
1542     if (command.getSize() > 0)
1543     {
1544       viewport.addToHistoryList(command);
1545       viewport.clearRedoList();
1546       updateEditMenuBar();
1547       viewport.updateHiddenColumns();
1548       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1549       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1550       // viewport.getColumnSelection()
1551       // .getHiddenColumns().size() > 0);
1552     }
1553   }
1554
1555   /**
1556    *
1557    * @return alignment objects for all views
1558    */
1559   AlignmentI[] getViewAlignments()
1560   {
1561     if (alignPanels != null)
1562     {
1563       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1564       int i = 0;
1565       for (AlignmentPanel ap : alignPanels)
1566       {
1567         als[i++] = ap.av.getAlignment();
1568       }
1569       return als;
1570     }
1571     if (viewport != null)
1572     {
1573       return new AlignmentI[] { viewport.getAlignment() };
1574     }
1575     return null;
1576   }
1577
1578   /**
1579    * DOCUMENT ME!
1580    *
1581    * @param e
1582    *          DOCUMENT ME!
1583    */
1584   @Override
1585   protected void undoMenuItem_actionPerformed(ActionEvent e)
1586   {
1587     if (viewport.getHistoryList().isEmpty())
1588     {
1589       return;
1590     }
1591     CommandI command = viewport.getHistoryList().pop();
1592     viewport.addToRedoList(command);
1593     command.undoCommand(getViewAlignments());
1594
1595     AlignmentViewport originalSource = getOriginatingSource(command);
1596     updateEditMenuBar();
1597
1598     if (originalSource != null)
1599     {
1600       if (originalSource != viewport)
1601       {
1602         Cache.log.warn(
1603                 "Implementation worry: mismatch of viewport origin for undo");
1604       }
1605       originalSource.updateHiddenColumns();
1606       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1607       // null
1608       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609       // viewport.getColumnSelection()
1610       // .getHiddenColumns().size() > 0);
1611       originalSource.firePropertyChange("alignment", null,
1612               originalSource.getAlignment().getSequences());
1613     }
1614   }
1615
1616   /**
1617    * DOCUMENT ME!
1618    *
1619    * @param e
1620    *          DOCUMENT ME!
1621    */
1622   @Override
1623   protected void redoMenuItem_actionPerformed(ActionEvent e)
1624   {
1625     if (viewport.getRedoList().size() < 1)
1626     {
1627       return;
1628     }
1629
1630     CommandI command = viewport.getRedoList().pop();
1631     viewport.addToHistoryList(command);
1632     command.doCommand(getViewAlignments());
1633
1634     AlignmentViewport originalSource = getOriginatingSource(command);
1635     updateEditMenuBar();
1636
1637     if (originalSource != null)
1638     {
1639
1640       if (originalSource != viewport)
1641       {
1642         Cache.log.warn(
1643                 "Implementation worry: mismatch of viewport origin for redo");
1644       }
1645       originalSource.updateHiddenColumns();
1646       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1647       // null
1648       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649       // viewport.getColumnSelection()
1650       // .getHiddenColumns().size() > 0);
1651       originalSource.firePropertyChange("alignment", null,
1652               originalSource.getAlignment().getSequences());
1653     }
1654   }
1655
1656   AlignmentViewport getOriginatingSource(CommandI command)
1657   {
1658     AlignmentViewport originalSource = null;
1659     // For sequence removal and addition, we need to fire
1660     // the property change event FROM the viewport where the
1661     // original alignment was altered
1662     AlignmentI al = null;
1663     if (command instanceof EditCommand)
1664     {
1665       EditCommand editCommand = (EditCommand) command;
1666       al = editCommand.getAlignment();
1667       List<Component> comps = PaintRefresher.components
1668               .get(viewport.getSequenceSetId());
1669
1670       for (Component comp : comps)
1671       {
1672         if (comp instanceof AlignmentPanel)
1673         {
1674           if (al == ((AlignmentPanel) comp).av.getAlignment())
1675           {
1676             originalSource = ((AlignmentPanel) comp).av;
1677             break;
1678           }
1679         }
1680       }
1681     }
1682
1683     if (originalSource == null)
1684     {
1685       // The original view is closed, we must validate
1686       // the current view against the closed view first
1687       if (al != null)
1688       {
1689         PaintRefresher.validateSequences(al, viewport.getAlignment());
1690       }
1691
1692       originalSource = viewport;
1693     }
1694
1695     return originalSource;
1696   }
1697
1698   /**
1699    * DOCUMENT ME!
1700    *
1701    * @param up
1702    *          DOCUMENT ME!
1703    */
1704   public void moveSelectedSequences(boolean up)
1705   {
1706     SequenceGroup sg = viewport.getSelectionGroup();
1707
1708     if (sg == null)
1709     {
1710       return;
1711     }
1712     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713             viewport.getHiddenRepSequences(), up);
1714     alignPanel.paintAlignment(true);
1715   }
1716
1717   synchronized void slideSequences(boolean right, int size)
1718   {
1719     List<SequenceI> sg = new ArrayList<>();
1720     if (viewport.cursorMode)
1721     {
1722       sg.add(viewport.getAlignment()
1723               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1724     }
1725     else if (viewport.getSelectionGroup() != null
1726             && viewport.getSelectionGroup().getSize() != viewport
1727                     .getAlignment().getHeight())
1728     {
1729       sg = viewport.getSelectionGroup()
1730               .getSequences(viewport.getHiddenRepSequences());
1731     }
1732
1733     if (sg.size() < 1)
1734     {
1735       return;
1736     }
1737
1738     List<SequenceI> invertGroup = new ArrayList<>();
1739
1740     for (SequenceI seq : viewport.getAlignment().getSequences())
1741     {
1742       if (!sg.contains(seq))
1743       {
1744         invertGroup.add(seq);
1745       }
1746     }
1747
1748     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1749
1750     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1751     for (int i = 0; i < invertGroup.size(); i++)
1752     {
1753       seqs2[i] = invertGroup.get(i);
1754     }
1755
1756     SlideSequencesCommand ssc;
1757     if (right)
1758     {
1759       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1760               viewport.getGapCharacter());
1761     }
1762     else
1763     {
1764       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1765               viewport.getGapCharacter());
1766     }
1767
1768     int groupAdjustment = 0;
1769     if (ssc.getGapsInsertedBegin() && right)
1770     {
1771       if (viewport.cursorMode)
1772       {
1773         alignPanel.getSeqPanel().moveCursor(size, 0);
1774       }
1775       else
1776       {
1777         groupAdjustment = size;
1778       }
1779     }
1780     else if (!ssc.getGapsInsertedBegin() && !right)
1781     {
1782       if (viewport.cursorMode)
1783       {
1784         alignPanel.getSeqPanel().moveCursor(-size, 0);
1785       }
1786       else
1787       {
1788         groupAdjustment = -size;
1789       }
1790     }
1791
1792     if (groupAdjustment != 0)
1793     {
1794       viewport.getSelectionGroup().setStartRes(
1795               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1796       viewport.getSelectionGroup().setEndRes(
1797               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1798     }
1799
1800     /*
1801      * just extend the last slide command if compatible; but not if in
1802      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1803      */
1804     boolean appendHistoryItem = false;
1805     Deque<CommandI> historyList = viewport.getHistoryList();
1806     boolean inSplitFrame = getSplitViewContainer() != null;
1807     if (!inSplitFrame && historyList != null && historyList.size() > 0
1808             && historyList.peek() instanceof SlideSequencesCommand)
1809     {
1810       appendHistoryItem = ssc.appendSlideCommand(
1811               (SlideSequencesCommand) historyList.peek());
1812     }
1813
1814     if (!appendHistoryItem)
1815     {
1816       addHistoryItem(ssc);
1817     }
1818
1819     repaint();
1820   }
1821
1822   /**
1823    * DOCUMENT ME!
1824    *
1825    * @param e
1826    *          DOCUMENT ME!
1827    */
1828   @Override
1829   protected void copy_actionPerformed(ActionEvent e)
1830   {
1831     System.gc();
1832     if (viewport.getSelectionGroup() == null)
1833     {
1834       return;
1835     }
1836     // TODO: preserve the ordering of displayed alignment annotation in any
1837     // internal paste (particularly sequence associated annotation)
1838     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1839     String[] omitHidden = null;
1840
1841     if (viewport.hasHiddenColumns())
1842     {
1843       omitHidden = viewport.getViewAsString(true);
1844     }
1845
1846     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1847             seqs, omitHidden, null);
1848
1849     StringSelection ss = new StringSelection(output);
1850
1851     try
1852     {
1853       jalview.gui.Desktop.internalCopy = true;
1854       // Its really worth setting the clipboard contents
1855       // to empty before setting the large StringSelection!!
1856       Toolkit.getDefaultToolkit().getSystemClipboard()
1857               .setContents(new StringSelection(""), null);
1858
1859       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1860               Desktop.instance);
1861     } catch (OutOfMemoryError er)
1862     {
1863       new OOMWarning("copying region", er);
1864       return;
1865     }
1866
1867     ArrayList<int[]> hiddenColumns = null;
1868     if (viewport.hasHiddenColumns())
1869     {
1870       hiddenColumns = new ArrayList<>();
1871       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1872       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1873       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1874               .getHiddenColumns().getHiddenColumnsCopy();
1875       for (int[] region : hiddenRegions)
1876       {
1877         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1878         {
1879           hiddenColumns
1880                   .add(new int[]
1881                   { region[0] - hiddenOffset, region[1] - hiddenOffset });
1882         }
1883       }
1884     }
1885
1886     Desktop.jalviewClipboard = new Object[] { seqs,
1887         viewport.getAlignment().getDataset(), hiddenColumns };
1888     statusBar.setText(MessageManager.formatMessage(
1889             "label.copied_sequences_to_clipboard", new Object[]
1890             { Integer.valueOf(seqs.length).toString() }));
1891   }
1892
1893   /**
1894    * DOCUMENT ME!
1895    *
1896    * @param e
1897    *          DOCUMENT ME!
1898    */
1899   @Override
1900   protected void pasteNew_actionPerformed(ActionEvent e)
1901   {
1902     paste(true);
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void pasteThis_actionPerformed(ActionEvent e)
1913   {
1914     paste(false);
1915   }
1916
1917   /**
1918    * Paste contents of Jalview clipboard
1919    *
1920    * @param newAlignment
1921    *          true to paste to a new alignment, otherwise add to this.
1922    */
1923   void paste(boolean newAlignment)
1924   {
1925     boolean externalPaste = true;
1926     try
1927     {
1928       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1929       Transferable contents = c.getContents(this);
1930
1931       if (contents == null)
1932       {
1933         return;
1934       }
1935
1936       String str;
1937       FileFormatI format;
1938       try
1939       {
1940         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941         if (str.length() < 1)
1942         {
1943           return;
1944         }
1945
1946         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1947
1948       } catch (OutOfMemoryError er)
1949       {
1950         new OOMWarning("Out of memory pasting sequences!!", er);
1951         return;
1952       }
1953
1954       SequenceI[] sequences;
1955       boolean annotationAdded = false;
1956       AlignmentI alignment = null;
1957
1958       if (Desktop.jalviewClipboard != null)
1959       {
1960         // The clipboard was filled from within Jalview, we must use the
1961         // sequences
1962         // And dataset from the copied alignment
1963         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964         // be doubly sure that we create *new* sequence objects.
1965         sequences = new SequenceI[newseq.length];
1966         for (int i = 0; i < newseq.length; i++)
1967         {
1968           sequences[i] = new Sequence(newseq[i]);
1969         }
1970         alignment = new Alignment(sequences);
1971         externalPaste = false;
1972       }
1973       else
1974       {
1975         // parse the clipboard as an alignment.
1976         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1977                 format);
1978         sequences = alignment.getSequencesArray();
1979       }
1980
1981       int alwidth = 0;
1982       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1983       int fgroup = -1;
1984
1985       if (newAlignment)
1986       {
1987
1988         if (Desktop.jalviewClipboard != null)
1989         {
1990           // dataset is inherited
1991           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1992         }
1993         else
1994         {
1995           // new dataset is constructed
1996           alignment.setDataset(null);
1997         }
1998         alwidth = alignment.getWidth() + 1;
1999       }
2000       else
2001       {
2002         AlignmentI pastedal = alignment; // preserve pasted alignment object
2003         // Add pasted sequences and dataset into existing alignment.
