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.PropertyChangeEvent;
  49 import java.io.File;
  50 import java.io.FileWriter;
  51 import java.io.IOException;
  52 import java.io.OutputStreamWriter;
  53 import java.io.PrintWriter;
  54 import java.net.URL;
  55 import java.util.ArrayList;
  56 import java.util.Arrays;
  57 import java.util.Deque;
  58 import java.util.Enumeration;
  59 import java.util.Hashtable;
  60 import java.util.List;
  61 import java.util.Locale;
  62 import java.util.Vector;
  63
  64 import javax.swing.ButtonGroup;
  65 import javax.swing.JCheckBoxMenuItem;
  66 import javax.swing.JComponent;
  67 import javax.swing.JEditorPane;
  68 import javax.swing.JInternalFrame;
  69 import javax.swing.JLabel;
  70 import javax.swing.JLayeredPane;
  71 import javax.swing.JMenu;
  72 import javax.swing.JMenuItem;
  73 import javax.swing.JPanel;
  74 import javax.swing.JScrollPane;
  75 import javax.swing.SwingUtilities;
  76
  77 import ext.vamsas.ServiceHandle;
  78 import jalview.analysis.AlignmentSorter;
  79 import jalview.analysis.AlignmentUtils;
  80 import jalview.analysis.CrossRef;
  81 import jalview.analysis.Dna;
  82 import jalview.analysis.GeneticCodeI;
  83 import jalview.analysis.ParseProperties;
  84 import jalview.analysis.SequenceIdMatcher;
  85 import jalview.api.AlignExportSettingsI;
  86 import jalview.api.AlignViewControllerGuiI;
  87 import jalview.api.AlignViewControllerI;
  88 import jalview.api.AlignViewportI;
  89 import jalview.api.AlignmentViewPanel;
  90 import jalview.api.FeatureSettingsControllerI;
  91 import jalview.api.FeatureSettingsModelI;
  92 import jalview.api.SplitContainerI;
  93 import jalview.api.ViewStyleI;
  94 import jalview.api.analysis.SimilarityParamsI;
  95 import jalview.bin.Cache;
  96 import jalview.bin.Console;
  97 import jalview.bin.Jalview;
  98 import jalview.commands.CommandI;
  99 import jalview.commands.EditCommand;
 100 import jalview.commands.EditCommand.Action;
 101 import jalview.commands.OrderCommand;
 102 import jalview.commands.RemoveGapColCommand;
 103 import jalview.commands.RemoveGapsCommand;
 104 import jalview.commands.SlideSequencesCommand;
 105 import jalview.commands.TrimRegionCommand;
 106 import jalview.datamodel.AlignExportSettingsAdapter;
 107 import jalview.datamodel.AlignedCodonFrame;
 108 import jalview.datamodel.Alignment;
 109 import jalview.datamodel.AlignmentAnnotation;
 110 import jalview.datamodel.AlignmentExportData;
 111 import jalview.datamodel.AlignmentI;
 112 import jalview.datamodel.AlignmentOrder;
 113 import jalview.datamodel.AlignmentView;
 114 import jalview.datamodel.ColumnSelection;
 115 import jalview.datamodel.ContactMatrixI;
 116 import jalview.datamodel.HiddenColumns;
 117 import jalview.datamodel.PDBEntry;
 118 import jalview.datamodel.SeqCigar;
 119 import jalview.datamodel.Sequence;
 120 import jalview.datamodel.SequenceGroup;
 121 import jalview.datamodel.SequenceI;
 122 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 123 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 124 import jalview.io.AlignmentProperties;
 125 import jalview.io.AnnotationFile;
 126 import jalview.io.BackupFiles;
 127 import jalview.io.BioJsHTMLOutput;
 128 import jalview.io.DataSourceType;
 129 import jalview.io.FileFormat;
 130 import jalview.io.FileFormatI;
 131 import jalview.io.FileFormats;
 132 import jalview.io.FileLoader;
 133 import jalview.io.FileParse;
 134 import jalview.io.FormatAdapter;
 135 import jalview.io.HtmlSvgOutput;
 136 import jalview.io.IdentifyFile;
 137 import jalview.io.JPredFile;
 138 import jalview.io.JalviewFileChooser;
 139 import jalview.io.JalviewFileView;
 140 import jalview.io.JnetAnnotationMaker;
 141 import jalview.io.NewickFile;
 142 import jalview.io.ScoreMatrixFile;
 143 import jalview.io.TCoffeeScoreFile;
 144 import jalview.io.exceptions.ImageOutputException;
 145 import jalview.io.vcf.VCFLoader;
 146 import jalview.jbgui.GAlignFrame;
 147 import jalview.project.Jalview2XML;
 148 import jalview.schemes.ColourSchemeI;
 149 import jalview.schemes.ColourSchemes;
 150 import jalview.schemes.ResidueColourScheme;
 151 import jalview.schemes.TCoffeeColourScheme;
 152 import jalview.util.HttpUtils;
 153 import jalview.util.ImageMaker.TYPE;
 154 import jalview.util.MessageManager;
 155 import jalview.util.Platform;
 156 import jalview.util.imagemaker.BitmapImageSizing;
 157 import jalview.viewmodel.AlignmentViewport;
 158 import jalview.viewmodel.ViewportRanges;
 159 import jalview.ws.DBRefFetcher;
 160 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 161 import jalview.ws.jws1.Discoverer;
 162 import jalview.ws.jws2.Jws2Discoverer;
 163 import jalview.ws.jws2.jabaws2.Jws2Instance;
 164 import jalview.ws.seqfetcher.DbSourceProxy;
 165
 166 /**
 167  * DOCUMENT ME!
 168  *
 169  * @author $author$
 170  * @version $Revision$
 171  */
 172 @SuppressWarnings("serial")
 173 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 174         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 175 {
 176
 177   public static final int DEFAULT_WIDTH = 700;
 178
 179   public static final int DEFAULT_HEIGHT = 500;
 180
 181   /*
 182    * The currently displayed panel (selected tabbed view if more than one)
 183    */
 184   public AlignmentPanel alignPanel;
 185
 186   AlignViewport viewport;
 187
 188   public AlignViewControllerI avc;
 189
 190   List<AlignmentPanel> alignPanels = new ArrayList<>();
 191
 192   /**
 193    * Last format used to load or save alignments in this window
 194    */
 195   FileFormatI currentFileFormat = null;
 196
 197   /**
 198    * Current filename for this alignment
 199    */
 200   String fileName = null;
 201
 202   File fileObject;
 203
 204   /**
 205    * Creates a new AlignFrame object with specific width and height.
 206    *
 207    * @param al
 208    * @param width
 209    * @param height
 210    */
 211   public AlignFrame(AlignmentI al, int width, int height)
 212   {
 213     this(al, null, width, height);
 214   }
 215
 216   /**
 217    * Creates a new AlignFrame object with specific width, height and
 218    * sequenceSetId
 219    *
 220    * @param al
 221    * @param width
 222    * @param height
 223    * @param sequenceSetId
 224    */
 225   public AlignFrame(AlignmentI al, int width, int height,
 226           String sequenceSetId)
 227   {
 228     this(al, null, width, height, sequenceSetId);
 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    * @param viewId
 240    */
 241   public AlignFrame(AlignmentI al, int width, int height,
 242           String sequenceSetId, String viewId)
 243   {
 244     this(al, null, width, height, sequenceSetId, viewId);
 245   }
 246
 247   /**
 248    * new alignment window with hidden columns
 249    *
 250    * @param al
 251    *          AlignmentI
 252    * @param hiddenColumns
 253    *          ColumnSelection or null
 254    * @param width
 255    *          Width of alignment frame
 256    * @param height
 257    *          height of frame.
 258    */
 259   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 260           int height)
 261   {
 262     this(al, hiddenColumns, width, height, null);
 263   }
 264
 265   /**
 266    * Create alignment frame for al with hiddenColumns, a specific width and
 267    * height, and specific sequenceId
 268    *
 269    * @param al
 270    * @param hiddenColumns
 271    * @param width
 272    * @param height
 273    * @param sequenceSetId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 277           int height, String sequenceSetId)
 278   {
 279     this(al, hiddenColumns, width, height, sequenceSetId, null);
 280   }
 281
 282   /**
 283    * Create alignment frame for al with hiddenColumns, a specific width and
 284    * height, and specific sequenceId
 285    *
 286    * @param al
 287    * @param hiddenColumns
 288    * @param width
 289    * @param height
 290    * @param sequenceSetId
 291    *          (may be null)
 292    * @param viewId
 293    *          (may be null)
 294    */
 295   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 296           int height, String sequenceSetId, String viewId)
 297   {
 298     setSize(width, height);
 299
 300     if (al.getDataset() == null)
 301     {
 302       al.setDataset(null);
 303     }
 304
 305     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 306
 307     alignPanel = new AlignmentPanel(this, viewport);
 308
 309     addAlignmentPanel(alignPanel, true);
 310     init();
 311   }
 312
 313   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 314           HiddenColumns hiddenColumns, int width, int height)
 315   {
 316     setSize(width, height);
 317
 318     if (al.getDataset() == null)
 319     {
 320       al.setDataset(null);
 321     }
 322
 323     viewport = new AlignViewport(al, hiddenColumns);
 324
 325     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 326     {
 327       viewport.hideSequence(hiddenSeqs);
 328     }
 329     alignPanel = new AlignmentPanel(this, viewport);
 330     addAlignmentPanel(alignPanel, true);
 331     init();
 332   }
 333
 334   /**
 335    * Make a new AlignFrame from existing alignmentPanels
 336    *
 337    * @param ap
 338    *          AlignmentPanel
 339    * @param av
 340    *          AlignViewport
 341    */
 342   public AlignFrame(AlignmentPanel ap)
 343   {
 344     viewport = ap.av;
 345     alignPanel = ap;
 346     addAlignmentPanel(ap, false);
 347     init();
 348   }
 349
 350   /**
 351    * initalise the alignframe from the underlying viewport data and the
 352    * configurations
 353    */
 354   void init()
 355   {
 356     setFrameIcon(null);
 357
 358     // setBackground(Color.white); // BH 2019
 359
 360     if (!Jalview.isHeadlessMode())
 361     {
 362       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 363     }
 364
 365     avc = new jalview.controller.AlignViewController(this, viewport,
 366             alignPanel);
 367     if (viewport.getAlignmentConservationAnnotation() == null)
 368     {
 369       // BLOSUM62Colour.setEnabled(false);
 370       conservationMenuItem.setEnabled(false);
 371       modifyConservation.setEnabled(false);
 372       // PIDColour.setEnabled(false);
 373       // abovePIDThreshold.setEnabled(false);
 374       // modifyPID.setEnabled(false);
 375     }
 376
 377     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 378
 379     if (sortby.equals("Id"))
 380     {
 381       sortIDMenuItem_actionPerformed(null);
 382     }
 383     else if (sortby.equals("Pairwise Identity"))
 384     {
 385       sortPairwiseMenuItem_actionPerformed(null);
 386     }
 387
 388     this.alignPanel.av
 389             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 390
 391     setMenusFromViewport(viewport);
 392     buildSortByAnnotationScoresMenu();
 393     calculateTree.addActionListener(new ActionListener()
 394     {
 395
 396       @Override
 397       public void actionPerformed(ActionEvent e)
 398       {
 399         openTreePcaDialog();
 400       }
 401     });
 402     buildColourMenu();
 403
 404     if (Desktop.desktop != null)
 405     {
 406       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 407       if (!Platform.isJS())
 408       {
 409         addServiceListeners();
 410       }
 411       setGUINucleotide();
 412     }
 413
 414     if (viewport.getWrapAlignment())
 415     {
 416       wrapMenuItem_actionPerformed(null);
 417     }
 418
 419     if (Cache.getDefault("SHOW_OVERVIEW", false))
 420     {
 421       this.overviewMenuItem_actionPerformed(null);
 422     }
 423
 424     addKeyListener();
 425
 426     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 427     final List<AlignmentPanel> origview = new ArrayList<>();
 428     final String menuLabel = MessageManager
 429             .getString("label.copy_format_from");
 430     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 431             new ViewSetProvider()
 432             {
 433
 434               @Override
 435               public AlignmentPanel[] getAllAlignmentPanels()
 436               {
 437                 origview.clear();
 438                 origview.add(alignPanel);
 439                 // make an array of all alignment panels except for this one
 440                 List<AlignmentPanel> aps = new ArrayList<>(
 441                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 442                 aps.remove(AlignFrame.this.alignPanel);
 443                 return aps.toArray(new AlignmentPanel[aps.size()]);
 444               }
 445             }, selviews, new ItemListener()
 446             {
 447
 448               @Override
 449               public void itemStateChanged(ItemEvent e)
 450               {
 451                 if (origview.size() > 0)
 452                 {
 453                   final AlignmentPanel ap = origview.get(0);
 454
 455                   /*
 456                    * Copy the ViewStyle of the selected panel to 'this one'.
 457                    * Don't change value of 'scaleProteinAsCdna' unless copying
 458                    * from a SplitFrame.
 459                    */
 460                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 461                           .getViewStyle();
 462                   boolean fromSplitFrame = selviews.get(0)
 463                           .getAlignViewport().getCodingComplement() != null;
 464                   if (!fromSplitFrame)
 465                   {
 466                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 467                             .getViewStyle().isScaleProteinAsCdna());
 468                   }
 469                   ap.getAlignViewport().setViewStyle(vs);
 470
 471                   /*
 472                    * Also rescale ViewStyle of SplitFrame complement if there is
 473                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 474                    * the whole ViewStyle (allow cDNA protein to have different
 475                    * fonts)
 476                    */
 477                   AlignViewportI complement = ap.getAlignViewport()
 478                           .getCodingComplement();
 479                   if (complement != null && vs.isScaleProteinAsCdna())
 480                   {
 481                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 482                     ((SplitFrame) af.getSplitViewContainer())
 483                             .adjustLayout();
 484                     af.setMenusForViewport();
 485                   }
 486
 487                   ap.updateLayout();
 488                   ap.setSelected(true);
 489                   ap.alignFrame.setMenusForViewport();
 490
 491                 }
 492               }
 493             });
 494     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 495             .indexOf("devel") > -1
 496             || Cache.getDefault("VERSION", "DEVELOPMENT")
 497                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 498     {
 499       formatMenu.add(vsel);
 500     }
 501     addFocusListener(new FocusAdapter()
 502     {
 503       @Override
 504       public void focusGained(FocusEvent e)
 505       {
 506         Jalview.setCurrentAlignFrame(AlignFrame.this);
 507       }
 508     });
 509
 510   }
 511
 512   /**
 513    * Change the filename and format for the alignment, and enable the 'reload'
 514    * button functionality.
 515    *
 516    * @param file
 517    *          valid filename
 518    * @param format
 519    *          format of file
 520    */
 521   public void setFileName(String file, FileFormatI format)
 522   {
 523     fileName = file;
 524     setFileFormat(format);
 525     reload.setEnabled(true);
 526   }
 527
 528   /**
 529    * JavaScript will have this, maybe others. More dependable than a file name
 530    * and maintains a reference to the actual bytes loaded.
