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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Rectangle;
  27 import java.awt.Toolkit;
  28 import java.awt.datatransfer.Clipboard;
  29 import java.awt.datatransfer.DataFlavor;
  30 import java.awt.datatransfer.StringSelection;
  31 import java.awt.datatransfer.Transferable;
  32 import java.awt.dnd.DnDConstants;
  33 import java.awt.dnd.DropTargetDragEvent;
  34 import java.awt.dnd.DropTargetDropEvent;
  35 import java.awt.dnd.DropTargetEvent;
  36 import java.awt.dnd.DropTargetListener;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.FocusAdapter;
  40 import java.awt.event.FocusEvent;
  41 import java.awt.event.ItemEvent;
  42 import java.awt.event.ItemListener;
  43 import java.awt.event.KeyAdapter;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.print.PageFormat;
  47 import java.awt.print.PrinterJob;
  48 import java.beans.PropertyChangeListener;
  49 import java.io.File;
  50 import java.io.FileWriter;
  51 import java.io.PrintWriter;
  52 import java.net.URL;
  53 import java.util.ArrayList;
  54 import java.util.Arrays;
  55 import java.util.Collection;
  56 import java.util.Deque;
  57 import java.util.List;
  58 import java.util.Vector;
  59
  60 import javax.swing.ButtonGroup;
  61 import javax.swing.JCheckBoxMenuItem;
  62 import javax.swing.JComponent;
  63 import javax.swing.JEditorPane;
  64 import javax.swing.JInternalFrame;
  65 import javax.swing.JLabel;
  66 import javax.swing.JLayeredPane;
  67 import javax.swing.JMenu;
  68 import javax.swing.JMenuItem;
  69 import javax.swing.JPanel;
  70 import javax.swing.JScrollPane;
  71 import javax.swing.SwingUtilities;
  72 import javax.swing.event.InternalFrameAdapter;
  73 import javax.swing.event.InternalFrameEvent;
  74
  75 import jalview.analysis.AlignmentSorter;
  76 import jalview.analysis.AlignmentUtils;
  77 import jalview.analysis.CrossRef;
  78 import jalview.analysis.Dna;
  79 import jalview.analysis.GeneticCodeI;
  80 import jalview.analysis.ParseProperties;
  81 import jalview.analysis.SequenceIdMatcher;
  82 import jalview.api.AlignExportSettingsI;
  83 import jalview.api.AlignViewControllerGuiI;
  84 import jalview.api.AlignViewControllerI;
  85 import jalview.api.AlignViewportI;
  86 import jalview.api.AlignmentViewPanel;
  87 import jalview.api.FeatureSettingsControllerI;
  88 import jalview.api.FeatureSettingsModelI;
  89 import jalview.api.SplitContainerI;
  90 import jalview.api.ViewStyleI;
  91 import jalview.api.analysis.SimilarityParamsI;
  92 import jalview.bin.Cache;
  93 import jalview.bin.Jalview;
  94 import jalview.commands.CommandI;
  95 import jalview.commands.EditCommand;
  96 import jalview.commands.EditCommand.Action;
  97 import jalview.commands.OrderCommand;
  98 import jalview.commands.RemoveGapColCommand;
  99 import jalview.commands.RemoveGapsCommand;
 100 import jalview.commands.SlideSequencesCommand;
 101 import jalview.commands.TrimRegionCommand;
 102 import jalview.datamodel.AlignExportSettingsAdapter;
 103 import jalview.datamodel.AlignedCodonFrame;
 104 import jalview.datamodel.Alignment;
 105 import jalview.datamodel.AlignmentAnnotation;
 106 import jalview.datamodel.AlignmentExportData;
 107 import jalview.datamodel.AlignmentI;
 108 import jalview.datamodel.AlignmentOrder;
 109 import jalview.datamodel.AlignmentView;
 110 import jalview.datamodel.ColumnSelection;
 111 import jalview.datamodel.HiddenColumns;
 112 import jalview.datamodel.PDBEntry;
 113 import jalview.datamodel.SeqCigar;
 114 import jalview.datamodel.Sequence;
 115 import jalview.datamodel.SequenceGroup;
 116 import jalview.datamodel.SequenceI;
 117 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 118 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 119 import jalview.hmmer.HMMAlign;
 120 import jalview.hmmer.HMMBuild;
 121 import jalview.hmmer.HMMERParamStore;
 122 import jalview.hmmer.HMMERPreset;
 123 import jalview.hmmer.HMMSearch;
 124 import jalview.hmmer.HmmerCommand;
 125 import jalview.hmmer.JackHMMER;
 126 import jalview.io.AlignmentProperties;
 127 import jalview.io.AnnotationFile;
 128 import jalview.io.BackupFiles;
 129 import jalview.io.BioJsHTMLOutput;
 130 import jalview.io.DataSourceType;
 131 import jalview.io.FileFormat;
 132 import jalview.io.FileFormatI;
 133 import jalview.io.FileFormats;
 134 import jalview.io.FileLoader;
 135 import jalview.io.FileParse;
 136 import jalview.io.FormatAdapter;
 137 import jalview.io.HtmlSvgOutput;
 138 import jalview.io.IdentifyFile;
 139 import jalview.io.JPredFile;
 140 import jalview.io.JalviewFileChooser;
 141 import jalview.io.JalviewFileView;
 142 import jalview.io.JnetAnnotationMaker;
 143 import jalview.io.NewickFile;
 144 import jalview.io.ScoreMatrixFile;
 145 import jalview.io.TCoffeeScoreFile;
 146 import jalview.io.vcf.VCFLoader;
 147 import jalview.jbgui.GAlignFrame;
 148 import jalview.project.Jalview2XML;
 149 import jalview.schemes.ColourSchemeI;
 150 import jalview.schemes.ColourSchemes;
 151 import jalview.schemes.ResidueColourScheme;
 152 import jalview.schemes.TCoffeeColourScheme;
 153 import jalview.util.ImageMaker.TYPE;
 154 import jalview.util.MessageManager;
 155 import jalview.util.Platform;
 156 import jalview.viewmodel.AlignmentViewport;
 157 import jalview.viewmodel.ViewportRanges;
 158 import jalview.ws.DBRefFetcher;
 159 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 160 import jalview.ws.ServiceChangeListener;
 161 import jalview.ws.WSDiscovererI;
 162 import jalview.ws.api.ServiceWithParameters;
 163 import jalview.ws.jws1.Discoverer;
 164 import jalview.ws.jws2.Jws2Discoverer;
 165 import jalview.ws.jws2.PreferredServiceRegistry;
 166 import jalview.ws.params.ArgumentI;
 167 import jalview.ws.params.ParamDatastoreI;
 168 import jalview.ws.params.WsParamSetI;
 169 import jalview.ws.seqfetcher.DbSourceProxy;
 170 import jalview.ws.slivkaws.SlivkaWSDiscoverer;
 171 import java.io.IOException;
 172 import java.util.HashSet;
 173 import java.util.Set;
 174
 175 import javax.swing.JFileChooser;
 176 import javax.swing.JOptionPane;
 177
 178 /**
 179  * DOCUMENT ME!
 180  *
 181  * @author $author$
 182  * @version $Revision$
 183  */
 184 @SuppressWarnings("serial")
 185 public class AlignFrame extends GAlignFrame
 186         implements DropTargetListener, IProgressIndicator,
 187         AlignViewControllerGuiI, ColourChangeListener, ServiceChangeListener
 188 {
 189   public static final int DEFAULT_WIDTH = 700;
 190
 191   public static final int DEFAULT_HEIGHT = 500;
 192
 193   /*
 194    * The currently displayed panel (selected tabbed view if more than one)
 195    */
 196   public AlignmentPanel alignPanel;
 197
 198   AlignViewport viewport;
 199
 200   public AlignViewControllerI avc;
 201
 202   List<AlignmentPanel> alignPanels = new ArrayList<>();
 203
 204   /**
 205    * Last format used to load or save alignments in this window
 206    */
 207   FileFormatI currentFileFormat = null;
 208
 209   /**
 210    * Current filename for this alignment
 211    */
 212   String fileName = null;
 213
 214   /**
 215    * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping
 216    */
 217   File fileObject;
 218
 219   /**
 220    * Creates a new AlignFrame object with specific width and height.
 221    *
 222    * @param al
 223    * @param width
 224    * @param height
 225    */
 226   public AlignFrame(AlignmentI al, int width, int height)
 227   {
 228     this(al, null, width, height);
 229   }
 230
 231   /**
 232    * Creates a new AlignFrame object with specific width, height and
 233    * sequenceSetId
 234    *
 235    * @param al
 236    * @param width
 237    * @param height
 238    * @param sequenceSetId
 239    */
 240   public AlignFrame(AlignmentI al, int width, int height,
 241           String sequenceSetId)
 242   {
 243     this(al, null, width, height, sequenceSetId);
 244   }
 245
 246   /**
 247    * Creates a new AlignFrame object with specific width, height and
 248    * sequenceSetId
 249    *
 250    * @param al
 251    * @param width
 252    * @param height
 253    * @param sequenceSetId
 254    * @param viewId
 255    */
 256   public AlignFrame(AlignmentI al, int width, int height,
 257           String sequenceSetId, String viewId)
 258   {
 259     this(al, null, width, height, sequenceSetId, viewId);
 260   }
 261
 262   /**
 263    * new alignment window with hidden columns
 264    *
 265    * @param al
 266    *          AlignmentI
 267    * @param hiddenColumns
 268    *          ColumnSelection or null
 269    * @param width
 270    *          Width of alignment frame
 271    * @param height
 272    *          height of frame.
 273    */
 274   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 275           int height)
 276   {
 277     this(al, hiddenColumns, width, height, null);
 278   }
 279
 280   /**
 281    * Create alignment frame for al with hiddenColumns, a specific width and
 282    * height, and specific sequenceId
 283    *
 284    * @param al
 285    * @param hiddenColumns
 286    * @param width
 287    * @param height
 288    * @param sequenceSetId
 289    *          (may be null)
 290    */
 291   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 292           int height, String sequenceSetId)
 293   {
 294     this(al, hiddenColumns, width, height, sequenceSetId, null);
 295   }
 296
 297   /**
 298    * Create alignment frame for al with hiddenColumns, a specific width and
 299    * height, and specific sequenceId
 300    *
 301    * @param al
 302    * @param hiddenColumns
 303    * @param width
 304    * @param height
 305    * @param sequenceSetId
 306    *          (may be null)
 307    * @param viewId
 308    *          (may be null)
 309    */
 310   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 311           int height, String sequenceSetId, String viewId)
 312   {
 313     setSize(width, height);
 314
 315     if (al.getDataset() == null)
 316     {
 317       al.setDataset(null);
 318     }
 319
 320     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 321
 322     alignPanel = new AlignmentPanel(this, viewport);
 323
 324     addAlignmentPanel(alignPanel, true);
 325     init();
 326   }
 327
 328   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 329           HiddenColumns hiddenColumns, int width, int height)
 330   {
 331     setSize(width, height);
 332
 333     if (al.getDataset() == null)
 334     {
 335       al.setDataset(null);
 336     }
 337
 338     viewport = new AlignViewport(al, hiddenColumns);
 339
 340     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 341     {
 342       viewport.hideSequence(hiddenSeqs);
 343     }
 344     alignPanel = new AlignmentPanel(this, viewport);
 345     addAlignmentPanel(alignPanel, true);
 346     init();
 347   }
 348
 349   /**
 350    * Make a new AlignFrame from existing alignmentPanels
 351    *
 352    * @param ap
 353    *          AlignmentPanel
 354    * @param av
 355    *          AlignViewport
 356    */
 357   public AlignFrame(AlignmentPanel ap)
 358   {
 359     viewport = ap.av;
 360     alignPanel = ap;
 361     addAlignmentPanel(ap, false);
 362     init();
 363   }
 364
 365   /**
 366    * initalise the alignframe from the underlying viewport data and the
 367    * configurations
 368    */
 369   void init()
 370   {
 371     // setBackground(Color.white); // BH 2019
 372
 373     if (!Jalview.isHeadlessMode())
 374     {
 375       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 376     }
 377
 378     avc = new jalview.controller.AlignViewController(this, viewport,
 379             alignPanel);
 380     if (viewport.getAlignmentConservationAnnotation() == null)
 381     {
 382       // BLOSUM62Colour.setEnabled(false);
 383       conservationMenuItem.setEnabled(false);
 384       modifyConservation.setEnabled(false);
 385       // PIDColour.setEnabled(false);
 386       // abovePIDThreshold.setEnabled(false);
 387       // modifyPID.setEnabled(false);
 388     }
 389
 390     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 391             "No sort");
 392
 393     if (sortby.equals("Id"))
 394     {
 395       sortIDMenuItem_actionPerformed(null);
 396     }
 397     else if (sortby.equals("Pairwise Identity"))
 398     {
 399       sortPairwiseMenuItem_actionPerformed(null);
 400     }
 401
 402     this.alignPanel.av
 403             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 404
 405     setMenusFromViewport(viewport);
 406     buildSortByAnnotationScoresMenu();
 407     calculateTree.addActionListener(new ActionListener()
 408     {
 409
 410       @Override
 411       public void actionPerformed(ActionEvent e)
 412       {
 413         openTreePcaDialog();
 414       }
 415     });
 416     buildColourMenu();
 417
 418     if (Desktop.desktop != null)
 419     {
 420       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 421       if (!Platform.isJS())
 422       {
 423         addServiceListeners();
 424       }
 425       setGUINucleotide();
 426     }
 427
 428     if (viewport.getWrapAlignment())
 429     {
 430       wrapMenuItem_actionPerformed(null);
 431     }
 432
 433     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 434     {
 435       this.overviewMenuItem_actionPerformed(null);
 436     }
 437
 438     addKeyListener();
 439
 440     final List<AlignmentPanel> selviews = new ArrayList<>();
 441     final List<AlignmentPanel> origview = new ArrayList<>();
 442     final String menuLabel = MessageManager
 443             .getString("label.copy_format_from");
 444     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 445             new ViewSetProvider()
 446             {
 447
 448               @Override
 449               public AlignmentPanel[] getAllAlignmentPanels()
 450               {
 451                 origview.clear();
 452                 origview.add(alignPanel);
 453                 // make an array of all alignment panels except for this one
 454                 List<AlignmentPanel> aps = new ArrayList<>(
 455                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 456                 aps.remove(AlignFrame.this.alignPanel);
 457                 return aps.toArray(new AlignmentPanel[aps.size()]);
 458               }
 459             }, selviews, new ItemListener()
 460             {
 461
 462               @Override
 463               public void itemStateChanged(ItemEvent e)
 464               {
 465                 if (origview.size() > 0)
 466                 {
 467                   final AlignmentPanel ap = origview.get(0);
 468
 469                   /*
 470                    * Copy the ViewStyle of the selected panel to 'this one'.
 471                    * Don't change value of 'scaleProteinAsCdna' unless copying
 472                    * from a SplitFrame.
 473                    */
 474                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 475                           .getViewStyle();
 476                   boolean fromSplitFrame = selviews.get(0)
 477                           .getAlignViewport().getCodingComplement() != null;
 478                   if (!fromSplitFrame)
 479                   {
 480                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 481                             .getViewStyle().isScaleProteinAsCdna());
 482                   }
 483                   ap.getAlignViewport().setViewStyle(vs);
 484
 485                   /*
 486                    * Also rescale ViewStyle of SplitFrame complement if there is
 487                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 488                    * the whole ViewStyle (allow cDNA protein to have different
 489                    * fonts)
 490                    */
 491                   AlignViewportI complement = ap.getAlignViewport()
 492                           .getCodingComplement();
 493                   if (complement != null && vs.isScaleProteinAsCdna())
 494                   {
 495                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 496                     ((SplitFrame) af.getSplitViewContainer())
 497                             .adjustLayout();
 498                     af.setMenusForViewport();
 499                   }
 500
 501                   ap.updateLayout();
 502                   ap.setSelected(true);
 503                   ap.alignFrame.setMenusForViewport();
 504
 505                 }
 506               }
 507             });
 508     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 509             .indexOf("devel") > -1
 510             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 511                     .indexOf("test") > -1)
 512     {
 513       formatMenu.add(vsel);
 514     }
 515     addFocusListener(new FocusAdapter()
 516     {
 517       @Override
 518       public void focusGained(FocusEvent e)
 519       {
 520         Jalview.setCurrentAlignFrame(AlignFrame.this);
 521       }
 522     });
 523
 524   }
 525
 526   /**
 527    * Change the filename and format for the alignment, and enable the 'reload'
 528    * button functionality.
 529    *
 530    * @param file
 531    *          valid filename
 532    * @param format
 533    *          format of file
 534    */
 535   public void setFileName(String file, FileFormatI format)
 536   {
 537     fileName = file;
 538     setFileFormat(format);
 539     reload.setEnabled(true);
 540   }
 541
 542   /**
 543    * JavaScript will have this, maybe others. More dependable than a file name
 544    * and maintains a reference to the actual bytes loaded.