2004         alignment = viewport.getAlignment();
2005         alwidth = alignment.getWidth() + 1;
2006         // decide if we need to import sequences from an existing dataset
2007         boolean importDs = Desktop.jalviewClipboard != null
2008                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2009         // importDs==true instructs us to copy over new dataset sequences from
2010         // an existing alignment
2011         Vector newDs = (importDs) ? new Vector() : null; // used to create
2012         // minimum dataset set
2013
2014         for (int i = 0; i < sequences.length; i++)
2015         {
2016           if (importDs)
2017           {
2018             newDs.addElement(null);
2019           }
2020           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2021           // paste
2022           if (importDs && ds != null)
2023           {
2024             if (!newDs.contains(ds))
2025             {
2026               newDs.setElementAt(ds, i);
2027               ds = new Sequence(ds);
2028               // update with new dataset sequence
2029               sequences[i].setDatasetSequence(ds);
2030             }
2031             else
2032             {
2033               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2034             }
2035           }
2036           else
2037           {
2038             // copy and derive new dataset sequence
2039             sequences[i] = sequences[i].deriveSequence();
2040             alignment.getDataset()
2041                     .addSequence(sequences[i].getDatasetSequence());
2042             // TODO: avoid creation of duplicate dataset sequences with a
2043             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2044           }
2045           alignment.addSequence(sequences[i]); // merges dataset
2046         }
2047         if (newDs != null)
2048         {
2049           newDs.clear(); // tidy up
2050         }
2051         if (alignment.getAlignmentAnnotation() != null)
2052         {
2053           for (AlignmentAnnotation alan : alignment
2054                   .getAlignmentAnnotation())
2055           {
2056             if (alan.graphGroup > fgroup)
2057             {
2058               fgroup = alan.graphGroup;
2059             }
2060           }
2061         }
2062         if (pastedal.getAlignmentAnnotation() != null)
2063         {
2064           // Add any annotation attached to alignment.
2065           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2066           for (int i = 0; i < alann.length; i++)
2067           {
2068             annotationAdded = true;
2069             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2070             {
2071               AlignmentAnnotation newann = new AlignmentAnnotation(
2072                       alann[i]);
2073               if (newann.graphGroup > -1)
2074               {
2075                 if (newGraphGroups.size() <= newann.graphGroup
2076                         || newGraphGroups.get(newann.graphGroup) == null)
2077                 {
2078                   for (int q = newGraphGroups
2079                           .size(); q <= newann.graphGroup; q++)
2080                   {
2081                     newGraphGroups.add(q, null);
2082                   }
2083                   newGraphGroups.set(newann.graphGroup,
2084                           new Integer(++fgroup));
2085                 }
2086                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2087                         .intValue();
2088               }
2089
2090               newann.padAnnotation(alwidth);
2091               alignment.addAnnotation(newann);
2092             }
2093           }
2094         }
2095       }
2096       if (!newAlignment)
2097       {
2098         // /////
2099         // ADD HISTORY ITEM
2100         //
2101         addHistoryItem(new EditCommand(
2102                 MessageManager.getString("label.add_sequences"),
2103                 Action.PASTE, sequences, 0, alignment.getWidth(),
2104                 alignment));
2105       }
2106       // Add any annotations attached to sequences
2107       for (int i = 0; i < sequences.length; i++)
2108       {
2109         if (sequences[i].getAnnotation() != null)
2110         {
2111           AlignmentAnnotation newann;
2112           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2113           {
2114             annotationAdded = true;
2115             newann = sequences[i].getAnnotation()[a];
2116             newann.adjustForAlignment();
2117             newann.padAnnotation(alwidth);
2118             if (newann.graphGroup > -1)
2119             {
2120               if (newann.graphGroup > -1)
2121               {
2122                 if (newGraphGroups.size() <= newann.graphGroup
2123                         || newGraphGroups.get(newann.graphGroup) == null)
2124                 {
2125                   for (int q = newGraphGroups
2126                           .size(); q <= newann.graphGroup; q++)
2127                   {
2128                     newGraphGroups.add(q, null);
2129                   }
2130                   newGraphGroups.set(newann.graphGroup,
2131                           new Integer(++fgroup));
2132                 }
2133                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2134                         .intValue();
2135               }
2136             }
2137             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2138             // was
2139             // duplicated
2140             // earlier
2141             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2142                     a);
2143           }
2144         }
2145       }
2146       if (!newAlignment)
2147       {
2148
2149         // propagate alignment changed.
2150         vpRanges.setEndSeq(alignment.getHeight());
2151         if (annotationAdded)
2152         {
2153           // Duplicate sequence annotation in all views.
2154           AlignmentI[] alview = this.getViewAlignments();
2155           for (int i = 0; i < sequences.length; i++)
2156           {
2157             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2158             if (sann == null)
2159             {
2160               continue;
2161             }
2162             for (int avnum = 0; avnum < alview.length; avnum++)
2163             {
2164               if (alview[avnum] != alignment)
2165               {
2166                 // duplicate in a view other than the one with input focus
2167                 int avwidth = alview[avnum].getWidth() + 1;
2168                 // this relies on sann being preserved after we
2169                 // modify the sequence's annotation array for each duplication
2170                 for (int a = 0; a < sann.length; a++)
2171                 {
2172                   AlignmentAnnotation newann = new AlignmentAnnotation(
2173                           sann[a]);
2174                   sequences[i].addAlignmentAnnotation(newann);
2175                   newann.padAnnotation(avwidth);
2176                   alview[avnum].addAnnotation(newann); // annotation was
2177                   // duplicated earlier
2178                   // TODO JAL-1145 graphGroups are not updated for sequence
2179                   // annotation added to several views. This may cause
2180                   // strangeness
2181                   alview[avnum].setAnnotationIndex(newann, a);
2182                 }
2183               }
2184             }
2185           }
2186           buildSortByAnnotationScoresMenu();
2187         }
2188         viewport.firePropertyChange("alignment", null,
2189                 alignment.getSequences());
2190         if (alignPanels != null)
2191         {
2192           for (AlignmentPanel ap : alignPanels)
2193           {
2194             ap.validateAnnotationDimensions(false);
2195           }
2196         }
2197         else
2198         {
2199           alignPanel.validateAnnotationDimensions(false);
2200         }
2201
2202       }
2203       else
2204       {
2205         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2206                 DEFAULT_HEIGHT);
2207         String newtitle = new String("Copied sequences");
2208
2209         if (Desktop.jalviewClipboard != null
2210                 && Desktop.jalviewClipboard[2] != null)
2211         {
2212           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2213           for (int[] region : hc)
2214           {
2215             af.viewport.hideColumns(region[0], region[1]);
2216           }
2217         }
2218
2219         // >>>This is a fix for the moment, until a better solution is
2220         // found!!<<<
2221         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2222                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2223                         .getFeatureRenderer());
2224
2225         // TODO: maintain provenance of an alignment, rather than just make the
2226         // title a concatenation of operations.
2227         if (!externalPaste)
2228         {
2229           if (title.startsWith("Copied sequences"))
2230           {
2231             newtitle = title;
2232           }
2233           else
2234           {
2235             newtitle = newtitle.concat("- from " + title);
2236           }
2237         }
2238         else
2239         {
2240           newtitle = new String("Pasted sequences");
2241         }
2242
2243         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2244                 DEFAULT_HEIGHT);
2245
2246       }
2247
2248     } catch (Exception ex)
2249     {
2250       ex.printStackTrace();
2251       System.out.println("Exception whilst pasting: " + ex);
2252       // could be anything being pasted in here
2253     }
2254
2255   }
2256
2257   @Override
2258   protected void expand_newalign(ActionEvent e)
2259   {
2260     try
2261     {
2262       AlignmentI alignment = AlignmentUtils
2263               .expandContext(getViewport().getAlignment(), -1);
2264       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2265               DEFAULT_HEIGHT);
2266       String newtitle = new String("Flanking alignment");
2267
2268       if (Desktop.jalviewClipboard != null
2269               && Desktop.jalviewClipboard[2] != null)
2270       {
2271         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2272         for (int region[] : hc)
2273         {
2274           af.viewport.hideColumns(region[0], region[1]);
2275         }
2276       }
2277
2278       // >>>This is a fix for the moment, until a better solution is
2279       // found!!<<<
2280       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2281               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2282                       .getFeatureRenderer());
2283
2284       // TODO: maintain provenance of an alignment, rather than just make the
2285       // title a concatenation of operations.
2286       {
2287         if (title.startsWith("Copied sequences"))
2288         {
2289           newtitle = title;
2290         }
2291         else
2292         {
2293           newtitle = newtitle.concat("- from " + title);
2294         }
2295       }
2296
2297       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2298
2299     } catch (Exception ex)
2300     {
2301       ex.printStackTrace();
2302       System.out.println("Exception whilst pasting: " + ex);
2303       // could be anything being pasted in here
2304     } catch (OutOfMemoryError oom)
2305     {
2306       new OOMWarning("Viewing flanking region of alignment", oom);
2307     }
2308   }
2309
2310   /**
2311    * DOCUMENT ME!
2312    *
2313    * @param e
2314    *          DOCUMENT ME!
2315    */
2316   @Override
2317   protected void cut_actionPerformed(ActionEvent e)
2318   {
2319     copy_actionPerformed(null);
2320     delete_actionPerformed(null);
2321   }
2322
2323   /**
2324    * DOCUMENT ME!
2325    *
2326    * @param e
2327    *          DOCUMENT ME!
2328    */
2329   @Override
2330   protected void delete_actionPerformed(ActionEvent evt)
2331   {
2332
2333     SequenceGroup sg = viewport.getSelectionGroup();
2334     if (sg == null)
2335     {
2336       return;
2337     }
2338
2339     /*
2340      * If the cut affects all sequences, warn, remove highlighted columns
2341      */
2342     if (sg.getSize() == viewport.getAlignment().getHeight())
2343     {
2344       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2345               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2346       if (isEntireAlignWidth)
2347       {
2348         int confirm = JvOptionPane.showConfirmDialog(this,
2349                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2350                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2351                 JvOptionPane.OK_CANCEL_OPTION);
2352
2353         if (confirm == JvOptionPane.CANCEL_OPTION
2354                 || confirm == JvOptionPane.CLOSED_OPTION)
2355         {
2356           return;
2357         }
2358       }
2359       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2360               sg.getEndRes() + 1);
2361     }
2362     SequenceI[] cut = sg.getSequences()
2363             .toArray(new SequenceI[sg.getSize()]);
2364
2365     addHistoryItem(new EditCommand(
2366             MessageManager.getString("label.cut_sequences"), Action.CUT,
2367             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2368             viewport.getAlignment()));
2369
2370     viewport.setSelectionGroup(null);
2371     viewport.sendSelection();
2372     viewport.getAlignment().deleteGroup(sg);
2373
2374     viewport.firePropertyChange("alignment", null,
2375             viewport.getAlignment().getSequences());
2376     if (viewport.getAlignment().getHeight() < 1)
2377     {
2378       try
2379       {
2380         this.setClosed(true);
2381       } catch (Exception ex)
2382       {
2383       }
2384     }
2385   }
2386
2387   /**
2388    * DOCUMENT ME!
2389    *
2390    * @param e
2391    *          DOCUMENT ME!
2392    */
2393   @Override
2394   protected void deleteGroups_actionPerformed(ActionEvent e)
2395   {
2396     if (avc.deleteGroups())
2397     {
2398       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2399       alignPanel.updateAnnotation();
2400       alignPanel.paintAlignment(true);
2401     }
2402   }
2403
2404   /**
2405    * DOCUMENT ME!
2406    *
2407    * @param e
2408    *          DOCUMENT ME!
2409    */
2410   @Override
2411   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2412   {
2413     SequenceGroup sg = new SequenceGroup();
2414
2415     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2416     {
2417       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2418     }
2419
2420     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2421     viewport.setSelectionGroup(sg);
2422     viewport.sendSelection();
2423     // JAL-2034 - should delegate to
2424     // alignPanel to decide if overview needs
2425     // updating.