 531    *
 532    * @param file
 533    */
 534   public void setFileObject(File file)
 535   {
 536     this.fileObject = file;
 537   }
 538
 539   /**
 540    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 541    * events
 542    */
 543   void addKeyListener()
 544   {
 545     addKeyListener(new KeyAdapter()
 546     {
 547       @Override
 548       public void keyPressed(KeyEvent evt)
 549       {
 550         if (viewport.cursorMode
 551                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 552                         && evt.getKeyCode() <= KeyEvent.VK_9)
 553                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 554                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 555                 && Character.isDigit(evt.getKeyChar()))
 556         {
 557           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 558         }
 559
 560         switch (evt.getKeyCode())
 561         {
 562
 563         case 27: // escape key
 564           deselectAllSequenceMenuItem_actionPerformed(null);
 565
 566           break;
 567
 568         case KeyEvent.VK_DOWN:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             moveSelectedSequences(false);
 572           }
 573           if (viewport.cursorMode)
 574           {
 575             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 576           }
 577           break;
 578
 579         case KeyEvent.VK_UP:
 580           if (evt.isAltDown() || !viewport.cursorMode)
 581           {
 582             moveSelectedSequences(true);
 583           }
 584           if (viewport.cursorMode)
 585           {
 586             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 587           }
 588
 589           break;
 590
 591         case KeyEvent.VK_LEFT:
 592           if (evt.isAltDown() || !viewport.cursorMode)
 593           {
 594             slideSequences(false,
 595                     alignPanel.getSeqPanel().getKeyboardNo1());
 596           }
 597           else
 598           {
 599             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 600           }
 601
 602           break;
 603
 604         case KeyEvent.VK_RIGHT:
 605           if (evt.isAltDown() || !viewport.cursorMode)
 606           {
 607             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 608           }
 609           else
 610           {
 611             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 612           }
 613           break;
 614
 615         case KeyEvent.VK_SPACE:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 619                     || evt.isShiftDown() || evt.isAltDown());
 620           }
 621           break;
 622
 623         // case KeyEvent.VK_A:
 624         // if (viewport.cursorMode)
 625         // {
 626         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 627         // //jalview.bin.Console.outPrintln("A");
 628         // }
 629         // break;
 630         /*
 631          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 632          * jalview.bin.Console.outPrintln("closing bracket"); } break;
 633          */
 634         case KeyEvent.VK_DELETE:
 635         case KeyEvent.VK_BACK_SPACE:
 636           if (!viewport.cursorMode)
 637           {
 638             cut_actionPerformed();
 639           }
 640           else
 641           {
 642             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 643                     || evt.isShiftDown() || evt.isAltDown());
 644           }
 645
 646           break;
 647
 648         case KeyEvent.VK_S:
 649           if (viewport.cursorMode)
 650           {
 651             alignPanel.getSeqPanel().setCursorRow();
 652           }
 653           break;
 654         case KeyEvent.VK_C:
 655           if (viewport.cursorMode && !evt.isControlDown())
 656           {
 657             alignPanel.getSeqPanel().setCursorColumn();
 658           }
 659           break;
 660         case KeyEvent.VK_P:
 661           if (viewport.cursorMode)
 662           {
 663             alignPanel.getSeqPanel().setCursorPosition();
 664           }
 665           break;
 666
 667         case KeyEvent.VK_ENTER:
 668         case KeyEvent.VK_COMMA:
 669           if (viewport.cursorMode)
 670           {
 671             alignPanel.getSeqPanel().setCursorRowAndColumn();
 672           }
 673           break;
 674
 675         case KeyEvent.VK_Q:
 676           if (viewport.cursorMode)
 677           {
 678             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 679           }
 680           break;
 681         case KeyEvent.VK_M:
 682           if (viewport.cursorMode)
 683           {
 684             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 685           }
 686           break;
 687
 688         case KeyEvent.VK_F2:
 689           viewport.cursorMode = !viewport.cursorMode;
 690           setStatus(MessageManager
 691                   .formatMessage("label.keyboard_editing_mode", new String[]
 692                   { (viewport.cursorMode ? "on" : "off") }));
 693           if (viewport.cursorMode)
 694           {
 695             ViewportRanges ranges = viewport.getRanges();
 696             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 697                     .getStartRes();
 698             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 699                     .getStartSeq();
 700           }
 701           alignPanel.getSeqPanel().seqCanvas.repaint();
 702           break;
 703
 704         case KeyEvent.VK_F1:
 705           try
 706           {
 707             Help.showHelpWindow();
 708           } catch (Exception ex)
 709           {
 710             ex.printStackTrace();
 711           }
 712           break;
 713         case KeyEvent.VK_H:
 714         {
 715           boolean toggleSeqs = !evt.isControlDown();
 716           boolean toggleCols = !evt.isShiftDown();
 717           toggleHiddenRegions(toggleSeqs, toggleCols);
 718           break;
 719         }
 720         case KeyEvent.VK_B:
 721         {
 722           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 723           boolean modifyExisting = true; // always modify, don't clear
 724                                          // evt.isShiftDown();
 725           boolean invertHighlighted = evt.isAltDown();
 726           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 727                   toggleSel);
 728           break;
 729         }
 730         case KeyEvent.VK_PAGE_UP:
 731           viewport.getRanges().pageUp();
 732           break;
 733         case KeyEvent.VK_PAGE_DOWN:
 734           viewport.getRanges().pageDown();
 735           break;
 736         }
 737       }
 738
 739       @Override
 740       public void keyReleased(KeyEvent evt)
 741       {
 742         switch (evt.getKeyCode())
 743         {
 744         case KeyEvent.VK_LEFT:
 745           if (evt.isAltDown() || !viewport.cursorMode)
 746           {
 747             viewport.firePropertyChange("alignment", null,
 748                     viewport.getAlignment().getSequences());
 749           }
 750           break;
 751
 752         case KeyEvent.VK_RIGHT:
 753           if (evt.isAltDown() || !viewport.cursorMode)
 754           {
 755             viewport.firePropertyChange("alignment", null,
 756                     viewport.getAlignment().getSequences());
 757           }
 758           break;
 759         }
 760       }
 761     });
 762   }
 763
 764   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 765   {
 766     ap.alignFrame = this;
 767     avc = new jalview.controller.AlignViewController(this, viewport,
 768             alignPanel);
 769
 770     alignPanels.add(ap);
 771
 772     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 773
 774     int aSize = alignPanels.size();
 775
 776     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 777
 778     if (aSize == 1 && ap.av.getViewName() == null)
 779     {
 780       this.getContentPane().add(ap, BorderLayout.CENTER);
 781     }
 782     else
 783     {
 784       if (aSize == 2)
 785       {
 786         setInitialTabVisible();
 787       }
 788
 789       expandViews.setEnabled(true);
 790       gatherViews.setEnabled(true);
 791       tabbedPane.addTab(ap.av.getViewName(), ap);
 792
 793       ap.setVisible(false);
 794     }
 795
 796     if (newPanel)
 797     {
 798       if (ap.av.isPadGaps())
 799       {
 800         ap.av.getAlignment().padGaps();
 801       }
 802       ap.av.updateConservation(ap);
 803       ap.av.updateConsensus(ap);
 804       ap.av.updateStrucConsensus(ap);
 805     }
 806   }
 807
 808   public void setInitialTabVisible()
 809   {
 810     expandViews.setEnabled(true);
 811     gatherViews.setEnabled(true);
 812     tabbedPane.setVisible(true);
 813     AlignmentPanel first = alignPanels.get(0);
 814     tabbedPane.addTab(first.av.getViewName(), first);
 815     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 816   }
 817
 818   public AlignViewport getViewport()
 819   {
 820     return viewport;
 821   }
 822
 823   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 824   private void addServiceListeners()
 825   {
 826     final java.beans.PropertyChangeListener thisListener;
 827     Desktop.instance.addJalviewPropertyChangeListener("services",
 828             thisListener = new java.beans.PropertyChangeListener()
 829             {
 830               @Override
 831               public void propertyChange(PropertyChangeEvent evt)
 832               {
 833                 // // jalview.bin.Console.outPrintln("Discoverer property
 834                 // change.");
 835                 // if (evt.getPropertyName().equals("services"))
 836                 {
 837                   SwingUtilities.invokeLater(new Runnable()
 838                   {
 839
 840                     @Override
 841                     public void run()
 842                     {
 843                       jalview.bin.Console.errPrintln(
 844                               "Rebuild WS Menu for service change");
 845                       BuildWebServiceMenu();
 846                     }
 847
 848                   });
 849                 }
 850               }
 851             });
 852     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 853     {
 854       @Override
 855       public void internalFrameClosed(
 856               javax.swing.event.InternalFrameEvent evt)
 857       {
 858         // jalview.bin.Console.outPrintln("deregistering discoverer listener");
 859         Desktop.instance.removeJalviewPropertyChangeListener("services",
 860                 thisListener);
 861         closeMenuItem_actionPerformed(true);
 862       }
 863     });
 864     // Finally, build the menu once to get current service state
 865     new Thread(new Runnable()
 866     {
 867       @Override
 868       public void run()
 869       {
 870         BuildWebServiceMenu();
 871       }
 872     }).start();
 873   }
 874
 875   /**
 876    * Configure menu items that vary according to whether the alignment is
 877    * nucleotide or protein
 878    */
 879   public void setGUINucleotide()
 880   {
 881     AlignmentI al = getViewport().getAlignment();
 882     boolean nucleotide = al.isNucleotide();
 883
 884     loadVcf.setVisible(nucleotide);
 885     showTranslation.setVisible(nucleotide);
 886     showReverse.setVisible(nucleotide);
 887     showReverseComplement.setVisible(nucleotide);
 888     conservationMenuItem.setEnabled(!nucleotide);
 889     modifyConservation
 890             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 891     showGroupConservation.setEnabled(!nucleotide);
 892
 893     showComplementMenuItem
 894             .setText(nucleotide ? MessageManager.getString("label.protein")
 895                     : MessageManager.getString("label.nucleotide"));
 896   }
 897
 898   /**
 899    * set up menus for the current viewport. This may be called after any
 900    * operation that affects the data in the current view (selection changed,
 901    * etc) to update the menus to reflect the new state.
 902    */
 903   @Override
 904   public void setMenusForViewport()
 905   {
 906     setMenusFromViewport(viewport);
 907   }
 908
 909   /**
 910    * Need to call this method when tabs are selected for multiple views, or when
 911    * loading from Jalview2XML.java
 912    *
 913    * @param av
 914    *          AlignViewport
 915    */
 916   public void setMenusFromViewport(AlignViewport av)
 917   {
 918     padGapsMenuitem.setSelected(av.isPadGaps());
 919     colourTextMenuItem.setSelected(av.isShowColourText());
 920     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 921     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 922     conservationMenuItem.setSelected(av.getConservationSelected());
 923     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 924     seqLimits.setSelected(av.getShowJVSuffix());
 925     idRightAlign.setSelected(av.isRightAlignIds());
 926     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 927     renderGapsMenuItem.setSelected(av.isRenderGaps());
 928     wrapMenuItem.setSelected(av.getWrapAlignment());
 929     scaleAbove.setVisible(av.getWrapAlignment());
 930     scaleLeft.setVisible(av.getWrapAlignment());
 931     scaleRight.setVisible(av.getWrapAlignment());
 932     annotationPanelMenuItem.setState(av.isShowAnnotation());
 933     /*
 934      * Show/hide annotations only enabled if annotation panel is shown
 935      */
 936     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 938     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 939     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 940     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 941     viewTextMenuItem.setSelected(av.getShowText());
 942     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 943     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 944     showGroupConservation.setSelected(av.isShowGroupConservation());
 945     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 946     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 947     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 948
 949     ColourMenuHelper.setColourSelected(colourMenu,
 950             av.getGlobalColourScheme());
 951
 952     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 953     hiddenMarkers.setState(av.getShowHiddenMarkers());
 954     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 955     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 956     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 957     autoCalculate.setSelected(av.autoCalculateConsensus);
 958     sortByTree.setSelected(av.sortByTree);
 959     listenToViewSelections.setSelected(av.followSelection);
 960
 961     showProducts.setEnabled(canShowProducts());
 962     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 963
 964     updateEditMenuBar();
 965   }
 966
 967   /**
 968    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 969    *
 970    * @param b
 971    */
 972   public void setGroovyEnabled(boolean b)
 973   {
 974     runGroovy.setEnabled(b);
 975   }
 976
 977   private IProgressIndicator progressBar;
 978
 979   /*
 980    * (non-Javadoc)
 981    *
 982    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 983    */
 984   @Override
 985   public void setProgressBar(String message, long id)
 986   {
 987     if (!Platform.isHeadless() && progressBar != null)
 988       progressBar.setProgressBar(message, id);
 989   }
 990
 991   @Override
 992   public void registerHandler(final long id,
 993           final IProgressIndicatorHandler handler)
 994   {
 995     if (progressBar != null)
 996       progressBar.registerHandler(id, handler);
 997   }
 998
 999   /**
1000    *
1001    * @return true if any progress bars are still active
1002    */
1003   @Override
1004   public boolean operationInProgress()
1005   {
1006     return progressBar == null ? false : progressBar.operationInProgress();
1007   }
1008
1009   /**
1010    * Sets the text of the status bar. Note that setting a null or empty value
1011    * will cause the status bar to be hidden, with possibly undesirable flicker
1012    * of the screen layout.
1013    */
1014   @Override
1015   public void setStatus(String text)
1016   {
1017     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1018   }
1019
1020   /*
1021    * Added so Castor Mapping file can obtain Jalview Version
1022    */
1023   public String getVersion()
1024   {
1025     return Cache.getProperty("VERSION");
1026   }
1027
1028   public FeatureRenderer getFeatureRenderer()
1029   {
1030     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1031   }
1032
1033   @Override
1034   public void fetchSequence_actionPerformed()
1035   {
1036     new SequenceFetcher(this);
1037   }
1038
1039   @Override
1040   public void addFromFile_actionPerformed(ActionEvent e)
1041   {
1042     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1043   }
1044
1045   @Override
1046   public void reload_actionPerformed(ActionEvent e)
1047   {
1048     if (fileName != null)
1049     {
1050       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1051       // originating file's format
1052       // TODO: work out how to recover feature settings for correct view(s) when
1053       // file is reloaded.
1054       if (FileFormat.Jalview.equals(currentFileFormat))
1055       {
1056         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1057         for (int i = 0; i < frames.length; i++)
1058         {
1059           if (frames[i] instanceof AlignFrame && frames[i] != this
1060                   && ((AlignFrame) frames[i]).fileName != null
1061                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1062           {
1063             try
1064             {
1065               frames[i].setSelected(true);
1066               Desktop.instance.closeAssociatedWindows();
1067             } catch (java.beans.PropertyVetoException ex)
1068             {
1069             }
1070           }
1071
1072         }
1073         Desktop.instance.closeAssociatedWindows();
1074
1075         FileLoader loader = new FileLoader();
1076         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1077                 ? DataSourceType.URL
1078                 : DataSourceType.FILE;
1079         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1080       }
1081       else
1082       {
1083         Rectangle bounds = this.getBounds();
1084
1085         FileLoader loader = new FileLoader();
1086
1087         AlignFrame newframe = null;
1088
1089         if (fileObject == null)
1090         {
1091
1092           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1093                   fileName) ? DataSourceType.URL : DataSourceType.FILE;
1094           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1095                   currentFileFormat);
1096         }
1097         else
1098         {
1099           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1100                   DataSourceType.FILE, currentFileFormat);
1101         }
1102
1103         newframe.setBounds(bounds);
1104         if (featureSettings != null && featureSettings.isShowing())
1105         {
1106           final Rectangle fspos = featureSettings.frame.getBounds();
1107           // TODO: need a 'show feature settings' function that takes bounds -
1108           // need to refactor Desktop.addFrame
1109           newframe.featureSettings_actionPerformed(null);
1110           final FeatureSettings nfs = newframe.featureSettings;
1111           SwingUtilities.invokeLater(new Runnable()
1112           {
1113             @Override
1114             public void run()
1115             {
1116               nfs.frame.setBounds(fspos);
1117             }
1118           });
1119           this.featureSettings.close();
1120           this.featureSettings = null;
1121         }
1122         this.closeMenuItem_actionPerformed(true);
1123       }
1124     }
1125   }
1126
1127   @Override
1128   public void addFromText_actionPerformed(ActionEvent e)
1129   {
1130     Desktop.instance
1131             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1132   }
1133
1134   @Override
1135   public void addFromURL_actionPerformed(ActionEvent e)
1136   {
1137     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1138   }
1139
1140   @Override
1141   public void save_actionPerformed(ActionEvent e)
1142   {
1143     if (fileName == null || (currentFileFormat == null)
1144             || HttpUtils.startsWithHttpOrHttps(fileName))
1145     {
1146       saveAs_actionPerformed();
1147     }
1148     else
1149     {
1150       saveAlignment(fileName, currentFileFormat);
1151     }
1152   }
1153
1154   /**
1155    * Saves the alignment to a file with a name chosen by the user, if necessary
1156    * warning if a file would be overwritten
1157    */
1158   @Override
1159   public void saveAs_actionPerformed()
1160   {
1161     String format = currentFileFormat == null ? null
1162             : currentFileFormat.getName();
1163     JalviewFileChooser chooser = JalviewFileChooser
1164             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1165
1166     chooser.setFileView(new JalviewFileView());
1167     chooser.setDialogTitle(
1168             MessageManager.getString("label.save_alignment_to_file"));
1169     chooser.setToolTipText(MessageManager.getString("action.save"));
1170
1171     int value = chooser.showSaveDialog(this);
1172
1173     if (value != JalviewFileChooser.APPROVE_OPTION)
1174     {
1175       return;
1176     }
1177     currentFileFormat = chooser.getSelectedFormat();
1178     // todo is this (2005) test now obsolete - value is never null?