 545    *
 546    * @param file
 547    */
 548   public void setFileObject(File file)
 549   {
 550     this.fileObject = file;
 551   }
 552
 553   /**
 554    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 555    * events
 556    */
 557   void addKeyListener()
 558   {
 559     addKeyListener(new KeyAdapter()
 560     {
 561       @Override
 562       public void keyPressed(KeyEvent evt)
 563       {
 564         if (viewport.cursorMode
 565                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 566                         && evt.getKeyCode() <= KeyEvent.VK_9)
 567                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 568                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 569                 && Character.isDigit(evt.getKeyChar()))
 570         {
 571           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 572         }
 573
 574         switch (evt.getKeyCode())
 575         {
 576
 577         case 27: // escape key
 578           deselectAllSequenceMenuItem_actionPerformed(null);
 579
 580           break;
 581
 582         case KeyEvent.VK_DOWN:
 583           if (evt.isAltDown() || !viewport.cursorMode)
 584           {
 585             moveSelectedSequences(false);
 586           }
 587           if (viewport.cursorMode)
 588           {
 589             alignPanel.getSeqPanel().moveCursor(0, 1);
 590           }
 591           break;
 592
 593         case KeyEvent.VK_UP:
 594           if (evt.isAltDown() || !viewport.cursorMode)
 595           {
 596             moveSelectedSequences(true);
 597           }
 598           if (viewport.cursorMode)
 599           {
 600             alignPanel.getSeqPanel().moveCursor(0, -1);
 601           }
 602
 603           break;
 604
 605         case KeyEvent.VK_LEFT:
 606           if (evt.isAltDown() || !viewport.cursorMode)
 607           {
 608             slideSequences(false,
 609                     alignPanel.getSeqPanel().getKeyboardNo1());
 610           }
 611           else
 612           {
 613             alignPanel.getSeqPanel().moveCursor(-1, 0);
 614           }
 615
 616           break;
 617
 618         case KeyEvent.VK_RIGHT:
 619           if (evt.isAltDown() || !viewport.cursorMode)
 620           {
 621             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 622           }
 623           else
 624           {
 625             alignPanel.getSeqPanel().moveCursor(1, 0);
 626           }
 627           break;
 628
 629         case KeyEvent.VK_SPACE:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 633                     || evt.isShiftDown() || evt.isAltDown());
 634           }
 635           break;
 636
 637         // case KeyEvent.VK_A:
 638         // if (viewport.cursorMode)
 639         // {
 640         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 641         // //System.out.println("A");
 642         // }
 643         // break;
 644         /*
 645          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 646          * System.out.println("closing bracket"); } break;
 647          */
 648         case KeyEvent.VK_DELETE:
 649         case KeyEvent.VK_BACK_SPACE:
 650           if (!viewport.cursorMode)
 651           {
 652             cut_actionPerformed();
 653           }
 654           else
 655           {
 656             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 657                     || evt.isShiftDown() || evt.isAltDown());
 658           }
 659
 660           break;
 661
 662         case KeyEvent.VK_S:
 663           if (viewport.cursorMode)
 664           {
 665             alignPanel.getSeqPanel().setCursorRow();
 666           }
 667           break;
 668         case KeyEvent.VK_C:
 669           if (viewport.cursorMode && !evt.isControlDown())
 670           {
 671             alignPanel.getSeqPanel().setCursorColumn();
 672           }
 673           break;
 674         case KeyEvent.VK_P:
 675           if (viewport.cursorMode)
 676           {
 677             alignPanel.getSeqPanel().setCursorPosition();
 678           }
 679           break;
 680
 681         case KeyEvent.VK_ENTER:
 682         case KeyEvent.VK_COMMA:
 683           if (viewport.cursorMode)
 684           {
 685             alignPanel.getSeqPanel().setCursorRowAndColumn();
 686           }
 687           break;
 688
 689         case KeyEvent.VK_Q:
 690           if (viewport.cursorMode)
 691           {
 692             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 693           }
 694           break;
 695         case KeyEvent.VK_M:
 696           if (viewport.cursorMode)
 697           {
 698             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 699           }
 700           break;
 701
 702         case KeyEvent.VK_F2:
 703           viewport.cursorMode = !viewport.cursorMode;
 704           setStatus(MessageManager
 705                   .formatMessage("label.keyboard_editing_mode", new String[]
 706                   { (viewport.cursorMode ? "on" : "off") }));
 707           if (viewport.cursorMode)
 708           {
 709             ViewportRanges ranges = viewport.getRanges();
 710             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 711                     .getStartRes();
 712             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 713                     .getStartSeq();
 714           }
 715           alignPanel.getSeqPanel().seqCanvas.repaint();
 716           break;
 717
 718         case KeyEvent.VK_F1:
 719           try
 720           {
 721             Help.showHelpWindow();
 722           } catch (Exception ex)
 723           {
 724             ex.printStackTrace();
 725           }
 726           break;
 727         case KeyEvent.VK_H:
 728         {
 729           boolean toggleSeqs = !evt.isControlDown();
 730           boolean toggleCols = !evt.isShiftDown();
 731           toggleHiddenRegions(toggleSeqs, toggleCols);
 732           break;
 733         }
 734         case KeyEvent.VK_B:
 735         {
 736           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 737           boolean modifyExisting = true; // always modify, don't clear
 738                                          // evt.isShiftDown();
 739           boolean invertHighlighted = evt.isAltDown();
 740           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 741                   toggleSel);
 742           break;
 743         }
 744         case KeyEvent.VK_PAGE_UP:
 745           viewport.getRanges().pageUp();
 746           break;
 747         case KeyEvent.VK_PAGE_DOWN:
 748           viewport.getRanges().pageDown();
 749           break;
 750         }
 751       }
 752
 753       @Override
 754       public void keyReleased(KeyEvent evt)
 755       {
 756         switch (evt.getKeyCode())
 757         {
 758         case KeyEvent.VK_LEFT:
 759           if (evt.isAltDown() || !viewport.cursorMode)
 760           {
 761             viewport.firePropertyChange("alignment", null,
 762                     viewport.getAlignment().getSequences());
 763           }
 764           break;
 765
 766         case KeyEvent.VK_RIGHT:
 767           if (evt.isAltDown() || !viewport.cursorMode)
 768           {
 769             viewport.firePropertyChange("alignment", null,
 770                     viewport.getAlignment().getSequences());
 771           }
 772           break;
 773         }
 774       }
 775     });
 776   }
 777
 778   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 779   {
 780     ap.alignFrame = this;
 781     avc = new jalview.controller.AlignViewController(this, viewport,
 782             alignPanel);
 783
 784     alignPanels.add(ap);
 785
 786     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 787
 788     int aSize = alignPanels.size();
 789
 790     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 791
 792     if (aSize == 1 && ap.av.getViewName() == null)
 793     {
 794       this.getContentPane().add(ap, BorderLayout.CENTER);
 795     }
 796     else
 797     {
 798       if (aSize == 2)
 799       {
 800         setInitialTabVisible();
 801       }
 802
 803       expandViews.setEnabled(true);
 804       gatherViews.setEnabled(true);
 805       tabbedPane.addTab(ap.av.getViewName(), ap);
 806
 807       ap.setVisible(false);
 808     }
 809
 810     if (newPanel)
 811     {
 812       if (ap.av.isPadGaps())
 813       {
 814         ap.av.getAlignment().padGaps();
 815       }
 816       ap.av.updateConservation(ap);
 817       ap.av.updateConsensus(ap);
 818       ap.av.updateStrucConsensus(ap);
 819       ap.av.initInformationWorker(ap);
 820     }
 821   }
 822
 823   public void setInitialTabVisible()
 824   {
 825     expandViews.setEnabled(true);
 826     gatherViews.setEnabled(true);
 827     tabbedPane.setVisible(true);
 828     AlignmentPanel first = alignPanels.get(0);
 829     tabbedPane.addTab(first.av.getViewName(), first);
 830     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 831   }
 832
 833   public AlignViewport getViewport()
 834   {
 835     return viewport;
 836   }
 837
 838   @Override
 839   public void servicesChanged(WSDiscovererI discoverer,
 840           Collection<? extends ServiceWithParameters> services)
 841   {
 842     buildWebServicesMenu();
 843   }
 844
 845   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 846   private void addServiceListeners()
 847   {
 848     if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
 849     {
 850       WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance();
 851       discoverer.addServiceChangeListener(this);
 852     }
 853     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
 854     {
 855       WSDiscovererI discoverer = Jws2Discoverer.getDiscoverer();
 856       discoverer.addServiceChangeListener(this);
 857     }
 858     // legacy event listener for compatibility with jws1
 859     PropertyChangeListener legacyListener = (changeEvent) -> {
 860       buildWebServicesMenu();
 861     };
 862     Desktop.instance.addJalviewPropertyChangeListener("services",legacyListener);
 863
 864     addInternalFrameListener(new InternalFrameAdapter() {
 865       @Override
 866       public void internalFrameClosed(InternalFrameEvent e) {
 867         System.out.println("deregistering discoverer listener");
 868         SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
 869         Jws2Discoverer.getDiscoverer().removeServiceChangeListener(AlignFrame.this);
 870         Desktop.instance.removeJalviewPropertyChangeListener("services", legacyListener);
 871         closeMenuItem_actionPerformed(true);
 872       }
 873     });
 874     buildWebServicesMenu();
 875   }
 876
 877   /**
 878    * Configure menu items that vary according to whether the alignment is
 879    * nucleotide or protein
 880    */
 881   public void setGUINucleotide()
 882   {
 883     AlignmentI al = getViewport().getAlignment();
 884     boolean nucleotide = al.isNucleotide();
 885
 886     loadVcf.setVisible(nucleotide);
 887     showTranslation.setVisible(nucleotide);
 888     showReverse.setVisible(nucleotide);
 889     showReverseComplement.setVisible(nucleotide);
 890     conservationMenuItem.setEnabled(!nucleotide);
 891     modifyConservation
 892             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 893     showGroupConservation.setEnabled(!nucleotide);
 894
 895     showComplementMenuItem
 896             .setText(nucleotide ? MessageManager.getString("label.protein")
 897                     : MessageManager.getString("label.nucleotide"));
 898   }
 899
 900   /**
 901    * set up menus for the current viewport. This may be called after any
 902    * operation that affects the data in the current view (selection changed,
 903    * etc) to update the menus to reflect the new state.
 904    */
 905   @Override
 906   public void setMenusForViewport()
 907   {
 908     setMenusFromViewport(viewport);
 909   }
 910
 911   /**
 912    * Need to call this method when tabs are selected for multiple views, or when
 913    * loading from Jalview2XML.java
 914    *
 915    * @param av
 916    *          AlignViewport
 917    */
 918   public void setMenusFromViewport(AlignViewport av)
 919   {
 920     padGapsMenuitem.setSelected(av.isPadGaps());
 921     colourTextMenuItem.setSelected(av.isShowColourText());
 922     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 923     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 924     conservationMenuItem.setSelected(av.getConservationSelected());
 925     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 926     seqLimits.setSelected(av.getShowJVSuffix());
 927     idRightAlign.setSelected(av.isRightAlignIds());
 928     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 929     renderGapsMenuItem.setSelected(av.isRenderGaps());
 930     wrapMenuItem.setSelected(av.getWrapAlignment());
 931     scaleAbove.setVisible(av.getWrapAlignment());
 932     scaleLeft.setVisible(av.getWrapAlignment());
 933     scaleRight.setVisible(av.getWrapAlignment());
 934     annotationPanelMenuItem.setState(av.isShowAnnotation());
 935     /*
 936      * Show/hide annotations only enabled if annotation panel is shown
 937      */
 938     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 939     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 940     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 941     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 942     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 943     viewTextMenuItem.setSelected(av.getShowText());
 944     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 945     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 946     showGroupConservation.setSelected(av.isShowGroupConservation());
 947     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 948     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 949     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 950     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 951     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 952     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 953
 954     ColourMenuHelper.setColourSelected(colourMenu,
 955             av.getGlobalColourScheme());
 956
 957     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 958     hiddenMarkers.setState(av.getShowHiddenMarkers());
 959     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 960     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 961     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 962     autoCalculate.setSelected(av.autoCalculateConsensus);
 963     sortByTree.setSelected(av.sortByTree);
 964     listenToViewSelections.setSelected(av.followSelection);
 965
 966     showProducts.setEnabled(canShowProducts());
 967     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 968
 969     updateEditMenuBar();
 970   }
 971
 972   /**
 973    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 974    *
 975    * @param b
 976    */
 977   public void setGroovyEnabled(boolean b)
 978   {
 979     runGroovy.setEnabled(b);
 980   }
 981
 982   private IProgressIndicator progressBar;
 983
 984   /*
 985    * (non-Javadoc)
 986    *
 987    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 988    */
 989   @Override
 990   public void setProgressBar(String message, long id)
 991   {
 992     progressBar.setProgressBar(message, id);
 993   }
 994
 995   @Override
 996   public void registerHandler(final long id,
 997           final IProgressIndicatorHandler handler)
 998   {
 999     progressBar.registerHandler(id, handler);
1000   }
1001
1002   /**
1003    *
1004    * @return true if any progress bars are still active
1005    */
1006   @Override
1007   public boolean operationInProgress()
1008   {
1009     return progressBar.operationInProgress();
1010   }
1011
1012   /**
1013    * Sets the text of the status bar. Note that setting a null or empty value
1014    * will cause the status bar to be hidden, with possibly undesirable flicker
1015    * of the screen layout.
1016    */
1017   @Override
1018   public void setStatus(String text)
1019   {
1020     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1021   }
1022
1023   /*
1024    * Added so Castor Mapping file can obtain Jalview Version
1025    */
1026   public String getVersion()
1027   {
1028     return jalview.bin.Cache.getProperty("VERSION");
1029   }
1030
1031   public FeatureRenderer getFeatureRenderer()
1032   {
1033     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1034   }
1035
1036   @Override
1037   public void fetchSequence_actionPerformed()
1038   {
1039     new SequenceFetcher(this);
1040   }
1041
1042   @Override
1043   public void addFromFile_actionPerformed(ActionEvent e)
1044   {
1045     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1046   }
1047
1048   @Override
1049   public void hmmBuild_actionPerformed(boolean withDefaults)
1050   {
1051     if (!alignmentIsSufficient(1))
1052     {
1053       return;
1054     }
1055
1056     /*
1057      * get default parameters, and optionally show a dialog
1058      * to allow them to be modified
1059      */
1060     ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
1061     List<ArgumentI> args = store.getServiceParameters();
1062
1063     if (!withDefaults)
1064     {
1065       WsParamSetI set = new HMMERPreset();
1066       WsJobParameters params = new WsJobParameters(store, set, args);
1067       if (params.showRunDialog())
1068       {
1069         args = params.getJobParams();
1070       }
1071       else
1072       {
1073         return; // user cancelled
1074       }
1075     }
1076     new Thread(new HMMBuild(this, args)).start();
1077   }
1078
1079   @Override
1080   public void hmmAlign_actionPerformed(boolean withDefaults)
1081   {
1082     if (!(checkForHMM() && alignmentIsSufficient(2)))
1083     {
1084       return;
1085     }
1086
1087     /*
1088      * get default parameters, and optionally show a dialog
1089      * to allow them to be modified
1090      */
1091     ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
1092     List<ArgumentI> args = store.getServiceParameters();
1093
1094     if (!withDefaults)
1095     {
1096       WsParamSetI set = new HMMERPreset();
1097       WsJobParameters params = new WsJobParameters(store, set, args);
1098       if (params.showRunDialog())
1099       {
1100         args = params.getJobParams();
1101       }
1102       else
1103       {
1104         return; // user cancelled
1105       }
1106     }
1107     new Thread(new HMMAlign(this, args)).start();
1108   }
1109
1110   @Override
1111   public void hmmSearch_actionPerformed(boolean withDefaults)
1112   {
1113     if (!checkForHMM())
1114     {
1115       return;
1116     }
1117
1118     /*
1119      * get default parameters, and (if requested) show
1120      * dialog to allow modification
1121      */
1122     ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
1123     List<ArgumentI> args = store.getServiceParameters();
1124
1125     if (!withDefaults)
1126     {
1127       WsParamSetI set = new HMMERPreset();
1128       WsJobParameters params = new WsJobParameters(store, set, args);
1129       if (params.showRunDialog())
1130       {
1131         args = params.getJobParams();
1132       }
1133       else
1134       {
1135         return; // user cancelled
1136       }
1137     }
1138     new Thread(new HMMSearch(this, args)).start();
1139     alignPanel.repaint();
1140   }
1141
1142   @Override
1143   public void jackhmmer_actionPerformed(boolean withDefaults)
1144   {
1145
1146     /*
1147      * get default parameters, and (if requested) show
1148      * dialog to allow modification
1149      */
1150
1151     ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
1152     List<ArgumentI> args = store.getServiceParameters();
1153
1154     if (!withDefaults)
1155     {
1156       WsParamSetI set = new HMMERPreset();
1157       WsJobParameters params = new WsJobParameters(store, set, args);
1158       if (params.showRunDialog())
1159       {
1160         args = params.getJobParams();
1161       }
1162       else
1163       {
1164         return; // user cancelled
1165       }
1166     }
1167     new Thread(new JackHMMER(this, args)).start();
1168     alignPanel.repaint();
1169
1170   }
1171
1172   /**
1173    * Checks if the alignment has at least one hidden Markov model, if not shows
1174    * a dialog advising to run hmmbuild or load an HMM profile
1175    *
1176    * @return
1177    */
1178   private boolean checkForHMM()
1179   {
1180     if (viewport.getAlignment().getHmmSequences().isEmpty())
1181     {
1182       JOptionPane.showMessageDialog(this,
1183               MessageManager.getString("warn.no_hmm"));
1184       return false;
1185     }
1186     return true;
1187   }
1188
1189   @Override
1190   protected void filterByEValue_actionPerformed()
1191   {
1192     viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
1193   }
1194
1195   @Override
1196   protected void filterByScore_actionPerformed()
1197   {
1198     viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
1199   }
1200
1201   private double inputDouble(String message)
1202   {
1203     String str = null;
1204     Double d = null;
1205     while (d == null || d <= 0)
1206     {
1207       str = JOptionPane.showInputDialog(this.alignPanel, message);
1208       try
1209       {
1210         d = Double.valueOf(str);
1211       } catch (NumberFormatException e)
1212       {
1213       }
1214     }
1215     return d;
1216   }
1217
1218   /**
1219    * Checks if the alignment contains the required number of sequences.
1220    *
1221    * @param required
1222    * @return
1223    */
1224   public boolean alignmentIsSufficient(int required)
1225   {
1226     if (getViewport().getSequenceSelection().length < required)
1227     {
1228       JOptionPane.showMessageDialog(this,
1229               MessageManager.getString("label.not_enough_sequences"));
1230       return false;
1231     }
1232     return true;
1233   }
1234
1235   /**
1236    * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
1237    * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
1238    * comma-separated list)
1239    */
1240   @Override
1241   public void addDatabase_actionPerformed() throws IOException
1242   {
1243     if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
1244     {
1245       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1246     }
1247
1248     String path = openFileChooser(false);
1249     if (path != null && new File(path).exists())
1250     {
1251       IdentifyFile identifier = new IdentifyFile();
1252       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1253       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1254               || format == FileFormat.Pfam)
1255       {
1256         String currentDbPaths = Cache
1257                 .getProperty(Preferences.HMMSEARCH_DBS);
1258         currentDbPaths += Preferences.COMMA + path;
1259         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1260       }
1261       else
1262       {
1263         JOptionPane.showMessageDialog(this,
1264                 MessageManager.getString("warn.invalid_format"));
1265       }
1266     }
1267   }
1268
1269   /**
1270    * Opens a file chooser, optionally restricted to selecting folders
1271    * (directories) only. Answers the path to the selected file or folder, or
1272    * null if none is chosen.
1273    *
1274    * @param
1275    * @return
1276    */
1277   protected String openFileChooser(boolean forFolder)
1278   {
1279     // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
1280     String choice = null;
1281     JFileChooser chooser = new JFileChooser();
1282     if (forFolder)
1283     {
1284       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1285     }
1286     chooser.setDialogTitle(
1287             MessageManager.getString("label.open_local_file"));
1288     chooser.setToolTipText(MessageManager.getString("action.open"));
1289
1290     int value = chooser.showOpenDialog(this);
1291
1292     if (value == JFileChooser.APPROVE_OPTION)
1293     {
1294       choice = chooser.getSelectedFile().getPath();
1295     }
1296     return choice;
1297   }
1298
1299   @Override
1300   public void reload_actionPerformed(ActionEvent e)
1301   {
1302     if (fileName != null)
1303     {
1304       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1305       // originating file's format
1306       // TODO: work out how to recover feature settings for correct view(s) when
1307       // file is reloaded.
1308       if (FileFormat.Jalview.equals(currentFileFormat))
1309       {
1310         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1311         for (int i = 0; i < frames.length; i++)
1312         {
1313           if (frames[i] instanceof AlignFrame && frames[i] != this
1314                   && ((AlignFrame) frames[i]).fileName != null
1315                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1316           {
1317             try
1318             {
1319               frames[i].setSelected(true);
1320               Desktop.instance.closeAssociatedWindows();
1321             } catch (java.beans.PropertyVetoException ex)
1322             {
1323             }
1324           }
1325
1326         }
1327         Desktop.instance.closeAssociatedWindows();
1328
1329         FileLoader loader = new FileLoader();
1330         DataSourceType protocol = fileName.startsWith("http:")
1331                 ? DataSourceType.URL
1332                 : DataSourceType.FILE;
1333         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1334       }
1335       else
1336       {
1337         Rectangle bounds = this.getBounds();
1338
1339         FileLoader loader = new FileLoader();
1340
1341         AlignFrame newframe = null;
1342
1343         if (fileObject == null)
1344         {
1345
1346           DataSourceType protocol = (fileName.startsWith("http:")
1347                   ? DataSourceType.URL
1348                   : DataSourceType.FILE);
1349           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1350                   currentFileFormat);
1351         }
1352         else
1353         {
1354           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1355                   DataSourceType.FILE, currentFileFormat);
1356         }
1357
1358         newframe.setBounds(bounds);
1359         if (featureSettings != null && featureSettings.isShowing())
1360         {
1361           final Rectangle fspos = featureSettings.frame.getBounds();
1362           // TODO: need a 'show feature settings' function that takes bounds -
1363           // need to refactor Desktop.addFrame
1364           newframe.featureSettings_actionPerformed(null);
1365           final FeatureSettings nfs = newframe.featureSettings;
1366           SwingUtilities.invokeLater(new Runnable()
1367           {
1368             @Override
1369             public void run()
1370             {
1371               nfs.frame.setBounds(fspos);
1372             }
1373           });
1374           this.featureSettings.close();
1375           this.featureSettings = null;
1376         }
1377         this.closeMenuItem_actionPerformed(true);
1378       }
1379     }
1380   }
1381
1382   @Override
1383   public void addFromText_actionPerformed(ActionEvent e)
1384   {
1385     Desktop.instance
1386             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1387   }
1388
1389   @Override
1390   public void addFromURL_actionPerformed(ActionEvent e)
1391   {
1392     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1393   }
1394
1395   @Override
1396   public void save_actionPerformed(ActionEvent e)
1397   {
1398     if (fileName == null || (currentFileFormat == null)
1399             || fileName.startsWith("http"))
1400     {
1401       saveAs_actionPerformed();
1402     }
1403     else
1404     {
1405       saveAlignment(fileName, currentFileFormat);
1406     }
1407   }
1408
1409   /**
1410    * Saves the alignment to a file with a name chosen by the user, if necessary
1411    * warning if a file would be overwritten
1412    */
1413   @Override
1414   public void saveAs_actionPerformed()
1415   {
1416     String format = currentFileFormat == null ? null
1417             : currentFileFormat.getName();
1418     JalviewFileChooser chooser = JalviewFileChooser
1419             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1420
1421     chooser.setFileView(new JalviewFileView());
1422     chooser.setDialogTitle(
1423             MessageManager.getString("label.save_alignment_to_file"));
1424     chooser.setToolTipText(MessageManager.getString("action.save"));
1425
1426     int value = chooser.showSaveDialog(this);
1427
1428     if (value != JalviewFileChooser.APPROVE_OPTION)
1429     {
1430       return;
1431     }
1432     currentFileFormat = chooser.getSelectedFormat();
1433     // todo is this (2005) test now obsolete - value is never null?
1434     while (currentFileFormat == null)
1435     {
1436       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1437               MessageManager
1438                       .getString("label.select_file_format_before_saving"),
1439               MessageManager.getString("label.file_format_not_specified"),
1440               JvOptionPane.WARNING_MESSAGE);
1441       currentFileFormat = chooser.getSelectedFormat();
1442       value = chooser.showSaveDialog(this);
1443       if (value != JalviewFileChooser.APPROVE_OPTION)
1444       {
1445         return;
1446       }
1447     }
1448
1449     fileName = chooser.getSelectedFile().getPath();
1450
1451     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1452     Cache.setProperty("LAST_DIRECTORY", fileName);
1453     saveAlignment(fileName, currentFileFormat);
1454   }
1455
1456   boolean lastSaveSuccessful = false;
1457
1458   FileFormatI lastFormatSaved;
1459
1460   String lastFilenameSaved;
1461
1462   /**
1463    * Raise a dialog or status message for the last call to saveAlignment.
1464    *
1465    * @return true if last call to saveAlignment(file, format) was successful.