2426     alignPanel.paintAlignment(false);
2427     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2428   }
2429
2430   /**
2431    * DOCUMENT ME!
2432    *
2433    * @param e
2434    *          DOCUMENT ME!
2435    */
2436   @Override
2437   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2438   {
2439     if (viewport.cursorMode)
2440     {
2441       alignPanel.getSeqPanel().keyboardNo1 = null;
2442       alignPanel.getSeqPanel().keyboardNo2 = null;
2443     }
2444     viewport.setSelectionGroup(null);
2445     viewport.getColumnSelection().clear();
2446     viewport.setSelectionGroup(null);
2447     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2448     // JAL-2034 - should delegate to
2449     // alignPanel to decide if overview needs
2450     // updating.
2451     alignPanel.paintAlignment(false);
2452     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2453     viewport.sendSelection();
2454   }
2455
2456   /**
2457    * DOCUMENT ME!
2458    *
2459    * @param e
2460    *          DOCUMENT ME!
2461    */
2462   @Override
2463   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2464   {
2465     SequenceGroup sg = viewport.getSelectionGroup();
2466
2467     if (sg == null)
2468     {
2469       selectAllSequenceMenuItem_actionPerformed(null);
2470
2471       return;
2472     }
2473
2474     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2475     {
2476       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2477     }
2478     // JAL-2034 - should delegate to
2479     // alignPanel to decide if overview needs
2480     // updating.
2481
2482     alignPanel.paintAlignment(true);
2483     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484     viewport.sendSelection();
2485   }
2486
2487   @Override
2488   public void invertColSel_actionPerformed(ActionEvent e)
2489   {
2490     viewport.invertColumnSelection();
2491     alignPanel.paintAlignment(true);
2492     viewport.sendSelection();
2493   }
2494
2495   /**
2496    * DOCUMENT ME!
2497    *
2498    * @param e
2499    *          DOCUMENT ME!
2500    */
2501   @Override
2502   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2503   {
2504     trimAlignment(true);
2505   }
2506
2507   /**
2508    * DOCUMENT ME!
2509    *
2510    * @param e
2511    *          DOCUMENT ME!
2512    */
2513   @Override
2514   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2515   {
2516     trimAlignment(false);
2517   }
2518
2519   void trimAlignment(boolean trimLeft)
2520   {
2521     ColumnSelection colSel = viewport.getColumnSelection();
2522     int column;
2523
2524     if (!colSel.isEmpty())
2525     {
2526       if (trimLeft)
2527       {
2528         column = colSel.getMin();
2529       }
2530       else
2531       {
2532         column = colSel.getMax();
2533       }
2534
2535       SequenceI[] seqs;
2536       if (viewport.getSelectionGroup() != null)
2537       {
2538         seqs = viewport.getSelectionGroup()
2539                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2540       }
2541       else
2542       {
2543         seqs = viewport.getAlignment().getSequencesArray();
2544       }
2545
2546       TrimRegionCommand trimRegion;
2547       if (trimLeft)
2548       {
2549         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2550                 column, viewport.getAlignment());
2551         vpRanges.setStartRes(0);
2552       }
2553       else
2554       {
2555         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2556                 column, viewport.getAlignment());
2557       }
2558
2559       statusBar.setText(MessageManager
2560               .formatMessage("label.removed_columns", new String[]
2561               { Integer.valueOf(trimRegion.getSize()).toString() }));
2562
2563       addHistoryItem(trimRegion);
2564
2565       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2566       {
2567         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2569         {
2570           viewport.getAlignment().deleteGroup(sg);
2571         }
2572       }
2573
2574       viewport.firePropertyChange("alignment", null,
2575               viewport.getAlignment().getSequences());
2576     }
2577   }
2578
2579   /**
2580    * DOCUMENT ME!
2581    *
2582    * @param e
2583    *          DOCUMENT ME!
2584    */
2585   @Override
2586   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2587   {
2588     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2589
2590     SequenceI[] seqs;
2591     if (viewport.getSelectionGroup() != null)
2592     {
2593       seqs = viewport.getSelectionGroup()
2594               .getSequencesAsArray(viewport.getHiddenRepSequences());
2595       start = viewport.getSelectionGroup().getStartRes();
2596       end = viewport.getSelectionGroup().getEndRes();
2597     }
2598     else
2599     {
2600       seqs = viewport.getAlignment().getSequencesArray();
2601     }
2602
2603     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604             "Remove Gapped Columns", seqs, start, end,
2605             viewport.getAlignment());
2606
2607     addHistoryItem(removeGapCols);
2608
2609     statusBar.setText(MessageManager
2610             .formatMessage("label.removed_empty_columns", new Object[]
2611             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2612
2613     // This is to maintain viewport position on first residue
2614     // of first sequence
2615     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2616     int startRes = seq.findPosition(vpRanges.getStartRes());
2617     // ShiftList shifts;
2618     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2619     // edit.alColumnChanges=shifts.getInverse();
2620     // if (viewport.hasHiddenColumns)
2621     // viewport.getColumnSelection().compensateForEdits(shifts);
2622     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2623     viewport.firePropertyChange("alignment", null,
2624             viewport.getAlignment().getSequences());
2625
2626   }
2627
2628   /**
2629    * DOCUMENT ME!
2630    *
2631    * @param e
2632    *          DOCUMENT ME!
2633    */
2634   @Override
2635   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2636   {
2637     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2638
2639     SequenceI[] seqs;
2640     if (viewport.getSelectionGroup() != null)
2641     {
2642       seqs = viewport.getSelectionGroup()
2643               .getSequencesAsArray(viewport.getHiddenRepSequences());
2644       start = viewport.getSelectionGroup().getStartRes();
2645       end = viewport.getSelectionGroup().getEndRes();
2646     }
2647     else
2648     {
2649       seqs = viewport.getAlignment().getSequencesArray();
2650     }
2651
2652     // This is to maintain viewport position on first residue
2653     // of first sequence
2654     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2655     int startRes = seq.findPosition(vpRanges.getStartRes());
2656
2657     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2658             viewport.getAlignment()));
2659
2660     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2661
2662     viewport.firePropertyChange("alignment", null,
2663             viewport.getAlignment().getSequences());
2664
2665   }
2666
2667   /**
2668    * DOCUMENT ME!
2669    *
2670    * @param e
2671    *          DOCUMENT ME!
2672    */
2673   @Override
2674   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2675   {
2676     viewport.setPadGaps(padGapsMenuitem.isSelected());
2677     viewport.firePropertyChange("alignment", null,
2678             viewport.getAlignment().getSequences());
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void findMenuItem_actionPerformed(ActionEvent e)
2689   {
2690     new Finder();
2691   }
2692
2693   /**
2694    * Create a new view of the current alignment.
2695    */
2696   @Override
2697   public void newView_actionPerformed(ActionEvent e)
2698   {
2699     newView(null, true);
2700   }
2701
2702   /**
2703    * Creates and shows a new view of the current alignment.
2704    *
2705    * @param viewTitle
2706    *          title of newly created view; if null, one will be generated
2707    * @param copyAnnotation
2708    *          if true then duplicate all annnotation, groups and settings
2709    * @return new alignment panel, already displayed.
2710    */
2711   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2712   {
2713     /*
2714      * Create a new AlignmentPanel (with its own, new Viewport)
2715      */
2716     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2717     if (!copyAnnotation)
2718     {
2719       /*
2720        * remove all groups and annotation except for the automatic stuff
2721        */
2722       newap.av.getAlignment().deleteAllGroups();
2723       newap.av.getAlignment().deleteAllAnnotations(false);
2724     }
2725
2726     newap.av.setGatherViewsHere(false);
2727
2728     if (viewport.viewName == null)
2729     {
2730       viewport.viewName = MessageManager
2731               .getString("label.view_name_original");
2732     }
2733
2734     /*
2735      * Views share the same edits undo and redo stacks
2736      */
2737     newap.av.setHistoryList(viewport.getHistoryList());
2738     newap.av.setRedoList(viewport.getRedoList());
2739
2740     /*
2741      * Views share the same mappings; need to deregister any new mappings
2742      * created by copyAlignPanel, and register the new reference to the shared
2743      * mappings
2744      */
2745     newap.av.replaceMappings(viewport.getAlignment());
2746
2747     /*
2748      * start up cDNA consensus (if applicable) now mappings are in place
2749      */
2750     if (newap.av.initComplementConsensus())
2751     {
2752       newap.refresh(true); // adjust layout of annotations
2753     }
2754
2755     newap.av.viewName = getNewViewName(viewTitle);
2756
2757     addAlignmentPanel(newap, true);
2758     newap.alignmentChanged();
2759
2760     if (alignPanels.size() == 2)
2761     {
2762       viewport.setGatherViewsHere(true);
2763     }
2764     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2765     return newap;
2766   }
2767
2768   /**
2769    * Make a new name for the view, ensuring it is unique within the current
2770    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2771    * these now use viewId. Unique view names are still desirable for usability.)
2772    *
2773    * @param viewTitle
2774    * @return
2775    */
2776   protected String getNewViewName(String viewTitle)
2777   {
2778     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2779     boolean addFirstIndex = false;
2780     if (viewTitle == null || viewTitle.trim().length() == 0)
2781     {
2782       viewTitle = MessageManager.getString("action.view");
2783       addFirstIndex = true;
2784     }
2785     else
2786     {
2787       index = 1;// we count from 1 if given a specific name
2788     }
2789     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2790
2791     List<Component> comps = PaintRefresher.components
2792             .get(viewport.getSequenceSetId());
2793
2794     List<String> existingNames = getExistingViewNames(comps);
2795
2796     while (existingNames.contains(newViewName))
2797     {
2798       newViewName = viewTitle + " " + (++index);
2799     }
2800     return newViewName;
2801   }
2802
2803   /**
2804    * Returns a list of distinct view names found in the given list of
2805    * components. View names are held on the viewport of an AlignmentPanel.
2806    *
2807    * @param comps
2808    * @return
2809    */
2810   protected List<String> getExistingViewNames(List<Component> comps)
2811   {
2812     List<String> existingNames = new ArrayList<>();
2813     for (Component comp : comps)
2814     {
2815       if (comp instanceof AlignmentPanel)
2816       {
2817         AlignmentPanel ap = (AlignmentPanel) comp;
2818         if (!existingNames.contains(ap.av.viewName))
2819         {
2820           existingNames.add(ap.av.viewName);
2821         }
2822       }
2823     }
2824     return existingNames;
2825   }
2826
2827   /**
2828    * Explode tabbed views into separate windows.
2829    */
2830   @Override
2831   public void expandViews_actionPerformed(ActionEvent e)
2832   {
2833     Desktop.explodeViews(this);
2834   }
2835
2836   /**
2837    * Gather views in separate windows back into a tabbed presentation.
2838    */
2839   @Override
2840   public void gatherViews_actionPerformed(ActionEvent e)
2841   {
2842     Desktop.instance.gatherViews(this);
2843   }
2844
2845   /**
2846    * DOCUMENT ME!
2847    *
2848    * @param e
2849    *          DOCUMENT ME!
2850    */
2851   @Override
2852   public void font_actionPerformed(ActionEvent e)
2853   {
2854     new FontChooser(alignPanel);
2855   }
2856
2857   /**
2858    * DOCUMENT ME!
2859    *
2860    * @param e
2861    *          DOCUMENT ME!
2862    */
2863   @Override
2864   protected void seqLimit_actionPerformed(ActionEvent e)
2865   {
2866     viewport.setShowJVSuffix(seqLimits.isSelected());
2867
2868     alignPanel.getIdPanel().getIdCanvas()
2869             .setPreferredSize(alignPanel.calculateIdWidth());
2870     alignPanel.paintAlignment(true);
2871   }
2872
2873   @Override
2874   public void idRightAlign_actionPerformed(ActionEvent e)
2875   {
2876     viewport.setRightAlignIds(idRightAlign.isSelected());
2877     alignPanel.paintAlignment(true);
2878   }
2879
2880   @Override
2881   public void centreColumnLabels_actionPerformed(ActionEvent e)
2882   {
2883     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   /*
2888    * (non-Javadoc)
2889    *
2890    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2891    */
2892   @Override
2893   protected void followHighlight_actionPerformed()
2894   {
2895     /*
2896      * Set the 'follow' flag on the Viewport (and scroll to position if now
2897      * true).