1179     while (currentFileFormat == null)
1180     {
1181       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1182               MessageManager
1183                       .getString("label.select_file_format_before_saving"),
1184               MessageManager.getString("label.file_format_not_specified"),
1185               JvOptionPane.WARNING_MESSAGE);
1186       currentFileFormat = chooser.getSelectedFormat();
1187       value = chooser.showSaveDialog(this);
1188       if (value != JalviewFileChooser.APPROVE_OPTION)
1189       {
1190         return;
1191       }
1192     }
1193
1194     fileName = chooser.getSelectedFile().getPath();
1195
1196     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1197     Cache.setProperty("LAST_DIRECTORY", fileName);
1198     saveAlignment(fileName, currentFileFormat);
1199   }
1200
1201   boolean lastSaveSuccessful = false;
1202
1203   FileFormatI lastFormatSaved;
1204
1205   String lastFilenameSaved;
1206
1207   /**
1208    * Raise a dialog or status message for the last call to saveAlignment.
1209    *
1210    * @return true if last call to saveAlignment(file, format) was successful.
1211    */
1212   public boolean isSaveAlignmentSuccessful()
1213   {
1214
1215     if (!lastSaveSuccessful)
1216     {
1217       if (!Platform.isHeadless())
1218       {
1219         JvOptionPane.showInternalMessageDialog(this, MessageManager
1220                 .formatMessage("label.couldnt_save_file", new Object[]
1221                 { lastFilenameSaved }),
1222                 MessageManager.getString("label.error_saving_file"),
1223                 JvOptionPane.WARNING_MESSAGE);
1224       }
1225       else
1226       {
1227         Console.error(MessageManager
1228                 .formatMessage("label.couldnt_save_file", new Object[]
1229                 { lastFilenameSaved }));
1230       }
1231     }
1232     else
1233     {
1234
1235       setStatus(MessageManager.formatMessage(
1236               "label.successfully_saved_to_file_in_format", new Object[]
1237               { lastFilenameSaved, lastFormatSaved }));
1238
1239     }
1240     return lastSaveSuccessful;
1241   }
1242
1243   /**
1244    * Saves the alignment to the specified file path, in the specified format,
1245    * which may be an alignment format, or Jalview project format. If the
1246    * alignment has hidden regions, or the format is one capable of including
1247    * non-sequence data (features, annotations, groups), then the user may be
1248    * prompted to specify what to include in the output.
1249    *
1250    * @param file
1251    * @param format
1252    */
1253   public void saveAlignment(String file, FileFormatI format)
1254   {
1255     saveAlignment(file, format, false);
1256   }
1257
1258   public void saveAlignment(String file, FileFormatI format, boolean stdout)
1259   {
1260     lastSaveSuccessful = true;
1261     if (!stdout)
1262     {
1263       lastFilenameSaved = file;
1264     }
1265     lastFormatSaved = format;
1266
1267     if (FileFormat.Jalview.equals(format))
1268     {
1269       String shortName = title;
1270       if (shortName.indexOf(File.separatorChar) > -1)
1271       {
1272         shortName = shortName
1273                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1274       }
1275       // TODO deal with stdout=true
1276       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1277               shortName);
1278
1279       Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1280       if (lastSaveSuccessful)
1281       {
1282         this.getViewport().setSavedUpToDate(true);
1283       }
1284
1285       statusBar.setText(MessageManager.formatMessage(
1286               "label.successfully_saved_to_file_in_format", new Object[]
1287               { file, format }));
1288
1289       return;
1290     }
1291
1292     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1293     Runnable cancelAction = () -> {
1294       lastSaveSuccessful = false;
1295     };
1296     Runnable outputAction = () -> {
1297       // todo defer this to inside formatSequences (or later)
1298       AlignmentExportData exportData = viewport.getAlignExportData(options);
1299       String output = new FormatAdapter(alignPanel, options)
1300               .formatSequences(format, exportData.getAlignment(),
1301                       exportData.getOmitHidden(),
1302                       exportData.getStartEndPostions(),
1303                       viewport.getAlignment().getHiddenColumns());
1304       if (output == null)
1305       {
1306         lastSaveSuccessful = false;
1307       }
1308       else
1309       {
1310         // create backupfiles object and get new temp filename destination
1311         boolean doBackup = BackupFiles.getEnabled() && !stdout;
1312         BackupFiles backupfiles = null;
1313         if (doBackup)
1314         {
1315           Console.trace("ALIGNFRAME making backupfiles object for " + file);
1316           backupfiles = new BackupFiles(file);
1317         }
1318         try
1319         {
1320           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1321                   : file;
1322           Console.trace("ALIGNFRAME setting PrintWriter");
1323           PrintWriter out = stdout
1324                   ? new PrintWriter(new OutputStreamWriter(System.out))
1325                   : new PrintWriter(new FileWriter(tempFilePath));
1326
1327           if (backupfiles != null)
1328           {
1329             Console.trace("ALIGNFRAME about to write to temp file "
1330                     + backupfiles.getTempFilePath());
1331           }
1332
1333           out.print(output);
1334           out.flush();
1335           if (!stdout)
1336           {
1337             Console.trace("ALIGNFRAME about to close file");
1338             out.close();
1339             Console.trace("ALIGNFRAME closed file");
1340           }
1341           AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
1342           if (stdout)
1343           {
1344             statusBar.setText(MessageManager.formatMessage(
1345                     "label.successfully_printed_to_stdout_in_format",
1346                     new Object[]
1347                     { format.getName() }));
1348           }
1349           else
1350           {
1351             statusBar.setText(MessageManager.formatMessage(
1352                     "label.successfully_saved_to_file_in_format",
1353                     new Object[]
1354                     { fileName, format.getName() }));
1355           }
1356           lastSaveSuccessful = true;
1357         } catch (IOException e)
1358         {
1359           lastSaveSuccessful = false;
1360           Console.error(
1361                   "ALIGNFRAME Something happened writing the temp file");
1362           Console.error(e.getMessage());
1363           Console.debug(Cache.getStackTraceString(e));
1364         } catch (Exception ex)
1365         {
1366           lastSaveSuccessful = false;
1367           Console.error(
1368                   "ALIGNFRAME Something unexpected happened writing the temp file");
1369           Console.error(ex.getMessage());
1370           Console.debug(Cache.getStackTraceString(ex));
1371         }
1372
1373         if (doBackup)
1374         {
1375           backupfiles.setWriteSuccess(lastSaveSuccessful);
1376           Console.debug("ALIGNFRAME writing temp file was "
1377                   + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1378           // do the backup file roll and rename the temp file to actual file
1379           Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1380           lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1381           Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1382                   + (lastSaveSuccessful ? "" : "un") + "successfully");
1383         }
1384
1385         Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1386         if (lastSaveSuccessful)
1387         {
1388           AlignFrame.this.getViewport().setSavedUpToDate(true);
1389         }
1390       }
1391     };
1392
1393     /*
1394      * show dialog with export options if applicable; else just do it
1395      */
1396     if (AlignExportOptions.isNeeded(viewport, format))
1397     {
1398       AlignExportOptions choices = new AlignExportOptions(
1399               alignPanel.getAlignViewport(), format, options);
1400       choices.setResponseAction(0, outputAction);
1401       choices.setResponseAction(1, cancelAction);
1402       choices.showDialog();
1403     }
1404     else
1405     {
1406       try
1407       {
1408         outputAction.run();
1409       } catch (Exception e)
1410       {
1411         // TODO Auto-generated catch block
1412         e.printStackTrace();
1413       }
1414     }
1415   }
1416
1417   /**
1418    * Outputs the alignment to textbox in the requested format, if necessary
1419    * first prompting the user for whether to include hidden regions or
1420    * non-sequence data
1421    *
1422    * @param fileFormatName
1423    */
1424   @Override
1425   protected void outputText_actionPerformed(String fileFormatName)
1426   {
1427     FileFormatI fileFormat = FileFormats.getInstance()
1428             .forName(fileFormatName);
1429     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1430     Runnable outputAction = () -> {
1431       // todo defer this to inside formatSequences (or later)
1432       AlignmentExportData exportData = viewport.getAlignExportData(options);
1433       CutAndPasteTransfer cap = new CutAndPasteTransfer();
1434       cap.setForInput(null);
1435       try
1436       {
1437         FileFormatI format = fileFormat;
1438         cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
1439                 format, exportData.getAlignment(),
1440                 exportData.getOmitHidden(),
1441                 exportData.getStartEndPostions(),
1442                 viewport.getAlignment().getHiddenColumns()));
1443         Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1444                 "label.alignment_output_command", new Object[]
1445                 { fileFormat.getName() }), 600, 500);
1446       } catch (OutOfMemoryError oom)
1447       {
1448         new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1449                 oom);
1450         cap.dispose();
1451       }
1452     };
1453
1454     /*
1455      * show dialog with export options if applicable; else just do it
1456      */
1457     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1458     {
1459       AlignExportOptions choices = new AlignExportOptions(
1460               alignPanel.getAlignViewport(), fileFormat, options);
1461       choices.setResponseAction(0, outputAction);
1462       choices.showDialog();
1463     }
1464     else
1465     {
1466       try
1467       {
1468         outputAction.run();
1469       } catch (Exception e)
1470       {
1471         e.printStackTrace();
1472       }
1473     }
1474   }
1475
1476   /**
1477    * DOCUMENT ME!
1478    *
1479    * @param e
1480    *          DOCUMENT ME!
1481    */
1482   @Override
1483   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1484   {
1485     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1486     try
1487     {
1488       htmlSVG.exportHTML(null);
1489     } catch (ImageOutputException x)
1490     {
1491       // report problem to console and raise dialog
1492     }
1493   }
1494
1495   @Override
1496   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1497   {
1498     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1499     try
1500     {
1501       bjs.exportHTML(null);
1502     } catch (ImageOutputException x)
1503     {
1504       // report problem to console and raise dialog
1505     }
1506   }
1507
1508   public void createImageMap(File file, String image)
1509   {
1510     try
1511     {
1512       alignPanel.makePNGImageMap(file, image);
1513     } catch (ImageOutputException x)
1514     {
1515       // report problem to console and raise dialog
1516     }
1517   }
1518
1519   @Override
1520   public void createPNG_actionPerformed(ActionEvent e)
1521   {
1522     try
1523     {
1524       createPNG(null);
1525     } catch (ImageOutputException ioex)
1526     {
1527       // raise dialog, and report via console
1528     }
1529   }
1530
1531   @Override
1532   public void createEPS_actionPerformed(ActionEvent e)
1533   {
1534     try
1535     {
1536       createEPS(null);
1537     } catch (ImageOutputException ioex)
1538     {
1539       // raise dialog, and report via console
1540     }
1541
1542   }
1543
1544   @Override
1545   public void createSVG_actionPerformed(ActionEvent e)
1546   {
1547     try
1548     {
1549       createSVG(null);
1550     } catch (ImageOutputException ioex)
1551     {
1552       // raise dialog, and report via console
1553     }
1554
1555   }
1556
1557   /**
1558    * Creates a PNG image of the alignment and writes it to the given file. If
1559    * the file is null, the user is prompted to choose a file.
1560    *
1561    * @param f
1562    */
1563   public void createPNG(File f) throws ImageOutputException
1564   {
1565     createPNG(f, null, BitmapImageSizing.defaultBitmapImageSizing());
1566   }
1567
1568   public void createPNG(File f, String renderer, BitmapImageSizing userBis)
1569           throws ImageOutputException
1570   {
1571     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
1572   }
1573
1574   /**
1575    * Creates an EPS image of the alignment and writes it to the given file. If
1576    * the file is null, the user is prompted to choose a file.
1577    *
1578    * @param f
1579    */
1580   public void createEPS(File f) throws ImageOutputException
1581   {
1582     createEPS(f, null);
1583   }
1584
1585   public void createEPS(File f, String renderer) throws ImageOutputException
1586   {
1587     alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
1588   }
1589
1590   /**
1591    * Creates an SVG image of the alignment and writes it to the given file. If
1592    * the file is null, the user is prompted to choose a file.
1593    *
1594    * @param f
1595    */
1596   public void createSVG(File f) throws ImageOutputException
1597   {
1598     createSVG(f, null);
1599   }
1600
1601   public void createSVG(File f, String renderer) throws ImageOutputException
1602   {
1603     alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
1604   }
1605
1606   @Override
1607   public void pageSetup_actionPerformed(ActionEvent e)
1608   {
1609     PrinterJob printJob = PrinterJob.getPrinterJob();
1610     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1611   }
1612
1613   /**
1614    * DOCUMENT ME!
1615    *
1616    * @param e
1617    *          DOCUMENT ME!
1618    */
1619   @Override
1620   public void printMenuItem_actionPerformed(ActionEvent e)
1621   {
1622     // Putting in a thread avoids Swing painting problems
1623     PrintThread thread = new PrintThread(alignPanel);
1624     thread.start();
1625   }
1626
1627   @Override
1628   public void exportFeatures_actionPerformed(ActionEvent e)
1629   {
1630     new AnnotationExporter(alignPanel).exportFeatures();
1631   }
1632
1633   @Override
1634   public void exportAnnotations_actionPerformed(ActionEvent e)
1635   {
1636     new AnnotationExporter(alignPanel).exportAnnotations();
1637   }
1638
1639   @Override
1640   public void associatedData_actionPerformed(ActionEvent e)
1641   {
1642     final JalviewFileChooser chooser = new JalviewFileChooser(
1643             Cache.getProperty("LAST_DIRECTORY"));
1644     chooser.setFileView(new JalviewFileView());
1645     String tooltip = MessageManager
1646             .getString("label.load_jalview_annotations");
1647     chooser.setDialogTitle(tooltip);
1648     chooser.setToolTipText(tooltip);
1649     chooser.setResponseHandler(0, () -> {
1650       String choice = chooser.getSelectedFile().getPath();
1651       Cache.setProperty("LAST_DIRECTORY", choice);
1652       loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1653     });
1654
1655     chooser.showOpenDialog(this);
1656   }
1657
1658   /**
1659    * Close the current view or all views in the alignment frame. If the frame
1660    * only contains one view then the alignment will be removed from memory.
1661    *
1662    * @param closeAllTabs
1663    */
1664   @Override
1665   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1666   {
1667     if (alignPanels != null && alignPanels.size() < 2)
1668     {
1669       closeAllTabs = true;
1670     }
1671
1672     Desktop.closeModal(this);
1673
1674     try
1675     {
1676       if (alignPanels != null)
1677       {
1678         if (closeAllTabs)
1679         {
1680           if (this.isClosed())
1681           {
1682             // really close all the windows - otherwise wait till
1683             // setClosed(true) is called
1684             for (int i = 0; i < alignPanels.size(); i++)
1685             {
1686               AlignmentPanel ap = alignPanels.get(i);
1687               ap.closePanel();
1688             }
1689           }
1690         }
1691         else
1692         {
1693           closeView(alignPanel);
1694         }
1695       }
1696       if (closeAllTabs)
1697       {
1698         if (featureSettings != null && featureSettings.isOpen())
1699         {
1700           featureSettings.close();
1701           featureSettings = null;
1702         }
1703
1704         /*
1705          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1706          * be called recursively, with the frame now in 'closed' state
1707          */
1708         this.setClosed(true);
1709       }
1710     } catch (Exception ex)
1711     {
1712       ex.printStackTrace();
1713     }
1714   }
1715
1716   /**
1717    * Close the specified panel and close up tabs appropriately.
1718    *
1719    * @param panelToClose
1720    */
1721   public void closeView(AlignmentPanel panelToClose)
1722   {
1723     int index = tabbedPane.getSelectedIndex();
1724     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1725     alignPanels.remove(panelToClose);
1726     panelToClose.closePanel();
1727     panelToClose = null;
1728
1729     tabbedPane.removeTabAt(closedindex);
1730     tabbedPane.validate();
1731
1732     if (index > closedindex || index == tabbedPane.getTabCount())
1733     {
1734       // modify currently selected tab index if necessary.
1735       index--;
1736     }
1737
1738     this.tabSelectionChanged(index);
1739   }
1740
1741   /**
1742    * DOCUMENT ME!