1466    */
1467   public boolean isSaveAlignmentSuccessful()
1468   {
1469
1470     if (!lastSaveSuccessful)
1471     {
1472       JvOptionPane.showInternalMessageDialog(this, MessageManager
1473               .formatMessage("label.couldnt_save_file", new Object[]
1474               { lastFilenameSaved }),
1475               MessageManager.getString("label.error_saving_file"),
1476               JvOptionPane.WARNING_MESSAGE);
1477     }
1478     else
1479     {
1480
1481       setStatus(MessageManager.formatMessage(
1482               "label.successfully_saved_to_file_in_format", new Object[]
1483               { lastFilenameSaved, lastFormatSaved }));
1484
1485     }
1486     return lastSaveSuccessful;
1487   }
1488
1489   /**
1490    * Saves the alignment to the specified file path, in the specified format,
1491    * which may be an alignment format, or Jalview project format. If the
1492    * alignment has hidden regions, or the format is one capable of including
1493    * non-sequence data (features, annotations, groups), then the user may be
1494    * prompted to specify what to include in the output.
1495    *
1496    * @param file
1497    * @param format
1498    */
1499   public void saveAlignment(String file, FileFormatI format)
1500   {
1501     lastSaveSuccessful = true;
1502     lastFilenameSaved = file;
1503     lastFormatSaved = format;
1504
1505     if (FileFormat.Jalview.equals(format))
1506     {
1507       String shortName = title;
1508       if (shortName.indexOf(File.separatorChar) > -1)
1509       {
1510         shortName = shortName
1511                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1512       }
1513       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1514               shortName);
1515
1516       statusBar.setText(MessageManager.formatMessage(
1517               "label.successfully_saved_to_file_in_format", new Object[]
1518               { fileName, format }));
1519
1520       return;
1521     }
1522
1523     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1524     Runnable cancelAction = new Runnable()
1525     {
1526       @Override
1527       public void run()
1528       {
1529         lastSaveSuccessful = false;
1530       }
1531     };
1532     Runnable outputAction = new Runnable()
1533     {
1534       @Override
1535       public void run()
1536       {
1537         // todo defer this to inside formatSequences (or later)
1538         AlignmentExportData exportData = viewport
1539                 .getAlignExportData(options);
1540         String output = new FormatAdapter(alignPanel, options)
1541                 .formatSequences(format, exportData.getAlignment(),
1542                         exportData.getOmitHidden(),
1543                         exportData.getStartEndPostions(),
1544                         viewport.getAlignment().getHiddenColumns());
1545         if (output == null)
1546         {
1547           lastSaveSuccessful = false;
1548         }
1549         else
1550         {
1551           // create backupfiles object and get new temp filename destination
1552           boolean doBackup = BackupFiles.getEnabled();
1553           BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1554           try
1555           {
1556             String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1557                     : file;
1558             PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1559
1560             out.print(output);
1561             out.close();
1562             AlignFrame.this.setTitle(file);
1563             statusBar.setText(MessageManager.formatMessage(
1564                     "label.successfully_saved_to_file_in_format",
1565                     new Object[]
1566                     { fileName, format.getName() }));
1567             lastSaveSuccessful = true;
1568           } catch (Exception ex)
1569           {
1570             lastSaveSuccessful = false;
1571             ex.printStackTrace();
1572           }
1573
1574           if (doBackup)
1575           {
1576             backupfiles.setWriteSuccess(lastSaveSuccessful);
1577             // do the backup file roll and rename the temp file to actual file
1578             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1579           }
1580         }
1581       }
1582     };
1583
1584     /*
1585      * show dialog with export options if applicable; else just do it
1586      */
1587     if (AlignExportOptions.isNeeded(viewport, format))
1588     {
1589       AlignExportOptions choices = new AlignExportOptions(
1590               alignPanel.getAlignViewport(), format, options);
1591       choices.setResponseAction(0, outputAction);
1592       choices.setResponseAction(1, cancelAction);
1593       choices.showDialog();
1594     }
1595     else
1596     {
1597       outputAction.run();
1598     }
1599   }
1600
1601   /**
1602    * Outputs the alignment to textbox in the requested format, if necessary
1603    * first prompting the user for whether to include hidden regions or
1604    * non-sequence data
1605    *
1606    * @param fileFormatName
1607    */
1608   @Override
1609   protected void outputText_actionPerformed(String fileFormatName)
1610   {
1611     FileFormatI fileFormat = FileFormats.getInstance()
1612             .forName(fileFormatName);
1613     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1614     Runnable outputAction = new Runnable()
1615     {
1616       @Override
1617       public void run()
1618       {
1619         // todo defer this to inside formatSequences (or later)
1620         AlignmentExportData exportData = viewport
1621                 .getAlignExportData(options);
1622         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1623         cap.setForInput(null);
1624         try
1625         {
1626           FileFormatI format = fileFormat;
1627           cap.setText(new FormatAdapter(alignPanel, options)
1628                   .formatSequences(format, exportData.getAlignment(),
1629                           exportData.getOmitHidden(),
1630                           exportData.getStartEndPostions(),
1631                           viewport.getAlignment().getHiddenColumns()));
1632           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1633                   "label.alignment_output_command", new Object[]
1634                   { fileFormat.getName() }), 600, 500);
1635         } catch (OutOfMemoryError oom)
1636         {
1637           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1638                   oom);
1639           cap.dispose();
1640         }
1641       }
1642     };
1643
1644     /*
1645      * show dialog with export options if applicable; else just do it
1646      */
1647     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1648     {
1649       AlignExportOptions choices = new AlignExportOptions(
1650               alignPanel.getAlignViewport(), fileFormat, options);
1651       choices.setResponseAction(0, outputAction);
1652       choices.showDialog();
1653     }
1654     else
1655     {
1656       outputAction.run();
1657     }
1658   }
1659
1660   /**
1661    * DOCUMENT ME!
1662    *
1663    * @param e
1664    *          DOCUMENT ME!
1665    */
1666   @Override
1667   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1668   {
1669     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1670     htmlSVG.exportHTML(null);
1671   }
1672
1673   @Override
1674   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1675   {
1676     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1677     bjs.exportHTML(null);
1678   }
1679
1680   public void createImageMap(File file, String image)
1681   {
1682     alignPanel.makePNGImageMap(file, image);
1683   }
1684
1685   /**
1686    * Creates a PNG image of the alignment and writes it to the given file. If
1687    * the file is null, the user is prompted to choose a file.
1688    *
1689    * @param f
1690    */
1691   @Override
1692   public void createPNG(File f)
1693   {
1694     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1695   }
1696
1697   /**
1698    * Creates an EPS image of the alignment and writes it to the given file. If
1699    * the file is null, the user is prompted to choose a file.
1700    *
1701    * @param f
1702    */
1703   @Override
1704   public void createEPS(File f)
1705   {
1706     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1707   }
1708
1709   /**
1710    * Creates an SVG image of the alignment and writes it to the given file. If
1711    * the file is null, the user is prompted to choose a file.
1712    *
1713    * @param f
1714    */
1715   @Override
1716   public void createSVG(File f)
1717   {
1718     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1719   }
1720
1721   @Override
1722   public void pageSetup_actionPerformed(ActionEvent e)
1723   {
1724     PrinterJob printJob = PrinterJob.getPrinterJob();
1725     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1726   }
1727
1728   /**
1729    * DOCUMENT ME!
1730    *
1731    * @param e
1732    *          DOCUMENT ME!
1733    */
1734   @Override
1735   public void printMenuItem_actionPerformed(ActionEvent e)
1736   {
1737     // Putting in a thread avoids Swing painting problems
1738     PrintThread thread = new PrintThread(alignPanel);
1739     thread.start();
1740   }
1741
1742   @Override
1743   public void exportFeatures_actionPerformed(ActionEvent e)
1744   {
1745     new AnnotationExporter(alignPanel).exportFeatures();
1746   }
1747
1748   @Override
1749   public void exportAnnotations_actionPerformed(ActionEvent e)
1750   {
1751     new AnnotationExporter(alignPanel).exportAnnotations();
1752   }
1753
1754   @Override
1755   public void associatedData_actionPerformed(ActionEvent e)
1756           throws IOException, InterruptedException
1757   {
1758     final JalviewFileChooser chooser = new JalviewFileChooser(
1759             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1760     chooser.setFileView(new JalviewFileView());
1761     String tooltip = MessageManager
1762             .getString("label.load_jalview_annotations");
1763     chooser.setDialogTitle(tooltip);
1764     chooser.setToolTipText(tooltip);
1765     chooser.setResponseHandler(0, new Runnable()
1766     {
1767       @Override
1768       public void run()
1769       {
1770         String choice = chooser.getSelectedFile().getPath();
1771         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1772         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1773       }
1774     });
1775
1776     chooser.showOpenDialog(this);
1777   }
1778
1779   /**
1780    * Close the current view or all views in the alignment frame. If the frame
1781    * only contains one view then the alignment will be removed from memory.
1782    *
1783    * @param closeAllTabs
1784    */
1785   @Override
1786   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1787   {
1788     if (alignPanels != null && alignPanels.size() < 2)
1789     {
1790       closeAllTabs = true;
1791     }
1792
1793     try
1794     {
1795       if (alignPanels != null)
1796       {
1797         if (closeAllTabs)
1798         {
1799           if (this.isClosed())
1800           {
1801             // really close all the windows - otherwise wait till
1802             // setClosed(true) is called
1803             for (int i = 0; i < alignPanels.size(); i++)
1804             {
1805               AlignmentPanel ap = alignPanels.get(i);
1806               ap.closePanel();
1807             }
1808           }
1809         }
1810         else
1811         {
1812           closeView(alignPanel);
1813         }
1814       }
1815       if (closeAllTabs)
1816       {
1817         if (featureSettings != null && featureSettings.isOpen())
1818         {
1819           featureSettings.close();
1820           featureSettings = null;
1821         }
1822         /*
1823          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1824          * be called recursively, with the frame now in 'closed' state
1825          */
1826         this.setClosed(true);
1827       }
1828     } catch (Exception ex)
1829     {
1830       ex.printStackTrace();
1831     }
1832   }
1833
1834   /**
1835    * Close the specified panel and close up tabs appropriately.
1836    *
1837    * @param panelToClose
1838    */
1839   public void closeView(AlignmentPanel panelToClose)
1840   {
1841     int index = tabbedPane.getSelectedIndex();
1842     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1843     alignPanels.remove(panelToClose);
1844     panelToClose.closePanel();
1845     panelToClose = null;
1846
1847     tabbedPane.removeTabAt(closedindex);
1848     tabbedPane.validate();
1849
1850     if (index > closedindex || index == tabbedPane.getTabCount())
1851     {
1852       // modify currently selected tab index if necessary.
1853       index--;
1854     }
1855
1856     this.tabSelectionChanged(index);
1857   }
1858
1859   /**
1860    * DOCUMENT ME!
1861    */
1862   void updateEditMenuBar()
1863   {
1864
1865     if (viewport.getHistoryList().size() > 0)
1866     {
1867       undoMenuItem.setEnabled(true);
1868       CommandI command = viewport.getHistoryList().peek();
1869       undoMenuItem.setText(MessageManager
1870               .formatMessage("label.undo_command", new Object[]
1871               { command.getDescription() }));
1872     }
1873     else
1874     {
1875       undoMenuItem.setEnabled(false);
1876       undoMenuItem.setText(MessageManager.getString("action.undo"));
1877     }
1878
1879     if (viewport.getRedoList().size() > 0)
1880     {
1881       redoMenuItem.setEnabled(true);
1882
1883       CommandI command = viewport.getRedoList().peek();
1884       redoMenuItem.setText(MessageManager
1885               .formatMessage("label.redo_command", new Object[]
1886               { command.getDescription() }));
1887     }
1888     else
1889     {
1890       redoMenuItem.setEnabled(false);
1891       redoMenuItem.setText(MessageManager.getString("action.redo"));
1892     }
1893   }
1894
1895   @Override
1896   public void addHistoryItem(CommandI command)
1897   {
1898     if (command.getSize() > 0)
1899     {
1900       viewport.addToHistoryList(command);
1901       viewport.clearRedoList();
1902       updateEditMenuBar();
1903       viewport.updateHiddenColumns();
1904       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1905       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1906       // viewport.getColumnSelection()
1907       // .getHiddenColumns().size() > 0);
1908     }
1909   }
1910
1911   /**
1912    *
1913    * @return alignment objects for all views
1914    */
1915   AlignmentI[] getViewAlignments()
1916   {
1917     if (alignPanels != null)
1918     {
1919       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1920       int i = 0;
1921       for (AlignmentPanel ap : alignPanels)
1922       {
1923         als[i++] = ap.av.getAlignment();
1924       }
1925       return als;
1926     }
1927     if (viewport != null)
1928     {
1929       return new AlignmentI[] { viewport.getAlignment() };
1930     }
1931     return null;
1932   }
1933
1934   /**
1935    * DOCUMENT ME!
1936    *
1937    * @param e
1938    *          DOCUMENT ME!
1939    */
1940   @Override
1941   protected void undoMenuItem_actionPerformed(ActionEvent e)
1942   {
1943     if (viewport.getHistoryList().isEmpty())
1944     {
1945       return;
1946     }
1947     CommandI command = viewport.getHistoryList().pop();
1948     viewport.addToRedoList(command);
1949     command.undoCommand(getViewAlignments());
1950
1951     AlignmentViewport originalSource = getOriginatingSource(command);
1952     updateEditMenuBar();
1953
1954     if (originalSource != null)
1955     {
1956       if (originalSource != viewport)
1957       {
1958         Cache.log.warn(
1959                 "Implementation worry: mismatch of viewport origin for undo");
1960       }
1961       originalSource.updateHiddenColumns();
1962       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1963       // null
1964       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1965       // viewport.getColumnSelection()
1966       // .getHiddenColumns().size() > 0);
1967       originalSource.firePropertyChange("alignment", null,
1968               originalSource.getAlignment().getSequences());
1969     }
1970   }
1971
1972   /**
1973    * DOCUMENT ME!
1974    *
1975    * @param e
1976    *          DOCUMENT ME!
1977    */
1978   @Override
1979   protected void redoMenuItem_actionPerformed(ActionEvent e)
1980   {
1981     if (viewport.getRedoList().size() < 1)
1982     {
1983       return;
1984     }
1985
1986     CommandI command = viewport.getRedoList().pop();
1987     viewport.addToHistoryList(command);
1988     command.doCommand(getViewAlignments());
1989
1990     AlignmentViewport originalSource = getOriginatingSource(command);
1991     updateEditMenuBar();
1992
1993     if (originalSource != null)
1994     {
1995
1996       if (originalSource != viewport)
1997       {
1998         Cache.log.warn(
1999                 "Implementation worry: mismatch of viewport origin for redo");
2000       }
2001       originalSource.updateHiddenColumns();
2002       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
2003       // null
2004       // && viewport.getColumnSelection().getHiddenColumns() != null &&
2005       // viewport.getColumnSelection()
2006       // .getHiddenColumns().size() > 0);
2007       originalSource.firePropertyChange("alignment", null,
2008               originalSource.getAlignment().getSequences());
2009     }
2010   }
2011
2012   AlignmentViewport getOriginatingSource(CommandI command)
2013   {
2014     AlignmentViewport originalSource = null;
2015     // For sequence removal and addition, we need to fire
2016     // the property change event FROM the viewport where the
2017     // original alignment was altered
2018     AlignmentI al = null;
2019     if (command instanceof EditCommand)
2020     {
2021       EditCommand editCommand = (EditCommand) command;
2022       al = editCommand.getAlignment();
2023       List<Component> comps = PaintRefresher.components
2024               .get(viewport.getSequenceSetId());
2025
2026       for (Component comp : comps)
2027       {
2028         if (comp instanceof AlignmentPanel)
2029         {
2030           if (al == ((AlignmentPanel) comp).av.getAlignment())
2031           {
2032             originalSource = ((AlignmentPanel) comp).av;
2033             break;
2034           }
2035         }
2036       }
2037     }
2038
2039     if (originalSource == null)
2040     {
2041       // The original view is closed, we must validate
2042       // the current view against the closed view first
2043       if (al != null)
2044       {
2045         PaintRefresher.validateSequences(al, viewport.getAlignment());
2046       }
2047
2048       originalSource = viewport;
2049     }
2050
2051     return originalSource;
2052   }
2053
2054   /**
2055    * DOCUMENT ME!
2056    *
2057    * @param up
2058    *          DOCUMENT ME!
2059    */
2060   public void moveSelectedSequences(boolean up)
2061   {
2062     SequenceGroup sg = viewport.getSelectionGroup();
2063
2064     if (sg == null)
2065     {
2066       return;
2067     }
2068     viewport.getAlignment().moveSelectedSequencesByOne(sg,
2069             viewport.getHiddenRepSequences(), up);
2070     alignPanel.paintAlignment(true, false);
2071   }
2072
2073   synchronized void slideSequences(boolean right, int size)
2074   {
2075     List<SequenceI> sg = new ArrayList<>();
2076     if (viewport.cursorMode)
2077     {
2078       sg.add(viewport.getAlignment()
2079               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
2080     }
2081     else if (viewport.getSelectionGroup() != null
2082             && viewport.getSelectionGroup().getSize() != viewport
2083                     .getAlignment().getHeight())
2084     {
2085       sg = viewport.getSelectionGroup()
2086               .getSequences(viewport.getHiddenRepSequences());
2087     }
2088
2089     if (sg.size() < 1)
2090     {
2091       return;
2092     }
2093
2094     List<SequenceI> invertGroup = new ArrayList<>();
2095
2096     for (SequenceI seq : viewport.getAlignment().getSequences())
2097     {
2098       if (!sg.contains(seq))
2099       {
2100         invertGroup.add(seq);
2101       }
2102     }
2103
2104     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
2105
2106     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
2107     for (int i = 0; i < invertGroup.size(); i++)
2108     {
2109       seqs2[i] = invertGroup.get(i);
2110     }
2111
2112     SlideSequencesCommand ssc;
2113     if (right)
2114     {
2115       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2116               viewport.getGapCharacter());
2117     }
2118     else
2119     {
2120       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2121               viewport.getGapCharacter());
2122     }
2123
2124     int groupAdjustment = 0;
2125     if (ssc.getGapsInsertedBegin() && right)
2126     {
2127       if (viewport.cursorMode)
2128       {
2129         alignPanel.getSeqPanel().moveCursor(size, 0);
2130       }
2131       else
2132       {
2133         groupAdjustment = size;
2134       }
2135     }
2136     else if (!ssc.getGapsInsertedBegin() && !right)
2137     {
2138       if (viewport.cursorMode)
2139       {
2140         alignPanel.getSeqPanel().moveCursor(-size, 0);
2141       }
2142       else
2143       {
2144         groupAdjustment = -size;
2145       }
2146     }
2147
2148     if (groupAdjustment != 0)
2149     {
2150       viewport.getSelectionGroup().setStartRes(
2151               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2152       viewport.getSelectionGroup().setEndRes(
2153               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2154     }
2155
2156     /*
2157      * just extend the last slide command if compatible; but not if in
2158      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2159      */
2160     boolean appendHistoryItem = false;
2161     Deque<CommandI> historyList = viewport.getHistoryList();
2162     boolean inSplitFrame = getSplitViewContainer() != null;
2163     if (!inSplitFrame && historyList != null && historyList.size() > 0
2164             && historyList.peek() instanceof SlideSequencesCommand)
2165     {
2166       appendHistoryItem = ssc.appendSlideCommand(
2167               (SlideSequencesCommand) historyList.peek());
2168     }
2169
2170     if (!appendHistoryItem)
2171     {
2172       addHistoryItem(ssc);
2173     }
2174
2175     repaint();
2176   }
2177
2178   /**
2179    * DOCUMENT ME!
2180    *
2181    * @param e
2182    *          DOCUMENT ME!
2183    */
2184   @Override
2185   protected void copy_actionPerformed()
2186   {
2187     if (viewport.getSelectionGroup() == null)
2188     {
2189       return;
2190     }
2191     // TODO: preserve the ordering of displayed alignment annotation in any
2192     // internal paste (particularly sequence associated annotation)
2193     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2194     String[] omitHidden = null;
2195
2196     if (viewport.hasHiddenColumns())
2197     {
2198       omitHidden = viewport.getViewAsString(true);
2199     }
2200
2201     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2202             seqs, omitHidden, null);
2203
2204     StringSelection ss = new StringSelection(output);
2205
2206     try
2207     {
2208       jalview.gui.Desktop.internalCopy = true;
2209       // Its really worth setting the clipboard contents
2210       // to empty before setting the large StringSelection!!
2211       Toolkit.getDefaultToolkit().getSystemClipboard()
2212               .setContents(new StringSelection(""), null);
2213
2214       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2215               Desktop.instance);
2216     } catch (OutOfMemoryError er)
2217     {
2218       new OOMWarning("copying region", er);
2219       return;
2220     }
2221
2222     HiddenColumns hiddenColumns = null;
2223     if (viewport.hasHiddenColumns())
2224     {
2225       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2226       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2227
2228       // create new HiddenColumns object with copy of hidden regions
2229       // between startRes and endRes, offset by startRes
2230       hiddenColumns = new HiddenColumns(
2231               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2232               hiddenCutoff, hiddenOffset);
2233     }
2234
2235     Desktop.jalviewClipboard = new Object[] { seqs,
2236         viewport.getAlignment().getDataset(), hiddenColumns };
2237     setStatus(MessageManager.formatMessage(
2238             "label.copied_sequences_to_clipboard", new Object[]
2239             { Integer.valueOf(seqs.length).toString() }));
2240   }
2241
2242   /**
2243    * DOCUMENT ME!