2898      */
2899     final boolean state = this.followHighlightMenuItem.getState();
2900     viewport.setFollowHighlight(state);
2901     if (state)
2902     {
2903       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2904     }
2905   }
2906
2907   /**
2908    * DOCUMENT ME!
2909    *
2910    * @param e
2911    *          DOCUMENT ME!
2912    */
2913   @Override
2914   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2915   {
2916     viewport.setColourText(colourTextMenuItem.isSelected());
2917     alignPanel.paintAlignment(true);
2918   }
2919
2920   /**
2921    * DOCUMENT ME!
2922    *
2923    * @param e
2924    *          DOCUMENT ME!
2925    */
2926   @Override
2927   public void wrapMenuItem_actionPerformed(ActionEvent e)
2928   {
2929     scaleAbove.setVisible(wrapMenuItem.isSelected());
2930     scaleLeft.setVisible(wrapMenuItem.isSelected());
2931     scaleRight.setVisible(wrapMenuItem.isSelected());
2932     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2933     alignPanel.updateLayout();
2934   }
2935
2936   @Override
2937   public void showAllSeqs_actionPerformed(ActionEvent e)
2938   {
2939     viewport.showAllHiddenSeqs();
2940   }
2941
2942   @Override
2943   public void showAllColumns_actionPerformed(ActionEvent e)
2944   {
2945     viewport.showAllHiddenColumns();
2946     alignPanel.paintAlignment(true);
2947     viewport.sendSelection();
2948   }
2949
2950   @Override
2951   public void hideSelSequences_actionPerformed(ActionEvent e)
2952   {
2953     viewport.hideAllSelectedSeqs();
2954   }
2955
2956   /**
2957    * called by key handler and the hide all/show all menu items
2958    *
2959    * @param toggleSeqs
2960    * @param toggleCols
2961    */
2962   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2963   {
2964
2965     boolean hide = false;
2966     SequenceGroup sg = viewport.getSelectionGroup();
2967     if (!toggleSeqs && !toggleCols)
2968     {
2969       // Hide everything by the current selection - this is a hack - we do the
2970       // invert and then hide
2971       // first check that there will be visible columns after the invert.
2972       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2973               && sg.getStartRes() <= sg.getEndRes()))
2974       {
2975         // now invert the sequence set, if required - empty selection implies
2976         // that no hiding is required.
2977         if (sg != null)
2978         {
2979           invertSequenceMenuItem_actionPerformed(null);
2980           sg = viewport.getSelectionGroup();
2981           toggleSeqs = true;
2982
2983         }
2984         viewport.expandColSelection(sg, true);
2985         // finally invert the column selection and get the new sequence
2986         // selection.
2987         invertColSel_actionPerformed(null);
2988         toggleCols = true;
2989       }
2990     }
2991
2992     if (toggleSeqs)
2993     {
2994       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2995       {
2996         hideSelSequences_actionPerformed(null);
2997         hide = true;
2998       }
2999       else if (!(toggleCols && viewport.hasSelectedColumns()))
3000       {
3001         showAllSeqs_actionPerformed(null);
3002       }
3003     }
3004
3005     if (toggleCols)
3006     {
3007       if (viewport.hasSelectedColumns())
3008       {
3009         hideSelColumns_actionPerformed(null);
3010         if (!toggleSeqs)
3011         {
3012           viewport.setSelectionGroup(sg);
3013         }
3014       }
3015       else if (!hide)
3016       {
3017         showAllColumns_actionPerformed(null);
3018       }
3019     }
3020   }
3021
3022   /*
3023    * (non-Javadoc)
3024    *
3025    * @see
3026    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3027    * event.ActionEvent)
3028    */
3029   @Override
3030   public void hideAllButSelection_actionPerformed(ActionEvent e)
3031   {
3032     toggleHiddenRegions(false, false);
3033     viewport.sendSelection();
3034   }
3035
3036   /*
3037    * (non-Javadoc)
3038    *
3039    * @see
3040    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3041    * .ActionEvent)
3042    */
3043   @Override
3044   public void hideAllSelection_actionPerformed(ActionEvent e)
3045   {
3046     SequenceGroup sg = viewport.getSelectionGroup();
3047     viewport.expandColSelection(sg, false);
3048     viewport.hideAllSelectedSeqs();
3049     viewport.hideSelectedColumns();
3050     alignPanel.paintAlignment(true);
3051     viewport.sendSelection();
3052   }
3053
3054   /*
3055    * (non-Javadoc)
3056    *
3057    * @see
3058    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3059    * ActionEvent)
3060    */
3061   @Override
3062   public void showAllhidden_actionPerformed(ActionEvent e)
3063   {
3064     viewport.showAllHiddenColumns();
3065     viewport.showAllHiddenSeqs();
3066     alignPanel.paintAlignment(true);
3067     viewport.sendSelection();
3068   }
3069
3070   @Override
3071   public void hideSelColumns_actionPerformed(ActionEvent e)
3072   {
3073     viewport.hideSelectedColumns();
3074     alignPanel.paintAlignment(true);
3075     viewport.sendSelection();
3076   }
3077
3078   @Override
3079   public void hiddenMarkers_actionPerformed(ActionEvent e)
3080   {
3081     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3082     repaint();
3083   }
3084
3085   /**
3086    * DOCUMENT ME!
3087    *
3088    * @param e
3089    *          DOCUMENT ME!
3090    */
3091   @Override
3092   protected void scaleAbove_actionPerformed(ActionEvent e)
3093   {
3094     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3095     alignPanel.paintAlignment(true);
3096   }
3097
3098   /**
3099    * DOCUMENT ME!
3100    *
3101    * @param e
3102    *          DOCUMENT ME!
3103    */
3104   @Override
3105   protected void scaleLeft_actionPerformed(ActionEvent e)
3106   {
3107     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3108     alignPanel.paintAlignment(true);
3109   }
3110
3111   /**
3112    * DOCUMENT ME!
3113    *
3114    * @param e
3115    *          DOCUMENT ME!
3116    */
3117   @Override
3118   protected void scaleRight_actionPerformed(ActionEvent e)
3119   {
3120     viewport.setScaleRightWrapped(scaleRight.isSelected());
3121     alignPanel.paintAlignment(true);
3122   }
3123
3124   /**
3125    * DOCUMENT ME!
3126    *
3127    * @param e
3128    *          DOCUMENT ME!
3129    */
3130   @Override
3131   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3132   {
3133     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3134     alignPanel.paintAlignment(true);
3135   }
3136
3137   /**
3138    * DOCUMENT ME!
3139    *
3140    * @param e
3141    *          DOCUMENT ME!
3142    */
3143   @Override
3144   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3145   {
3146     viewport.setShowText(viewTextMenuItem.isSelected());
3147     alignPanel.paintAlignment(true);
3148   }
3149
3150   /**
3151    * DOCUMENT ME!
3152    *
3153    * @param e
3154    *          DOCUMENT ME!
3155    */
3156   @Override
3157   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3158   {
3159     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3160     alignPanel.paintAlignment(true);
3161   }
3162
3163   public FeatureSettings featureSettings;
3164
3165   @Override
3166   public FeatureSettingsControllerI getFeatureSettingsUI()
3167   {
3168     return featureSettings;
3169   }
3170
3171   @Override
3172   public void featureSettings_actionPerformed(ActionEvent e)
3173   {
3174     if (featureSettings != null)
3175     {
3176       featureSettings.close();
3177       featureSettings = null;
3178     }
3179     if (!showSeqFeatures.isSelected())
3180     {
3181       // make sure features are actually displayed
3182       showSeqFeatures.setSelected(true);
3183       showSeqFeatures_actionPerformed(null);
3184     }
3185     featureSettings = new FeatureSettings(this);
3186   }
3187
3188   /**
3189    * Set or clear 'Show Sequence Features'
3190    *
3191    * @param evt
3192    *          DOCUMENT ME!
3193    */
3194   @Override
3195   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3196   {
3197     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3198     alignPanel.paintAlignment(true);
3199   }
3200
3201   /**
3202    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3203    * the annotations panel as a whole.
3204    *
3205    * The options to show/hide all annotations should be enabled when the panel
3206    * is shown, and disabled when the panel is hidden.
3207    *
3208    * @param e
3209    */
3210   @Override
3211   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3212   {
3213     final boolean setVisible = annotationPanelMenuItem.isSelected();
3214     viewport.setShowAnnotation(setVisible);
3215     this.showAllSeqAnnotations.setEnabled(setVisible);
3216     this.hideAllSeqAnnotations.setEnabled(setVisible);
3217     this.showAllAlAnnotations.setEnabled(setVisible);
3218     this.hideAllAlAnnotations.setEnabled(setVisible);
3219     alignPanel.updateLayout();
3220   }
3221
3222   @Override
3223   public void alignmentProperties()
3224   {
3225     JEditorPane editPane = new JEditorPane("text/html", "");
3226     editPane.setEditable(false);
3227     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3228             .formatAsHtml();
3229     editPane.setText(
3230             MessageManager.formatMessage("label.html_content", new Object[]
3231             { contents.toString() }));
3232     JInternalFrame frame = new JInternalFrame();
3233     frame.getContentPane().add(new JScrollPane(editPane));
3234
3235     Desktop.addInternalFrame(frame, MessageManager
3236             .formatMessage("label.alignment_properties", new Object[]
3237             { getTitle() }), 500, 400);
3238   }
3239
3240   /**
3241    * DOCUMENT ME!
3242    *
3243    * @param e
3244    *          DOCUMENT ME!
3245    */
3246   @Override
3247   public void overviewMenuItem_actionPerformed(ActionEvent e)
3248   {
3249     if (alignPanel.overviewPanel != null)
3250     {
3251       return;
3252     }
3253
3254     JInternalFrame frame = new JInternalFrame();
3255     final OverviewPanel overview = new OverviewPanel(alignPanel);
3256     frame.setContentPane(overview);
3257     Desktop.addInternalFrame(frame, MessageManager
3258             .formatMessage("label.overview_params", new Object[]
3259             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3260             true, true);
3261     frame.pack();
3262     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3263     frame.addInternalFrameListener(
3264             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_MENU.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, viewport.getResidueShading(),
3365             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(),
3437             viewport.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(
3455             new OrderCommand("ID Sort", oldOrder, 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,
3517               MessageManager.getString(
3518                       "label.you_must_select_least_two_sequences"),
3519               MessageManager.getString("label.invalid_selection"),
3520               JvOptionPane.WARNING_MESSAGE);
3521     }
3522     else
3523     {
3524       JInternalFrame frame = new JInternalFrame();
3525       frame.setContentPane(new PairwiseAlignPanel(viewport));
3526       Desktop.addInternalFrame(frame,
3527               MessageManager.getString("action.pairwise_alignment"), 600,
3528               500);
3529     }
3530   }
3531
3532   @Override
3533   public void autoCalculate_actionPerformed(ActionEvent e)
3534   {
3535     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3536     if (viewport.autoCalculateConsensus)
3537     {
3538       viewport.firePropertyChange("alignment", null,
3539               viewport.getAlignment().getSequences());
3540     }
3541   }
3542
3543   @Override
3544   public void sortByTreeOption_actionPerformed(ActionEvent e)
3545   {
3546     viewport.sortByTree = sortByTree.isSelected();
3547   }
3548
3549   @Override
3550   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3551   {
3552     viewport.followSelection = listenToViewSelections.isSelected();
3553   }
3554
3555   /**
3556    * Constructs a tree panel and adds it to the desktop
3557    *
3558    * @param type
3559    *          tree type (NJ or AV)
3560    * @param modelName
3561    *          name of score model used to compute the tree
3562    * @param options
3563    *          parameters for the distance or similarity calculation
3564    */
3565   void newTreePanel(String type, String modelName,
3566           SimilarityParamsI options)
3567   {
3568     String frameTitle = "";
3569     TreePanel tp;
3570
3571     boolean onSelection = false;
3572     if (viewport.getSelectionGroup() != null
3573             && viewport.getSelectionGroup().getSize() > 0)
3574     {
3575       SequenceGroup sg = viewport.getSelectionGroup();
3576
3577       /* Decide if the selection is a column region */
3578       for (SequenceI _s : sg.getSequences())
3579       {
3580         if (_s.getLength() < sg.getEndRes())
3581         {
3582           JvOptionPane.showMessageDialog(Desktop.desktop,
3583                   MessageManager.getString(
3584                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3585                   MessageManager.getString(
3586                           "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
3629             .formatMessage("action.by_title_param", new Object[]
3630             { title }));
3631     sort.add(item);
3632     item.addActionListener(new java.awt.event.ActionListener()
3633     {
3634       @Override
3635       public void actionPerformed(ActionEvent e)
3636       {
3637         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3638
3639         // TODO: JBPNote - have to map order entries to curent SequenceI
3640         // pointers
3641         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3642
3643         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3644                 viewport.getAlignment()));
3645
3646         alignPanel.paintAlignment(true);
3647       }
3648     });
3649   }
3650
3651   /**
3652    * Add a new sort by annotation score menu item
3653    *
3654    * @param sort
3655    *          the menu to add the option to
3656    * @param scoreLabel
3657    *          the label used to retrieve scores for each sequence on the
3658    *          alignment
3659    */
3660   public void addSortByAnnotScoreMenuItem(JMenu sort,
3661           final String scoreLabel)
3662   {
3663     final JMenuItem item = new JMenuItem(scoreLabel);
3664     sort.add(item);
3665     item.addActionListener(new java.awt.event.ActionListener()
3666     {
3667       @Override
3668       public void actionPerformed(ActionEvent e)
3669       {
3670         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3671         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3672                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3673         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3674                 viewport.getAlignment()));
3675         alignPanel.paintAlignment(true);
3676       }
3677     });
3678   }
3679
3680   /**
3681    * last hash for alignment's annotation array - used to minimise cost of
3682    * rebuild.