1743    */
1744   void updateEditMenuBar()
1745   {
1746
1747     if (viewport.getHistoryList().size() > 0)
1748     {
1749       undoMenuItem.setEnabled(true);
1750       CommandI command = viewport.getHistoryList().peek();
1751       undoMenuItem.setText(MessageManager
1752               .formatMessage("label.undo_command", new Object[]
1753               { command.getDescription() }));
1754     }
1755     else
1756     {
1757       undoMenuItem.setEnabled(false);
1758       undoMenuItem.setText(MessageManager.getString("action.undo"));
1759     }
1760
1761     if (viewport.getRedoList().size() > 0)
1762     {
1763       redoMenuItem.setEnabled(true);
1764
1765       CommandI command = viewport.getRedoList().peek();
1766       redoMenuItem.setText(MessageManager
1767               .formatMessage("label.redo_command", new Object[]
1768               { command.getDescription() }));
1769     }
1770     else
1771     {
1772       redoMenuItem.setEnabled(false);
1773       redoMenuItem.setText(MessageManager.getString("action.redo"));
1774     }
1775   }
1776
1777   @Override
1778   public void addHistoryItem(CommandI command)
1779   {
1780     if (command.getSize() > 0)
1781     {
1782       viewport.addToHistoryList(command);
1783       viewport.clearRedoList();
1784       updateEditMenuBar();
1785       viewport.updateHiddenColumns();
1786       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1787       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1788       // viewport.getColumnSelection()
1789       // .getHiddenColumns().size() > 0);
1790     }
1791   }
1792
1793   /**
1794    *
1795    * @return alignment objects for all views
1796    */
1797   public AlignmentI[] getViewAlignments()
1798   {
1799     if (alignPanels != null)
1800     {
1801       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1802       int i = 0;
1803       for (AlignmentPanel ap : alignPanels)
1804       {
1805         als[i++] = ap.av.getAlignment();
1806       }
1807       return als;
1808     }
1809     if (viewport != null)
1810     {
1811       return new AlignmentI[] { viewport.getAlignment() };
1812     }
1813     return null;
1814   }
1815
1816   /**
1817    * DOCUMENT ME!
1818    *
1819    * @param e
1820    *          DOCUMENT ME!
1821    */
1822   @Override
1823   protected void undoMenuItem_actionPerformed(ActionEvent e)
1824   {
1825     if (viewport.getHistoryList().isEmpty())
1826     {
1827       return;
1828     }
1829     CommandI command = viewport.getHistoryList().pop();
1830     viewport.addToRedoList(command);
1831     command.undoCommand(getViewAlignments());
1832
1833     AlignmentViewport originalSource = getOriginatingSource(command);
1834     updateEditMenuBar();
1835
1836     if (originalSource != null)
1837     {
1838       if (originalSource != viewport)
1839       {
1840         Console.warn(
1841                 "Implementation worry: mismatch of viewport origin for undo");
1842       }
1843       originalSource.updateHiddenColumns();
1844       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1845       // null
1846       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1847       // viewport.getColumnSelection()
1848       // .getHiddenColumns().size() > 0);
1849       originalSource.firePropertyChange("alignment", null,
1850               originalSource.getAlignment().getSequences());
1851     }
1852   }
1853
1854   /**
1855    * DOCUMENT ME!
1856    *
1857    * @param e
1858    *          DOCUMENT ME!
1859    */
1860   @Override
1861   protected void redoMenuItem_actionPerformed(ActionEvent e)
1862   {
1863     if (viewport.getRedoList().size() < 1)
1864     {
1865       return;
1866     }
1867
1868     CommandI command = viewport.getRedoList().pop();
1869     viewport.addToHistoryList(command);
1870     command.doCommand(getViewAlignments());
1871
1872     AlignmentViewport originalSource = getOriginatingSource(command);
1873     updateEditMenuBar();
1874
1875     if (originalSource != null)
1876     {
1877
1878       if (originalSource != viewport)
1879       {
1880         Console.warn(
1881                 "Implementation worry: mismatch of viewport origin for redo");
1882       }
1883       originalSource.updateHiddenColumns();
1884       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1885       // null
1886       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1887       // viewport.getColumnSelection()
1888       // .getHiddenColumns().size() > 0);
1889       originalSource.firePropertyChange("alignment", null,
1890               originalSource.getAlignment().getSequences());
1891     }
1892   }
1893
1894   AlignmentViewport getOriginatingSource(CommandI command)
1895   {
1896     AlignmentViewport originalSource = null;
1897     // For sequence removal and addition, we need to fire
1898     // the property change event FROM the viewport where the
1899     // original alignment was altered
1900     AlignmentI al = null;
1901     if (command instanceof EditCommand)
1902     {
1903       EditCommand editCommand = (EditCommand) command;
1904       al = editCommand.getAlignment();
1905       List<Component> comps = PaintRefresher.components
1906               .get(viewport.getSequenceSetId());
1907
1908       for (Component comp : comps)
1909       {
1910         if (comp instanceof AlignmentPanel)
1911         {
1912           if (al == ((AlignmentPanel) comp).av.getAlignment())
1913           {
1914             originalSource = ((AlignmentPanel) comp).av;
1915             break;
1916           }
1917         }
1918       }
1919     }
1920
1921     if (originalSource == null)
1922     {
1923       // The original view is closed, we must validate
1924       // the current view against the closed view first
1925       if (al != null)
1926       {
1927         PaintRefresher.validateSequences(al, viewport.getAlignment());
1928       }
1929
1930       originalSource = viewport;
1931     }
1932
1933     return originalSource;
1934   }
1935
1936   /**
1937    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1938    * or the sequence under cursor in keyboard mode
1939    *
1940    * @param up
1941    *          or down (if !up)
1942    */
1943   public void moveSelectedSequences(boolean up)
1944   {
1945     SequenceGroup sg = viewport.getSelectionGroup();
1946
1947     if (sg == null)
1948     {
1949       if (viewport.cursorMode)
1950       {
1951         sg = new SequenceGroup();
1952         sg.addSequence(viewport.getAlignment().getSequenceAt(
1953                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1954       }
1955       else
1956       {
1957         return;
1958       }
1959     }
1960
1961     if (sg.getSize() < 1)
1962     {
1963       return;
1964     }
1965
1966     // TODO: JAL-3733 - add an event to the undo buffer for this !
1967
1968     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1969             viewport.getHiddenRepSequences(), up);
1970     alignPanel.paintAlignment(true, false);
1971   }
1972
1973   synchronized void slideSequences(boolean right, int size)
1974   {
1975     List<SequenceI> sg = new ArrayList<>();
1976     if (viewport.cursorMode)
1977     {
1978       sg.add(viewport.getAlignment()
1979               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1980     }
1981     else if (viewport.getSelectionGroup() != null
1982             && viewport.getSelectionGroup().getSize() != viewport
1983                     .getAlignment().getHeight())
1984     {
1985       sg = viewport.getSelectionGroup()
1986               .getSequences(viewport.getHiddenRepSequences());
1987     }
1988
1989     if (sg.size() < 1)
1990     {
1991       return;
1992     }
1993
1994     List<SequenceI> invertGroup = new ArrayList<>();
1995
1996     for (SequenceI seq : viewport.getAlignment().getSequences())
1997     {
1998       if (!sg.contains(seq))
1999       {
2000         invertGroup.add(seq);
2001       }
2002     }
2003
2004     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
2005
2006     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
2007     for (int i = 0; i < invertGroup.size(); i++)
2008     {
2009       seqs2[i] = invertGroup.get(i);
2010     }
2011
2012     SlideSequencesCommand ssc;
2013     if (right)
2014     {
2015       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2016               viewport.getGapCharacter());
2017     }
2018     else
2019     {
2020       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2021               viewport.getGapCharacter());
2022     }
2023
2024     int groupAdjustment = 0;
2025     if (ssc.getGapsInsertedBegin() && right)
2026     {
2027       if (viewport.cursorMode)
2028       {
2029         alignPanel.getSeqPanel().moveCursor(size, 0);
2030       }
2031       else
2032       {
2033         groupAdjustment = size;
2034       }
2035     }
2036     else if (!ssc.getGapsInsertedBegin() && !right)
2037     {
2038       if (viewport.cursorMode)
2039       {
2040         alignPanel.getSeqPanel().moveCursor(-size, 0);
2041       }
2042       else
2043       {
2044         groupAdjustment = -size;
2045       }
2046     }
2047
2048     if (groupAdjustment != 0)
2049     {
2050       viewport.getSelectionGroup().setStartRes(
2051               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2052       viewport.getSelectionGroup().setEndRes(
2053               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2054     }
2055
2056     /*
2057      * just extend the last slide command if compatible; but not if in
2058      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2059      */
2060     boolean appendHistoryItem = false;
2061     Deque<CommandI> historyList = viewport.getHistoryList();
2062     boolean inSplitFrame = getSplitViewContainer() != null;
2063     if (!inSplitFrame && historyList != null && historyList.size() > 0
2064             && historyList.peek() instanceof SlideSequencesCommand)
2065     {
2066       appendHistoryItem = ssc.appendSlideCommand(
2067               (SlideSequencesCommand) historyList.peek());
2068     }
2069
2070     if (!appendHistoryItem)
2071     {
2072       addHistoryItem(ssc);
2073     }
2074
2075     repaint();
2076   }
2077
2078   /**
2079    * DOCUMENT ME!
2080    *
2081    * @param e
2082    *          DOCUMENT ME!
2083    */
2084   @Override
2085   protected void copy_actionPerformed()
2086   {
2087     if (viewport.getSelectionGroup() == null)
2088     {
2089       return;
2090     }
2091     // TODO: preserve the ordering of displayed alignment annotation in any
2092     // internal paste (particularly sequence associated annotation)
2093     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2094     String[] omitHidden = null;
2095
2096     if (viewport.hasHiddenColumns())
2097     {
2098       omitHidden = viewport.getViewAsString(true);
2099     }
2100
2101     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2102             seqs, omitHidden, null);
2103
2104     StringSelection ss = new StringSelection(output);
2105
2106     try
2107     {
2108       jalview.gui.Desktop.internalCopy = true;
2109       // Its really worth setting the clipboard contents
2110       // to empty before setting the large StringSelection!!
2111       Toolkit.getDefaultToolkit().getSystemClipboard()
2112               .setContents(new StringSelection(""), null);
2113
2114       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2115               Desktop.instance);
2116     } catch (OutOfMemoryError er)
2117     {
2118       new OOMWarning("copying region", er);
2119       return;
2120     }
2121
2122     HiddenColumns hiddenColumns = null;
2123     if (viewport.hasHiddenColumns())
2124     {
2125       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2126       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2127
2128       // create new HiddenColumns object with copy of hidden regions
2129       // between startRes and endRes, offset by startRes
2130       hiddenColumns = new HiddenColumns(
2131               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2132               hiddenCutoff, hiddenOffset);
2133     }
2134
2135     Desktop.jalviewClipboard = new Object[] { seqs,
2136         viewport.getAlignment().getDataset(), hiddenColumns };
2137     setStatus(MessageManager.formatMessage(
2138             "label.copied_sequences_to_clipboard", new Object[]
2139             { Integer.valueOf(seqs.length).toString() }));
2140   }
2141
2142   /**
2143    * DOCUMENT ME!
2144    *
2145    * @param e
2146    *          DOCUMENT ME!
2147    */
2148   @Override
2149   protected void pasteNew_actionPerformed(ActionEvent e)
2150   {
2151     paste(true);
2152   }
2153
2154   /**
2155    * DOCUMENT ME!
2156    *
2157    * @param e
2158    *          DOCUMENT ME!
2159    */
2160   @Override
2161   protected void pasteThis_actionPerformed(ActionEvent e)
2162   {
2163     paste(false);
2164   }
2165
2166   /**
2167    * Paste contents of Jalview clipboard
2168    *
2169    * @param newAlignment
2170    *          true to paste to a new alignment, otherwise add to this.
2171    */
2172   void paste(boolean newAlignment)
2173   {
2174     boolean externalPaste = true;
2175     try
2176     {
2177       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2178       Transferable contents = c.getContents(this);
2179
2180       if (contents == null)
2181       {
2182         return;
2183       }
2184
2185       String str;
2186       FileFormatI format;
2187       try
2188       {
2189         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2190         if (str.length() < 1)
2191         {
2192           return;
2193         }
2194
2195         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2196
2197       } catch (OutOfMemoryError er)
2198       {
2199         new OOMWarning("Out of memory pasting sequences!!", er);
2200         return;
2201       }
2202
2203       SequenceI[] sequences;
2204       boolean annotationAdded = false;
2205       AlignmentI alignment = null;
2206
2207       if (Desktop.jalviewClipboard != null)
2208       {
2209         // The clipboard was filled from within Jalview, we must use the
2210         // sequences
2211         // And dataset from the copied alignment
2212         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2213         // be doubly sure that we create *new* sequence objects.
2214         sequences = new SequenceI[newseq.length];
2215         for (int i = 0; i < newseq.length; i++)
2216         {
2217           sequences[i] = new Sequence(newseq[i]);
2218         }
2219         alignment = new Alignment(sequences);
2220         externalPaste = false;
2221       }
2222       else
2223       {
2224         // parse the clipboard as an alignment.
2225         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2226                 format);
2227         sequences = alignment.getSequencesArray();
2228       }
2229
2230       int alwidth = 0;
2231       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2232       int fgroup = -1;
2233
2234       if (newAlignment)
2235       {
2236
2237         if (Desktop.jalviewClipboard != null)
2238         {
2239           // dataset is inherited
2240           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2241         }
2242         else
2243         {
2244           // new dataset is constructed
2245           alignment.setDataset(null);
2246         }
2247         alwidth = alignment.getWidth() + 1;
2248       }
2249       else
2250       {
2251         AlignmentI pastedal = alignment; // preserve pasted alignment object
2252         // Add pasted sequences and dataset into existing alignment.
2253         alignment = viewport.getAlignment();
2254         alwidth = alignment.getWidth() + 1;
2255         // decide if we need to import sequences from an existing dataset
2256         boolean importDs = Desktop.jalviewClipboard != null
2257                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2258         // importDs==true instructs us to copy over new dataset sequences from
2259         // an existing alignment
2260         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2261                                                                       // create
2262         // minimum dataset set
2263
2264         for (int i = 0; i < sequences.length; i++)
2265         {
2266           if (importDs)
2267           {
2268             newDs.addElement(null);
2269           }
2270           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2271           // paste
2272           if (importDs && ds != null)
2273           {
2274             if (!newDs.contains(ds))
2275             {
2276               newDs.setElementAt(ds, i);
2277               ds = new Sequence(ds);
2278               // update with new dataset sequence
2279               sequences[i].setDatasetSequence(ds);
2280             }
2281             else
2282             {
2283               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2284             }
2285           }
2286           else
2287           {
2288             // copy and derive new dataset sequence
2289             sequences[i] = sequences[i].deriveSequence();
2290             alignment.getDataset()
2291                     .addSequence(sequences[i].getDatasetSequence());
2292             // TODO: avoid creation of duplicate dataset sequences with a
2293             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2294           }
2295           alignment.addSequence(sequences[i]); // merges dataset
2296         }
2297         if (newDs != null)
2298         {
2299           newDs.clear(); // tidy up
2300         }
2301         if (alignment.getAlignmentAnnotation() != null)
2302         {
2303           for (AlignmentAnnotation alan : alignment
2304                   .getAlignmentAnnotation())
2305           {
2306             if (alan.graphGroup > fgroup)
2307             {
2308               fgroup = alan.graphGroup;
2309             }
2310           }
2311         }
2312         if (pastedal.getAlignmentAnnotation() != null)
2313         {
2314           // Add any annotation attached to alignment.