2244    *
2245    * @param e
2246    *          DOCUMENT ME!
2247    * @throws InterruptedException
2248    * @throws IOException
2249    */
2250   @Override
2251   protected void pasteNew_actionPerformed(ActionEvent e)
2252           throws IOException, InterruptedException
2253   {
2254     paste(true);
2255   }
2256
2257   /**
2258    * DOCUMENT ME!
2259    *
2260    * @param e
2261    *          DOCUMENT ME!
2262    * @throws InterruptedException
2263    * @throws IOException
2264    */
2265   @Override
2266   protected void pasteThis_actionPerformed(ActionEvent e)
2267           throws IOException, InterruptedException
2268   {
2269     paste(false);
2270   }
2271
2272   /**
2273    * Paste contents of Jalview clipboard
2274    *
2275    * @param newAlignment
2276    *          true to paste to a new alignment, otherwise add to this.
2277    * @throws InterruptedException
2278    * @throws IOException
2279    */
2280   void paste(boolean newAlignment) throws IOException, InterruptedException
2281   {
2282     boolean externalPaste = true;
2283     try
2284     {
2285       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2286       Transferable contents = c.getContents(this);
2287
2288       if (contents == null)
2289       {
2290         return;
2291       }
2292
2293       String str;
2294       FileFormatI format;
2295       try
2296       {
2297         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2298         if (str.length() < 1)
2299         {
2300           return;
2301         }
2302
2303         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2304
2305       } catch (OutOfMemoryError er)
2306       {
2307         new OOMWarning("Out of memory pasting sequences!!", er);
2308         return;
2309       }
2310
2311       SequenceI[] sequences;
2312       boolean annotationAdded = false;
2313       AlignmentI alignment = null;
2314
2315       if (Desktop.jalviewClipboard != null)
2316       {
2317         // The clipboard was filled from within Jalview, we must use the
2318         // sequences
2319         // And dataset from the copied alignment
2320         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2321         // be doubly sure that we create *new* sequence objects.
2322         sequences = new SequenceI[newseq.length];
2323         for (int i = 0; i < newseq.length; i++)
2324         {
2325           sequences[i] = new Sequence(newseq[i]);
2326         }
2327         alignment = new Alignment(sequences);
2328         externalPaste = false;
2329       }
2330       else
2331       {
2332         // parse the clipboard as an alignment.
2333         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2334                 format);
2335         sequences = alignment.getSequencesArray();
2336       }
2337
2338       int alwidth = 0;
2339       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2340       int fgroup = -1;
2341
2342       if (newAlignment)
2343       {
2344
2345         if (Desktop.jalviewClipboard != null)
2346         {
2347           // dataset is inherited
2348           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2349         }
2350         else
2351         {
2352           // new dataset is constructed
2353           alignment.setDataset(null);
2354         }
2355         alwidth = alignment.getWidth() + 1;
2356       }
2357       else
2358       {
2359         AlignmentI pastedal = alignment; // preserve pasted alignment object
2360         // Add pasted sequences and dataset into existing alignment.
2361         alignment = viewport.getAlignment();
2362         alwidth = alignment.getWidth() + 1;
2363         // decide if we need to import sequences from an existing dataset
2364         boolean importDs = Desktop.jalviewClipboard != null
2365                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2366         // importDs==true instructs us to copy over new dataset sequences from
2367         // an existing alignment
2368         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2369                                                                       // create
2370         // minimum dataset set
2371
2372         for (int i = 0; i < sequences.length; i++)
2373         {
2374           if (importDs)
2375           {
2376             newDs.addElement(null);
2377           }
2378           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2379           // paste
2380           if (importDs && ds != null)
2381           {
2382             if (!newDs.contains(ds))
2383             {
2384               newDs.setElementAt(ds, i);
2385               ds = new Sequence(ds);
2386               // update with new dataset sequence
2387               sequences[i].setDatasetSequence(ds);
2388             }
2389             else
2390             {
2391               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2392             }
2393           }
2394           else
2395           {
2396             // copy and derive new dataset sequence
2397             sequences[i] = sequences[i].deriveSequence();
2398             alignment.getDataset()
2399                     .addSequence(sequences[i].getDatasetSequence());
2400             // TODO: avoid creation of duplicate dataset sequences with a
2401             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2402           }
2403           alignment.addSequence(sequences[i]); // merges dataset
2404         }
2405         if (newDs != null)
2406         {
2407           newDs.clear(); // tidy up
2408         }
2409         if (alignment.getAlignmentAnnotation() != null)
2410         {
2411           for (AlignmentAnnotation alan : alignment
2412                   .getAlignmentAnnotation())
2413           {
2414             if (alan.graphGroup > fgroup)
2415             {
2416               fgroup = alan.graphGroup;
2417             }
2418           }
2419         }
2420         if (pastedal.getAlignmentAnnotation() != null)
2421         {
2422           // Add any annotation attached to alignment.
2423           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2424           for (int i = 0; i < alann.length; i++)
2425           {
2426             annotationAdded = true;
2427             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2428             {
2429               AlignmentAnnotation newann = new AlignmentAnnotation(
2430                       alann[i]);
2431               if (newann.graphGroup > -1)
2432               {
2433                 if (newGraphGroups.size() <= newann.graphGroup
2434                         || newGraphGroups.get(newann.graphGroup) == null)
2435                 {
2436                   for (int q = newGraphGroups
2437                           .size(); q <= newann.graphGroup; q++)
2438                   {
2439                     newGraphGroups.add(q, null);
2440                   }
2441                   newGraphGroups.set(newann.graphGroup,
2442                           Integer.valueOf(++fgroup));
2443                 }
2444                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2445                         .intValue();
2446               }
2447
2448               newann.padAnnotation(alwidth);
2449               alignment.addAnnotation(newann);
2450             }
2451           }
2452         }
2453       }
2454       if (!newAlignment)
2455       {
2456         // /////
2457         // ADD HISTORY ITEM
2458         //
2459         addHistoryItem(new EditCommand(
2460                 MessageManager.getString("label.add_sequences"),
2461                 Action.PASTE, sequences, 0, alignment.getWidth(),
2462                 alignment));
2463       }
2464       // Add any annotations attached to sequences
2465       for (int i = 0; i < sequences.length; i++)
2466       {
2467         if (sequences[i].getAnnotation() != null)
2468         {
2469           AlignmentAnnotation newann;
2470           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2471           {
2472             annotationAdded = true;
2473             newann = sequences[i].getAnnotation()[a];
2474             newann.adjustForAlignment();
2475             newann.padAnnotation(alwidth);
2476             if (newann.graphGroup > -1)
2477             {
2478               if (newann.graphGroup > -1)
2479               {
2480                 if (newGraphGroups.size() <= newann.graphGroup
2481                         || newGraphGroups.get(newann.graphGroup) == null)
2482                 {
2483                   for (int q = newGraphGroups
2484                           .size(); q <= newann.graphGroup; q++)
2485                   {
2486                     newGraphGroups.add(q, null);
2487                   }
2488                   newGraphGroups.set(newann.graphGroup,
2489                           Integer.valueOf(++fgroup));
2490                 }
2491                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2492                         .intValue();
2493               }
2494             }
2495             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2496             // was
2497             // duplicated
2498             // earlier
2499             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2500                     a);
2501           }
2502         }
2503       }
2504       if (!newAlignment)
2505       {
2506
2507         // propagate alignment changed.
2508         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2509         if (annotationAdded)
2510         {
2511           // Duplicate sequence annotation in all views.
2512           AlignmentI[] alview = this.getViewAlignments();
2513           for (int i = 0; i < sequences.length; i++)
2514           {
2515             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2516             if (sann == null)
2517             {
2518               continue;
2519             }
2520             for (int avnum = 0; avnum < alview.length; avnum++)
2521             {
2522               if (alview[avnum] != alignment)
2523               {
2524                 // duplicate in a view other than the one with input focus
2525                 int avwidth = alview[avnum].getWidth() + 1;
2526                 // this relies on sann being preserved after we
2527                 // modify the sequence's annotation array for each duplication
2528                 for (int a = 0; a < sann.length; a++)
2529                 {
2530                   AlignmentAnnotation newann = new AlignmentAnnotation(
2531                           sann[a]);
2532                   sequences[i].addAlignmentAnnotation(newann);
2533                   newann.padAnnotation(avwidth);
2534                   alview[avnum].addAnnotation(newann); // annotation was
2535                   // duplicated earlier
2536                   // TODO JAL-1145 graphGroups are not updated for sequence
2537                   // annotation added to several views. This may cause
2538                   // strangeness
2539                   alview[avnum].setAnnotationIndex(newann, a);
2540                 }
2541               }
2542             }
2543           }
2544           buildSortByAnnotationScoresMenu();
2545         }
2546         viewport.firePropertyChange("alignment", null,
2547                 alignment.getSequences());
2548         if (alignPanels != null)
2549         {
2550           for (AlignmentPanel ap : alignPanels)
2551           {
2552             ap.validateAnnotationDimensions(false);
2553           }
2554         }
2555         else
2556         {
2557           alignPanel.validateAnnotationDimensions(false);
2558         }
2559
2560       }
2561       else
2562       {
2563         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2564                 DEFAULT_HEIGHT);
2565         String newtitle = new String("Copied sequences");
2566
2567         if (Desktop.jalviewClipboard != null
2568                 && Desktop.jalviewClipboard[2] != null)
2569         {
2570           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2571           af.viewport.setHiddenColumns(hc);
2572         }
2573
2574         // >>>This is a fix for the moment, until a better solution is
2575         // found!!<<<
2576         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2577                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2578                         .getFeatureRenderer());
2579
2580         // TODO: maintain provenance of an alignment, rather than just make the
2581         // title a concatenation of operations.
2582         if (!externalPaste)
2583         {
2584           if (title.startsWith("Copied sequences"))
2585           {
2586             newtitle = title;
2587           }
2588           else
2589           {
2590             newtitle = newtitle.concat("- from " + title);
2591           }
2592         }
2593         else
2594         {
2595           newtitle = new String("Pasted sequences");
2596         }
2597
2598         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2599                 DEFAULT_HEIGHT);
2600
2601       }
2602
2603     } catch (Exception ex)
2604     {
2605       ex.printStackTrace();
2606       System.out.println("Exception whilst pasting: " + ex);
2607       // could be anything being pasted in here
2608     }
2609   }
2610
2611   @Override
2612   protected void expand_newalign(ActionEvent e)
2613   {
2614     try
2615     {
2616       AlignmentI alignment = AlignmentUtils
2617               .expandContext(getViewport().getAlignment(), -1);
2618       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2619               DEFAULT_HEIGHT);
2620       String newtitle = new String("Flanking alignment");
2621
2622       if (Desktop.jalviewClipboard != null
2623               && Desktop.jalviewClipboard[2] != null)
2624       {
2625         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2626         af.viewport.setHiddenColumns(hc);
2627       }
2628
2629       // >>>This is a fix for the moment, until a better solution is
2630       // found!!<<<
2631       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2632               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2633                       .getFeatureRenderer());
2634
2635       // TODO: maintain provenance of an alignment, rather than just make the
2636       // title a concatenation of operations.
2637       {
2638         if (title.startsWith("Copied sequences"))
2639         {
2640           newtitle = title;
2641         }
2642         else
2643         {
2644           newtitle = newtitle.concat("- from " + title);
2645         }
2646       }
2647
2648       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2649
2650     } catch (Exception ex)
2651     {
2652       ex.printStackTrace();
2653       System.out.println("Exception whilst pasting: " + ex);
2654       // could be anything being pasted in here
2655     } catch (OutOfMemoryError oom)
2656     {
2657       new OOMWarning("Viewing flanking region of alignment", oom);
2658     }
2659   }
2660
2661   /**
2662    * Action Cut (delete and copy) the selected region
2663    */
2664   @Override
2665   protected void cut_actionPerformed()
2666   {
2667     copy_actionPerformed();
2668     delete_actionPerformed();
2669   }
2670
2671   /**
2672    * Performs menu option to Delete the currently selected region
2673    */
2674   @Override
2675   protected void delete_actionPerformed()
2676   {
2677
2678     SequenceGroup sg = viewport.getSelectionGroup();
2679     if (sg == null)
2680     {
2681       return;
2682     }
2683
2684     Runnable okAction = new Runnable()
2685     {
2686       @Override
2687       public void run()
2688       {
2689         SequenceI[] cut = sg.getSequences()
2690                 .toArray(new SequenceI[sg.getSize()]);
2691
2692         addHistoryItem(new EditCommand(
2693                 MessageManager.getString("label.cut_sequences"), Action.CUT,
2694                 cut, sg.getStartRes(),
2695                 sg.getEndRes() - sg.getStartRes() + 1,
2696                 viewport.getAlignment()));
2697
2698         viewport.setSelectionGroup(null);
2699         viewport.sendSelection();
2700         viewport.getAlignment().deleteGroup(sg);
2701
2702         viewport.firePropertyChange("alignment", null,
2703                 viewport.getAlignment().getSequences());
2704         if (viewport.getAlignment().getHeight() < 1)
2705         {
2706           try
2707           {
2708             AlignFrame.this.setClosed(true);
2709           } catch (Exception ex)
2710           {
2711           }
2712         }
2713       }
2714     };
2715
2716     /*
2717      * If the cut affects all sequences, prompt for confirmation
2718      */
2719     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2720             .getHeight();
2721     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2722             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2723     if (wholeHeight && wholeWidth)
2724     {
2725       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2726       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2727       Object[] options = new Object[] {
2728           MessageManager.getString("action.ok"),
2729           MessageManager.getString("action.cancel") };
2730       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2731               MessageManager.getString("label.delete_all"),
2732               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2733               options, options[0]);
2734     }
2735     else
2736     {
2737       okAction.run();
2738     }
2739   }
2740
2741   /**
2742    * DOCUMENT ME!
2743    *
2744    * @param e
2745    *          DOCUMENT ME!
2746    */
2747   @Override
2748   protected void deleteGroups_actionPerformed(ActionEvent e)
2749   {
2750     if (avc.deleteGroups())
2751     {
2752       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2753       alignPanel.updateAnnotation();
2754       alignPanel.paintAlignment(true, true);
2755     }
2756   }
2757
2758   /**
2759    * DOCUMENT ME!
2760    *
2761    * @param e
2762    *          DOCUMENT ME!
2763    */
2764   @Override
2765   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2766   {
2767     SequenceGroup sg = new SequenceGroup(
2768             viewport.getAlignment().getSequences());
2769
2770     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2771     viewport.setSelectionGroup(sg);
2772     viewport.isSelectionGroupChanged(true);
2773     viewport.sendSelection();
2774     // JAL-2034 - should delegate to
2775     // alignPanel to decide if overview needs
2776     // updating.
2777     alignPanel.paintAlignment(false, false);
2778     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2779   }
2780
2781   /**
2782    * DOCUMENT ME!
2783    *
2784    * @param e
2785    *          DOCUMENT ME!
2786    */
2787   @Override
2788   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2789   {
2790     if (viewport.cursorMode)
2791     {
2792       alignPanel.getSeqPanel().keyboardNo1 = null;
2793       alignPanel.getSeqPanel().keyboardNo2 = null;
2794     }
2795     viewport.setSelectionGroup(null);
2796     viewport.getColumnSelection().clear();
2797     viewport.setSelectionGroup(null);
2798     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2799     // JAL-2034 - should delegate to
2800     // alignPanel to decide if overview needs
2801     // updating.
2802     alignPanel.paintAlignment(false, false);
2803     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2804     viewport.sendSelection();
2805   }
2806
2807   /**
2808    * DOCUMENT ME!
2809    *
2810    * @param e
2811    *          DOCUMENT ME!
2812    */
2813   @Override
2814   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2815   {
2816     SequenceGroup sg = viewport.getSelectionGroup();
2817
2818     if (sg == null)
2819     {
2820       selectAllSequenceMenuItem_actionPerformed(null);
2821
2822       return;
2823     }
2824
2825     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2826     {
2827       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2828     }
2829     // JAL-2034 - should delegate to
2830     // alignPanel to decide if overview needs
2831     // updating.
2832
2833     alignPanel.paintAlignment(true, false);
2834     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2835     viewport.sendSelection();
2836   }
2837
2838   @Override
2839   public void invertColSel_actionPerformed(ActionEvent e)
2840   {
2841     viewport.invertColumnSelection();
2842     alignPanel.paintAlignment(true, false);
2843     viewport.sendSelection();
2844   }
2845
2846   /**
2847    * DOCUMENT ME!
2848    *
2849    * @param e
2850    *          DOCUMENT ME!
2851    */
2852   @Override
2853   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2854   {
2855     trimAlignment(true);
2856   }
2857
2858   /**
2859    * DOCUMENT ME!
2860    *
2861    * @param e
2862    *          DOCUMENT ME!
2863    */
2864   @Override
2865   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2866   {
2867     trimAlignment(false);
2868   }
2869
2870   void trimAlignment(boolean trimLeft)
2871   {
2872     ColumnSelection colSel = viewport.getColumnSelection();
2873     int column;
2874
2875     if (!colSel.isEmpty())
2876     {
2877       if (trimLeft)
2878       {
2879         column = colSel.getMin();
2880       }
2881       else
2882       {
2883         column = colSel.getMax();
2884       }
2885
2886       SequenceI[] seqs;
2887       if (viewport.getSelectionGroup() != null)
2888       {
2889         seqs = viewport.getSelectionGroup()
2890                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2891       }
2892       else
2893       {
2894         seqs = viewport.getAlignment().getSequencesArray();
2895       }
2896
2897       TrimRegionCommand trimRegion;
2898       if (trimLeft)
2899       {
2900         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2901                 column, viewport.getAlignment());
2902         viewport.getRanges().setStartRes(0);
2903       }
2904       else
2905       {
2906         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2907                 column, viewport.getAlignment());
2908       }
2909
2910       setStatus(MessageManager
2911               .formatMessage("label.removed_columns", new String[]
2912               { Integer.valueOf(trimRegion.getSize()).toString() }));
2913
2914       addHistoryItem(trimRegion);
2915
2916       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2917       {
2918         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2919                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2920         {
2921           viewport.getAlignment().deleteGroup(sg);
2922         }
2923       }
2924
2925       viewport.firePropertyChange("alignment", null,
2926               viewport.getAlignment().getSequences());
2927     }
2928   }
2929
2930   /**
2931    * DOCUMENT ME!
2932    *
2933    * @param e
2934    *          DOCUMENT ME!
2935    */
2936   @Override
2937   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2938   {
2939     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2940
2941     SequenceI[] seqs;
2942     if (viewport.getSelectionGroup() != null)
2943     {
2944       seqs = viewport.getSelectionGroup()
2945               .getSequencesAsArray(viewport.getHiddenRepSequences());
2946       start = viewport.getSelectionGroup().getStartRes();
2947       end = viewport.getSelectionGroup().getEndRes();
2948     }
2949     else
2950     {
2951       seqs = viewport.getAlignment().getSequencesArray();
2952     }
2953
2954     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2955             "Remove Gapped Columns", seqs, start, end,
2956             viewport.getAlignment());
2957
2958     addHistoryItem(removeGapCols);
2959
2960     setStatus(MessageManager
2961             .formatMessage("label.removed_empty_columns", new Object[]
2962             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2963
2964     // This is to maintain viewport position on first residue
2965     // of first sequence
2966     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2967     ViewportRanges ranges = viewport.getRanges();
2968     int startRes = seq.findPosition(ranges.getStartRes());
2969     // ShiftList shifts;
2970     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2971     // edit.alColumnChanges=shifts.getInverse();
2972     // if (viewport.hasHiddenColumns)
2973     // viewport.getColumnSelection().compensateForEdits(shifts);
2974     ranges.setStartRes(seq.findIndex(startRes) - 1);
2975     viewport.firePropertyChange("alignment", null,
2976             viewport.getAlignment().getSequences());
2977
2978   }
2979
2980   /**
2981    * DOCUMENT ME!
2982    *
2983    * @param e
2984    *          DOCUMENT ME!
2985    */
2986   @Override
2987   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2988   {
2989     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2990
2991     SequenceI[] seqs;
2992     if (viewport.getSelectionGroup() != null)
2993     {
2994       seqs = viewport.getSelectionGroup()
2995               .getSequencesAsArray(viewport.getHiddenRepSequences());
2996       start = viewport.getSelectionGroup().getStartRes();
2997       end = viewport.getSelectionGroup().getEndRes();
2998     }
2999     else
3000     {
3001       seqs = viewport.getAlignment().getSequencesArray();
3002     }
3003
3004     // This is to maintain viewport position on first residue
3005     // of first sequence
3006     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
3007     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
3008
3009     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
3010             viewport.getAlignment()));
3011
3012     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
3013
3014     viewport.firePropertyChange("alignment", null,
3015             viewport.getAlignment().getSequences());
3016
3017   }
3018
3019   /**
3020    * DOCUMENT ME!
3021    *
3022    * @param e
3023    *          DOCUMENT ME!