3683    */
3684   protected int _annotationScoreVectorHash;
3685
3686   /**
3687    * search the alignment and rebuild the sort by annotation score submenu the
3688    * last alignment annotation vector hash is stored to minimize cost of
3689    * rebuilding in subsequence calls.
3690    *
3691    */
3692   @Override
3693   public void buildSortByAnnotationScoresMenu()
3694   {
3695     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3696     {
3697       return;
3698     }
3699
3700     if (viewport.getAlignment().getAlignmentAnnotation()
3701             .hashCode() != _annotationScoreVectorHash)
3702     {
3703       sortByAnnotScore.removeAll();
3704       // almost certainly a quicker way to do this - but we keep it simple
3705       Hashtable scoreSorts = new Hashtable();
3706       AlignmentAnnotation aann[];
3707       for (SequenceI sqa : viewport.getAlignment().getSequences())
3708       {
3709         aann = sqa.getAnnotation();
3710         for (int i = 0; aann != null && i < aann.length; i++)
3711         {
3712           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3713           {
3714             scoreSorts.put(aann[i].label, aann[i].label);
3715           }
3716         }
3717       }
3718       Enumeration labels = scoreSorts.keys();
3719       while (labels.hasMoreElements())
3720       {
3721         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3722                 (String) labels.nextElement());
3723       }
3724       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3725       scoreSorts.clear();
3726
3727       _annotationScoreVectorHash = viewport.getAlignment()
3728               .getAlignmentAnnotation().hashCode();
3729     }
3730   }
3731
3732   /**
3733    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3734    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3735    * call. Listeners are added to remove the menu item when the treePanel is
3736    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3737    * modified.
3738    */
3739   @Override
3740   public void buildTreeSortMenu()
3741   {
3742     sortByTreeMenu.removeAll();
3743
3744     List<Component> comps = PaintRefresher.components
3745             .get(viewport.getSequenceSetId());
3746     List<TreePanel> treePanels = new ArrayList<>();
3747     for (Component comp : comps)
3748     {
3749       if (comp instanceof TreePanel)
3750       {
3751         treePanels.add((TreePanel) comp);
3752       }
3753     }
3754
3755     if (treePanels.size() < 1)
3756     {
3757       sortByTreeMenu.setVisible(false);
3758       return;
3759     }
3760
3761     sortByTreeMenu.setVisible(true);
3762
3763     for (final TreePanel tp : treePanels)
3764     {
3765       final JMenuItem item = new JMenuItem(tp.getTitle());
3766       item.addActionListener(new java.awt.event.ActionListener()
3767       {
3768         @Override
3769         public void actionPerformed(ActionEvent e)
3770         {
3771           tp.sortByTree_actionPerformed();
3772           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3773
3774         }
3775       });
3776
3777       sortByTreeMenu.add(item);
3778     }
3779   }
3780
3781   public boolean sortBy(AlignmentOrder alorder, String undoname)
3782   {
3783     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3784     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3785     if (undoname != null)
3786     {
3787       addHistoryItem(new OrderCommand(undoname, oldOrder,
3788               viewport.getAlignment()));
3789     }
3790     alignPanel.paintAlignment(true);
3791     return true;
3792   }
3793
3794   /**
3795    * Work out whether the whole set of sequences or just the selected set will
3796    * be submitted for multiple alignment.
3797    *
3798    */
3799   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3800   {
3801     // Now, check we have enough sequences
3802     AlignmentView msa = null;
3803
3804     if ((viewport.getSelectionGroup() != null)
3805             && (viewport.getSelectionGroup().getSize() > 1))
3806     {
3807       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3808       // some common interface!
3809       /*
3810        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3811        * SequenceI[sz = seqs.getSize(false)];
3812        *
3813        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3814        * seqs.getSequenceAt(i); }
3815        */
3816       msa = viewport.getAlignmentView(true);
3817     }
3818     else if (viewport.getSelectionGroup() != null
3819             && viewport.getSelectionGroup().getSize() == 1)
3820     {
3821       int option = JvOptionPane.showConfirmDialog(this,
3822               MessageManager.getString("warn.oneseq_msainput_selection"),
3823               MessageManager.getString("label.invalid_selection"),
3824               JvOptionPane.OK_CANCEL_OPTION);
3825       if (option == JvOptionPane.OK_OPTION)
3826       {
3827         msa = viewport.getAlignmentView(false);
3828       }
3829     }
3830     else
3831     {
3832       msa = viewport.getAlignmentView(false);
3833     }
3834     return msa;
3835   }
3836
3837   /**
3838    * Decides what is submitted to a secondary structure prediction service: the
3839    * first sequence in the alignment, or in the current selection, or, if the
3840    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3841    * region or the whole alignment. (where the first sequence in the set is the
3842    * one that the prediction will be for).
3843    */
3844   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3845   {
3846     AlignmentView seqs = null;
3847
3848     if ((viewport.getSelectionGroup() != null)
3849             && (viewport.getSelectionGroup().getSize() > 0))
3850     {
3851       seqs = viewport.getAlignmentView(true);
3852     }
3853     else
3854     {
3855       seqs = viewport.getAlignmentView(false);
3856     }
3857     // limit sequences - JBPNote in future - could spawn multiple prediction
3858     // jobs
3859     // TODO: viewport.getAlignment().isAligned is a global state - the local
3860     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3861     if (!viewport.getAlignment().isAligned(false))
3862     {
3863       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3864       // TODO: if seqs.getSequences().length>1 then should really have warned
3865       // user!
3866
3867     }
3868     return seqs;
3869   }
3870
3871   /**
3872    * DOCUMENT ME!
3873    *
3874    * @param e
3875    *          DOCUMENT ME!
3876    */
3877   @Override
3878   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3879   {
3880     // Pick the tree file
3881     JalviewFileChooser chooser = new JalviewFileChooser(
3882             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3883     chooser.setFileView(new JalviewFileView());
3884     chooser.setDialogTitle(
3885             MessageManager.getString("label.select_newick_like_tree_file"));
3886     chooser.setToolTipText(
3887             MessageManager.getString("label.load_tree_file"));
3888
3889     int value = chooser.showOpenDialog(null);
3890
3891     if (value == JalviewFileChooser.APPROVE_OPTION)
3892     {
3893       String filePath = chooser.getSelectedFile().getPath();
3894       Cache.setProperty("LAST_DIRECTORY", filePath);
3895       NewickFile fin = null;
3896       try
3897       {
3898         fin = new NewickFile(filePath, DataSourceType.FILE);
3899         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3900       } catch (Exception ex)
3901       {
3902         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3903                 MessageManager.getString("label.problem_reading_tree_file"),
3904                 JvOptionPane.WARNING_MESSAGE);
3905         ex.printStackTrace();
3906       }
3907       if (fin != null && fin.hasWarningMessage())
3908       {
3909         JvOptionPane.showMessageDialog(Desktop.desktop,
3910                 fin.getWarningMessage(),
3911                 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.debug(
4143                         "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,
4230                     source);
4231           }
4232         });
4233         showProducts.add(xtype);
4234       }
4235       showProducts.setVisible(showp);
4236       showProducts.setEnabled(showp);
4237     } catch (Exception e)
4238     {
4239       Cache.log.warn(
4240               "canShowProducts threw an exception - please report to help@jalview.org",
4241               e);
4242       return false;
4243     }
4244     return showp;
4245   }
4246
4247   /**
4248    * Finds and displays cross-references for the selected sequences (protein
4249    * products for nucleotide sequences, dna coding sequences for peptides).
4250    *
4251    * @param sel
4252    *          the sequences to show cross-references for
4253    * @param dna
4254    *          true if from a nucleotide alignment (so showing proteins)
4255    * @param source
4256    *          the database to show cross-references for
4257    */
4258   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4259           final String source)
4260   {
4261     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4262             .start();
4263   }
4264
4265   /**
4266    * Construct and display a new frame containing the translation of this
4267    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4268    */
4269   @Override
4270   public void showTranslation_actionPerformed(ActionEvent e)
4271   {
4272     AlignmentI al = null;
4273     try
4274     {
4275       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4276
4277       al = dna.translateCdna();
4278     } catch (Exception ex)
4279     {
4280       jalview.bin.Cache.log.error(
4281               "Exception during translation. Please report this !", ex);
4282       final String msg = MessageManager.getString(
4283               "label.error_when_translating_sequences_submit_bug_report");
4284       final String errorTitle = MessageManager
4285               .getString("label.implementation_error")
4286               + MessageManager.getString("label.translation_failed");
4287       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4288               JvOptionPane.ERROR_MESSAGE);
4289       return;
4290     }
4291     if (al == null || al.getHeight() == 0)
4292     {
4293       final String msg = MessageManager.getString(
4294               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4295       final String errorTitle = MessageManager
4296               .getString("label.translation_failed");
4297       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4298               JvOptionPane.WARNING_MESSAGE);
4299     }
4300     else
4301     {
4302       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4303       af.setFileFormat(this.currentFileFormat);
4304       final String newTitle = MessageManager
4305               .formatMessage("label.translation_of_params", new Object[]
4306               { this.getTitle() });
4307       af.setTitle(newTitle);
4308       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4309       {
4310         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4311         viewport.openSplitFrame(af, new Alignment(seqs));
4312       }
4313       else
4314       {
4315         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4316                 DEFAULT_HEIGHT);
4317       }
4318     }
4319   }
4320
4321   /**
4322    * Set the file format
4323    *
4324    * @param format
4325    */
4326   public void setFileFormat(FileFormatI format)
4327   {
4328     this.currentFileFormat = format;
4329   }
4330
4331   /**
4332    * Try to load a features file onto the alignment.
4333    *
4334    * @param file
4335    *          contents or path to retrieve file
4336    * @param sourceType
4337    *          access mode of file (see jalview.io.AlignFile)
4338    * @return true if features file was parsed correctly.