2315           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2316           for (int i = 0; i < alann.length; i++)
2317           {
2318             annotationAdded = true;
2319             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2320             {
2321               AlignmentAnnotation newann = new AlignmentAnnotation(
2322                       alann[i]);
2323               if (newann.graphGroup > -1)
2324               {
2325                 if (newGraphGroups.size() <= newann.graphGroup
2326                         || newGraphGroups.get(newann.graphGroup) == null)
2327                 {
2328                   for (int q = newGraphGroups
2329                           .size(); q <= newann.graphGroup; q++)
2330                   {
2331                     newGraphGroups.add(q, null);
2332                   }
2333                   newGraphGroups.set(newann.graphGroup,
2334                           Integer.valueOf(++fgroup));
2335                 }
2336                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2337                         .intValue();
2338               }
2339
2340               newann.padAnnotation(alwidth);
2341               alignment.addAnnotation(newann);
2342             }
2343           }
2344         }
2345       }
2346       if (!newAlignment)
2347       {
2348         // /////
2349         // ADD HISTORY ITEM
2350         //
2351         addHistoryItem(new EditCommand(
2352                 MessageManager.getString("label.add_sequences"),
2353                 Action.PASTE, sequences, 0, alignment.getWidth(),
2354                 alignment));
2355       }
2356       // Add any annotations attached to sequences
2357       for (int i = 0; i < sequences.length; i++)
2358       {
2359         if (sequences[i].getAnnotation() != null)
2360         {
2361           AlignmentAnnotation newann;
2362           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2363           {
2364             annotationAdded = true;
2365             newann = sequences[i].getAnnotation()[a];
2366             newann.adjustForAlignment();
2367             newann.padAnnotation(alwidth);
2368             if (newann.graphGroup > -1)
2369             {
2370               if (newann.graphGroup > -1)
2371               {
2372                 if (newGraphGroups.size() <= newann.graphGroup
2373                         || newGraphGroups.get(newann.graphGroup) == null)
2374                 {
2375                   for (int q = newGraphGroups
2376                           .size(); q <= newann.graphGroup; q++)
2377                   {
2378                     newGraphGroups.add(q, null);
2379                   }
2380                   newGraphGroups.set(newann.graphGroup,
2381                           Integer.valueOf(++fgroup));
2382                 }
2383                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2384                         .intValue();
2385               }
2386             }
2387             // annotation was duplicated earlier
2388             alignment.addAnnotation(sequences[i].getAnnotation()[a]);
2389             // take care of contact matrix too
2390             ContactMatrixI cm = sequences[i]
2391                     .getContactMatrixFor(sequences[i].getAnnotation()[a]);
2392             if (cm != null)
2393             {
2394               alignment.addContactListFor(sequences[i].getAnnotation()[a],
2395                       cm);
2396             }
2397
2398             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2399                     a);
2400           }
2401         }
2402       }
2403       if (!newAlignment)
2404       {
2405
2406         // propagate alignment changed.
2407         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2408         if (annotationAdded)
2409         {
2410           // Duplicate sequence annotation in all views.
2411           AlignmentI[] alview = this.getViewAlignments();
2412           for (int i = 0; i < sequences.length; i++)
2413           {
2414             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2415             if (sann == null)
2416             {
2417               continue;
2418             }
2419             for (int avnum = 0; avnum < alview.length; avnum++)
2420             {
2421               if (alview[avnum] != alignment)
2422               {
2423                 // duplicate in a view other than the one with input focus
2424                 int avwidth = alview[avnum].getWidth() + 1;
2425                 // this relies on sann being preserved after we
2426                 // modify the sequence's annotation array for each duplication
2427                 for (int a = 0; a < sann.length; a++)
2428                 {
2429                   AlignmentAnnotation newann = new AlignmentAnnotation(
2430                           sann[a]);
2431                   sequences[i].addAlignmentAnnotation(newann);
2432                   newann.padAnnotation(avwidth);
2433                   alview[avnum].addAnnotation(newann); // annotation was
2434                   // duplicated earlier
2435                   // TODO JAL-1145 graphGroups are not updated for sequence
2436                   // annotation added to several views. This may cause
2437                   // strangeness
2438                   alview[avnum].setAnnotationIndex(newann, a);
2439                 }
2440               }
2441             }
2442           }
2443           buildSortByAnnotationScoresMenu();
2444         }
2445         viewport.firePropertyChange("alignment", null,
2446                 alignment.getSequences());
2447         if (alignPanels != null)
2448         {
2449           for (AlignmentPanel ap : alignPanels)
2450           {
2451             ap.validateAnnotationDimensions(false);
2452           }
2453         }
2454         else
2455         {
2456           alignPanel.validateAnnotationDimensions(false);
2457         }
2458
2459       }
2460       else
2461       {
2462         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2463                 DEFAULT_HEIGHT);
2464         String newtitle = new String("Copied sequences");
2465
2466         if (Desktop.jalviewClipboard != null
2467                 && Desktop.jalviewClipboard[2] != null)
2468         {
2469           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2470           af.viewport.setHiddenColumns(hc);
2471         }
2472
2473         // >>>This is a fix for the moment, until a better solution is
2474         // found!!<<<
2475         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2476                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2477                         .getFeatureRenderer());
2478
2479         // TODO: maintain provenance of an alignment, rather than just make the
2480         // title a concatenation of operations.
2481         if (!externalPaste)
2482         {
2483           if (title.startsWith("Copied sequences"))
2484           {
2485             newtitle = title;
2486           }
2487           else
2488           {
2489             newtitle = newtitle.concat("- from " + title);
2490           }
2491         }
2492         else
2493         {
2494           newtitle = new String("Pasted sequences");
2495         }
2496
2497         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2498                 DEFAULT_HEIGHT);
2499
2500       }
2501
2502     } catch (Exception ex)
2503     {
2504       ex.printStackTrace();
2505       jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
2506       // could be anything being pasted in here
2507     }
2508
2509   }
2510
2511   @Override
2512   protected void expand_newalign(ActionEvent e)
2513   {
2514     try
2515     {
2516       AlignmentI alignment = AlignmentUtils
2517               .expandContext(getViewport().getAlignment(), -1);
2518       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2519               DEFAULT_HEIGHT);
2520       String newtitle = new String("Flanking alignment");
2521
2522       if (Desktop.jalviewClipboard != null
2523               && Desktop.jalviewClipboard[2] != null)
2524       {
2525         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2526         af.viewport.setHiddenColumns(hc);
2527       }
2528
2529       // >>>This is a fix for the moment, until a better solution is
2530       // found!!<<<
2531       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2532               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2533                       .getFeatureRenderer());
2534
2535       // TODO: maintain provenance of an alignment, rather than just make the
2536       // title a concatenation of operations.
2537       {
2538         if (title.startsWith("Copied sequences"))
2539         {
2540           newtitle = title;
2541         }
2542         else
2543         {
2544           newtitle = newtitle.concat("- from " + title);
2545         }
2546       }
2547
2548       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2549
2550     } catch (Exception ex)
2551     {
2552       ex.printStackTrace();
2553       jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
2554       // could be anything being pasted in here
2555     } catch (OutOfMemoryError oom)
2556     {
2557       new OOMWarning("Viewing flanking region of alignment", oom);
2558     }
2559   }
2560
2561   /**
2562    * Action Cut (delete and copy) the selected region
2563    */
2564   @Override
2565   protected void cut_actionPerformed()
2566   {
2567     copy_actionPerformed();
2568     delete_actionPerformed();
2569   }
2570
2571   /**
2572    * Performs menu option to Delete the currently selected region
2573    */
2574   @Override
2575   protected void delete_actionPerformed()
2576   {
2577
2578     SequenceGroup sg = viewport.getSelectionGroup();
2579     if (sg == null)
2580     {
2581       return;
2582     }
2583
2584     Runnable okAction = () -> {
2585       SequenceI[] cut = sg.getSequences()
2586               .toArray(new SequenceI[sg.getSize()]);
2587
2588       addHistoryItem(new EditCommand(
2589               MessageManager.getString("label.cut_sequences"), Action.CUT,
2590               cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2591               viewport.getAlignment()));
2592
2593       viewport.setSelectionGroup(null);
2594       viewport.sendSelection();
2595       viewport.getAlignment().deleteGroup(sg);
2596
2597       viewport.firePropertyChange("alignment", null,
2598               viewport.getAlignment().getSequences());
2599       if (viewport.getAlignment().getHeight() < 1)
2600       {
2601         try
2602         {
2603           AlignFrame.this.setClosed(true);
2604         } catch (Exception ex)
2605         {
2606         }
2607       }
2608     };
2609
2610     /*
2611      * If the cut affects all sequences, prompt for confirmation
2612      */
2613     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2614             .getHeight();
2615     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2616             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2617     if (wholeHeight && wholeWidth)
2618     {
2619       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2620       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2621       Object[] options = new Object[] {
2622           MessageManager.getString("action.ok"),
2623           MessageManager.getString("action.cancel") };
2624       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2625               MessageManager.getString("label.delete_all"),
2626               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2627               options, options[0]);
2628     }
2629     else
2630     {
2631       try
2632       {
2633         okAction.run();
2634       } catch (Exception e)
2635       {
2636         e.printStackTrace();
2637       }
2638     }
2639   }
2640
2641   /**
2642    * DOCUMENT ME!
2643    *
2644    * @param e
2645    *          DOCUMENT ME!
2646    */
2647   @Override
2648   protected void deleteGroups_actionPerformed(ActionEvent e)
2649   {
2650     if (avc.deleteGroups())
2651     {
2652       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2653       alignPanel.updateAnnotation();
2654       alignPanel.paintAlignment(true, true);
2655     }
2656   }
2657
2658   /**
2659    * DOCUMENT ME!
2660    *
2661    * @param e
2662    *          DOCUMENT ME!
2663    */
2664   @Override
2665   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2666   {
2667     SequenceGroup sg = new SequenceGroup(
2668             viewport.getAlignment().getSequences());
2669
2670     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2671     viewport.setSelectionGroup(sg);
2672     viewport.isSelectionGroupChanged(true);
2673     viewport.sendSelection();
2674     // JAL-2034 - should delegate to
2675     // alignPanel to decide if overview needs
2676     // updating.
2677     alignPanel.paintAlignment(false, false);
2678     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2689   {
2690     if (viewport.cursorMode)
2691     {
2692       alignPanel.getSeqPanel().keyboardNo1 = null;
2693       alignPanel.getSeqPanel().keyboardNo2 = null;
2694     }
2695     viewport.setSelectionGroup(null);
2696     viewport.getColumnSelection().clear();
2697     viewport.setSearchResults(null);
2698     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2699     // JAL-2034 - should delegate to
2700     // alignPanel to decide if overview needs
2701     // updating.
2702     alignPanel.paintAlignment(false, false);
2703     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2704     viewport.sendSelection();
2705   }
2706
2707   /**
2708    * DOCUMENT ME!
2709    *
2710    * @param e
2711    *          DOCUMENT ME!
2712    */
2713   @Override
2714   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2715   {
2716     SequenceGroup sg = viewport.getSelectionGroup();
2717
2718     if (sg == null)
2719     {
2720       selectAllSequenceMenuItem_actionPerformed(null);
2721
2722       return;
2723     }
2724
2725     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2726     {
2727       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2728     }
2729     // JAL-2034 - should delegate to
2730     // alignPanel to decide if overview needs
2731     // updating.
2732
2733     alignPanel.paintAlignment(true, false);
2734     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2735     viewport.sendSelection();
2736   }
2737
2738   @Override
2739   public void invertColSel_actionPerformed(ActionEvent e)
2740   {
2741     viewport.invertColumnSelection();
2742     alignPanel.paintAlignment(true, false);
2743     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2744     viewport.sendSelection();
2745   }
2746
2747   /**
2748    * DOCUMENT ME!
2749    *
2750    * @param e
2751    *          DOCUMENT ME!
2752    */
2753   @Override
2754   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2755   {
2756     trimAlignment(true);
2757   }
2758
2759   /**
2760    * DOCUMENT ME!
2761    *
2762    * @param e
2763    *          DOCUMENT ME!
2764    */
2765   @Override
2766   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2767   {
2768     trimAlignment(false);
2769   }
2770
2771   void trimAlignment(boolean trimLeft)
2772   {
2773     ColumnSelection colSel = viewport.getColumnSelection();
2774     int column;
2775
2776     if (!colSel.isEmpty())
2777     {
2778       if (trimLeft)
2779       {
2780         column = colSel.getMin();
2781       }
2782       else
2783       {
2784         column = colSel.getMax();
2785       }
2786
2787       SequenceI[] seqs;
2788       if (viewport.getSelectionGroup() != null)
2789       {
2790         seqs = viewport.getSelectionGroup()
2791                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2792       }
2793       else
2794       {
2795         seqs = viewport.getAlignment().getSequencesArray();
2796       }
2797
2798       TrimRegionCommand trimRegion;
2799       if (trimLeft)
2800       {
2801         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2802                 column, viewport.getAlignment());
2803         viewport.getRanges().setStartRes(0);
2804       }
2805       else
2806       {
2807         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2808                 column, viewport.getAlignment());
2809       }
2810
2811       setStatus(MessageManager.formatMessage("label.removed_columns",
2812               new String[]
2813               { Integer.valueOf(trimRegion.getSize()).toString() }));
2814
2815       addHistoryItem(trimRegion);
2816
2817       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2818       {
2819         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2820                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2821         {
2822           viewport.getAlignment().deleteGroup(sg);
2823         }
2824       }
2825
2826       viewport.firePropertyChange("alignment", null,
2827               viewport.getAlignment().getSequences());
2828     }
2829   }
2830
2831   /**
2832    * DOCUMENT ME!
2833    *
2834    * @param e
2835    *          DOCUMENT ME!
2836    */
2837   @Override
2838   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2839   {
2840     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2841
2842     SequenceI[] seqs;
2843     if (viewport.getSelectionGroup() != null)
2844     {
2845       seqs = viewport.getSelectionGroup()
2846               .getSequencesAsArray(viewport.getHiddenRepSequences());
2847       start = viewport.getSelectionGroup().getStartRes();
2848       end = viewport.getSelectionGroup().getEndRes();
2849     }
2850     else
2851     {
2852       seqs = viewport.getAlignment().getSequencesArray();
2853     }
2854
2855     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2856             "Remove Gapped Columns", seqs, start, end,
2857             viewport.getAlignment());
2858
2859     addHistoryItem(removeGapCols);
2860
2861     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2862             new Object[]
2863             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2864
2865     // This is to maintain viewport position on first residue
2866     // of first sequence
2867     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2868     ViewportRanges ranges = viewport.getRanges();
2869     int startRes = seq.findPosition(ranges.getStartRes());
2870     // ShiftList shifts;
2871     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2872     // edit.alColumnChanges=shifts.getInverse();
2873     // if (viewport.hasHiddenColumns)
2874     // viewport.getColumnSelection().compensateForEdits(shifts);
2875     ranges.setStartRes(seq.findIndex(startRes) - 1);
2876     viewport.firePropertyChange("alignment", null,
2877             viewport.getAlignment().getSequences());
2878
2879   }
2880
2881   /**
2882    * DOCUMENT ME!
2883    *
2884    * @param e
2885    *          DOCUMENT ME!
2886    */
2887   @Override
2888   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2889   {
2890     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2891
2892     SequenceI[] seqs;
2893     if (viewport.getSelectionGroup() != null)
2894     {
2895       seqs = viewport.getSelectionGroup()
2896               .getSequencesAsArray(viewport.getHiddenRepSequences());
2897       start = viewport.getSelectionGroup().getStartRes();
2898       end = viewport.getSelectionGroup().getEndRes();
2899     }
2900     else
2901     {
2902       seqs = viewport.getAlignment().getSequencesArray();
2903     }
2904
2905     // This is to maintain viewport position on first residue
2906     // of first sequence
2907     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2908     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2909
2910     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2911             viewport.getAlignment()));
2912
2913     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2914
2915     viewport.firePropertyChange("alignment", null,
2916             viewport.getAlignment().getSequences());
2917
2918   }
2919
2920   /**
2921    * DOCUMENT ME!
2922    *
2923    * @param e
2924    *          DOCUMENT ME!
2925    */
2926   @Override
2927   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2928   {
2929     viewport.setPadGaps(padGapsMenuitem.isSelected());
2930     viewport.firePropertyChange("alignment", null,
2931             viewport.getAlignment().getSequences());
2932   }
2933
2934   /**
2935    * Opens a Finder dialog
2936    *
2937    * @param e
2938    */
2939   @Override
2940   public void findMenuItem_actionPerformed(ActionEvent e)
2941   {
2942     new Finder(alignPanel, false, null);
2943   }
2944
2945   /**
2946    * Create a new view of the current alignment.
2947    */
2948   @Override
2949   public void newView_actionPerformed(ActionEvent e)
2950   {
2951     newView(null, true);
2952   }
2953
2954   /**
2955    * Creates and shows a new view of the current alignment.