3024    */
3025   @Override
3026   public void padGapsMenuitem_actionPerformed(ActionEvent e)
3027   {
3028     viewport.setPadGaps(padGapsMenuitem.isSelected());
3029     viewport.firePropertyChange("alignment", null,
3030             viewport.getAlignment().getSequences());
3031   }
3032
3033   /**
3034    * DOCUMENT ME!
3035    *
3036    * @param e
3037    *          DOCUMENT ME!
3038    */
3039   @Override
3040   public void findMenuItem_actionPerformed(ActionEvent e)
3041   {
3042     new Finder();
3043   }
3044
3045   /**
3046    * Create a new view of the current alignment.
3047    */
3048   @Override
3049   public void newView_actionPerformed(ActionEvent e)
3050   {
3051     newView(null, true);
3052   }
3053
3054   /**
3055    * Creates and shows a new view of the current alignment.
3056    *
3057    * @param viewTitle
3058    *          title of newly created view; if null, one will be generated
3059    * @param copyAnnotation
3060    *          if true then duplicate all annnotation, groups and settings
3061    * @return new alignment panel, already displayed.
3062    */
3063   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
3064   {
3065     /*
3066      * Create a new AlignmentPanel (with its own, new Viewport)
3067      */
3068     AlignmentPanel newap = new jalview.project.Jalview2XML()
3069             .copyAlignPanel(alignPanel);
3070     if (!copyAnnotation)
3071     {
3072       /*
3073        * remove all groups and annotation except for the automatic stuff
3074        */
3075       newap.av.getAlignment().deleteAllGroups();
3076       newap.av.getAlignment().deleteAllAnnotations(false);
3077     }
3078
3079     newap.av.setGatherViewsHere(false);
3080
3081     if (viewport.getViewName() == null)
3082     {
3083       viewport.setViewName(MessageManager
3084               .getString("label.view_name_original"));
3085     }
3086
3087     /*
3088      * Views share the same edits undo and redo stacks
3089      */
3090     newap.av.setHistoryList(viewport.getHistoryList());
3091     newap.av.setRedoList(viewport.getRedoList());
3092
3093     /*
3094      * copy any visualisation settings that are not saved in the project
3095      */
3096     newap.av.setColourAppliesToAllGroups(
3097             viewport.getColourAppliesToAllGroups());
3098
3099     /*
3100      * Views share the same mappings; need to deregister any new mappings
3101      * created by copyAlignPanel, and register the new reference to the shared
3102      * mappings
3103      */
3104     newap.av.replaceMappings(viewport.getAlignment());
3105
3106     /*
3107      * start up cDNA consensus (if applicable) now mappings are in place
3108      */
3109     if (newap.av.initComplementConsensus())
3110     {
3111       newap.refresh(true); // adjust layout of annotations
3112     }
3113
3114     newap.av.setViewName(getNewViewName(viewTitle));
3115
3116     addAlignmentPanel(newap, true);
3117     newap.alignmentChanged();
3118
3119     if (alignPanels.size() == 2)
3120     {
3121       viewport.setGatherViewsHere(true);
3122     }
3123     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3124     return newap;
3125   }
3126
3127   /**
3128    * Make a new name for the view, ensuring it is unique within the current
3129    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3130    * these now use viewId. Unique view names are still desirable for usability.)
3131    *
3132    * @param viewTitle
3133    * @return
3134    */
3135   protected String getNewViewName(String viewTitle)
3136   {
3137     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3138     boolean addFirstIndex = false;
3139     if (viewTitle == null || viewTitle.trim().length() == 0)
3140     {
3141       viewTitle = MessageManager.getString("action.view");
3142       addFirstIndex = true;
3143     }
3144     else
3145     {
3146       index = 1;// we count from 1 if given a specific name
3147     }
3148     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3149
3150     List<Component> comps = PaintRefresher.components
3151             .get(viewport.getSequenceSetId());
3152
3153     List<String> existingNames = getExistingViewNames(comps);
3154
3155     while (existingNames.contains(newViewName))
3156     {
3157       newViewName = viewTitle + " " + (++index);
3158     }
3159     return newViewName;
3160   }
3161
3162   /**
3163    * Returns a list of distinct view names found in the given list of
3164    * components. View names are held on the viewport of an AlignmentPanel.
3165    *
3166    * @param comps
3167    * @return
3168    */
3169   protected List<String> getExistingViewNames(List<Component> comps)
3170   {
3171     List<String> existingNames = new ArrayList<>();
3172     for (Component comp : comps)
3173     {
3174       if (comp instanceof AlignmentPanel)
3175       {
3176         AlignmentPanel ap = (AlignmentPanel) comp;
3177         if (!existingNames.contains(ap.av.getViewName()))
3178         {
3179           existingNames.add(ap.av.getViewName());
3180         }
3181       }
3182     }
3183     return existingNames;
3184   }
3185
3186   /**
3187    * Explode tabbed views into separate windows.
3188    */
3189   @Override
3190   public void expandViews_actionPerformed(ActionEvent e)
3191   {
3192     Desktop.explodeViews(this);
3193   }
3194
3195   /**
3196    * Gather views in separate windows back into a tabbed presentation.
3197    */
3198   @Override
3199   public void gatherViews_actionPerformed(ActionEvent e)
3200   {
3201     Desktop.instance.gatherViews(this);
3202   }
3203
3204   /**
3205    * DOCUMENT ME!
3206    *
3207    * @param e
3208    *          DOCUMENT ME!
3209    */
3210   @Override
3211   public void font_actionPerformed(ActionEvent e)
3212   {
3213     new FontChooser(alignPanel);
3214   }
3215
3216   /**
3217    * DOCUMENT ME!
3218    *
3219    * @param e
3220    *          DOCUMENT ME!
3221    */
3222   @Override
3223   protected void seqLimit_actionPerformed(ActionEvent e)
3224   {
3225     viewport.setShowJVSuffix(seqLimits.isSelected());
3226
3227     alignPanel.getIdPanel().getIdCanvas()
3228             .setPreferredSize(alignPanel.calculateIdWidth());
3229     alignPanel.paintAlignment(true, false);
3230   }
3231
3232   @Override
3233   public void idRightAlign_actionPerformed(ActionEvent e)
3234   {
3235     viewport.setRightAlignIds(idRightAlign.isSelected());
3236     alignPanel.paintAlignment(false, false);
3237   }
3238
3239   @Override
3240   public void centreColumnLabels_actionPerformed(ActionEvent e)
3241   {
3242     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3243     alignPanel.paintAlignment(false, false);
3244   }
3245
3246   /*
3247    * (non-Javadoc)
3248    *
3249    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3250    */
3251   @Override
3252   protected void followHighlight_actionPerformed()
3253   {
3254     /*
3255      * Set the 'follow' flag on the Viewport (and scroll to position if now
3256      * true).
3257      */
3258     final boolean state = this.followHighlightMenuItem.getState();
3259     viewport.setFollowHighlight(state);
3260     if (state)
3261     {
3262       alignPanel.scrollToPosition(viewport.getSearchResults());
3263     }
3264   }
3265
3266   /**
3267    * DOCUMENT ME!
3268    *
3269    * @param e
3270    *          DOCUMENT ME!
3271    */
3272   @Override
3273   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3274   {
3275     viewport.setColourText(colourTextMenuItem.isSelected());
3276     alignPanel.paintAlignment(false, false);
3277   }
3278
3279   /**
3280    * DOCUMENT ME!
3281    *
3282    * @param e
3283    *          DOCUMENT ME!
3284    */
3285   @Override
3286   public void wrapMenuItem_actionPerformed(ActionEvent e)
3287   {
3288     scaleAbove.setVisible(wrapMenuItem.isSelected());
3289     scaleLeft.setVisible(wrapMenuItem.isSelected());
3290     scaleRight.setVisible(wrapMenuItem.isSelected());
3291     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3292     alignPanel.updateLayout();
3293   }
3294
3295   @Override
3296   public void showAllSeqs_actionPerformed(ActionEvent e)
3297   {
3298     viewport.showAllHiddenSeqs();
3299   }
3300
3301   @Override
3302   public void showAllColumns_actionPerformed(ActionEvent e)
3303   {
3304     viewport.showAllHiddenColumns();
3305     alignPanel.paintAlignment(true, true);
3306     viewport.sendSelection();
3307   }
3308
3309   @Override
3310   public void hideSelSequences_actionPerformed(ActionEvent e)
3311   {
3312     viewport.hideAllSelectedSeqs();
3313   }
3314
3315   /**
3316    * called by key handler and the hide all/show all menu items
3317    *
3318    * @param toggleSeqs
3319    * @param toggleCols
3320    */
3321   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3322   {
3323
3324     boolean hide = false;
3325     SequenceGroup sg = viewport.getSelectionGroup();
3326     if (!toggleSeqs && !toggleCols)
3327     {
3328       // Hide everything by the current selection - this is a hack - we do the
3329       // invert and then hide
3330       // first check that there will be visible columns after the invert.
3331       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3332               && sg.getStartRes() <= sg.getEndRes()))
3333       {
3334         // now invert the sequence set, if required - empty selection implies
3335         // that no hiding is required.
3336         if (sg != null)
3337         {
3338           invertSequenceMenuItem_actionPerformed(null);
3339           sg = viewport.getSelectionGroup();
3340           toggleSeqs = true;
3341
3342         }
3343         viewport.expandColSelection(sg, true);
3344         // finally invert the column selection and get the new sequence
3345         // selection.
3346         invertColSel_actionPerformed(null);
3347         toggleCols = true;
3348       }
3349     }
3350
3351     if (toggleSeqs)
3352     {
3353       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3354       {
3355         hideSelSequences_actionPerformed(null);
3356         hide = true;
3357       }
3358       else if (!(toggleCols && viewport.hasSelectedColumns()))
3359       {
3360         showAllSeqs_actionPerformed(null);
3361       }
3362     }
3363
3364     if (toggleCols)
3365     {
3366       if (viewport.hasSelectedColumns())
3367       {
3368         hideSelColumns_actionPerformed(null);
3369         if (!toggleSeqs)
3370         {
3371           viewport.setSelectionGroup(sg);
3372         }
3373       }
3374       else if (!hide)
3375       {
3376         showAllColumns_actionPerformed(null);
3377       }
3378     }
3379   }
3380
3381   /*
3382    * (non-Javadoc)
3383    *
3384    * @see
3385    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3386    * event.ActionEvent)
3387    */
3388   @Override
3389   public void hideAllButSelection_actionPerformed(ActionEvent e)
3390   {
3391     toggleHiddenRegions(false, false);
3392     viewport.sendSelection();
3393   }
3394
3395   /*
3396    * (non-Javadoc)
3397    *
3398    * @see
3399    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3400    * .ActionEvent)
3401    */
3402   @Override
3403   public void hideAllSelection_actionPerformed(ActionEvent e)
3404   {
3405     SequenceGroup sg = viewport.getSelectionGroup();
3406     viewport.expandColSelection(sg, false);
3407     viewport.hideAllSelectedSeqs();
3408     viewport.hideSelectedColumns();
3409     alignPanel.updateLayout();
3410     alignPanel.paintAlignment(true, true);
3411     viewport.sendSelection();
3412   }
3413
3414   /*
3415    * (non-Javadoc)
3416    *
3417    * @see
3418    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3419    * ActionEvent)
3420    */
3421   @Override
3422   public void showAllhidden_actionPerformed(ActionEvent e)
3423   {
3424     viewport.showAllHiddenColumns();
3425     viewport.showAllHiddenSeqs();
3426     alignPanel.paintAlignment(true, true);
3427     viewport.sendSelection();
3428   }
3429
3430   @Override
3431   public void hideSelColumns_actionPerformed(ActionEvent e)
3432   {
3433     viewport.hideSelectedColumns();
3434     alignPanel.updateLayout();
3435     alignPanel.paintAlignment(true, true);
3436     viewport.sendSelection();
3437   }
3438
3439   @Override
3440   public void hiddenMarkers_actionPerformed(ActionEvent e)
3441   {
3442     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3443     repaint();
3444   }
3445
3446   /**
3447    * DOCUMENT ME!
3448    *
3449    * @param e
3450    *          DOCUMENT ME!
3451    */
3452   @Override
3453   protected void scaleAbove_actionPerformed(ActionEvent e)
3454   {
3455     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3456     alignPanel.updateLayout();
3457     alignPanel.paintAlignment(true, false);
3458   }
3459
3460   /**
3461    * DOCUMENT ME!
3462    *
3463    * @param e
3464    *          DOCUMENT ME!
3465    */
3466   @Override
3467   protected void scaleLeft_actionPerformed(ActionEvent e)
3468   {
3469     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3470     alignPanel.updateLayout();
3471     alignPanel.paintAlignment(true, false);
3472   }
3473
3474   /**
3475    * DOCUMENT ME!
3476    *
3477    * @param e
3478    *          DOCUMENT ME!
3479    */
3480   @Override
3481   protected void scaleRight_actionPerformed(ActionEvent e)
3482   {
3483     viewport.setScaleRightWrapped(scaleRight.isSelected());
3484     alignPanel.updateLayout();
3485     alignPanel.paintAlignment(true, false);
3486   }
3487
3488   /**
3489    * DOCUMENT ME!
3490    *
3491    * @param e
3492    *          DOCUMENT ME!
3493    */
3494   @Override
3495   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3496   {
3497     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3498     alignPanel.paintAlignment(false, false);
3499   }
3500
3501   /**
3502    * DOCUMENT ME!
3503    *
3504    * @param e
3505    *          DOCUMENT ME!
3506    */
3507   @Override
3508   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3509   {
3510     viewport.setShowText(viewTextMenuItem.isSelected());
3511     alignPanel.paintAlignment(false, false);
3512   }
3513
3514   /**
3515    * DOCUMENT ME!
3516    *
3517    * @param e
3518    *          DOCUMENT ME!
3519    */
3520   @Override
3521   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3522   {
3523     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3524     alignPanel.paintAlignment(false, false);
3525   }
3526
3527   public FeatureSettings featureSettings;
3528
3529   @Override
3530   public FeatureSettingsControllerI getFeatureSettingsUI()
3531   {
3532     return featureSettings;
3533   }
3534
3535   @Override
3536   public void featureSettings_actionPerformed(ActionEvent e)
3537   {
3538     showFeatureSettingsUI();
3539   }
3540
3541   @Override
3542   public FeatureSettingsControllerI showFeatureSettingsUI()
3543   {
3544     if (featureSettings != null)
3545     {
3546       featureSettings.closeOldSettings();
3547       featureSettings = null;
3548     }
3549     if (!showSeqFeatures.isSelected())
3550     {
3551       // make sure features are actually displayed
3552       showSeqFeatures.setSelected(true);
3553       showSeqFeatures_actionPerformed(null);
3554     }
3555     featureSettings = new FeatureSettings(this);
3556     return featureSettings;
3557   }
3558
3559   /**
3560    * Set or clear 'Show Sequence Features'
3561    *
3562    * @param evt
3563    *          DOCUMENT ME!
3564    */
3565   @Override
3566   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3567   {
3568     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3569     alignPanel.paintAlignment(true, true);
3570   }
3571
3572   /**
3573    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3574    * the annotations panel as a whole.
3575    *
3576    * The options to show/hide all annotations should be enabled when the panel
3577    * is shown, and disabled when the panel is hidden.
3578    *
3579    * @param e
3580    */
3581   @Override
3582   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3583   {
3584     final boolean setVisible = annotationPanelMenuItem.isSelected();
3585     viewport.setShowAnnotation(setVisible);
3586     this.showAllSeqAnnotations.setEnabled(setVisible);
3587     this.hideAllSeqAnnotations.setEnabled(setVisible);
3588     this.showAllAlAnnotations.setEnabled(setVisible);
3589     this.hideAllAlAnnotations.setEnabled(setVisible);
3590     alignPanel.updateLayout();
3591   }
3592
3593   @Override
3594   public void alignmentProperties()
3595   {
3596     JComponent pane;
3597     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3598
3599             .formatAsHtml();
3600     String content = MessageManager.formatMessage("label.html_content",
3601             new Object[]
3602             { contents.toString() });
3603     contents = null;
3604
3605     if (Platform.isJS())
3606     {
3607       JLabel textLabel = new JLabel();
3608       textLabel.setText(content);
3609       textLabel.setBackground(Color.WHITE);
3610
3611       pane = new JPanel(new BorderLayout());
3612       ((JPanel) pane).setOpaque(true);
3613       pane.setBackground(Color.WHITE);
3614       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3615     }
3616     else
3617     /**
3618      * Java only
3619      *
3620      * @j2sIgnore
3621      */
3622     {
3623       JEditorPane editPane = new JEditorPane("text/html", "");
3624       editPane.setEditable(false);
3625       editPane.setText(content);
3626       pane = editPane;
3627     }
3628
3629     JInternalFrame frame = new JInternalFrame();
3630
3631     frame.getContentPane().add(new JScrollPane(pane));
3632
3633     Desktop.addInternalFrame(frame, MessageManager
3634             .formatMessage("label.alignment_properties", new Object[]
3635             { getTitle() }), 500, 400);
3636   }
3637
3638   /**
3639    * DOCUMENT ME!
3640    *
3641    * @param e
3642    *          DOCUMENT ME!
3643    */
3644   @Override
3645   public void overviewMenuItem_actionPerformed(ActionEvent e)
3646   {
3647     if (alignPanel.overviewPanel != null)
3648     {
3649       return;
3650     }
3651
3652     JInternalFrame frame = new JInternalFrame();
3653     final OverviewPanel overview = new OverviewPanel(alignPanel);
3654     frame.setContentPane(overview);
3655     Desktop.addInternalFrame(frame, MessageManager
3656             .formatMessage("label.overview_params", new Object[]
3657             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3658             true, true);
3659     frame.pack();
3660     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3661     frame.addInternalFrameListener(
3662             new javax.swing.event.InternalFrameAdapter()
3663             {
3664               @Override
3665               public void internalFrameClosed(
3666                       javax.swing.event.InternalFrameEvent evt)
3667               {
3668                 overview.dispose();
3669                 alignPanel.setOverviewPanel(null);
3670               }
3671             });
3672     if (getKeyListeners().length > 0)
3673     {
3674       frame.addKeyListener(getKeyListeners()[0]);
3675     }
3676
3677     alignPanel.setOverviewPanel(overview);
3678   }
3679
3680   @Override
3681   public void textColour_actionPerformed()
3682   {
3683     new TextColourChooser().chooseColour(alignPanel, null);
3684   }
3685
3686   /*
3687    * public void covariationColour_actionPerformed() {
3688    * changeColour(new
3689    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3690    * ()[0])); }
3691    */
3692   @Override
3693   public void annotationColour_actionPerformed()
3694   {
3695     new AnnotationColourChooser(viewport, alignPanel);
3696   }
3697
3698   @Override
3699   public void annotationColumn_actionPerformed(ActionEvent e)
3700   {
3701     new AnnotationColumnChooser(viewport, alignPanel);
3702   }
3703
3704   /**
3705    * Action on the user checking or unchecking the option to apply the selected
3706    * colour scheme to all groups. If unchecked, groups may have their own
3707    * independent colour schemes.
3708    *
3709    * @param selected
3710    */
3711   @Override
3712   public void applyToAllGroups_actionPerformed(boolean selected)
3713   {
3714     viewport.setColourAppliesToAllGroups(selected);
3715   }
3716
3717   /**
3718    * Action on user selecting a colour from the colour menu
3719    *
3720    * @param name
3721    *          the name (not the menu item label!) of the colour scheme
3722    */
3723   @Override
3724   public void changeColour_actionPerformed(String name)
3725   {
3726     /*
3727      * 'User Defined' opens a panel to configure or load a
3728      * user-defined colour scheme
3729      */
3730     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3731     {
3732       new UserDefinedColours(alignPanel);
3733       return;
3734     }
3735
3736     /*
3737      * otherwise set the chosen colour scheme (or null for 'None')
3738      */
3739     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3740             viewport, viewport.getAlignment(),
3741             viewport.getHiddenRepSequences());
3742     changeColour(cs);
3743   }
3744
3745   /**
3746    * Actions on setting or changing the alignment colour scheme
3747    *
3748    * @param cs
3749    */
3750   @Override
3751   public void changeColour(ColourSchemeI cs)
3752   {
3753     // TODO: pull up to controller method
3754     ColourMenuHelper.setColourSelected(colourMenu, cs);
3755
3756     viewport.setGlobalColourScheme(cs);
3757
3758     alignPanel.paintAlignment(true, true);
3759   }
3760
3761   /**
3762    * Show the PID threshold slider panel
3763    */
3764   @Override
3765   protected void modifyPID_actionPerformed()
3766   {
3767     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3768             alignPanel.getViewName());
3769     SliderPanel.showPIDSlider();
3770   }
3771
3772   /**
3773    * Show the Conservation slider panel
3774    */
3775   @Override
3776   protected void modifyConservation_actionPerformed()
3777   {
3778     SliderPanel.setConservationSlider(alignPanel,
3779             viewport.getResidueShading(), alignPanel.getViewName());
3780     SliderPanel.showConservationSlider();
3781   }
3782
3783   /**
3784    * Action on selecting or deselecting (Colour) By Conservation
3785    */
3786   @Override
3787   public void conservationMenuItem_actionPerformed(boolean selected)
3788   {
3789     modifyConservation.setEnabled(selected);
3790     viewport.setConservationSelected(selected);
3791     viewport.getResidueShading().setConservationApplied(selected);
3792
3793     changeColour(viewport.getGlobalColourScheme());
3794     if (selected)
3795     {
3796       modifyConservation_actionPerformed();
3797     }
3798     else
3799     {
3800       SliderPanel.hideConservationSlider();
3801     }
3802   }
3803
3804   /**
3805    * Action on selecting or deselecting (Colour) Above PID Threshold
3806    */
3807   @Override
3808   public void abovePIDThreshold_actionPerformed(boolean selected)
3809   {
3810     modifyPID.setEnabled(selected);
3811     viewport.setAbovePIDThreshold(selected);
3812     if (!selected)
3813     {
3814       viewport.getResidueShading().setThreshold(0,
3815               viewport.isIgnoreGapsConsensus());
3816     }
3817
3818     changeColour(viewport.getGlobalColourScheme());
3819     if (selected)
3820     {
3821       modifyPID_actionPerformed();
3822     }
3823     else
3824     {
3825       SliderPanel.hidePIDSlider();
3826     }
3827   }
3828
3829   /**
3830    * DOCUMENT ME!