4339    */
4340   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4341   {
4342     return avc.parseFeaturesFile(file, sourceType,
4343             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4344
4345   }
4346
4347   @Override
4348   public void refreshFeatureUI(boolean enableIfNecessary)
4349   {
4350     // note - currently this is only still here rather than in the controller
4351     // because of the featureSettings hard reference that is yet to be
4352     // abstracted
4353     if (enableIfNecessary)
4354     {
4355       viewport.setShowSequenceFeatures(true);
4356       showSeqFeatures.setSelected(true);
4357     }
4358
4359   }
4360
4361   @Override
4362   public void dragEnter(DropTargetDragEvent evt)
4363   {
4364   }
4365
4366   @Override
4367   public void dragExit(DropTargetEvent evt)
4368   {
4369   }
4370
4371   @Override
4372   public void dragOver(DropTargetDragEvent evt)
4373   {
4374   }
4375
4376   @Override
4377   public void dropActionChanged(DropTargetDragEvent evt)
4378   {
4379   }
4380
4381   @Override
4382   public void drop(DropTargetDropEvent evt)
4383   {
4384     // JAL-1552 - acceptDrop required before getTransferable call for
4385     // Java's Transferable for native dnd
4386     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4387     Transferable t = evt.getTransferable();
4388     final AlignFrame thisaf = this;
4389     final List<String> files = new ArrayList<>();
4390     List<DataSourceType> protocols = new ArrayList<>();
4391
4392     try
4393     {
4394       Desktop.transferFromDropTarget(files, protocols, evt, t);
4395     } catch (Exception e)
4396     {
4397       e.printStackTrace();
4398     }
4399     if (files != null)
4400     {
4401       new Thread(new Runnable()
4402       {
4403         @Override
4404         public void run()
4405         {
4406           try
4407           {
4408             // check to see if any of these files have names matching sequences
4409             // in
4410             // the alignment
4411             SequenceIdMatcher idm = new SequenceIdMatcher(
4412                     viewport.getAlignment().getSequencesArray());
4413             /**
4414              * Object[] { String,SequenceI}
4415              */
4416             ArrayList<Object[]> filesmatched = new ArrayList<>();
4417             ArrayList<String> filesnotmatched = new ArrayList<>();
4418             for (int i = 0; i < files.size(); i++)
4419             {
4420               String file = files.get(i).toString();
4421               String pdbfn = "";
4422               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4423               if (protocol == DataSourceType.FILE)
4424               {
4425                 File fl = new File(file);
4426                 pdbfn = fl.getName();
4427               }
4428               else if (protocol == DataSourceType.URL)
4429               {
4430                 URL url = new URL(file);
4431                 pdbfn = url.getFile();
4432               }
4433               if (pdbfn.length() > 0)
4434               {
4435                 // attempt to find a match in the alignment
4436                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4437                 int l = 0, c = pdbfn.indexOf(".");
4438                 while (mtch == null && c != -1)
4439                 {
4440                   do
4441                   {
4442                     l = c;
4443                   } while ((c = pdbfn.indexOf(".", l)) > l);
4444                   if (l > -1)
4445                   {
4446                     pdbfn = pdbfn.substring(0, l);
4447                   }
4448                   mtch = idm.findAllIdMatches(pdbfn);
4449                 }
4450                 if (mtch != null)
4451                 {
4452                   FileFormatI type = null;
4453                   try
4454                   {
4455                     type = new IdentifyFile().identify(file, protocol);
4456                   } catch (Exception ex)
4457                   {
4458                     type = null;
4459                   }
4460                   if (type != null && type.isStructureFile())
4461                   {
4462                     filesmatched.add(new Object[] { file, protocol, mtch });
4463                     continue;
4464                   }
4465                 }
4466                 // File wasn't named like one of the sequences or wasn't a PDB
4467                 // file.
4468                 filesnotmatched.add(file);
4469               }
4470             }
4471             int assocfiles = 0;
4472             if (filesmatched.size() > 0)
4473             {
4474               if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4475                       || JvOptionPane.showConfirmDialog(thisaf,
4476                               MessageManager.formatMessage(
4477                                       "label.automatically_associate_structure_files_with_sequences_same_name",
4478                                       new Object[]
4479                                       { Integer.valueOf(filesmatched.size())
4480                                               .toString() }),
4481                               MessageManager.getString(
4482                                       "label.automatically_associate_structure_files_by_name"),
4483                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4484
4485               {
4486                 for (Object[] fm : filesmatched)
4487                 {
4488                   // try and associate
4489                   // TODO: may want to set a standard ID naming formalism for
4490                   // associating PDB files which have no IDs.
4491                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4492                   {
4493                     PDBEntry pe = new AssociatePdbFileWithSeq()
4494                             .associatePdbWithSeq((String) fm[0],
4495                                     (DataSourceType) fm[1], toassoc, false,
4496                                     Desktop.instance);
4497                     if (pe != null)
4498                     {
4499                       System.err.println("Associated file : "
4500                               + ((String) fm[0]) + " with "
4501                               + toassoc.getDisplayId(true));
4502                       assocfiles++;
4503                     }
4504                   }
4505                   alignPanel.paintAlignment(true);
4506                 }
4507               }
4508             }
4509             if (filesnotmatched.size() > 0)
4510             {
4511               if (assocfiles > 0 && (Cache.getDefault(
4512                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4513                       || JvOptionPane.showConfirmDialog(thisaf,
4514                               "<html>" + MessageManager.formatMessage(
4515                                       "label.ignore_unmatched_dropped_files_info",
4516                                       new Object[]
4517                                       { Integer.valueOf(
4518                                               filesnotmatched.size())
4519                                               .toString() })
4520                                       + "</html>",
4521                               MessageManager.getString(
4522                                       "label.ignore_unmatched_dropped_files"),
4523                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4524               {
4525                 return;
4526               }
4527               for (String fn : filesnotmatched)
4528               {
4529                 loadJalviewDataFile(fn, null, null, null);
4530               }
4531
4532             }
4533           } catch (Exception ex)
4534           {
4535             ex.printStackTrace();
4536           }
4537         }
4538       }).start();
4539     }
4540   }
4541
4542   /**
4543    * Attempt to load a "dropped" file or URL string, by testing in turn for
4544    * <ul>
4545    * <li>an Annotation file</li>
4546    * <li>a JNet file</li>
4547    * <li>a features file</li>
4548    * <li>else try to interpret as an alignment file</li>
4549    * </ul>
4550    *
4551    * @param file
4552    *          either a filename or a URL string.
4553    */
4554   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4555           FileFormatI format, SequenceI assocSeq)
4556   {
4557     try
4558     {
4559       if (sourceType == null)
4560       {
4561         sourceType = FormatAdapter.checkProtocol(file);
4562       }
4563       // if the file isn't identified, or not positively identified as some
4564       // other filetype (PFAM is default unidentified alignment file type) then
4565       // try to parse as annotation.
4566       boolean isAnnotation = (format == null
4567               || FileFormat.Pfam.equals(format))
4568                       ? new AnnotationFile().annotateAlignmentView(viewport,
4569                               file, sourceType)
4570                       : false;
4571
4572       if (!isAnnotation)
4573       {
4574         // first see if its a T-COFFEE score file
4575         TCoffeeScoreFile tcf = null;
4576         try
4577         {
4578           tcf = new TCoffeeScoreFile(file, sourceType);
4579           if (tcf.isValid())
4580           {
4581             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4582             {
4583               buildColourMenu();
4584               changeColour(
4585                       new TCoffeeColourScheme(viewport.getAlignment()));
4586               isAnnotation = true;
4587               statusBar.setText(MessageManager.getString(
4588                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4589             }
4590             else
4591             {
4592               // some problem - if no warning its probable that the ID matching
4593               // process didn't work
4594               JvOptionPane.showMessageDialog(Desktop.desktop,
4595                       tcf.getWarningMessage() == null
4596                               ? MessageManager.getString(
4597                                       "label.check_file_matches_sequence_ids_alignment")
4598                               : tcf.getWarningMessage(),
4599                       MessageManager.getString(
4600                               "label.problem_reading_tcoffee_score_file"),
4601                       JvOptionPane.WARNING_MESSAGE);
4602             }
4603           }
4604           else
4605           {
4606             tcf = null;
4607           }
4608         } catch (Exception x)
4609         {
4610           Cache.log.debug(
4611                   "Exception when processing data source as T-COFFEE score file",
4612                   x);
4613           tcf = null;
4614         }
4615         if (tcf == null)
4616         {
4617           // try to see if its a JNet 'concise' style annotation file *before*
4618           // we
4619           // try to parse it as a features file
4620           if (format == null)
4621           {
4622             format = new IdentifyFile().identify(file, sourceType);
4623           }
4624           if (FileFormat.ScoreMatrix == format)
4625           {
4626             ScoreMatrixFile sm = new ScoreMatrixFile(
4627                     new FileParse(file, sourceType));
4628             sm.parse();
4629             // todo: i18n this message
4630             statusBar.setText(MessageManager.formatMessage(
4631                     "label.successfully_loaded_matrix",
4632                     sm.getMatrixName()));
4633           }
4634           else if (FileFormat.Jnet.equals(format))
4635           {
4636             JPredFile predictions = new JPredFile(file, sourceType);
4637             new JnetAnnotationMaker();
4638             JnetAnnotationMaker.add_annotation(predictions,
4639                     viewport.getAlignment(), 0, false);
4640             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4641             viewport.getAlignment().setSeqrep(repseq);
4642             HiddenColumns cs = new HiddenColumns();
4643             cs.hideInsertionsFor(repseq);
4644             viewport.getAlignment().setHiddenColumns(cs);
4645             isAnnotation = true;
4646           }
4647           // else if (IdentifyFile.FeaturesFile.equals(format))
4648           else if (FileFormat.Features.equals(format))
4649           {
4650             if (parseFeaturesFile(file, sourceType))
4651             {
4652               alignPanel.paintAlignment(true);
4653             }
4654           }
4655           else
4656           {
4657             new FileLoader().LoadFile(viewport, file, sourceType, format);
4658           }
4659         }
4660       }
4661       if (isAnnotation)
4662       {
4663
4664         alignPanel.adjustAnnotationHeight();
4665         viewport.updateSequenceIdColours();
4666         buildSortByAnnotationScoresMenu();
4667         alignPanel.paintAlignment(true);
4668       }
4669     } catch (Exception ex)
4670     {
4671       ex.printStackTrace();
4672     } catch (OutOfMemoryError oom)
4673     {
4674       try
4675       {
4676         System.gc();
4677       } catch (Exception x)
4678       {
4679       }
4680       new OOMWarning(
4681               "loading data "
4682                       + (sourceType != null
4683                               ? (sourceType == DataSourceType.PASTE
4684                                       ? "from clipboard."
4685                                       : "using " + sourceType + " from "
4686                                               + file)
4687                               : ".")
4688                       + (format != null
4689                               ? "(parsing as '" + format + "' file)"
4690                               : ""),
4691               oom, Desktop.desktop);
4692     }
4693   }
4694
4695   /**
4696    * Method invoked by the ChangeListener on the tabbed pane, in other words
4697    * when a different tabbed pane is selected by the user or programmatically.
4698    */
4699   @Override
4700   public void tabSelectionChanged(int index)
4701   {
4702     if (index > -1)
4703     {
4704       alignPanel = alignPanels.get(index);
4705       viewport = alignPanel.av;
4706       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4707       setMenusFromViewport(viewport);
4708     }
4709
4710     /*
4711      * 'focus' any colour slider that is open to the selected viewport
4712      */
4713     if (viewport.getConservationSelected())
4714     {
4715       SliderPanel.setConservationSlider(alignPanel,
4716               viewport.getResidueShading(), alignPanel.getViewName());
4717     }
4718     else
4719     {
4720       SliderPanel.hideConservationSlider();
4721     }
4722     if (viewport.getAbovePIDThreshold())
4723     {
4724       SliderPanel.setPIDSliderSource(alignPanel,
4725               viewport.getResidueShading(), alignPanel.getViewName());
4726     }
4727     else
4728     {
4729       SliderPanel.hidePIDSlider();
4730     }
4731
4732     /*
4733      * If there is a frame linked to this one in a SplitPane, switch it to the
4734      * same view tab index. No infinite recursion of calls should happen, since
4735      * tabSelectionChanged() should not get invoked on setting the selected
4736      * index to an unchanged value. Guard against setting an invalid index
4737      * before the new view peer tab has been created.
4738      */
4739     final AlignViewportI peer = viewport.getCodingComplement();
4740     if (peer != null)
4741     {
4742       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4743               .getAlignPanel().alignFrame;
4744       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4745       {
4746         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4747       }
4748     }
4749   }
4750
4751   /**
4752    * On right mouse click on view tab, prompt for and set new view name.