2956    *
2957    * @param viewTitle
2958    *          title of newly created view; if null, one will be generated
2959    * @param copyAnnotation
2960    *          if true then duplicate all annnotation, groups and settings
2961    * @return new alignment panel, already displayed.
2962    */
2963   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2964   {
2965     /*
2966      * Create a new AlignmentPanel (with its own, new Viewport)
2967      */
2968     AlignmentPanel newap = new jalview.project.Jalview2XML()
2969             .copyAlignPanel(alignPanel);
2970     if (!copyAnnotation)
2971     {
2972       /*
2973        * remove all groups and annotation except for the automatic stuff
2974        */
2975       newap.av.getAlignment().deleteAllGroups();
2976       newap.av.getAlignment().deleteAllAnnotations(false);
2977     }
2978
2979     newap.av.setGatherViewsHere(false);
2980
2981     if (viewport.getViewName() == null)
2982     {
2983       viewport.setViewName(
2984               MessageManager.getString("label.view_name_original"));
2985     }
2986
2987     /*
2988      * Views share the same edits undo and redo stacks
2989      */
2990     newap.av.setHistoryList(viewport.getHistoryList());
2991     newap.av.setRedoList(viewport.getRedoList());
2992
2993     /*
2994      * copy any visualisation settings that are not saved in the project
2995      */
2996     newap.av.setColourAppliesToAllGroups(
2997             viewport.getColourAppliesToAllGroups());
2998
2999     /*
3000      * Views share the same mappings; need to deregister any new mappings
3001      * created by copyAlignPanel, and register the new reference to the shared
3002      * mappings
3003      */
3004     newap.av.replaceMappings(viewport.getAlignment());
3005
3006     /*
3007      * start up cDNA consensus (if applicable) now mappings are in place
3008      */
3009     if (newap.av.initComplementConsensus())
3010     {
3011       newap.refresh(true); // adjust layout of annotations
3012     }
3013
3014     newap.av.setViewName(getNewViewName(viewTitle));
3015
3016     addAlignmentPanel(newap, true);
3017     newap.alignmentChanged();
3018
3019     if (alignPanels.size() == 2)
3020     {
3021       viewport.setGatherViewsHere(true);
3022     }
3023     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3024
3025     return newap;
3026   }
3027
3028   /**
3029    * Make a new name for the view, ensuring it is unique within the current
3030    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3031    * these now use viewId. Unique view names are still desirable for usability.)
3032    *
3033    * @param viewTitle
3034    * @return
3035    */
3036   protected String getNewViewName(String viewTitle)
3037   {
3038     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3039     boolean addFirstIndex = false;
3040     if (viewTitle == null || viewTitle.trim().length() == 0)
3041     {
3042       viewTitle = MessageManager.getString("action.view");
3043       addFirstIndex = true;
3044     }
3045     else
3046     {
3047       index = 1;// we count from 1 if given a specific name
3048     }
3049     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3050
3051     List<Component> comps = PaintRefresher.components
3052             .get(viewport.getSequenceSetId());
3053
3054     List<String> existingNames = getExistingViewNames(comps);
3055
3056     while (existingNames.contains(newViewName))
3057     {
3058       newViewName = viewTitle + " " + (++index);
3059     }
3060     return newViewName;
3061   }
3062
3063   /**
3064    * Returns a list of distinct view names found in the given list of
3065    * components. View names are held on the viewport of an AlignmentPanel.
3066    *
3067    * @param comps
3068    * @return
3069    */
3070   protected List<String> getExistingViewNames(List<Component> comps)
3071   {
3072     List<String> existingNames = new ArrayList<>();
3073     for (Component comp : comps)
3074     {
3075       if (comp instanceof AlignmentPanel)
3076       {
3077         AlignmentPanel ap = (AlignmentPanel) comp;
3078         if (!existingNames.contains(ap.av.getViewName()))
3079         {
3080           existingNames.add(ap.av.getViewName());
3081         }
3082       }
3083     }
3084     return existingNames;
3085   }
3086
3087   /**
3088    * Explode tabbed views into separate windows.
3089    */
3090   @Override
3091   public void expandViews_actionPerformed(ActionEvent e)
3092   {
3093     Desktop.explodeViews(this);
3094   }
3095
3096   /**
3097    * Gather views in separate windows back into a tabbed presentation.
3098    */
3099   @Override
3100   public void gatherViews_actionPerformed(ActionEvent e)
3101   {
3102     Desktop.instance.gatherViews(this);
3103   }
3104
3105   /**
3106    * DOCUMENT ME!
3107    *
3108    * @param e
3109    *          DOCUMENT ME!
3110    */
3111   @Override
3112   public void font_actionPerformed(ActionEvent e)
3113   {
3114     new FontChooser(alignPanel);
3115   }
3116
3117   /**
3118    * DOCUMENT ME!
3119    *
3120    * @param e
3121    *          DOCUMENT ME!
3122    */
3123   @Override
3124   protected void seqLimit_actionPerformed(ActionEvent e)
3125   {
3126     viewport.setShowJVSuffix(seqLimits.isSelected());
3127
3128     alignPanel.getIdPanel().getIdCanvas()
3129             .setPreferredSize(alignPanel.calculateIdWidth());
3130     alignPanel.paintAlignment(true, false);
3131   }
3132
3133   @Override
3134   public void idRightAlign_actionPerformed(ActionEvent e)
3135   {
3136     viewport.setRightAlignIds(idRightAlign.isSelected());
3137     alignPanel.paintAlignment(false, false);
3138   }
3139
3140   @Override
3141   public void centreColumnLabels_actionPerformed(ActionEvent e)
3142   {
3143     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3144     alignPanel.paintAlignment(false, false);
3145   }
3146
3147   /*
3148    * (non-Javadoc)
3149    *
3150    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3151    */
3152   @Override
3153   protected void followHighlight_actionPerformed()
3154   {
3155     /*
3156      * Set the 'follow' flag on the Viewport (and scroll to position if now
3157      * true).
3158      */
3159     final boolean state = this.followHighlightMenuItem.getState();
3160     viewport.setFollowHighlight(state);
3161     if (state)
3162     {
3163       alignPanel.scrollToPosition(viewport.getSearchResults());
3164     }
3165   }
3166
3167   /**
3168    * DOCUMENT ME!
3169    *
3170    * @param e
3171    *          DOCUMENT ME!
3172    */
3173   @Override
3174   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3175   {
3176     viewport.setColourText(colourTextMenuItem.isSelected());
3177     alignPanel.paintAlignment(false, false);
3178   }
3179
3180   /**
3181    * DOCUMENT ME!
3182    *
3183    * @param e
3184    *          DOCUMENT ME!
3185    */
3186   @Override
3187   public void wrapMenuItem_actionPerformed(ActionEvent e)
3188   {
3189     setWrapFormat(wrapMenuItem.isSelected(), false);
3190   }
3191
3192   public void setWrapFormat(boolean b, boolean setMenuItem)
3193   {
3194     scaleAbove.setVisible(b);
3195     scaleLeft.setVisible(b);
3196     scaleRight.setVisible(b);
3197     viewport.setWrapAlignment(b);
3198     alignPanel.updateLayout();
3199     if (setMenuItem)
3200     {
3201       wrapMenuItem.setSelected(b);
3202     }
3203   }
3204
3205   @Override
3206   public void showAllSeqs_actionPerformed(ActionEvent e)
3207   {
3208     viewport.showAllHiddenSeqs();
3209   }
3210
3211   @Override
3212   public void showAllColumns_actionPerformed(ActionEvent e)
3213   {
3214     viewport.showAllHiddenColumns();
3215     alignPanel.paintAlignment(true, true);
3216     viewport.sendSelection();
3217   }
3218
3219   @Override
3220   public void hideSelSequences_actionPerformed(ActionEvent e)
3221   {
3222     viewport.hideAllSelectedSeqs();
3223   }
3224
3225   /**
3226    * called by key handler and the hide all/show all menu items
3227    *
3228    * @param toggleSeqs
3229    * @param toggleCols
3230    */
3231   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3232   {
3233
3234     boolean hide = false;
3235     SequenceGroup sg = viewport.getSelectionGroup();
3236     if (!toggleSeqs && !toggleCols)
3237     {
3238       // Hide everything by the current selection - this is a hack - we do the
3239       // invert and then hide
3240       // first check that there will be visible columns after the invert.
3241       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3242               && sg.getStartRes() <= sg.getEndRes()))
3243       {
3244         // now invert the sequence set, if required - empty selection implies
3245         // that no hiding is required.
3246         if (sg != null)
3247         {
3248           invertSequenceMenuItem_actionPerformed(null);
3249           sg = viewport.getSelectionGroup();
3250           toggleSeqs = true;
3251
3252         }
3253         viewport.expandColSelection(sg, true);
3254         // finally invert the column selection and get the new sequence
3255         // selection.
3256         invertColSel_actionPerformed(null);
3257         toggleCols = true;
3258       }
3259     }
3260
3261     if (toggleSeqs)
3262     {
3263       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3264       {
3265         hideSelSequences_actionPerformed(null);
3266         hide = true;
3267       }
3268       else if (!(toggleCols && viewport.hasSelectedColumns()))
3269       {
3270         showAllSeqs_actionPerformed(null);
3271       }
3272     }
3273
3274     if (toggleCols)
3275     {
3276       if (viewport.hasSelectedColumns())
3277       {
3278         hideSelColumns_actionPerformed(null);
3279         if (!toggleSeqs)
3280         {
3281           viewport.setSelectionGroup(sg);
3282         }
3283       }
3284       else if (!hide)
3285       {
3286         showAllColumns_actionPerformed(null);
3287       }
3288     }
3289   }
3290
3291   /*
3292    * (non-Javadoc)
3293    *
3294    * @see
3295    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3296    * event.ActionEvent)
3297    */
3298   @Override
3299   public void hideAllButSelection_actionPerformed(ActionEvent e)
3300   {
3301     toggleHiddenRegions(false, false);
3302     viewport.sendSelection();
3303   }
3304
3305   /*
3306    * (non-Javadoc)
3307    *
3308    * @see
3309    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3310    * .ActionEvent)
3311    */
3312   @Override
3313   public void hideAllSelection_actionPerformed(ActionEvent e)
3314   {
3315     SequenceGroup sg = viewport.getSelectionGroup();
3316     viewport.expandColSelection(sg, false);
3317     viewport.hideAllSelectedSeqs();
3318     viewport.hideSelectedColumns();
3319     alignPanel.updateLayout();
3320     alignPanel.paintAlignment(true, true);
3321     viewport.sendSelection();
3322   }
3323
3324   /*
3325    * (non-Javadoc)
3326    *
3327    * @see
3328    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3329    * ActionEvent)
3330    */
3331   @Override
3332   public void showAllhidden_actionPerformed(ActionEvent e)
3333   {
3334     viewport.showAllHiddenColumns();
3335     viewport.showAllHiddenSeqs();
3336     alignPanel.paintAlignment(true, true);
3337     viewport.sendSelection();
3338   }
3339
3340   @Override
3341   public void hideSelColumns_actionPerformed(ActionEvent e)
3342   {
3343     viewport.hideSelectedColumns();
3344     alignPanel.updateLayout();
3345     alignPanel.paintAlignment(true, true);
3346     viewport.sendSelection();
3347   }
3348
3349   @Override
3350   public void hiddenMarkers_actionPerformed(ActionEvent e)
3351   {
3352     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3353     repaint();
3354   }
3355
3356   /**
3357    * DOCUMENT ME!
3358    *
3359    * @param e
3360    *          DOCUMENT ME!
3361    */
3362   @Override
3363   protected void scaleAbove_actionPerformed(ActionEvent e)
3364   {
3365     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3366     alignPanel.updateLayout();
3367     alignPanel.paintAlignment(true, false);
3368   }
3369
3370   /**
3371    * DOCUMENT ME!
3372    *
3373    * @param e
3374    *          DOCUMENT ME!
3375    */
3376   @Override
3377   protected void scaleLeft_actionPerformed(ActionEvent e)
3378   {
3379     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3380     alignPanel.updateLayout();
3381     alignPanel.paintAlignment(true, false);
3382   }
3383
3384   /**
3385    * DOCUMENT ME!
3386    *
3387    * @param e
3388    *          DOCUMENT ME!
3389    */
3390   @Override
3391   protected void scaleRight_actionPerformed(ActionEvent e)
3392   {
3393     viewport.setScaleRightWrapped(scaleRight.isSelected());
3394     alignPanel.updateLayout();
3395     alignPanel.paintAlignment(true, false);
3396   }
3397
3398   /**
3399    * DOCUMENT ME!
3400    *
3401    * @param e
3402    *          DOCUMENT ME!
3403    */
3404   @Override
3405   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3406   {
3407     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3408     alignPanel.paintAlignment(false, false);
3409   }
3410
3411   /**
3412    * DOCUMENT ME!
3413    *
3414    * @param e
3415    *          DOCUMENT ME!
3416    */
3417   @Override
3418   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3419   {
3420     viewport.setShowText(viewTextMenuItem.isSelected());
3421     alignPanel.paintAlignment(false, false);
3422   }
3423
3424   /**
3425    * DOCUMENT ME!
3426    *
3427    * @param e
3428    *          DOCUMENT ME!
3429    */
3430   @Override
3431   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3432   {
3433     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3434     alignPanel.paintAlignment(false, false);
3435   }
3436
3437   public FeatureSettings featureSettings;
3438
3439   @Override
3440   public FeatureSettingsControllerI getFeatureSettingsUI()
3441   {
3442     return featureSettings;
3443   }
3444
3445   @Override
3446   public void featureSettings_actionPerformed(ActionEvent e)
3447   {
3448     showFeatureSettingsUI();
3449   }
3450
3451   @Override
3452   public FeatureSettingsControllerI showFeatureSettingsUI()
3453   {
3454     if (featureSettings != null)
3455     {
3456       featureSettings.closeOldSettings();
3457       featureSettings = null;
3458     }
3459     if (!showSeqFeatures.isSelected())
3460     {
3461       // make sure features are actually displayed
3462       showSeqFeatures.setSelected(true);
3463       showSeqFeatures_actionPerformed(null);
3464     }
3465     featureSettings = new FeatureSettings(this);
3466     return featureSettings;
3467   }
3468
3469   /**
3470    * Set or clear 'Show Sequence Features'
3471    *
3472    * @param evt
3473    *          DOCUMENT ME!
3474    */
3475   @Override
3476   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3477   {
3478     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3479     alignPanel.paintAlignment(true, true);
3480   }
3481
3482   /**
3483    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3484    * the annotations panel as a whole.
3485    *
3486    * The options to show/hide all annotations should be enabled when the panel
3487    * is shown, and disabled when the panel is hidden.