3831    *
3832    * @param e
3833    *          DOCUMENT ME!
3834    */
3835   @Override
3836   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3837   {
3838     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3839     AlignmentSorter.sortByPID(viewport.getAlignment(),
3840             viewport.getAlignment().getSequenceAt(0));
3841     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3842             viewport.getAlignment()));
3843     alignPanel.paintAlignment(true, false);
3844   }
3845
3846   /**
3847    * DOCUMENT ME!
3848    *
3849    * @param e
3850    *          DOCUMENT ME!
3851    */
3852   @Override
3853   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3854   {
3855     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3856     AlignmentSorter.sortByID(viewport.getAlignment());
3857     addHistoryItem(
3858             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3859     alignPanel.paintAlignment(true, false);
3860   }
3861
3862   /**
3863    * DOCUMENT ME!
3864    *
3865    * @param e
3866    *          DOCUMENT ME!
3867    */
3868   @Override
3869   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3870   {
3871     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3872     AlignmentSorter.sortByLength(viewport.getAlignment());
3873     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3874             viewport.getAlignment()));
3875     alignPanel.paintAlignment(true, false);
3876   }
3877
3878   /**
3879    * DOCUMENT ME!
3880    *
3881    * @param e
3882    *          DOCUMENT ME!
3883    */
3884   @Override
3885   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3886   {
3887     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3888     AlignmentSorter.sortByGroup(viewport.getAlignment());
3889     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3890             viewport.getAlignment()));
3891
3892     alignPanel.paintAlignment(true, false);
3893   }
3894
3895   @Override
3896   public void sortEValueMenuItem_actionPerformed(ActionEvent e)
3897   {
3898     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3899     AlignmentSorter.sortByEValue(viewport.getAlignment());
3900     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3901             viewport.getAlignment()));
3902     alignPanel.paintAlignment(true, false);
3903
3904   }
3905
3906   @Override
3907   public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
3908   {
3909     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3910     AlignmentSorter.sortByBitScore(viewport.getAlignment());
3911     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3912             viewport.getAlignment()));
3913     alignPanel.paintAlignment(true, false);
3914
3915   }
3916
3917   /**
3918    * DOCUMENT ME!
3919    *
3920    * @param e
3921    *          DOCUMENT ME!
3922    */
3923   @Override
3924   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3925   {
3926     new RedundancyPanel(alignPanel, this);
3927   }
3928
3929   /**
3930    * DOCUMENT ME!
3931    *
3932    * @param e
3933    *          DOCUMENT ME!
3934    */
3935   @Override
3936   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3937   {
3938     if ((viewport.getSelectionGroup() == null)
3939             || (viewport.getSelectionGroup().getSize() < 2))
3940     {
3941       JvOptionPane.showInternalMessageDialog(this,
3942               MessageManager.getString(
3943                       "label.you_must_select_least_two_sequences"),
3944               MessageManager.getString("label.invalid_selection"),
3945               JvOptionPane.WARNING_MESSAGE);
3946     }
3947     else
3948     {
3949       JInternalFrame frame = new JInternalFrame();
3950       frame.setContentPane(new PairwiseAlignPanel(viewport));
3951       Desktop.addInternalFrame(frame,
3952               MessageManager.getString("action.pairwise_alignment"), 600,
3953               500);
3954     }
3955   }
3956
3957   @Override
3958   public void autoCalculate_actionPerformed(ActionEvent e)
3959   {
3960     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3961     if (viewport.autoCalculateConsensus)
3962     {
3963       viewport.firePropertyChange("alignment", null,
3964               viewport.getAlignment().getSequences());
3965     }
3966   }
3967
3968   @Override
3969   public void sortByTreeOption_actionPerformed(ActionEvent e)
3970   {
3971     viewport.sortByTree = sortByTree.isSelected();
3972   }
3973
3974   @Override
3975   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3976   {
3977     viewport.followSelection = listenToViewSelections.isSelected();
3978   }
3979
3980   /**
3981    * Constructs a tree panel and adds it to the desktop
3982    *
3983    * @param type
3984    *          tree type (NJ or AV)
3985    * @param modelName
3986    *          name of score model used to compute the tree
3987    * @param options
3988    *          parameters for the distance or similarity calculation
3989    */
3990   void newTreePanel(String type, String modelName,
3991           SimilarityParamsI options)
3992   {
3993     String frameTitle = "";
3994     TreePanel tp;
3995
3996     boolean onSelection = false;
3997     if (viewport.getSelectionGroup() != null
3998             && viewport.getSelectionGroup().getSize() > 0)
3999     {
4000       SequenceGroup sg = viewport.getSelectionGroup();
4001
4002       /* Decide if the selection is a column region */
4003       for (SequenceI _s : sg.getSequences())
4004       {
4005         if (_s.getLength() < sg.getEndRes())
4006         {
4007           JvOptionPane.showMessageDialog(Desktop.desktop,
4008                   MessageManager.getString(
4009                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4010                   MessageManager.getString(
4011                           "label.sequences_selection_not_aligned"),
4012                   JvOptionPane.WARNING_MESSAGE);
4013
4014           return;
4015         }
4016       }
4017       onSelection = true;
4018     }
4019     else
4020     {
4021       if (viewport.getAlignment().getHeight() < 2)
4022       {
4023         return;
4024       }
4025     }
4026
4027     tp = new TreePanel(alignPanel, type, modelName, options);
4028     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
4029
4030     frameTitle += " from ";
4031
4032     if (viewport.getViewName() != null)
4033     {
4034       frameTitle += viewport.getViewName() + " of ";
4035     }
4036
4037     frameTitle += this.title;
4038
4039     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
4040   }
4041
4042   /**
4043    * DOCUMENT ME!
4044    *
4045    * @param title
4046    *          DOCUMENT ME!
4047    * @param order
4048    *          DOCUMENT ME!
4049    */
4050   public void addSortByOrderMenuItem(String title,
4051           final AlignmentOrder order)
4052   {
4053     final JMenuItem item = new JMenuItem(MessageManager
4054             .formatMessage("action.by_title_param", new Object[]
4055             { title }));
4056     sort.add(item);
4057     item.addActionListener(new java.awt.event.ActionListener()
4058     {
4059       @Override
4060       public void actionPerformed(ActionEvent e)
4061       {
4062         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4063
4064         // TODO: JBPNote - have to map order entries to curent SequenceI
4065         // pointers
4066         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4067
4068         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
4069                 viewport.getAlignment()));
4070
4071         alignPanel.paintAlignment(true, false);
4072       }
4073     });
4074   }
4075
4076   /**
4077    * Add a new sort by annotation score menu item
4078    *
4079    * @param sort
4080    *          the menu to add the option to
4081    * @param scoreLabel
4082    *          the label used to retrieve scores for each sequence on the
4083    *          alignment
4084    */
4085   public void addSortByAnnotScoreMenuItem(JMenu sort,
4086           final String scoreLabel)
4087   {
4088     final JMenuItem item = new JMenuItem(scoreLabel);
4089     sort.add(item);
4090     item.addActionListener(new java.awt.event.ActionListener()
4091     {
4092       @Override
4093       public void actionPerformed(ActionEvent e)
4094       {
4095         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4096         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4097                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4098         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4099                 viewport.getAlignment()));
4100         alignPanel.paintAlignment(true, false);
4101       }
4102     });
4103   }
4104
4105   /**
4106    * last hash for alignment's annotation array - used to minimise cost of
4107    * rebuild.
4108    */
4109   protected int _annotationScoreVectorHash;
4110
4111   /**
4112    * search the alignment and rebuild the sort by annotation score submenu the
4113    * last alignment annotation vector hash is stored to minimize cost of
4114    * rebuilding in subsequence calls.
4115    *
4116    */
4117   @Override
4118   public void buildSortByAnnotationScoresMenu()
4119   {
4120     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4121     {
4122       return;
4123     }
4124
4125     if (viewport.getAlignment().getAlignmentAnnotation()
4126             .hashCode() == _annotationScoreVectorHash)
4127     {
4128       return;
4129     }
4130
4131     sortByAnnotScore.removeAll();
4132     Set<String> scoreSorts = new HashSet<>();
4133     for (SequenceI sqa : viewport.getAlignment().getSequences())
4134     {
4135       AlignmentAnnotation[] anns = sqa.getAnnotation();
4136       for (int i = 0; anns != null && i < anns.length; i++)
4137       {
4138         AlignmentAnnotation aa = anns[i];
4139         if (aa != null && aa.hasScore() && aa.sequenceRef != null)
4140         {
4141           scoreSorts.add(aa.label);
4142         }
4143       }
4144     }
4145     for (String label : scoreSorts)
4146     {
4147       addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
4148     }
4149     sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
4150
4151     _annotationScoreVectorHash = viewport.getAlignment()
4152             .getAlignmentAnnotation().hashCode();
4153   }
4154
4155   /**
4156    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4157    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4158    * call. Listeners are added to remove the menu item when the treePanel is
4159    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4160    * modified.
4161    */
4162   @Override
4163   public void buildTreeSortMenu()
4164   {
4165     sortByTreeMenu.removeAll();
4166
4167     List<Component> comps = PaintRefresher.components
4168             .get(viewport.getSequenceSetId());
4169     List<TreePanel> treePanels = new ArrayList<>();
4170     for (Component comp : comps)
4171     {
4172       if (comp instanceof TreePanel)
4173       {
4174         treePanels.add((TreePanel) comp);
4175       }
4176     }
4177
4178     if (treePanels.size() < 1)
4179     {
4180       sortByTreeMenu.setVisible(false);
4181       return;
4182     }
4183
4184     sortByTreeMenu.setVisible(true);
4185
4186     for (final TreePanel tp : treePanels)
4187     {
4188       final JMenuItem item = new JMenuItem(tp.getTitle());
4189       item.addActionListener(new java.awt.event.ActionListener()
4190       {
4191         @Override
4192         public void actionPerformed(ActionEvent e)
4193         {
4194           tp.sortByTree_actionPerformed();
4195           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4196
4197         }
4198       });
4199
4200       sortByTreeMenu.add(item);
4201     }
4202   }
4203
4204   public boolean sortBy(AlignmentOrder alorder, String undoname)
4205   {
4206     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4207     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4208     if (undoname != null)
4209     {
4210       addHistoryItem(new OrderCommand(undoname, oldOrder,
4211               viewport.getAlignment()));
4212     }
4213     alignPanel.paintAlignment(true, false);
4214     return true;
4215   }
4216
4217   /**
4218    * Work out whether the whole set of sequences or just the selected set will
4219    * be submitted for multiple alignment.
4220    *
4221    */
4222   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4223   {
4224     // Now, check we have enough sequences
4225     AlignmentView msa = null;
4226
4227     if ((viewport.getSelectionGroup() != null)
4228             && (viewport.getSelectionGroup().getSize() > 1))
4229     {
4230       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4231       // some common interface!
4232       /*
4233        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4234        * SequenceI[sz = seqs.getSize(false)];
4235        *
4236        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4237        * seqs.getSequenceAt(i); }
4238        */
4239       msa = viewport.getAlignmentView(true);
4240     }
4241     else if (viewport.getSelectionGroup() != null
4242             && viewport.getSelectionGroup().getSize() == 1)
4243     {
4244       int option = JvOptionPane.showConfirmDialog(this,
4245               MessageManager.getString("warn.oneseq_msainput_selection"),
4246               MessageManager.getString("label.invalid_selection"),
4247               JvOptionPane.OK_CANCEL_OPTION);
4248       if (option == JvOptionPane.OK_OPTION)
4249       {
4250         msa = viewport.getAlignmentView(false);
4251       }
4252     }
4253     else
4254     {
4255       msa = viewport.getAlignmentView(false);
4256     }
4257     return msa;
4258   }
4259
4260   /**
4261    * Decides what is submitted to a secondary structure prediction service: the
4262    * first sequence in the alignment, or in the current selection, or, if the
4263    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4264    * region or the whole alignment. (where the first sequence in the set is the
4265    * one that the prediction will be for).
4266    */
4267   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4268   {
4269     AlignmentView seqs = null;
4270
4271     if ((viewport.getSelectionGroup() != null)
4272             && (viewport.getSelectionGroup().getSize() > 0))
4273     {
4274       seqs = viewport.getAlignmentView(true);
4275     }
4276     else
4277     {
4278       seqs = viewport.getAlignmentView(false);
4279     }
4280     // limit sequences - JBPNote in future - could spawn multiple prediction
4281     // jobs
4282     // TODO: viewport.getAlignment().isAligned is a global state - the local
4283     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4284     if (!viewport.getAlignment().isAligned(false))
4285     {
4286       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4287       // TODO: if seqs.getSequences().length>1 then should really have warned
4288       // user!
4289
4290     }
4291     return seqs;
4292   }
4293
4294   /**
4295    * DOCUMENT ME!
4296    *
4297    * @param e
4298    *          DOCUMENT ME!
4299    */
4300   @Override
4301   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4302   {
4303     // Pick the tree file
4304     JalviewFileChooser chooser = new JalviewFileChooser(
4305             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4306     chooser.setFileView(new JalviewFileView());
4307     chooser.setDialogTitle(
4308             MessageManager.getString("label.select_newick_like_tree_file"));
4309     chooser.setToolTipText(
4310             MessageManager.getString("label.load_tree_file"));
4311
4312     chooser.setResponseHandler(0, new Runnable()
4313     {
4314       @Override
4315       public void run()
4316       {
4317         String filePath = chooser.getSelectedFile().getPath();
4318         Cache.setProperty("LAST_DIRECTORY", filePath);
4319         NewickFile fin = null;
4320         try
4321         {
4322           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4323                   DataSourceType.FILE));
4324           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4325         } catch (Exception ex)
4326         {
4327           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4328                   MessageManager
4329                           .getString("label.problem_reading_tree_file"),
4330                   JvOptionPane.WARNING_MESSAGE);
4331           ex.printStackTrace();
4332         }
4333         if (fin != null && fin.hasWarningMessage())
4334         {
4335           JvOptionPane.showMessageDialog(Desktop.desktop,
4336                   fin.getWarningMessage(),
4337                   MessageManager.getString(
4338                           "label.possible_problem_with_tree_file"),
4339                   JvOptionPane.WARNING_MESSAGE);
4340         }
4341       }
4342     });
4343     chooser.showOpenDialog(this);
4344   }
4345
4346   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4347   {
4348     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4349   }
4350
4351   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4352           int h, int x, int y)
4353   {
4354     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4355   }
4356
4357   /**
4358    * Add a treeviewer for the tree extracted from a Newick file object to the
4359    * current alignment view
4360    *
4361    * @param nf
4362    *          the tree
4363    * @param title
4364    *          tree viewer title
4365    * @param input
4366    *          Associated alignment input data (or null)
4367    * @param w
4368    *          width
4369    * @param h
4370    *          height
4371    * @param x
4372    *          position
4373    * @param y
4374    *          position
4375    * @return TreePanel handle
4376    */
4377   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4378           AlignmentView input, int w, int h, int x, int y)
4379   {
4380     TreePanel tp = null;
4381
4382     try
4383     {
4384       nf.parse();
4385
4386       if (nf.getTree() != null)
4387       {
4388         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4389
4390         tp.setSize(w, h);
4391
4392         if (x > 0 && y > 0)
4393         {
4394           tp.setLocation(x, y);
4395         }
4396
4397         Desktop.addInternalFrame(tp, treeTitle, w, h);
4398       }
4399     } catch (Exception ex)
4400     {
4401       ex.printStackTrace();
4402     }
4403
4404     return tp;
4405   }
4406
4407   /**
4408    * Schedule the web services menu rebuild to the event dispatch thread.
4409    */
4410   public void buildWebServicesMenu()
4411   {
4412     SwingUtilities.invokeLater(() -> {
4413       Cache.log.info("Rebuiling WS menu");
4414       webService.removeAll();
4415       if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
4416       {
4417         SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance();
4418         JMenu submenu = new JMenu("Slivka");
4419         buildWebServicesMenu(discoverer, submenu);
4420         webService.add(submenu);
4421       }
4422       if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4423       {
4424         WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer();
4425         JMenu submenu = new JMenu("JABAWS");
4426         buildLegacyWebServicesMenu(submenu);
4427         buildWebServicesMenu(jws2servs, submenu);
4428         webService.add(submenu);
4429       }
4430     });
4431   }
4432
4433   private void buildLegacyWebServicesMenu(JMenu menu)
4434   {
4435     JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
4436     if (Discoverer.services != null && Discoverer.services.size() > 0)
4437     {
4438       var secstrpred = Discoverer.services.get("SecStrPred");
4439       if (secstrpred != null)
4440       {
4441         for (ext.vamsas.ServiceHandle sh : secstrpred)
4442         {
4443           var menuProvider = Discoverer.getServiceClient(sh);
4444           menuProvider.attachWSMenuEntry(secstrmenu, this);
4445         }
4446       }
4447     }
4448     menu.add(secstrmenu);
4449   }
4450
4451   /**
4452    * Constructs the web services menu for the given discoverer under the
4453    * specified menu. This method must be called on the EDT
4454    *
4455    * @param discoverer
4456    *          the discoverer used to build the menu
4457    * @param menu
4458    *          parent component which the elements will be attached to
4459    */
4460   private void buildWebServicesMenu(WSDiscovererI discoverer, JMenu menu)
4461   {
4462     if (discoverer.hasServices())
4463     {
4464       PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
4465               discoverer.getServices(), sv -> buildWebServicesMenu(), menu,
4466               this, null);
4467     }
4468     if (discoverer.isRunning())
4469     {
4470       JMenuItem item = new JMenuItem("Service discovery in progress.");
4471       item.setEnabled(false);
4472       menu.add(item);
4473     }
4474     else if (!discoverer.hasServices())
4475     {
4476       JMenuItem item = new JMenuItem("No services available.");
4477       item.setEnabled(false);
4478       menu.add(item);
4479     }
4480   }
4481
4482   /**
4483    * construct any groupURL type service menu entries.
4484    *
4485    * @param webService
4486    */
4487   protected void build_urlServiceMenu(JMenu webService)
4488   {
4489     // TODO: remove this code when 2.7 is released
4490     // DEBUG - alignmentView
4491     /*
4492      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4493      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4494      *
4495      * @Override public void actionPerformed(ActionEvent e) {
4496      * jalview.datamodel.AlignmentView
4497      * .testSelectionViews(af.viewport.getAlignment(),
4498      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4499      *
4500      * }); webService.add(testAlView);
4501      */
4502     // TODO: refactor to RestClient discoverer and merge menu entries for
4503     // rest-style services with other types of analysis/calculation service
4504     // SHmmr test client - still being implemented.
4505     // DEBUG - alignmentView
4506
4507     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4508             .getRestClients())
4509     {
4510       client.attachWSMenuEntry(
4511               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4512               this);
4513     }
4514   }
4515
4516   /**
4517    * Searches the alignment sequences for xRefs and builds the Show
4518    * Cross-References menu (formerly called Show Products), with database
4519    * sources for which cross-references are found (protein sources for a
4520    * nucleotide alignment and vice versa)
4521    *
4522    * @return true if Show Cross-references menu should be enabled
4523    */
4524   public boolean canShowProducts()
4525   {
4526     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4527     AlignmentI dataset = viewport.getAlignment().getDataset();
4528
4529     showProducts.removeAll();
4530     final boolean dna = viewport.getAlignment().isNucleotide();
4531
4532     if (seqs == null || seqs.length == 0)
4533     {
4534       // nothing to see here.
4535       return false;
4536     }
4537
4538     boolean showp = false;
4539     try
4540     {
4541       List<String> ptypes = new CrossRef(seqs, dataset)
4542               .findXrefSourcesForSequences(dna);
4543
4544       for (final String source : ptypes)
4545       {
4546         showp = true;
4547         final AlignFrame af = this;
4548         JMenuItem xtype = new JMenuItem(source);
4549         xtype.addActionListener(new ActionListener()
4550         {
4551           @Override
4552           public void actionPerformed(ActionEvent e)
4553           {
4554             showProductsFor(af.viewport.getSequenceSelection(), dna,
4555                     source);
4556           }
4557         });
4558         showProducts.add(xtype);
4559       }
4560       showProducts.setVisible(showp);
4561       showProducts.setEnabled(showp);
4562     } catch (Exception e)
4563     {
4564       Cache.log.warn(
4565               "canShowProducts threw an exception - please report to help@jalview.org",
4566               e);
4567       return false;
4568     }
4569     return showp;
4570   }
4571
4572   /**
4573    * Finds and displays cross-references for the selected sequences (protein
4574    * products for nucleotide sequences, dna coding sequences for peptides).