4753    */
4754   @Override
4755   public void tabbedPane_mousePressed(MouseEvent e)
4756   {
4757     if (e.isPopupTrigger())
4758     {
4759       String msg = MessageManager.getString("label.enter_view_name");
4760       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4761               JvOptionPane.QUESTION_MESSAGE);
4762
4763       if (reply != null)
4764       {
4765         viewport.viewName = reply;
4766         // TODO warn if reply is in getExistingViewNames()?
4767         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4768       }
4769     }
4770   }
4771
4772   public AlignViewport getCurrentView()
4773   {
4774     return viewport;
4775   }
4776
4777   /**
4778    * Open the dialog for regex description parsing.
4779    */
4780   @Override
4781   protected void extractScores_actionPerformed(ActionEvent e)
4782   {
4783     ParseProperties pp = new jalview.analysis.ParseProperties(
4784             viewport.getAlignment());
4785     // TODO: verify regex and introduce GUI dialog for version 2.5
4786     // if (pp.getScoresFromDescription("col", "score column ",
4787     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4788     // true)>0)
4789     if (pp.getScoresFromDescription("description column",
4790             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4791     {
4792       buildSortByAnnotationScoresMenu();
4793     }
4794   }
4795
4796   /*
4797    * (non-Javadoc)
4798    *
4799    * @see
4800    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4801    * )
4802    */
4803   @Override
4804   protected void showDbRefs_actionPerformed(ActionEvent e)
4805   {
4806     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4807   }
4808
4809   /*
4810    * (non-Javadoc)
4811    *
4812    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4813    * ActionEvent)
4814    */
4815   @Override
4816   protected void showNpFeats_actionPerformed(ActionEvent e)
4817   {
4818     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4819   }
4820
4821   /**
4822    * find the viewport amongst the tabs in this alignment frame and close that
4823    * tab
4824    *
4825    * @param av
4826    */
4827   public boolean closeView(AlignViewportI av)
4828   {
4829     if (viewport == av)
4830     {
4831       this.closeMenuItem_actionPerformed(false);
4832       return true;
4833     }
4834     Component[] comp = tabbedPane.getComponents();
4835     for (int i = 0; comp != null && i < comp.length; i++)
4836     {
4837       if (comp[i] instanceof AlignmentPanel)
4838       {
4839         if (((AlignmentPanel) comp[i]).av == av)
4840         {
4841           // close the view.
4842           closeView((AlignmentPanel) comp[i]);
4843           return true;
4844         }
4845       }
4846     }
4847     return false;
4848   }
4849
4850   protected void build_fetchdbmenu(JMenu webService)
4851   {
4852     // Temporary hack - DBRef Fetcher always top level ws entry.
4853     // TODO We probably want to store a sequence database checklist in
4854     // preferences and have checkboxes.. rather than individual sources selected
4855     // here
4856     final JMenu rfetch = new JMenu(
4857             MessageManager.getString("action.fetch_db_references"));
4858     rfetch.setToolTipText(MessageManager.getString(
4859             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4860     webService.add(rfetch);
4861
4862     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4863             MessageManager.getString("option.trim_retrieved_seqs"));
4864     trimrs.setToolTipText(
4865             MessageManager.getString("label.trim_retrieved_sequences"));
4866     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4867     trimrs.addActionListener(new ActionListener()
4868     {
4869       @Override
4870       public void actionPerformed(ActionEvent e)
4871       {
4872         trimrs.setSelected(trimrs.isSelected());
4873         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4874                 Boolean.valueOf(trimrs.isSelected()).toString());
4875       };
4876     });
4877     rfetch.add(trimrs);
4878     JMenuItem fetchr = new JMenuItem(
4879             MessageManager.getString("label.standard_databases"));
4880     fetchr.setToolTipText(
4881             MessageManager.getString("label.fetch_embl_uniprot"));
4882     fetchr.addActionListener(new ActionListener()
4883     {
4884
4885       @Override
4886       public void actionPerformed(ActionEvent e)
4887       {
4888         new Thread(new Runnable()
4889         {
4890           @Override
4891           public void run()
4892           {
4893             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4894                     .getAlignment().isNucleotide();
4895             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4896                     alignPanel.av.getSequenceSelection(),
4897                     alignPanel.alignFrame, null,
4898                     alignPanel.alignFrame.featureSettings, isNucleotide);
4899             dbRefFetcher.addListener(new FetchFinishedListenerI()
4900             {
4901               @Override
4902               public void finished()
4903               {
4904                 AlignFrame.this.setMenusForViewport();
4905               }
4906             });
4907             dbRefFetcher.fetchDBRefs(false);
4908           }
4909         }).start();
4910
4911       }
4912
4913     });
4914     rfetch.add(fetchr);
4915     final AlignFrame me = this;
4916     new Thread(new Runnable()
4917     {
4918       @Override
4919       public void run()
4920       {
4921         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4922                 .getSequenceFetcherSingleton(me);
4923         javax.swing.SwingUtilities.invokeLater(new Runnable()
4924         {
4925           @Override
4926           public void run()
4927           {
4928             String[] dbclasses = sf.getOrderedSupportedSources();
4929             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4930             // jalview.util.QuickSort.sort(otherdb, otherdb);
4931             List<DbSourceProxy> otherdb;
4932             JMenu dfetch = new JMenu();
4933             JMenu ifetch = new JMenu();
4934             JMenuItem fetchr = null;
4935             int comp = 0, icomp = 0, mcomp = 15;
4936             String mname = null;
4937             int dbi = 0;
4938             for (String dbclass : dbclasses)
4939             {
4940               otherdb = sf.getSourceProxy(dbclass);
4941               // add a single entry for this class, or submenu allowing 'fetch
4942               // all' or pick one
4943               if (otherdb == null || otherdb.size() < 1)
4944               {
4945                 continue;
4946               }
4947               // List<DbSourceProxy> dbs=otherdb;
4948               // otherdb=new ArrayList<DbSourceProxy>();
4949               // for (DbSourceProxy db:dbs)
4950               // {
4951               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4952               // }
4953               if (mname == null)
4954               {
4955                 mname = "From " + dbclass;
4956               }
4957               if (otherdb.size() == 1)
4958               {
4959                 final DbSourceProxy[] dassource = otherdb
4960                         .toArray(new DbSourceProxy[0]);
4961                 DbSourceProxy src = otherdb.get(0);
4962                 fetchr = new JMenuItem(src.getDbSource());
4963                 fetchr.addActionListener(new ActionListener()
4964                 {
4965
4966                   @Override
4967                   public void actionPerformed(ActionEvent e)
4968                   {
4969                     new Thread(new Runnable()
4970                     {
4971
4972                       @Override
4973                       public void run()
4974                       {
4975                         boolean isNucleotide = alignPanel.alignFrame
4976                                 .getViewport().getAlignment()
4977                                 .isNucleotide();
4978                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4979                                 alignPanel.av.getSequenceSelection(),
4980                                 alignPanel.alignFrame, dassource,
4981                                 alignPanel.alignFrame.featureSettings,
4982                                 isNucleotide);
4983                         dbRefFetcher
4984                                 .addListener(new FetchFinishedListenerI()
4985                                 {
4986                                   @Override
4987                                   public void finished()
4988                                   {
4989                                     AlignFrame.this.setMenusForViewport();
4990                                   }
4991                                 });
4992                         dbRefFetcher.fetchDBRefs(false);
4993                       }
4994                     }).start();
4995                   }
4996
4997                 });
4998                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4999                         MessageManager.formatMessage(
5000                                 "label.fetch_retrieve_from", new Object[]
5001                                 { src.getDbName() })));
5002                 dfetch.add(fetchr);
5003                 comp++;
5004               }
5005               else
5006               {
5007                 final DbSourceProxy[] dassource = otherdb
5008                         .toArray(new DbSourceProxy[0]);
5009                 // fetch all entry
5010                 DbSourceProxy src = otherdb.get(0);
5011                 fetchr = new JMenuItem(MessageManager
5012                         .formatMessage("label.fetch_all_param", new Object[]
5013                         { src.getDbSource() }));
5014                 fetchr.addActionListener(new ActionListener()
5015                 {
5016                   @Override
5017                   public void actionPerformed(ActionEvent e)
5018                   {
5019                     new Thread(new Runnable()
5020                     {
5021
5022                       @Override
5023                       public void run()
5024                       {
5025                         boolean isNucleotide = alignPanel.alignFrame
5026                                 .getViewport().getAlignment()
5027                                 .isNucleotide();
5028                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5029                                 alignPanel.av.getSequenceSelection(),
5030                                 alignPanel.alignFrame, dassource,
5031                                 alignPanel.alignFrame.featureSettings,
5032                                 isNucleotide);
5033                         dbRefFetcher
5034                                 .addListener(new FetchFinishedListenerI()
5035                                 {
5036                                   @Override
5037                                   public void finished()
5038                                   {
5039                                     AlignFrame.this.setMenusForViewport();
5040                                   }
5041                                 });
5042                         dbRefFetcher.fetchDBRefs(false);
5043                       }
5044                     }).start();
5045                   }
5046                 });
5047
5048                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5049                         MessageManager.formatMessage(
5050                                 "label.fetch_retrieve_from_all_sources",
5051                                 new Object[]
5052                                 { Integer.valueOf(otherdb.size())
5053                                         .toString(),
5054                                     src.getDbSource(), src.getDbName() })));
5055                 dfetch.add(fetchr);
5056                 comp++;
5057                 // and then build the rest of the individual menus
5058                 ifetch = new JMenu(MessageManager.formatMessage(
5059                         "label.source_from_db_source", new Object[]
5060                         { src.getDbSource() }));
5061                 icomp = 0;
5062                 String imname = null;
5063                 int i = 0;
5064                 for (DbSourceProxy sproxy : otherdb)
5065                 {
5066                   String dbname = sproxy.getDbName();
5067                   String sname = dbname.length() > 5
5068                           ? dbname.substring(0, 5) + "..."
5069                           : dbname;
5070                   String msname = dbname.length() > 10
5071                           ? dbname.substring(0, 10) + "..."
5072                           : dbname;
5073                   if (imname == null)
5074                   {
5075                     imname = MessageManager
5076                             .formatMessage("label.from_msname", new Object[]
5077                             { sname });
5078                   }
5079                   fetchr = new JMenuItem(msname);
5080                   final DbSourceProxy[] dassrc = { sproxy };
5081                   fetchr.addActionListener(new ActionListener()
5082                   {
5083
5084                     @Override
5085                     public void actionPerformed(ActionEvent e)
5086                     {
5087                       new Thread(new Runnable()
5088                       {
5089
5090                         @Override
5091                         public void run()
5092                         {
5093                           boolean isNucleotide = alignPanel.alignFrame
5094                                   .getViewport().getAlignment()
5095                                   .isNucleotide();
5096                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5097                                   alignPanel.av.getSequenceSelection(),
5098                                   alignPanel.alignFrame, dassrc,
5099                                   alignPanel.alignFrame.featureSettings,
5100                                   isNucleotide);
5101                           dbRefFetcher
5102                                   .addListener(new FetchFinishedListenerI()
5103                                   {
5104                                     @Override
5105                                     public void finished()
5106                                     {
5107                                       AlignFrame.this.setMenusForViewport();
5108                                     }
5109                                   });
5110                           dbRefFetcher.fetchDBRefs(false);
5111                         }
5112                       }).start();
5113                     }
5114
5115                   });
5116                   fetchr.setToolTipText(
5117                           "<html>" + MessageManager.formatMessage(
5118                                   "label.fetch_retrieve_from", new Object[]
5119                                   { dbname }));
5120                   ifetch.add(fetchr);
5121                   ++i;
5122                   if (++icomp >= mcomp || i == (otherdb.size()))
5123                   {
5124                     ifetch.setText(MessageManager.formatMessage(
5125                             "label.source_to_target", imname, sname));
5126                     dfetch.add(ifetch);
5127                     ifetch = new JMenu();
5128                     imname = null;
5129                     icomp = 0;
5130                     comp++;
5131                   }
5132                 }
5133               }
5134               ++dbi;
5135               if (comp >= mcomp || dbi >= (dbclasses.length))
5136               {
5137                 dfetch.setText(MessageManager.formatMessage(
5138                         "label.source_to_target", mname, dbclass));
5139                 rfetch.add(dfetch);
5140                 dfetch = new JMenu();
5141                 mname = null;
5142                 comp = 0;
5143               }
5144             }
5145           }
5146         });
5147       }
5148     }).start();
5149
5150   }
5151
5152   /**
5153    * Left justify the whole alignment.