3488    *
3489    * @param e
3490    */
3491   @Override
3492   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3493   {
3494     final boolean setVisible = annotationPanelMenuItem.isSelected();
3495     viewport.setShowAnnotation(setVisible);
3496     this.showAllSeqAnnotations.setEnabled(setVisible);
3497     this.hideAllSeqAnnotations.setEnabled(setVisible);
3498     this.showAllAlAnnotations.setEnabled(setVisible);
3499     this.hideAllAlAnnotations.setEnabled(setVisible);
3500     alignPanel.updateLayout();
3501   }
3502
3503   @Override
3504   public void alignmentProperties()
3505   {
3506     JComponent pane;
3507     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3508
3509             .formatAsHtml();
3510     String content = MessageManager.formatMessage("label.html_content",
3511             new Object[]
3512             { contents.toString() });
3513     contents = null;
3514
3515     if (Platform.isJS())
3516     {
3517       JLabel textLabel = new JLabel();
3518       textLabel.setText(content);
3519       textLabel.setBackground(Color.WHITE);
3520
3521       pane = new JPanel(new BorderLayout());
3522       ((JPanel) pane).setOpaque(true);
3523       pane.setBackground(Color.WHITE);
3524       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3525     }
3526     else
3527     /**
3528      * Java only
3529      *
3530      * @j2sIgnore
3531      */
3532     {
3533       JEditorPane editPane = new JEditorPane("text/html", "");
3534       editPane.setEditable(false);
3535       editPane.setText(content);
3536       pane = editPane;
3537     }
3538
3539     JInternalFrame frame = new JInternalFrame();
3540     frame.setFrameIcon(null);
3541     frame.getContentPane().add(new JScrollPane(pane));
3542
3543     Desktop.addInternalFrame(frame, MessageManager
3544             .formatMessage("label.alignment_properties", new Object[]
3545             { getTitle() }), 500, 400);
3546   }
3547
3548   /**
3549    * Opens an Overview panel for the alignment, unless one is open already
3550    *
3551    * @param e
3552    */
3553   @Override
3554   public void overviewMenuItem_actionPerformed(ActionEvent e)
3555   {
3556     boolean showHiddenRegions = Cache
3557             .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
3558     openOverviewPanel(showHiddenRegions);
3559   }
3560
3561   public OverviewPanel openOverviewPanel(boolean showHidden)
3562   {
3563     if (alignPanel.overviewPanel != null)
3564     {
3565       return alignPanel.overviewPanel;
3566     }
3567     JInternalFrame frame = new JInternalFrame();
3568     frame.setFrameIcon(null);
3569     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
3570             showHidden);
3571     frame.setContentPane(overview);
3572     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
3573             frame.getHeight(), true, true);
3574     frame.pack();
3575     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3576     final AlignmentPanel thePanel = this.alignPanel;
3577     frame.addInternalFrameListener(
3578             new javax.swing.event.InternalFrameAdapter()
3579             {
3580               @Override
3581               public void internalFrameClosed(
3582                       javax.swing.event.InternalFrameEvent evt)
3583               {
3584                 overview.dispose();
3585                 thePanel.setOverviewPanel(null);
3586               }
3587             });
3588     if (getKeyListeners().length > 0)
3589     {
3590       frame.addKeyListener(getKeyListeners()[0]);
3591     }
3592
3593     alignPanel.setOverviewPanel(overview);
3594     alignPanel.setOverviewTitle(this);
3595
3596     return overview;
3597   }
3598
3599   @Override
3600   public void textColour_actionPerformed()
3601   {
3602     new TextColourChooser().chooseColour(alignPanel, null);
3603   }
3604
3605   /*
3606    * public void covariationColour_actionPerformed() {
3607    * changeColour(new
3608    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3609    * ()[0])); }
3610    */
3611   @Override
3612   public void annotationColour_actionPerformed()
3613   {
3614     new AnnotationColourChooser(viewport, alignPanel);
3615   }
3616
3617   @Override
3618   public void annotationColumn_actionPerformed(ActionEvent e)
3619   {
3620     new AnnotationColumnChooser(viewport, alignPanel);
3621   }
3622
3623   /**
3624    * Action on the user checking or unchecking the option to apply the selected
3625    * colour scheme to all groups. If unchecked, groups may have their own
3626    * independent colour schemes.
3627    *
3628    * @param selected
3629    */
3630   @Override
3631   public void applyToAllGroups_actionPerformed(boolean selected)
3632   {
3633     viewport.setColourAppliesToAllGroups(selected);
3634   }
3635
3636   /**
3637    * Action on user selecting a colour from the colour menu
3638    *
3639    * @param name
3640    *          the name (not the menu item label!) of the colour scheme
3641    */
3642   @Override
3643   public void changeColour_actionPerformed(String name)
3644   {
3645     /*
3646      * 'User Defined' opens a panel to configure or load a
3647      * user-defined colour scheme
3648      */
3649     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3650     {
3651       new UserDefinedColours(alignPanel);
3652       return;
3653     }
3654
3655     /*
3656      * otherwise set the chosen colour scheme (or null for 'None')
3657      */
3658     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3659             viewport, viewport.getAlignment(),
3660             viewport.getHiddenRepSequences());
3661     changeColour(cs);
3662   }
3663
3664   /**
3665    * Actions on setting or changing the alignment colour scheme
3666    *
3667    * @param cs
3668    */
3669   @Override
3670   public void changeColour(ColourSchemeI cs)
3671   {
3672     // TODO: pull up to controller method
3673     ColourMenuHelper.setColourSelected(colourMenu, cs);
3674
3675     viewport.setGlobalColourScheme(cs);
3676
3677     alignPanel.paintAlignment(true, true);
3678   }
3679
3680   /**
3681    * Show the PID threshold slider panel
3682    */
3683   @Override
3684   protected void modifyPID_actionPerformed()
3685   {
3686     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3687             alignPanel.getViewName());
3688     SliderPanel.showPIDSlider();
3689   }
3690
3691   /**
3692    * Show the Conservation slider panel
3693    */
3694   @Override
3695   protected void modifyConservation_actionPerformed()
3696   {
3697     SliderPanel.setConservationSlider(alignPanel,
3698             viewport.getResidueShading(), alignPanel.getViewName());
3699     SliderPanel.showConservationSlider();
3700   }
3701
3702   /**
3703    * Action on selecting or deselecting (Colour) By Conservation
3704    */
3705   @Override
3706   public void conservationMenuItem_actionPerformed(boolean selected)
3707   {
3708     modifyConservation.setEnabled(selected);
3709     viewport.setConservationSelected(selected);
3710     viewport.getResidueShading().setConservationApplied(selected);
3711
3712     changeColour(viewport.getGlobalColourScheme());
3713     if (selected)
3714     {
3715       modifyConservation_actionPerformed();
3716     }
3717     else
3718     {
3719       SliderPanel.hideConservationSlider();
3720     }
3721   }
3722
3723   /**
3724    * Action on selecting or deselecting (Colour) Above PID Threshold
3725    */
3726   @Override
3727   public void abovePIDThreshold_actionPerformed(boolean selected)
3728   {
3729     modifyPID.setEnabled(selected);
3730     viewport.setAbovePIDThreshold(selected);
3731     if (!selected)
3732     {
3733       viewport.getResidueShading().setThreshold(0,
3734               viewport.isIgnoreGapsConsensus());
3735     }
3736
3737     changeColour(viewport.getGlobalColourScheme());
3738     if (selected)
3739     {
3740       modifyPID_actionPerformed();
3741     }
3742     else
3743     {
3744       SliderPanel.hidePIDSlider();
3745     }
3746   }
3747
3748   /**
3749    * DOCUMENT ME!
3750    *
3751    * @param e
3752    *          DOCUMENT ME!
3753    */
3754   @Override
3755   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3756   {
3757     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3758     AlignmentSorter.sortByPID(viewport.getAlignment(),
3759             viewport.getAlignment().getSequenceAt(0));
3760     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3761             viewport.getAlignment()));
3762     alignPanel.paintAlignment(true, false);
3763   }
3764
3765   /**
3766    * DOCUMENT ME!
3767    *
3768    * @param e
3769    *          DOCUMENT ME!
3770    */
3771   @Override
3772   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3773   {
3774     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3775     AlignmentSorter.sortByID(viewport.getAlignment());
3776     addHistoryItem(
3777             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3778     alignPanel.paintAlignment(true, false);
3779   }
3780
3781   /**
3782    * DOCUMENT ME!
3783    *
3784    * @param e
3785    *          DOCUMENT ME!
3786    */
3787   @Override
3788   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3789   {
3790     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3791     AlignmentSorter.sortByLength(viewport.getAlignment());
3792     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3793             viewport.getAlignment()));
3794     alignPanel.paintAlignment(true, false);
3795   }
3796
3797   /**
3798    * DOCUMENT ME!
3799    *
3800    * @param e
3801    *          DOCUMENT ME!
3802    */
3803   @Override
3804   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3805   {
3806     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3807     AlignmentSorter.sortByGroup(viewport.getAlignment());
3808     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3809             viewport.getAlignment()));
3810
3811     alignPanel.paintAlignment(true, false);
3812   }
3813
3814   /**
3815    * DOCUMENT ME!
3816    *
3817    * @param e
3818    *          DOCUMENT ME!
3819    */
3820   @Override
3821   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3822   {
3823     new RedundancyPanel(alignPanel, this);
3824   }
3825
3826   /**
3827    * DOCUMENT ME!
3828    *
3829    * @param e
3830    *          DOCUMENT ME!
3831    */
3832   @Override
3833   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3834   {
3835     if ((viewport.getSelectionGroup() == null)
3836             || (viewport.getSelectionGroup().getSize() < 2))
3837     {
3838       JvOptionPane.showInternalMessageDialog(this,
3839               MessageManager.getString(
3840                       "label.you_must_select_least_two_sequences"),
3841               MessageManager.getString("label.invalid_selection"),
3842               JvOptionPane.WARNING_MESSAGE);
3843     }
3844     else
3845     {
3846       JInternalFrame frame = new JInternalFrame();
3847       frame.setFrameIcon(null);
3848       frame.setContentPane(new PairwiseAlignPanel(viewport));
3849       Desktop.addInternalFrame(frame,
3850               MessageManager.getString("action.pairwise_alignment"), 600,
3851               500);
3852     }
3853   }
3854
3855   @Override
3856   public void autoCalculate_actionPerformed(ActionEvent e)
3857   {
3858     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3859     if (viewport.autoCalculateConsensus)
3860     {
3861       viewport.firePropertyChange("alignment", null,
3862               viewport.getAlignment().getSequences());
3863     }
3864   }
3865
3866   @Override
3867   public void sortByTreeOption_actionPerformed(ActionEvent e)
3868   {
3869     viewport.sortByTree = sortByTree.isSelected();
3870   }
3871
3872   @Override
3873   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3874   {
3875     viewport.followSelection = listenToViewSelections.isSelected();
3876   }
3877
3878   /**
3879    * Constructs a tree panel and adds it to the desktop
3880    *
3881    * @param type
3882    *          tree type (NJ or AV)
3883    * @param modelName
3884    *          name of score model used to compute the tree
3885    * @param options
3886    *          parameters for the distance or similarity calculation
3887    */
3888   void newTreePanel(String type, String modelName,
3889           SimilarityParamsI options)
3890   {
3891     String frameTitle = "";
3892     TreePanel tp;
3893
3894     boolean onSelection = false;
3895     if (viewport.getSelectionGroup() != null
3896             && viewport.getSelectionGroup().getSize() > 0)
3897     {
3898       SequenceGroup sg = viewport.getSelectionGroup();
3899
3900       /* Decide if the selection is a column region */
3901       for (SequenceI _s : sg.getSequences())
3902       {
3903         if (_s.getLength() < sg.getEndRes())
3904         {
3905           JvOptionPane.showMessageDialog(Desktop.desktop,
3906                   MessageManager.getString(
3907                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3908                   MessageManager.getString(
3909                           "label.sequences_selection_not_aligned"),
3910                   JvOptionPane.WARNING_MESSAGE);
3911
3912           return;
3913         }
3914       }
3915       onSelection = true;
3916     }
3917     else
3918     {
3919       if (viewport.getAlignment().getHeight() < 2)
3920       {
3921         return;
3922       }
3923     }
3924
3925     tp = new TreePanel(alignPanel, type, modelName, options);
3926     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3927
3928     frameTitle += " from ";
3929
3930     if (viewport.getViewName() != null)
3931     {
3932       frameTitle += viewport.getViewName() + " of ";
3933     }
3934
3935     frameTitle += this.title;
3936
3937     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3938   }
3939
3940   /**
3941    * DOCUMENT ME!
3942    *
3943    * @param title
3944    *          DOCUMENT ME!
3945    * @param order
3946    *          DOCUMENT ME!
3947    */
3948   public void addSortByOrderMenuItem(String title,
3949           final AlignmentOrder order)
3950   {
3951     final JMenuItem item = new JMenuItem(MessageManager
3952             .formatMessage("action.by_title_param", new Object[]
3953             { title }));
3954     sort.add(item);
3955     item.addActionListener(new java.awt.event.ActionListener()
3956     {
3957       @Override
3958       public void actionPerformed(ActionEvent e)
3959       {
3960         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3961
3962         // TODO: JBPNote - have to map order entries to curent SequenceI
3963         // pointers
3964         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3965
3966         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3967                 viewport.getAlignment()));
3968
3969         alignPanel.paintAlignment(true, false);
3970       }
3971     });
3972   }
3973
3974   /**
3975    * Add a new sort by annotation score menu item
3976    *
3977    * @param sort
3978    *          the menu to add the option to
3979    * @param scoreLabel
3980    *          the label used to retrieve scores for each sequence on the
3981    *          alignment
3982    */
3983   public void addSortByAnnotScoreMenuItem(JMenu sort,
3984           final String scoreLabel)
3985   {
3986     final JMenuItem item = new JMenuItem(scoreLabel);
3987     sort.add(item);
3988     item.addActionListener(new java.awt.event.ActionListener()
3989     {
3990       @Override
3991       public void actionPerformed(ActionEvent e)
3992       {
3993         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3994         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3995                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3996         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3997                 viewport.getAlignment()));
3998         alignPanel.paintAlignment(true, false);
3999       }
4000     });
4001   }
4002
4003   /**
4004    * last hash for alignment's annotation array - used to minimise cost of
4005    * rebuild.
4006    */
4007   protected int _annotationScoreVectorHash;
4008
4009   /**
4010    * search the alignment and rebuild the sort by annotation score submenu the
4011    * last alignment annotation vector hash is stored to minimize cost of
4012    * rebuilding in subsequence calls.
4013    *
4014    */
4015   @Override
4016   public void buildSortByAnnotationScoresMenu()
4017   {
4018     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4019     {
4020       return;
4021     }
4022
4023     if (viewport.getAlignment().getAlignmentAnnotation()
4024             .hashCode() != _annotationScoreVectorHash)
4025     {
4026       sortByAnnotScore.removeAll();
4027       // almost certainly a quicker way to do this - but we keep it simple
4028       Hashtable<String, String> scoreSorts = new Hashtable<>();
4029       AlignmentAnnotation aann[];
4030       for (SequenceI sqa : viewport.getAlignment().getSequences())
4031       {
4032         aann = sqa.getAnnotation();
4033         for (int i = 0; aann != null && i < aann.length; i++)
4034         {
4035           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4036           {
4037             scoreSorts.put(aann[i].label, aann[i].label);
4038           }
4039         }
4040       }
4041       Enumeration<String> labels = scoreSorts.keys();
4042       while (labels.hasMoreElements())
4043       {
4044         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
4045       }
4046       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4047       scoreSorts.clear();
4048
4049       _annotationScoreVectorHash = viewport.getAlignment()
4050               .getAlignmentAnnotation().hashCode();
4051     }
4052   }
4053
4054   /**
4055    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4056    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4057    * call. Listeners are added to remove the menu item when the treePanel is
4058    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4059    * modified.
4060    */
4061   @Override
4062   public void buildTreeSortMenu()
4063   {
4064     sortByTreeMenu.removeAll();
4065
4066     List<Component> comps = PaintRefresher.components
4067             .get(viewport.getSequenceSetId());
4068     List<TreePanel> treePanels = new ArrayList<>();
4069     for (Component comp : comps)
4070     {
4071       if (comp instanceof TreePanel)
4072       {
4073         treePanels.add((TreePanel) comp);
4074       }
4075     }
4076
4077     if (treePanels.size() < 1)
4078     {
4079       sortByTreeMenu.setVisible(false);
4080       return;
4081     }
4082
4083     sortByTreeMenu.setVisible(true);
4084
4085     for (final TreePanel tp : treePanels)
4086     {
4087       final JMenuItem item = new JMenuItem(tp.getTitle());
4088       item.addActionListener(new java.awt.event.ActionListener()
4089       {
4090         @Override
4091         public void actionPerformed(ActionEvent e)
4092         {
4093           tp.sortByTree_actionPerformed();
4094           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4095
4096         }
4097       });
4098
4099       sortByTreeMenu.add(item);
4100     }
4101   }
4102
4103   public boolean sortBy(AlignmentOrder alorder, String undoname)
4104   {
4105     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4106     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4107     if (undoname != null)
4108     {
4109       addHistoryItem(new OrderCommand(undoname, oldOrder,
4110               viewport.getAlignment()));
4111     }
4112     alignPanel.paintAlignment(true, false);
4113     return true;
4114   }
4115
4116   /**
4117    * Work out whether the whole set of sequences or just the selected set will
4118    * be submitted for multiple alignment.
4119    *
4120    */
4121   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4122   {
4123     // Now, check we have enough sequences
4124     AlignmentView msa = null;
4125
4126     if ((viewport.getSelectionGroup() != null)
4127             && (viewport.getSelectionGroup().getSize() > 1))
4128     {
4129       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4130       // some common interface!