4575    *
4576    * @param sel
4577    *          the sequences to show cross-references for
4578    * @param dna
4579    *          true if from a nucleotide alignment (so showing proteins)
4580    * @param source
4581    *          the database to show cross-references for
4582    */
4583   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4584           final String source)
4585   {
4586     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4587             .start();
4588   }
4589
4590   /**
4591    * Construct and display a new frame containing the translation of this
4592    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4593    */
4594   @Override
4595   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4596   {
4597     AlignmentI al = null;
4598     try
4599     {
4600       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4601
4602       al = dna.translateCdna(codeTable);
4603     } catch (Exception ex)
4604     {
4605       jalview.bin.Cache.log.error(
4606               "Exception during translation. Please report this !", ex);
4607       final String msg = MessageManager.getString(
4608               "label.error_when_translating_sequences_submit_bug_report");
4609       final String errorTitle = MessageManager
4610               .getString("label.implementation_error")
4611               + MessageManager.getString("label.translation_failed");
4612       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4613               JvOptionPane.ERROR_MESSAGE);
4614       return;
4615     }
4616     if (al == null || al.getHeight() == 0)
4617     {
4618       final String msg = MessageManager.getString(
4619               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4620       final String errorTitle = MessageManager
4621               .getString("label.translation_failed");
4622       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4623               JvOptionPane.WARNING_MESSAGE);
4624     }
4625     else
4626     {
4627       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4628       af.setFileFormat(this.currentFileFormat);
4629       final String newTitle = MessageManager
4630               .formatMessage("label.translation_of_params", new Object[]
4631               { this.getTitle(), codeTable.getId() });
4632       af.setTitle(newTitle);
4633       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4634       {
4635         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4636         viewport.openSplitFrame(af, new Alignment(seqs));
4637       }
4638       else
4639       {
4640         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4641                 DEFAULT_HEIGHT);
4642       }
4643     }
4644   }
4645
4646   /**
4647    * Set the file format
4648    *
4649    * @param format
4650    */
4651   public void setFileFormat(FileFormatI format)
4652   {
4653     this.currentFileFormat = format;
4654   }
4655
4656   /**
4657    * Try to load a features file onto the alignment.
4658    *
4659    * @param file
4660    *          contents or path to retrieve file or a File object
4661    * @param sourceType
4662    *          access mode of file (see jalview.io.AlignFile)
4663    * @return true if features file was parsed correctly.
4664    */
4665   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4666   {
4667     // BH 2018
4668     return avc.parseFeaturesFile(file, sourceType,
4669             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4670
4671   }
4672
4673   @Override
4674   public void refreshFeatureUI(boolean enableIfNecessary)
4675   {
4676     // note - currently this is only still here rather than in the controller
4677     // because of the featureSettings hard reference that is yet to be
4678     // abstracted
4679     if (enableIfNecessary)
4680     {
4681       viewport.setShowSequenceFeatures(true);
4682       showSeqFeatures.setSelected(true);
4683     }
4684
4685   }
4686
4687   @Override
4688   public void dragEnter(DropTargetDragEvent evt)
4689   {
4690   }
4691
4692   @Override
4693   public void dragExit(DropTargetEvent evt)
4694   {
4695   }
4696
4697   @Override
4698   public void dragOver(DropTargetDragEvent evt)
4699   {
4700   }
4701
4702   @Override
4703   public void dropActionChanged(DropTargetDragEvent evt)
4704   {
4705   }
4706
4707   @Override
4708   public void drop(DropTargetDropEvent evt)
4709   {
4710     // JAL-1552 - acceptDrop required before getTransferable call for
4711     // Java's Transferable for native dnd
4712     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4713     Transferable t = evt.getTransferable();
4714
4715     final AlignFrame thisaf = this;
4716     final List<Object> files = new ArrayList<>();
4717     List<DataSourceType> protocols = new ArrayList<>();
4718
4719     try
4720     {
4721       Desktop.transferFromDropTarget(files, protocols, evt, t);
4722     } catch (Exception e)
4723     {
4724       e.printStackTrace();
4725     }
4726     if (files != null)
4727     {
4728       new Thread(new Runnable()
4729       {
4730         @Override
4731         public void run()
4732         {
4733           try
4734           {
4735             // check to see if any of these files have names matching sequences
4736             // in
4737             // the alignment
4738             SequenceIdMatcher idm = new SequenceIdMatcher(
4739                     viewport.getAlignment().getSequencesArray());
4740             /**
4741              * Object[] { String,SequenceI}
4742              */
4743             ArrayList<Object[]> filesmatched = new ArrayList<>();
4744             ArrayList<Object> filesnotmatched = new ArrayList<>();
4745             for (int i = 0; i < files.size(); i++)
4746             {
4747               // BH 2018
4748               Object file = files.get(i);
4749               String fileName = file.toString();
4750               String pdbfn = "";
4751               DataSourceType protocol = (file instanceof File
4752                       ? DataSourceType.FILE
4753                       : FormatAdapter.checkProtocol(fileName));
4754               if (protocol == DataSourceType.FILE)
4755               {
4756                 File fl;
4757                 if (file instanceof File)
4758                 {
4759                   fl = (File) file;
4760                   Platform.cacheFileData(fl);
4761                 }
4762                 else
4763                 {
4764                   fl = new File(fileName);
4765                 }
4766                 pdbfn = fl.getName();
4767               }
4768               else if (protocol == DataSourceType.URL)
4769               {
4770                 URL url = new URL(fileName);
4771                 pdbfn = url.getFile();
4772               }
4773               if (pdbfn.length() > 0)
4774               {
4775                 // attempt to find a match in the alignment
4776                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4777                 int l = 0, c = pdbfn.indexOf(".");
4778                 while (mtch == null && c != -1)
4779                 {
4780                   do
4781                   {
4782                     l = c;
4783                   } while ((c = pdbfn.indexOf(".", l)) > l);
4784                   if (l > -1)
4785                   {
4786                     pdbfn = pdbfn.substring(0, l);
4787                   }
4788                   mtch = idm.findAllIdMatches(pdbfn);
4789                 }
4790                 if (mtch != null)
4791                 {
4792                   FileFormatI type;
4793                   try
4794                   {
4795                     type = new IdentifyFile().identify(file, protocol);
4796                   } catch (Exception ex)
4797                   {
4798                     type = null;
4799                   }
4800                   if (type != null && type.isStructureFile())
4801                   {
4802                     filesmatched.add(new Object[] { file, protocol, mtch });
4803                     continue;
4804                   }
4805                 }
4806                 // File wasn't named like one of the sequences or wasn't a PDB
4807                 // file.
4808                 filesnotmatched.add(file);
4809               }
4810             }
4811             int assocfiles = 0;
4812             if (filesmatched.size() > 0)
4813             {
4814               boolean autoAssociate = Cache
4815                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4816               if (!autoAssociate)
4817               {
4818                 String msg = MessageManager.formatMessage(
4819                         "label.automatically_associate_structure_files_with_sequences_same_name",
4820                         new Object[]
4821                         { Integer.valueOf(filesmatched.size())
4822                                 .toString() });
4823                 String ttl = MessageManager.getString(
4824                         "label.automatically_associate_structure_files_by_name");
4825                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4826                         ttl, JvOptionPane.YES_NO_OPTION);
4827                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4828               }
4829               if (autoAssociate)
4830               {
4831                 for (Object[] fm : filesmatched)
4832                 {
4833                   // try and associate
4834                   // TODO: may want to set a standard ID naming formalism for
4835                   // associating PDB files which have no IDs.
4836                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4837                   {
4838                     PDBEntry pe = new AssociatePdbFileWithSeq()
4839                             .associatePdbWithSeq(fm[0].toString(),
4840                                     (DataSourceType) fm[1], toassoc, false,
4841                                     Desktop.instance);
4842                     if (pe != null)
4843                     {
4844                       System.err.println("Associated file : "
4845                               + (fm[0].toString()) + " with "
4846                               + toassoc.getDisplayId(true));
4847                       assocfiles++;
4848                     }
4849                   }
4850                   // TODO: do we need to update overview ? only if features are
4851                   // shown I guess
4852                   alignPanel.paintAlignment(true, false);
4853                 }
4854               }
4855               else
4856               {
4857                 /*
4858                  * add declined structures as sequences
4859                  */
4860                 for (Object[] o : filesmatched)
4861                 {
4862                   filesnotmatched.add(o[0]);
4863                 }
4864               }
4865             }
4866             if (filesnotmatched.size() > 0)
4867             {
4868               if (assocfiles > 0 && (Cache.getDefault(
4869                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4870                       || JvOptionPane.showConfirmDialog(thisaf,
4871                               "<html>" + MessageManager.formatMessage(
4872                                       "label.ignore_unmatched_dropped_files_info",
4873                                       new Object[]
4874                                       { Integer.valueOf(
4875                                               filesnotmatched.size())
4876                                               .toString() })
4877                                       + "</html>",
4878                               MessageManager.getString(
4879                                       "label.ignore_unmatched_dropped_files"),
4880                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4881               {
4882                 return;
4883               }
4884               for (Object fn : filesnotmatched)
4885               {
4886                 loadJalviewDataFile(fn, null, null, null);
4887               }
4888
4889             }
4890           } catch (Exception ex)
4891           {
4892             ex.printStackTrace();
4893           }
4894         }
4895       }).start();
4896     }
4897   }
4898
4899   /**
4900    * Attempt to load a "dropped" file or URL string, by testing in turn for
4901    * <ul>
4902    * <li>an Annotation file</li>
4903    * <li>a JNet file</li>
4904    * <li>a features file</li>
4905    * <li>else try to interpret as an alignment file</li>
4906    * </ul>
4907    *
4908    * @param file
4909    *          either a filename or a URL string.
4910    * @throws InterruptedException
4911    * @throws IOException
4912    */
4913   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4914           FileFormatI format, SequenceI assocSeq)
4915   {
4916     // BH 2018 was String file
4917     try
4918     {
4919       if (sourceType == null)
4920       {
4921         sourceType = FormatAdapter.checkProtocol(file);
4922       }
4923       // if the file isn't identified, or not positively identified as some
4924       // other filetype (PFAM is default unidentified alignment file type) then
4925       // try to parse as annotation.
4926       boolean isAnnotation = (format == null
4927               || FileFormat.Pfam.equals(format))
4928                       ? new AnnotationFile().annotateAlignmentView(viewport,
4929                               file, sourceType)
4930                       : false;
4931
4932       if (!isAnnotation)
4933       {
4934         // first see if its a T-COFFEE score file
4935         TCoffeeScoreFile tcf = null;
4936         try
4937         {
4938           tcf = new TCoffeeScoreFile(file, sourceType);
4939           if (tcf.isValid())
4940           {
4941             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4942             {
4943               buildColourMenu();
4944               changeColour(
4945                       new TCoffeeColourScheme(viewport.getAlignment()));
4946               isAnnotation = true;
4947               setStatus(MessageManager.getString(
4948                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4949             }
4950             else
4951             {
4952               // some problem - if no warning its probable that the ID matching
4953               // process didn't work
4954               JvOptionPane.showMessageDialog(Desktop.desktop,
4955                       tcf.getWarningMessage() == null
4956                               ? MessageManager.getString(
4957                                       "label.check_file_matches_sequence_ids_alignment")
4958                               : tcf.getWarningMessage(),
4959                       MessageManager.getString(
4960                               "label.problem_reading_tcoffee_score_file"),
4961                       JvOptionPane.WARNING_MESSAGE);
4962             }
4963           }
4964           else
4965           {
4966             tcf = null;
4967           }
4968         } catch (Exception x)
4969         {
4970           Cache.log.debug(
4971                   "Exception when processing data source as T-COFFEE score file",
4972                   x);
4973           tcf = null;
4974         }
4975         if (tcf == null)
4976         {
4977           // try to see if its a JNet 'concise' style annotation file *before*
4978           // we
4979           // try to parse it as a features file
4980           if (format == null)
4981           {
4982             format = new IdentifyFile().identify(file, sourceType);
4983           }
4984           if (FileFormat.ScoreMatrix == format)
4985           {
4986             ScoreMatrixFile sm = new ScoreMatrixFile(
4987                     new FileParse(file, sourceType));
4988             sm.parse();
4989             // todo: i18n this message
4990             setStatus(MessageManager.formatMessage(
4991                     "label.successfully_loaded_matrix",
4992                     sm.getMatrixName()));
4993           }
4994           else if (FileFormat.Jnet.equals(format))
4995           {
4996             JPredFile predictions = new JPredFile(file, sourceType);
4997             new JnetAnnotationMaker();
4998             JnetAnnotationMaker.add_annotation(predictions,
4999                     viewport.getAlignment(), 0, false);
5000             viewport.getAlignment().setupJPredAlignment();
5001             isAnnotation = true;
5002           }
5003           // else if (IdentifyFile.FeaturesFile.equals(format))
5004           else if (FileFormat.Features.equals(format))
5005           {
5006             if (parseFeaturesFile(file, sourceType))
5007             {
5008               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
5009               if (splitFrame != null)
5010               {
5011                 splitFrame.repaint();
5012               }
5013               else
5014               {
5015                 alignPanel.paintAlignment(true, true);
5016               }
5017             }
5018           }
5019           else
5020           {
5021             new FileLoader().LoadFile(viewport, file, sourceType, format);
5022           }
5023         }
5024       }
5025       if (isAnnotation)
5026       {
5027         alignPanel.adjustAnnotationHeight();
5028         viewport.updateSequenceIdColours();
5029         buildSortByAnnotationScoresMenu();
5030         alignPanel.paintAlignment(true, true);
5031       }
5032     } catch (Exception ex)
5033     {
5034       ex.printStackTrace();
5035     } catch (OutOfMemoryError oom)
5036     {
5037       try
5038       {
5039         System.gc();
5040       } catch (Exception x)
5041       {
5042       }
5043       new OOMWarning(
5044               "loading data "
5045                       + (sourceType != null
5046                               ? (sourceType == DataSourceType.PASTE
5047                                       ? "from clipboard."
5048                                       : "using " + sourceType + " from "
5049                                               + file)
5050                               : ".")
5051                       + (format != null
5052                               ? "(parsing as '" + format + "' file)"
5053                               : ""),
5054               oom, Desktop.desktop);
5055     }
5056   }
5057
5058   /**
5059    * Method invoked by the ChangeListener on the tabbed pane, in other words
5060    * when a different tabbed pane is selected by the user or programmatically.
5061    */
5062   @Override
5063   public void tabSelectionChanged(int index)
5064   {
5065     if (index > -1)
5066     {
5067       alignPanel = alignPanels.get(index);
5068       viewport = alignPanel.av;
5069       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5070       setMenusFromViewport(viewport);
5071       if (featureSettings != null && featureSettings.isOpen()
5072               && featureSettings.fr.getViewport() != viewport)
5073       {
5074         if (viewport.isShowSequenceFeatures())
5075         {
5076           // refresh the featureSettings to reflect UI change
5077           showFeatureSettingsUI();
5078         }
5079         else
5080         {
5081           // close feature settings for this view.
5082           featureSettings.close();
5083         }
5084       }
5085
5086     }
5087
5088     /*
5089      * 'focus' any colour slider that is open to the selected viewport
5090      */
5091     if (viewport.getConservationSelected())
5092     {
5093       SliderPanel.setConservationSlider(alignPanel,
5094               viewport.getResidueShading(), alignPanel.getViewName());
5095     }
5096     else
5097     {
5098       SliderPanel.hideConservationSlider();
5099     }
5100     if (viewport.getAbovePIDThreshold())
5101     {
5102       SliderPanel.setPIDSliderSource(alignPanel,
5103               viewport.getResidueShading(), alignPanel.getViewName());
5104     }
5105     else
5106     {
5107       SliderPanel.hidePIDSlider();
5108     }
5109
5110     /*
5111      * If there is a frame linked to this one in a SplitPane, switch it to the
5112      * same view tab index. No infinite recursion of calls should happen, since
5113      * tabSelectionChanged() should not get invoked on setting the selected
5114      * index to an unchanged value. Guard against setting an invalid index
5115      * before the new view peer tab has been created.
5116      */
5117     final AlignViewportI peer = viewport.getCodingComplement();
5118     if (peer != null)
5119     {
5120       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5121               .getAlignPanel().alignFrame;
5122       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5123       {
5124         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5125       }
5126     }
5127   }
5128
5129   /**
5130    * On right mouse click on view tab, prompt for and set new view name.
5131    */
5132   @Override
5133   public void tabbedPane_mousePressed(MouseEvent e)
5134   {
5135     if (e.isPopupTrigger())
5136     {
5137       String msg = MessageManager.getString("label.enter_view_name");
5138       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5139       String reply = JvOptionPane.showInputDialog(msg, ttl);
5140
5141       if (reply != null)
5142       {
5143         viewport.setViewName(reply);
5144         // TODO warn if reply is in getExistingViewNames()?
5145         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5146       }
5147     }
5148   }
5149
5150   public AlignViewport getCurrentView()
5151   {
5152     return viewport;
5153   }
5154
5155   /**
5156    * Open the dialog for regex description parsing.
5157    */
5158   @Override
5159   protected void extractScores_actionPerformed(ActionEvent e)
5160   {
5161     ParseProperties pp = new jalview.analysis.ParseProperties(
5162             viewport.getAlignment());
5163     // TODO: verify regex and introduce GUI dialog for version 2.5
5164     // if (pp.getScoresFromDescription("col", "score column ",
5165     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5166     // true)>0)
5167     if (pp.getScoresFromDescription("description column",
5168             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5169     {
5170       buildSortByAnnotationScoresMenu();
5171     }
5172   }
5173
5174   /*
5175    * (non-Javadoc)
5176    *
5177    * @see
5178    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5179    * )
5180    */
5181   @Override
5182   protected void showDbRefs_actionPerformed(ActionEvent e)
5183   {
5184     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5185   }
5186
5187   /*
5188    * (non-Javadoc)
5189    *
5190    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5191    * ActionEvent)
5192    */
5193   @Override
5194   protected void showNpFeats_actionPerformed(ActionEvent e)
5195   {
5196     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5197   }
5198
5199   /**
5200    * find the viewport amongst the tabs in this alignment frame and close that
5201    * tab
5202    *
5203    * @param av
5204    */
5205   public boolean closeView(AlignViewportI av)
5206   {
5207     if (viewport == av)
5208     {
5209       this.closeMenuItem_actionPerformed(false);
5210       return true;
5211     }
5212     Component[] comp = tabbedPane.getComponents();
5213     for (int i = 0; comp != null && i < comp.length; i++)
5214     {
5215       if (comp[i] instanceof AlignmentPanel)
5216       {
5217         if (((AlignmentPanel) comp[i]).av == av)
5218         {
5219           // close the view.
5220           closeView((AlignmentPanel) comp[i]);
5221           return true;
5222         }
5223       }
5224     }
5225     return false;
5226   }
5227
5228   protected void build_fetchdbmenu(JMenu webService)
5229   {
5230     // Temporary hack - DBRef Fetcher always top level ws entry.