5154    */
5155   @Override
5156   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5157   {
5158     AlignmentI al = viewport.getAlignment();
5159     al.justify(false);
5160     viewport.firePropertyChange("alignment", null, al);
5161   }
5162
5163   /**
5164    * Right justify the whole alignment.
5165    */
5166   @Override
5167   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5168   {
5169     AlignmentI al = viewport.getAlignment();
5170     al.justify(true);
5171     viewport.firePropertyChange("alignment", null, al);
5172   }
5173
5174   @Override
5175   public void setShowSeqFeatures(boolean b)
5176   {
5177     showSeqFeatures.setSelected(b);
5178     viewport.setShowSequenceFeatures(b);
5179   }
5180
5181   /*
5182    * (non-Javadoc)
5183    *
5184    * @see
5185    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5186    * awt.event.ActionEvent)
5187    */
5188   @Override
5189   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5190   {
5191     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5192     alignPanel.paintAlignment(true);
5193   }
5194
5195   /*
5196    * (non-Javadoc)
5197    *
5198    * @see
5199    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5200    * .ActionEvent)
5201    */
5202   @Override
5203   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5204   {
5205     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5206     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5207
5208   }
5209
5210   /*
5211    * (non-Javadoc)
5212    *
5213    * @see
5214    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5215    * .event.ActionEvent)
5216    */
5217   @Override
5218   protected void showGroupConservation_actionPerformed(ActionEvent e)
5219   {
5220     viewport.setShowGroupConservation(showGroupConservation.getState());
5221     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5222   }
5223
5224   /*
5225    * (non-Javadoc)
5226    *
5227    * @see
5228    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5229    * .event.ActionEvent)
5230    */
5231   @Override
5232   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5233   {
5234     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5235     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5236   }
5237
5238   /*
5239    * (non-Javadoc)
5240    *
5241    * @see
5242    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5243    * .event.ActionEvent)
5244    */
5245   @Override
5246   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5247   {
5248     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5249     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5250   }
5251
5252   @Override
5253   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5254   {
5255     showSequenceLogo.setState(true);
5256     viewport.setShowSequenceLogo(true);
5257     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5258     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5259   }
5260
5261   @Override
5262   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5263   {
5264     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5265   }
5266
5267   /*
5268    * (non-Javadoc)
5269    *
5270    * @see
5271    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5272    * .event.ActionEvent)
5273    */
5274   @Override
5275   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5276   {
5277     if (avc.makeGroupsFromSelection())
5278     {
5279       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5280       alignPanel.updateAnnotation();
5281       alignPanel.paintAlignment(true);
5282     }
5283   }
5284
5285   public void clearAlignmentSeqRep()
5286   {
5287     // TODO refactor alignmentseqrep to controller
5288     if (viewport.getAlignment().hasSeqrep())
5289     {
5290       viewport.getAlignment().setSeqrep(null);
5291       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5292       alignPanel.updateAnnotation();
5293       alignPanel.paintAlignment(true);
5294     }
5295   }
5296
5297   @Override
5298   protected void createGroup_actionPerformed(ActionEvent e)
5299   {
5300     if (avc.createGroup())
5301     {
5302       alignPanel.alignmentChanged();
5303     }
5304   }
5305
5306   @Override
5307   protected void unGroup_actionPerformed(ActionEvent e)
5308   {
5309     if (avc.unGroup())
5310     {
5311       alignPanel.alignmentChanged();
5312     }
5313   }
5314
5315   /**
5316    * make the given alignmentPanel the currently selected tab
5317    *
5318    * @param alignmentPanel
5319    */
5320   public void setDisplayedView(AlignmentPanel alignmentPanel)
5321   {
5322     if (!viewport.getSequenceSetId()
5323             .equals(alignmentPanel.av.getSequenceSetId()))
5324     {
5325       throw new Error(MessageManager.getString(
5326               "error.implementation_error_cannot_show_view_alignment_frame"));
5327     }
5328     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5329             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5330     {
5331       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5332     }
5333   }
5334
5335   /**
5336    * Action on selection of menu options to Show or Hide annotations.
5337    *
5338    * @param visible
5339    * @param forSequences
5340    *          update sequence-related annotations
5341    * @param forAlignment
5342    *          update non-sequence-related annotations
5343    */
5344   @Override
5345   protected void setAnnotationsVisibility(boolean visible,
5346           boolean forSequences, boolean forAlignment)
5347   {
5348     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5349             .getAlignmentAnnotation();
5350     if (anns == null)
5351     {
5352       return;
5353     }
5354     for (AlignmentAnnotation aa : anns)
5355     {
5356       /*
5357        * don't display non-positional annotations on an alignment
5358        */
5359       if (aa.annotations == null)
5360       {
5361         continue;
5362       }
5363       boolean apply = (aa.sequenceRef == null && forAlignment)
5364               || (aa.sequenceRef != null && forSequences);
5365       if (apply)
5366       {
5367         aa.visible = visible;
5368       }
5369     }
5370     alignPanel.validateAnnotationDimensions(true);
5371     alignPanel.alignmentChanged();
5372   }
5373
5374   /**
5375    * Store selected annotation sort order for the view and repaint.
5376    */
5377   @Override
5378   protected void sortAnnotations_actionPerformed()
5379   {
5380     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5381     this.alignPanel.av
5382             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5383     alignPanel.paintAlignment(true);
5384   }
5385
5386   /**
5387    *
5388    * @return alignment panels in this alignment frame
5389    */
5390   public List<? extends AlignmentViewPanel> getAlignPanels()
5391   {
5392     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5393   }
5394
5395   /**
5396    * Open a new alignment window, with the cDNA associated with this (protein)
5397    * alignment, aligned as is the protein.
5398    */
5399   protected void viewAsCdna_actionPerformed()
5400   {
5401     // TODO no longer a menu action - refactor as required
5402     final AlignmentI alignment = getViewport().getAlignment();
5403     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5404     if (mappings == null)
5405     {
5406       return;
5407     }
5408     List<SequenceI> cdnaSeqs = new ArrayList<>();
5409     for (SequenceI aaSeq : alignment.getSequences())
5410     {
5411       for (AlignedCodonFrame acf : mappings)
5412       {
5413         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5414         if (dnaSeq != null)
5415         {
5416           /*
5417            * There is a cDNA mapping for this protein sequence - add to new
5418            * alignment. It will share the same dataset sequence as other mapped
5419            * cDNA (no new mappings need to be created).
5420            */
5421           final Sequence newSeq = new Sequence(dnaSeq);
5422           newSeq.setDatasetSequence(dnaSeq);
5423           cdnaSeqs.add(newSeq);
5424         }
5425       }
5426     }
5427     if (cdnaSeqs.size() == 0)
5428     {
5429       // show a warning dialog no mapped cDNA
5430       return;
5431     }
5432     AlignmentI cdna = new Alignment(
5433             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5434     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5435             AlignFrame.DEFAULT_HEIGHT);
5436     cdna.alignAs(alignment);
5437     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5438             + this.title;
5439     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5440             AlignFrame.DEFAULT_HEIGHT);
5441   }
5442
5443   /**
5444    * Set visibility of dna/protein complement view (available when shown in a
5445    * split frame).
5446    *
5447    * @param show
5448    */
5449   @Override
5450   protected void showComplement_actionPerformed(boolean show)
5451   {
5452     SplitContainerI sf = getSplitViewContainer();
5453     if (sf != null)
5454     {
5455       sf.setComplementVisible(this, show);
5456     }
5457   }
5458
5459   /**
5460    * Generate the reverse (optionally complemented) of the selected sequences,
5461    * and add them to the alignment
5462    */
5463   @Override
5464   protected void showReverse_actionPerformed(boolean complement)
5465   {
5466     AlignmentI al = null;
5467     try
5468     {
5469       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5470       al = dna.reverseCdna(complement);
5471       viewport.addAlignment(al, "");
5472       addHistoryItem(new EditCommand(
5473               MessageManager.getString("label.add_sequences"), Action.PASTE,
5474               al.getSequencesArray(), 0, al.getWidth(),
5475               viewport.getAlignment()));
5476     } catch (Exception ex)
5477     {
5478       System.err.println(ex.getMessage());
5479       return;
5480     }
5481   }
5482
5483   /**
5484    * Try to run a script in the Groovy console, having first ensured that this
5485    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5486    * be targeted at this alignment.
5487    */
5488   @Override
5489   protected void runGroovy_actionPerformed()
5490   {
5491     Jalview.setCurrentAlignFrame(this);
5492     groovy.ui.Console console = Desktop.getGroovyConsole();
5493     if (console != null)
5494     {
5495       try
5496       {
5497         console.runScript();
5498       } catch (Exception ex)
5499       {
5500         System.err.println((ex.toString()));
5501         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5502                 MessageManager.getString("label.couldnt_run_groovy_script"),
5503                 MessageManager.getString("label.groovy_support_failed"),
5504                 JvOptionPane.ERROR_MESSAGE);
5505       }
5506     }
5507     else
5508     {
5509       System.err.println("Can't run Groovy script as console not found");
5510     }
5511   }
5512
5513   /**
5514    * Hides columns containing (or not containing) a specified feature, provided
5515    * that would not leave all columns hidden
5516    *
5517    * @param featureType
5518    * @param columnsContaining
5519    * @return
5520    */
5521   public boolean hideFeatureColumns(String featureType,
5522           boolean columnsContaining)
5523   {
5524     boolean notForHiding = avc.markColumnsContainingFeatures(
5525             columnsContaining, false, false, featureType);
5526     if (notForHiding)
5527     {
5528       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5529               false, featureType))
5530       {
5531         getViewport().hideSelectedColumns();
5532         return true;
5533       }
5534     }
5535     return false;
5536   }
5537
5538   @Override
5539   protected void selectHighlightedColumns_actionPerformed(
5540           ActionEvent actionEvent)
5541   {
5542     // include key modifier check in case user selects from menu
5543     avc.markHighlightedColumns(
5544             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5545             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5546                     | ActionEvent.CTRL_MASK)) != 0);
5547   }
5548
5549   /**
5550    * Rebuilds the Colour menu, including any user-defined colours which have
5551    * been loaded either on startup or during the session
5552    */
5553   public void buildColourMenu()
5554   {
5555     colourMenu.removeAll();
5556
5557     colourMenu.add(applyToAllGroups);
5558     colourMenu.add(textColour);
5559     colourMenu.addSeparator();
5560
5561     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5562             false);
5563
5564     colourMenu.addSeparator();
5565     colourMenu.add(conservationMenuItem);
5566     colourMenu.add(modifyConservation);
5567     colourMenu.add(abovePIDThreshold);
5568     colourMenu.add(modifyPID);
5569     colourMenu.add(annotationColour);
5570
5571     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5572     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5573   }
5574
5575   /**
5576    * Open a dialog (if not already open) that allows the user to select and
5577    * calculate PCA or Tree analysis
5578    */
5579   protected void openTreePcaDialog()
5580   {
5581     if (alignPanel.getCalculationDialog() == null)
5582     {
5583       new CalculationChooser(AlignFrame.this);
5584     }
5585   }
5586 }
5587
5588 class PrintThread extends Thread
5589 {
5590   AlignmentPanel ap;
5591
5592   public PrintThread(AlignmentPanel ap)
5593   {
5594     this.ap = ap;
5595   }
5596
5597   static PageFormat pf;
5598
5599   @Override
5600   public void run()
5601   {
5602     PrinterJob printJob = PrinterJob.getPrinterJob();
5603
5604     if (pf != null)
5605     {
5606       printJob.setPrintable(ap, pf);
5607     }
5608     else
5609     {
5610       printJob.setPrintable(ap);
5611     }
5612
5613     if (printJob.printDialog())
5614     {
5615       try
5616       {
5617         printJob.print();
5618       } catch (Exception PrintException)
5619       {
5620         PrintException.printStackTrace();
5621       }
5622     }
5623   }
5624 }