5231     // TODO We probably want to store a sequence database checklist in
5232     // preferences and have checkboxes.. rather than individual sources selected
5233     // here
5234     final JMenu rfetch = new JMenu(
5235             MessageManager.getString("action.fetch_db_references"));
5236     rfetch.setToolTipText(MessageManager.getString(
5237             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5238     webService.add(rfetch);
5239
5240     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5241             MessageManager.getString("option.trim_retrieved_seqs"));
5242     trimrs.setToolTipText(
5243             MessageManager.getString("label.trim_retrieved_sequences"));
5244     trimrs.setSelected(
5245             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5246     trimrs.addActionListener(new ActionListener()
5247     {
5248       @Override
5249       public void actionPerformed(ActionEvent e)
5250       {
5251         trimrs.setSelected(trimrs.isSelected());
5252         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5253                 Boolean.valueOf(trimrs.isSelected()).toString());
5254       }
5255     });
5256     rfetch.add(trimrs);
5257     JMenuItem fetchr = new JMenuItem(
5258             MessageManager.getString("label.standard_databases"));
5259     fetchr.setToolTipText(
5260             MessageManager.getString("label.fetch_embl_uniprot"));
5261     fetchr.addActionListener(new ActionListener()
5262     {
5263
5264       @Override
5265       public void actionPerformed(ActionEvent e)
5266       {
5267         new Thread(new Runnable()
5268         {
5269           @Override
5270           public void run()
5271           {
5272             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5273                     .getAlignment().isNucleotide();
5274             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5275                     alignPanel.av.getSequenceSelection(),
5276                     alignPanel.alignFrame, null,
5277                     alignPanel.alignFrame.featureSettings, isNucleotide);
5278             dbRefFetcher.addListener(new FetchFinishedListenerI()
5279             {
5280               @Override
5281               public void finished()
5282               {
5283
5284                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5285                         .getFeatureSettingsModels())
5286                 {
5287
5288                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5289                 }
5290                 AlignFrame.this.setMenusForViewport();
5291               }
5292             });
5293             dbRefFetcher.fetchDBRefs(false);
5294           }
5295         }).start();
5296
5297       }
5298
5299     });
5300     rfetch.add(fetchr);
5301     new Thread(new Runnable()
5302     {
5303       @Override
5304       public void run()
5305       {
5306         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5307                 .getSequenceFetcherSingleton();
5308         javax.swing.SwingUtilities.invokeLater(new Runnable()
5309         {
5310           @Override
5311           public void run()
5312           {
5313             String[] dbclasses = sf.getNonAlignmentSources();
5314             List<DbSourceProxy> otherdb;
5315             JMenu dfetch = new JMenu();
5316             JMenu ifetch = new JMenu();
5317             JMenuItem fetchr = null;
5318             int comp = 0, icomp = 0, mcomp = 15;
5319             String mname = null;
5320             int dbi = 0;
5321             for (String dbclass : dbclasses)
5322             {
5323               otherdb = sf.getSourceProxy(dbclass);
5324               // add a single entry for this class, or submenu allowing 'fetch
5325               // all' or pick one
5326               if (otherdb == null || otherdb.size() < 1)
5327               {
5328                 continue;
5329               }
5330               if (mname == null)
5331               {
5332                 mname = "From " + dbclass;
5333               }
5334               if (otherdb.size() == 1)
5335               {
5336                 final DbSourceProxy[] dassource = otherdb
5337                         .toArray(new DbSourceProxy[0]);
5338                 DbSourceProxy src = otherdb.get(0);
5339                 fetchr = new JMenuItem(src.getDbSource());
5340                 fetchr.addActionListener(new ActionListener()
5341                 {
5342
5343                   @Override
5344                   public void actionPerformed(ActionEvent e)
5345                   {
5346                     new Thread(new Runnable()
5347                     {
5348
5349                       @Override
5350                       public void run()
5351                       {
5352                         boolean isNucleotide = alignPanel.alignFrame
5353                                 .getViewport().getAlignment()
5354                                 .isNucleotide();
5355                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5356                                 alignPanel.av.getSequenceSelection(),
5357                                 alignPanel.alignFrame, dassource,
5358                                 alignPanel.alignFrame.featureSettings,
5359                                 isNucleotide);
5360                         dbRefFetcher
5361                                 .addListener(new FetchFinishedListenerI()
5362                                 {
5363                                   @Override
5364                                   public void finished()
5365                                   {
5366                                     FeatureSettingsModelI srcSettings = dassource[0]
5367                                             .getFeatureColourScheme();
5368                                     alignPanel.av.mergeFeaturesStyle(
5369                                             srcSettings);
5370                                     AlignFrame.this.setMenusForViewport();
5371                                   }
5372                                 });
5373                         dbRefFetcher.fetchDBRefs(false);
5374                       }
5375                     }).start();
5376                   }
5377
5378                 });
5379                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5380                         MessageManager.formatMessage(
5381                                 "label.fetch_retrieve_from", new Object[]
5382                                 { src.getDbName() })));
5383                 dfetch.add(fetchr);
5384                 comp++;
5385               }
5386               else
5387               {
5388                 final DbSourceProxy[] dassource = otherdb
5389                         .toArray(new DbSourceProxy[0]);
5390                 // fetch all entry
5391                 DbSourceProxy src = otherdb.get(0);
5392                 fetchr = new JMenuItem(MessageManager
5393                         .formatMessage("label.fetch_all_param", new Object[]
5394                         { src.getDbSource() }));
5395                 fetchr.addActionListener(new ActionListener()
5396                 {
5397                   @Override
5398                   public void actionPerformed(ActionEvent e)
5399                   {
5400                     new Thread(new Runnable()
5401                     {
5402
5403                       @Override
5404                       public void run()
5405                       {
5406                         boolean isNucleotide = alignPanel.alignFrame
5407                                 .getViewport().getAlignment()
5408                                 .isNucleotide();
5409                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5410                                 alignPanel.av.getSequenceSelection(),
5411                                 alignPanel.alignFrame, dassource,
5412                                 alignPanel.alignFrame.featureSettings,
5413                                 isNucleotide);
5414                         dbRefFetcher
5415                                 .addListener(new FetchFinishedListenerI()
5416                                 {
5417                                   @Override
5418                                   public void finished()
5419                                   {
5420                                     AlignFrame.this.setMenusForViewport();
5421                                   }
5422                                 });
5423                         dbRefFetcher.fetchDBRefs(false);
5424                       }
5425                     }).start();
5426                   }
5427                 });
5428
5429                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5430                         MessageManager.formatMessage(
5431                                 "label.fetch_retrieve_from_all_sources",
5432                                 new Object[]
5433                                 { Integer.valueOf(otherdb.size())
5434                                         .toString(),
5435                                     src.getDbSource(), src.getDbName() })));
5436                 dfetch.add(fetchr);
5437                 comp++;
5438                 // and then build the rest of the individual menus
5439                 ifetch = new JMenu(MessageManager.formatMessage(
5440                         "label.source_from_db_source", new Object[]
5441                         { src.getDbSource() }));
5442                 icomp = 0;
5443                 String imname = null;
5444                 int i = 0;
5445                 for (DbSourceProxy sproxy : otherdb)
5446                 {
5447                   String dbname = sproxy.getDbName();
5448                   String sname = dbname.length() > 5
5449                           ? dbname.substring(0, 5) + "..."
5450                           : dbname;
5451                   String msname = dbname.length() > 10
5452                           ? dbname.substring(0, 10) + "..."
5453                           : dbname;
5454                   if (imname == null)
5455                   {
5456                     imname = MessageManager
5457                             .formatMessage("label.from_msname", new Object[]
5458                             { sname });
5459                   }
5460                   fetchr = new JMenuItem(msname);
5461                   final DbSourceProxy[] dassrc = { sproxy };
5462                   fetchr.addActionListener(new ActionListener()
5463                   {
5464
5465                     @Override
5466                     public void actionPerformed(ActionEvent e)
5467                     {
5468                       new Thread(new Runnable()
5469                       {
5470
5471                         @Override
5472                         public void run()
5473                         {
5474                           boolean isNucleotide = alignPanel.alignFrame
5475                                   .getViewport().getAlignment()
5476                                   .isNucleotide();
5477                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5478                                   alignPanel.av.getSequenceSelection(),
5479                                   alignPanel.alignFrame, dassrc,
5480                                   alignPanel.alignFrame.featureSettings,
5481                                   isNucleotide);
5482                           dbRefFetcher
5483                                   .addListener(new FetchFinishedListenerI()
5484                                   {
5485                                     @Override
5486                                     public void finished()
5487                                     {
5488                                       AlignFrame.this.setMenusForViewport();
5489                                     }
5490                                   });
5491                           dbRefFetcher.fetchDBRefs(false);
5492                         }
5493                       }).start();
5494                     }
5495
5496                   });
5497                   fetchr.setToolTipText(
5498                           "<html>" + MessageManager.formatMessage(
5499                                   "label.fetch_retrieve_from", new Object[]
5500                                   { dbname }));
5501                   ifetch.add(fetchr);
5502                   ++i;
5503                   if (++icomp >= mcomp || i == (otherdb.size()))
5504                   {
5505                     ifetch.setText(MessageManager.formatMessage(
5506                             "label.source_to_target", imname, sname));
5507                     dfetch.add(ifetch);
5508                     ifetch = new JMenu();
5509                     imname = null;
5510                     icomp = 0;
5511                     comp++;
5512                   }
5513                 }
5514               }
5515               ++dbi;
5516               if (comp >= mcomp || dbi >= (dbclasses.length))
5517               {
5518                 dfetch.setText(MessageManager.formatMessage(
5519                         "label.source_to_target", mname, dbclass));
5520                 rfetch.add(dfetch);
5521                 dfetch = new JMenu();
5522                 mname = null;
5523                 comp = 0;
5524               }
5525             }
5526           }
5527         });
5528       }
5529     }).start();
5530
5531   }
5532
5533   /**
5534    * Left justify the whole alignment.
5535    */
5536   @Override
5537   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5538   {
5539     AlignmentI al = viewport.getAlignment();
5540     al.justify(false);
5541     viewport.firePropertyChange("alignment", null, al);
5542   }
5543
5544   /**
5545    * Right justify the whole alignment.
5546    */
5547   @Override
5548   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5549   {
5550     AlignmentI al = viewport.getAlignment();
5551     al.justify(true);
5552     viewport.firePropertyChange("alignment", null, al);
5553   }
5554
5555   @Override
5556   public void setShowSeqFeatures(boolean b)
5557   {
5558     showSeqFeatures.setSelected(b);
5559     viewport.setShowSequenceFeatures(b);
5560   }
5561
5562   /*
5563    * (non-Javadoc)
5564    *
5565    * @see
5566    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5567    * awt.event.ActionEvent)
5568    */
5569   @Override
5570   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5571   {
5572     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5573     alignPanel.paintAlignment(false, false);
5574   }
5575
5576   /*
5577    * (non-Javadoc)
5578    *
5579    * @see
5580    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5581    * .ActionEvent)
5582    */
5583   @Override
5584   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5585   {
5586     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5587     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5588
5589   }
5590
5591   /*
5592    * (non-Javadoc)
5593    *
5594    * @see
5595    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5596    * .event.ActionEvent)
5597    */
5598   @Override
5599   protected void showGroupConservation_actionPerformed(ActionEvent e)
5600   {
5601     viewport.setShowGroupConservation(showGroupConservation.getState());
5602     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5603   }
5604
5605   /*
5606    * (non-Javadoc)
5607    *
5608    * @see
5609    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5610    * .event.ActionEvent)
5611    */
5612   @Override
5613   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5614   {
5615     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5616     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5617   }
5618
5619   /*
5620    * (non-Javadoc)
5621    *
5622    * @see
5623    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5624    * .event.ActionEvent)
5625    */
5626   @Override
5627   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5628   {
5629     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5630     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5631   }
5632
5633   @Override
5634   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5635   {
5636     showSequenceLogo.setState(true);
5637     viewport.setShowSequenceLogo(true);
5638     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5639     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5640   }
5641
5642   @Override
5643   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5644   {
5645     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5646   }
5647
5648   /*
5649    * (non-Javadoc)
5650    *
5651    * @see
5652    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5653    * .event.ActionEvent)
5654    */
5655   @Override
5656   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5657   {
5658     if (avc.makeGroupsFromSelection())
5659     {
5660       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5661       alignPanel.updateAnnotation();
5662       alignPanel.paintAlignment(true,
5663               viewport.needToUpdateStructureViews());
5664     }
5665   }
5666
5667   public void clearAlignmentSeqRep()
5668   {
5669     // TODO refactor alignmentseqrep to controller
5670     if (viewport.getAlignment().hasSeqrep())
5671     {
5672       viewport.getAlignment().setSeqrep(null);
5673       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5674       alignPanel.updateAnnotation();
5675       alignPanel.paintAlignment(true, true);
5676     }
5677   }
5678
5679   @Override
5680   protected void createGroup_actionPerformed(ActionEvent e)
5681   {
5682     if (avc.createGroup())
5683     {
5684       if (applyAutoAnnotationSettings.isSelected())
5685       {
5686         alignPanel.updateAnnotation(true, false);
5687       }
5688       alignPanel.alignmentChanged();
5689     }
5690   }
5691
5692   @Override
5693   protected void unGroup_actionPerformed(ActionEvent e)
5694   {
5695     if (avc.unGroup())
5696     {
5697       alignPanel.alignmentChanged();
5698     }
5699   }
5700
5701   /**
5702    * make the given alignmentPanel the currently selected tab
5703    *
5704    * @param alignmentPanel
5705    */
5706   public void setDisplayedView(AlignmentPanel alignmentPanel)
5707   {
5708     if (!viewport.getSequenceSetId()
5709             .equals(alignmentPanel.av.getSequenceSetId()))
5710     {
5711       throw new Error(MessageManager.getString(
5712               "error.implementation_error_cannot_show_view_alignment_frame"));
5713     }
5714     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5715             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5716     {
5717       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5718     }
5719   }
5720
5721   /**
5722    * Action on selection of menu options to Show or Hide annotations.
5723    *
5724    * @param visible
5725    * @param forSequences
5726    *          update sequence-related annotations
5727    * @param forAlignment
5728    *          update non-sequence-related annotations
5729    */
5730   @Override
5731   protected void setAnnotationsVisibility(boolean visible,
5732           boolean forSequences, boolean forAlignment)
5733   {
5734     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5735             .getAlignmentAnnotation();
5736     if (anns == null)
5737     {
5738       return;
5739     }
5740     for (AlignmentAnnotation aa : anns)
5741     {
5742       /*
5743        * don't display non-positional annotations on an alignment
5744        */
5745       if (aa.annotations == null)
5746       {
5747         continue;
5748       }
5749       boolean apply = (aa.sequenceRef == null && forAlignment)
5750               || (aa.sequenceRef != null && forSequences);
5751       if (apply)
5752       {
5753         aa.visible = visible;
5754       }
5755     }
5756     alignPanel.validateAnnotationDimensions(true);
5757     alignPanel.alignmentChanged();
5758   }
5759
5760   /**
5761    * Store selected annotation sort order for the view and repaint.
5762    */
5763   @Override
5764   protected void sortAnnotations_actionPerformed()
5765   {
5766     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5767     this.alignPanel.av
5768             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5769     alignPanel.paintAlignment(false, false);
5770   }
5771
5772   /**
5773    *
5774    * @return alignment panels in this alignment frame
5775    */
5776   public List<? extends AlignmentViewPanel> getAlignPanels()
5777   {
5778     // alignPanels is never null
5779     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5780     return alignPanels;
5781   }
5782
5783   /**
5784    * Open a new alignment window, with the cDNA associated with this (protein)
5785    * alignment, aligned as is the protein.
5786    */
5787   protected void viewAsCdna_actionPerformed()
5788   {
5789     // TODO no longer a menu action - refactor as required
5790     final AlignmentI alignment = getViewport().getAlignment();
5791     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5792     if (mappings == null)
5793     {
5794       return;
5795     }
5796     List<SequenceI> cdnaSeqs = new ArrayList<>();
5797     for (SequenceI aaSeq : alignment.getSequences())
5798     {
5799       for (AlignedCodonFrame acf : mappings)
5800       {
5801         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5802         if (dnaSeq != null)
5803         {
5804           /*
5805            * There is a cDNA mapping for this protein sequence - add to new
5806            * alignment. It will share the same dataset sequence as other mapped
5807            * cDNA (no new mappings need to be created).
5808            */
5809           final Sequence newSeq = new Sequence(dnaSeq);
5810           newSeq.setDatasetSequence(dnaSeq);
5811           cdnaSeqs.add(newSeq);
5812         }
5813       }
5814     }
5815     if (cdnaSeqs.size() == 0)
5816     {
5817       // show a warning dialog no mapped cDNA
5818       return;
5819     }
5820     AlignmentI cdna = new Alignment(
5821             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5822     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5823             AlignFrame.DEFAULT_HEIGHT);
5824     cdna.alignAs(alignment);
5825     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5826             + this.title;
5827     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5828             AlignFrame.DEFAULT_HEIGHT);
5829   }
5830
5831   /**
5832    * Set visibility of dna/protein complement view (available when shown in a
5833    * split frame).
5834    *
5835    * @param show
5836    */
5837   @Override
5838   protected void showComplement_actionPerformed(boolean show)
5839   {
5840     SplitContainerI sf = getSplitViewContainer();
5841     if (sf != null)
5842     {
5843       sf.setComplementVisible(this, show);
5844     }
5845   }
5846
5847   /**
5848    * Generate the reverse (optionally complemented) of the selected sequences,
5849    * and add them to the alignment
5850    */
5851   @Override
5852   protected void showReverse_actionPerformed(boolean complement)
5853   {
5854     AlignmentI al = null;
5855     try
5856     {
5857       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5858       al = dna.reverseCdna(complement);
5859       viewport.addAlignment(al, "");
5860       addHistoryItem(new EditCommand(
5861               MessageManager.getString("label.add_sequences"), Action.PASTE,
5862               al.getSequencesArray(), 0, al.getWidth(),
5863               viewport.getAlignment()));
5864     } catch (Exception ex)
5865     {
5866       System.err.println(ex.getMessage());
5867       return;
5868     }
5869   }
5870
5871   /**
5872    * Try to run a script in the Groovy console, having first ensured that this
5873    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5874    * be targeted at this alignment.
5875    */
5876   @Override
5877   protected void runGroovy_actionPerformed()
5878   {
5879     Jalview.setCurrentAlignFrame(this);
5880     groovy.ui.Console console = Desktop.getGroovyConsole();
5881     if (console != null)
5882     {
5883       try
5884       {
5885         console.runScript();
5886       } catch (Exception ex)
5887       {
5888         System.err.println((ex.toString()));
5889         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5890                 MessageManager.getString("label.couldnt_run_groovy_script"),
5891                 MessageManager.getString("label.groovy_support_failed"),
5892                 JvOptionPane.ERROR_MESSAGE);
5893       }
5894     }
5895     else
5896     {
5897       System.err.println("Can't run Groovy script as console not found");
5898     }
5899   }
5900
5901   /**
5902    * Hides columns containing (or not containing) a specified feature, provided
5903    * that would not leave all columns hidden
5904    *
5905    * @param featureType
5906    * @param columnsContaining
5907    * @return
5908    */
5909   public boolean hideFeatureColumns(String featureType,
5910           boolean columnsContaining)
5911   {
5912     boolean notForHiding = avc.markColumnsContainingFeatures(
5913             columnsContaining, false, false, featureType);
5914     if (notForHiding)
5915     {
5916       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5917               false, featureType))
5918       {
5919         getViewport().hideSelectedColumns();
5920         return true;
5921       }
5922     }
5923     return false;
5924   }
5925
5926   @Override
5927   protected void selectHighlightedColumns_actionPerformed(
5928           ActionEvent actionEvent)
5929   {
5930     // include key modifier check in case user selects from menu
5931     avc.markHighlightedColumns(
5932             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5933             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5934                     | ActionEvent.CTRL_MASK)) != 0);
5935   }
5936
5937   /**
5938    * Rebuilds the Colour menu, including any user-defined colours which have
5939    * been loaded either on startup or during the session
5940    */
5941   public void buildColourMenu()
5942   {
5943     colourMenu.removeAll();
5944
5945     colourMenu.add(applyToAllGroups);
5946     colourMenu.add(textColour);
5947     colourMenu.addSeparator();
5948
5949     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5950             viewport.getAlignment(), false);
5951
5952     colourMenu.add(annotationColour);
5953     bg.add(annotationColour);
5954     colourMenu.addSeparator();
5955     colourMenu.add(conservationMenuItem);
5956     colourMenu.add(modifyConservation);
5957     colourMenu.add(abovePIDThreshold);
5958     colourMenu.add(modifyPID);
5959
5960     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5961     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5962   }
5963
5964   /**
5965    * Open a dialog (if not already open) that allows the user to select and
5966    * calculate PCA or Tree analysis
5967    */
5968   protected void openTreePcaDialog()
5969   {
5970     if (alignPanel.getCalculationDialog() == null)
5971     {
5972       new CalculationChooser(AlignFrame.this);
5973     }
5974   }
5975
5976   /**
5977    * Sets the status of the HMMER menu
5978    */
5979   public void updateHMMERStatus()
5980   {
5981     hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5982   }
5983
5984   @Override
5985   protected void loadVcf_actionPerformed()
5986   {
5987     JalviewFileChooser chooser = new JalviewFileChooser(
5988             Cache.getProperty("LAST_DIRECTORY"));
5989     chooser.setFileView(new JalviewFileView());
5990     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5991     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5992     final AlignFrame us = this;
5993     chooser.setResponseHandler(0, new Runnable()
5994     {
5995       @Override
5996       public void run()
5997       {
5998         String choice = chooser.getSelectedFile().getPath();
5999         Cache.setProperty("LAST_DIRECTORY", choice);
6000         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
6001         new VCFLoader(choice).loadVCF(seqs, us);
6002       }
6003     });
6004     chooser.showOpenDialog(null);
6005
6006   }
6007
6008   private Rectangle lastFeatureSettingsBounds = null;
6009
6010   @Override
6011   public void setFeatureSettingsGeometry(Rectangle bounds)
6012   {
6013     lastFeatureSettingsBounds = bounds;
6014   }
6015
6016   @Override
6017   public Rectangle getFeatureSettingsGeometry()
6018   {
6019     return lastFeatureSettingsBounds;
6020   }
6021 }
6022
6023 class PrintThread extends Thread
6024 {
6025   AlignmentPanel ap;
6026
6027   public PrintThread(AlignmentPanel ap)
6028   {
6029     this.ap = ap;
6030   }
6031
6032   static PageFormat pf;
6033
6034   @Override
6035   public void run()
6036   {
6037     PrinterJob printJob = PrinterJob.getPrinterJob();
6038
6039     if (pf != null)
6040     {
6041       printJob.setPrintable(ap, pf);
6042     }
6043     else
6044     {
6045       printJob.setPrintable(ap);
6046     }
6047
6048     if (printJob.printDialog())
6049     {
6050       try
6051       {
6052         printJob.print();
6053       } catch (Exception PrintException)
6054       {
6055         PrintException.printStackTrace();
6056       }
6057     }
6058   }
6059 }