4131       /*
4132        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4133        * SequenceI[sz = seqs.getSize(false)];
4134        *
4135        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4136        * seqs.getSequenceAt(i); }
4137        */
4138       msa = viewport.getAlignmentView(true);
4139     }
4140     else if (viewport.getSelectionGroup() != null
4141             && viewport.getSelectionGroup().getSize() == 1)
4142     {
4143       int option = JvOptionPane.showConfirmDialog(this,
4144               MessageManager.getString("warn.oneseq_msainput_selection"),
4145               MessageManager.getString("label.invalid_selection"),
4146               JvOptionPane.OK_CANCEL_OPTION);
4147       if (option == JvOptionPane.OK_OPTION)
4148       {
4149         msa = viewport.getAlignmentView(false);
4150       }
4151     }
4152     else
4153     {
4154       msa = viewport.getAlignmentView(false);
4155     }
4156     return msa;
4157   }
4158
4159   /**
4160    * Decides what is submitted to a secondary structure prediction service: the
4161    * first sequence in the alignment, or in the current selection, or, if the
4162    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4163    * region or the whole alignment. (where the first sequence in the set is the
4164    * one that the prediction will be for).
4165    */
4166   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4167   {
4168     AlignmentView seqs = null;
4169
4170     if ((viewport.getSelectionGroup() != null)
4171             && (viewport.getSelectionGroup().getSize() > 0))
4172     {
4173       seqs = viewport.getAlignmentView(true);
4174     }
4175     else
4176     {
4177       seqs = viewport.getAlignmentView(false);
4178     }
4179     // limit sequences - JBPNote in future - could spawn multiple prediction
4180     // jobs
4181     // TODO: viewport.getAlignment().isAligned is a global state - the local
4182     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4183     if (!viewport.getAlignment().isAligned(false))
4184     {
4185       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4186       // TODO: if seqs.getSequences().length>1 then should really have warned
4187       // user!
4188
4189     }
4190     return seqs;
4191   }
4192
4193   /**
4194    * DOCUMENT ME!
4195    *
4196    * @param e
4197    *          DOCUMENT ME!
4198    */
4199   @Override
4200   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4201   {
4202     // Pick the tree file
4203     JalviewFileChooser chooser = new JalviewFileChooser(
4204             Cache.getProperty("LAST_DIRECTORY"));
4205     chooser.setFileView(new JalviewFileView());
4206     chooser.setDialogTitle(
4207             MessageManager.getString("label.select_newick_like_tree_file"));
4208     chooser.setToolTipText(
4209             MessageManager.getString("label.load_tree_file"));
4210
4211     chooser.setResponseHandler(0, () -> {
4212       String filePath = chooser.getSelectedFile().getPath();
4213       Cache.setProperty("LAST_DIRECTORY", filePath);
4214       NewickFile fin = null;
4215       try
4216       {
4217         fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4218                 DataSourceType.FILE));
4219         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4220       } catch (Exception ex)
4221       {
4222         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4223                 MessageManager.getString("label.problem_reading_tree_file"),
4224                 JvOptionPane.WARNING_MESSAGE);
4225         ex.printStackTrace();
4226       }
4227       if (fin != null && fin.hasWarningMessage())
4228       {
4229         JvOptionPane.showMessageDialog(Desktop.desktop,
4230                 fin.getWarningMessage(),
4231                 MessageManager
4232                         .getString("label.possible_problem_with_tree_file"),
4233                 JvOptionPane.WARNING_MESSAGE);
4234       }
4235     });
4236     chooser.showOpenDialog(this);
4237   }
4238
4239   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4240   {
4241     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4242   }
4243
4244   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4245           int h, int x, int y)
4246   {
4247     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4248   }
4249
4250   /**
4251    * Add a treeviewer for the tree extracted from a Newick file object to the
4252    * current alignment view
4253    *
4254    * @param nf
4255    *          the tree
4256    * @param title
4257    *          tree viewer title
4258    * @param input
4259    *          Associated alignment input data (or null)
4260    * @param w
4261    *          width
4262    * @param h
4263    *          height
4264    * @param x
4265    *          position
4266    * @param y
4267    *          position
4268    * @return TreePanel handle
4269    */
4270   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4271           AlignmentView input, int w, int h, int x, int y)
4272   {
4273     TreePanel tp = null;
4274
4275     try
4276     {
4277       nf.parse();
4278
4279       if (nf.getTree() != null)
4280       {
4281         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4282
4283         tp.setSize(w, h);
4284
4285         if (x > 0 && y > 0)
4286         {
4287           tp.setLocation(x, y);
4288         }
4289
4290         Desktop.addInternalFrame(tp, treeTitle, w, h);
4291       }
4292     } catch (Exception ex)
4293     {
4294       ex.printStackTrace();
4295     }
4296
4297     return tp;
4298   }
4299
4300   public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
4301   {
4302     int x = 4, y = 5;
4303     int w = 400, h = 500;
4304
4305     try
4306     {
4307       NewickFile fin = new NewickFile(
4308               new FileParse(cm.getNewick(), DataSourceType.PASTE));
4309       String title = aa.label + " " + cm.getTreeMethod() + " tree"
4310               + (aa.sequenceRef != null
4311                       ? (" for " + aa.sequenceRef.getDisplayId(false))
4312                       : "");
4313
4314       showColumnWiseTree(fin, aa, title, w, h, x, y);
4315     } catch (Throwable xx)
4316     {
4317       Console.error("Unexpected exception showing tree for contact matrix",
4318               xx);
4319     }
4320   }
4321
4322   public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
4323           String treeTitle, int w, int h, int x, int y)
4324   {
4325     try
4326     {
4327       nf.parse();
4328       if (nf.getTree() == null)
4329       {
4330         return null;
4331       }
4332       TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle);
4333
4334       tp.setSize(w, h);
4335
4336       if (x > 0 && y > 0)
4337       {
4338         tp.setLocation(x, y);
4339       }
4340
4341       Desktop.addInternalFrame(tp, treeTitle, w, h);
4342       return tp;
4343     } catch (Throwable xx)
4344     {
4345       Console.error("Unexpected exception showing tree for contact matrix",
4346               xx);
4347     }
4348     return null;
4349   }
4350
4351   private boolean buildingMenu = false;
4352
4353   /**
4354    * Generates menu items and listener event actions for web service clients
4355    *
4356    */
4357   public void BuildWebServiceMenu()
4358   {
4359     while (buildingMenu)
4360     {
4361       try
4362       {
4363         jalview.bin.Console
4364                 .errPrintln("Waiting for building menu to finish.");
4365         Thread.sleep(10);
4366       } catch (Exception e)
4367       {
4368       }
4369     }
4370     final AlignFrame me = this;
4371     buildingMenu = true;
4372     new Thread(new Runnable()
4373     {
4374       @Override
4375       public void run()
4376       {
4377         final List<JMenuItem> legacyItems = new ArrayList<>();
4378         try
4379         {
4380           // jalview.bin.Console.errPrintln("Building ws menu again "
4381           // + Thread.currentThread());
4382           // TODO: add support for context dependent disabling of services based
4383           // on
4384           // alignment and current selection
4385           // TODO: add additional serviceHandle parameter to specify abstract
4386           // handler
4387           // class independently of AbstractName
4388           // TODO: add in rediscovery GUI function to restart discoverer
4389           // TODO: group services by location as well as function and/or
4390           // introduce
4391           // object broker mechanism.
4392           final Vector<JMenu> wsmenu = new Vector<>();
4393           final IProgressIndicator af = me;
4394
4395           /*
4396            * do not i18n these strings - they are hard-coded in class
4397            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4398            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4399            */
4400           final JMenu msawsmenu = new JMenu("Alignment");
4401           final JMenu secstrmenu = new JMenu(
4402                   "Secondary Structure Prediction");
4403           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4404           final JMenu analymenu = new JMenu("Analysis");
4405           final JMenu dismenu = new JMenu("Protein Disorder");
4406           // JAL-940 - only show secondary structure prediction services from
4407           // the legacy server
4408           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4409               // &&
4410           Discoverer.services != null && (Discoverer.services.size() > 0))
4411           {
4412             // TODO: refactor to allow list of AbstractName/Handler bindings to
4413             // be
4414             // stored or retrieved from elsewhere
4415             // No MSAWS used any more:
4416             // Vector msaws = null; // (Vector)
4417             // Discoverer.services.get("MsaWS");
4418             Vector<ServiceHandle> secstrpr = Discoverer.services
4419                     .get("SecStrPred");
4420             if (secstrpr != null)
4421             {
4422               // Add any secondary structure prediction services
4423               for (int i = 0, j = secstrpr.size(); i < j; i++)
4424               {
4425                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4426                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4427                         .getServiceClient(sh);
4428                 int p = secstrmenu.getItemCount();
4429                 impl.attachWSMenuEntry(secstrmenu, me);
4430                 int q = secstrmenu.getItemCount();
4431                 for (int litm = p; litm < q; litm++)
4432                 {
4433                   legacyItems.add(secstrmenu.getItem(litm));
4434                 }
4435               }
4436             }
4437           }
4438
4439           // Add all submenus in the order they should appear on the web
4440           // services menu
4441           wsmenu.add(msawsmenu);
4442           wsmenu.add(secstrmenu);
4443           wsmenu.add(dismenu);
4444           wsmenu.add(analymenu);
4445           // No search services yet
4446           // wsmenu.add(seqsrchmenu);
4447
4448           javax.swing.SwingUtilities.invokeLater(new Runnable()
4449           {
4450             @Override
4451             public void run()
4452             {
4453               try
4454               {
4455                 webService.removeAll();
4456                 // first, add discovered services onto the webservices menu
4457                 if (wsmenu.size() > 0)
4458                 {
4459                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4460                   {
4461                     webService.add(wsmenu.get(i));
4462                   }
4463                 }
4464                 else
4465                 {
4466                   webService.add(me.webServiceNoServices);
4467                 }
4468                 // TODO: move into separate menu builder class.
4469                 {
4470                   // logic for 2.11.1.4 is
4471                   // always look to see if there is a discover. if there isn't
4472                   // we can't show any Jws2 services
4473                   // if there are services available, show them - regardless of
4474                   // the 'show JWS2 preference'
4475                   // if the discoverer is running then say so
4476                   // otherwise offer to trigger discovery if 'show JWS2' is not
4477                   // enabled
4478                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4479                   if (jws2servs != null)
4480                   {
4481                     if (jws2servs.hasServices())
4482                     {
4483                       jws2servs.attachWSMenuEntry(webService, me);
4484                       for (Jws2Instance sv : jws2servs.getServices())
4485                       {
4486                         if (sv.description.toLowerCase(Locale.ROOT)
4487                                 .contains("jpred"))
4488                         {
4489                           for (JMenuItem jmi : legacyItems)
4490                           {
4491                             jmi.setVisible(false);
4492                           }
4493                         }
4494                       }
4495                     }
4496
4497                     if (jws2servs.isRunning())
4498                     {
4499                       JMenuItem tm = new JMenuItem(
4500                               "Still discovering JABA Services");
4501                       tm.setEnabled(false);
4502                       webService.add(tm);
4503                     }
4504                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4505                     {
4506                       JMenuItem enableJws2 = new JMenuItem(
4507                               "Discover Web Services");
4508                       enableJws2.setToolTipText(
4509                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4510                       enableJws2.setEnabled(true);
4511                       enableJws2.addActionListener(new ActionListener()
4512                       {
4513
4514                         @Override
4515                         public void actionPerformed(ActionEvent e)
4516                         {
4517                           // start service discoverer, but ignore preference
4518                           Desktop.instance.startServiceDiscovery(false,
4519                                   true);
4520                         }
4521                       });
4522                       webService.add(enableJws2);
4523                     }
4524                   }
4525                 }
4526                 build_urlServiceMenu(me.webService);
4527                 build_fetchdbmenu(webService);
4528                 for (JMenu item : wsmenu)
4529                 {
4530                   if (item.getItemCount() == 0)
4531                   {
4532                     item.setEnabled(false);
4533                   }
4534                   else
4535                   {
4536                     item.setEnabled(true);
4537                   }
4538                 }
4539               } catch (Exception e)
4540               {
4541                 Console.debug(
4542                         "Exception during web service menu building process.",
4543                         e);
4544               }
4545             }
4546           });
4547         } catch (Exception e)
4548         {
4549         }
4550         buildingMenu = false;
4551       }
4552     }).start();
4553
4554   }
4555
4556   /**
4557    * construct any groupURL type service menu entries.
4558    *
4559    * @param webService
4560    */
4561   protected void build_urlServiceMenu(JMenu webService)
4562   {
4563     // TODO: remove this code when 2.7 is released
4564     // DEBUG - alignmentView
4565     /*
4566      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4567      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4568      *
4569      * @Override public void actionPerformed(ActionEvent e) {
4570      * jalview.datamodel.AlignmentView
4571      * .testSelectionViews(af.viewport.getAlignment(),
4572      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4573      *
4574      * }); webService.add(testAlView);
4575      */
4576     // TODO: refactor to RestClient discoverer and merge menu entries for
4577     // rest-style services with other types of analysis/calculation service
4578     // SHmmr test client - still being implemented.
4579     // DEBUG - alignmentView
4580
4581     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4582             .getRestClients())
4583     {
4584       client.attachWSMenuEntry(
4585               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4586               this);
4587     }
4588   }
4589
4590   /**
4591    * Searches the alignment sequences for xRefs and builds the Show
4592    * Cross-References menu (formerly called Show Products), with database
4593    * sources for which cross-references are found (protein sources for a
4594    * nucleotide alignment and vice versa)
4595    *
4596    * @return true if Show Cross-references menu should be enabled
4597    */
4598   public boolean canShowProducts()
4599   {
4600     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4601     AlignmentI dataset = viewport.getAlignment().getDataset();
4602
4603     showProducts.removeAll();
4604     final boolean dna = viewport.getAlignment().isNucleotide();
4605
4606     if (seqs == null || seqs.length == 0)
4607     {
4608       // nothing to see here.
4609       return false;
4610     }
4611
4612     boolean showp = false;
4613     try
4614     {
4615       List<String> ptypes = new CrossRef(seqs, dataset)
4616               .findXrefSourcesForSequences(dna);
4617
4618       for (final String source : ptypes)
4619       {
4620         showp = true;
4621         final AlignFrame af = this;
4622         JMenuItem xtype = new JMenuItem(source);
4623         xtype.addActionListener(new ActionListener()
4624         {
4625           @Override
4626           public void actionPerformed(ActionEvent e)
4627           {
4628             showProductsFor(af.viewport.getSequenceSelection(), dna,
4629                     source);
4630           }
4631         });
4632         showProducts.add(xtype);
4633       }
4634       showProducts.setVisible(showp);
4635       showProducts.setEnabled(showp);
4636     } catch (Exception e)
4637     {
4638       Console.warn(
4639               "canShowProducts threw an exception - please report to help@jalview.org",
4640               e);
4641       return false;
4642     }
4643     return showp;
4644   }
4645
4646   /**
4647    * Finds and displays cross-references for the selected sequences (protein
4648    * products for nucleotide sequences, dna coding sequences for peptides).
4649    *
4650    * @param sel
4651    *          the sequences to show cross-references for
4652    * @param dna
4653    *          true if from a nucleotide alignment (so showing proteins)
4654    * @param source
4655    *          the database to show cross-references for
4656    */
4657   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4658           final String source)
4659   {
4660     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4661             .start();
4662   }
4663
4664   /**
4665    * Construct and display a new frame containing the translation of this
4666    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4667    */
4668   @Override
4669   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4670   {
4671     AlignmentI al = null;
4672     try
4673     {
4674       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4675
4676       al = dna.translateCdna(codeTable);
4677     } catch (Exception ex)
4678     {
4679       Console.error("Exception during translation. Please report this !",
4680               ex);
4681       final String msg = MessageManager.getString(
4682               "label.error_when_translating_sequences_submit_bug_report");
4683       final String errorTitle = MessageManager
4684               .getString("label.implementation_error")
4685               + MessageManager.getString("label.translation_failed");
4686       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4687               JvOptionPane.ERROR_MESSAGE);
4688       return;
4689     }
4690     if (al == null || al.getHeight() == 0)
4691     {
4692       final String msg = MessageManager.getString(
4693               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4694       final String errorTitle = MessageManager
4695               .getString("label.translation_failed");
4696       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4697               JvOptionPane.WARNING_MESSAGE);
4698     }
4699     else
4700     {
4701       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4702       af.setFileFormat(this.currentFileFormat);
4703       final String newTitle = MessageManager
4704               .formatMessage("label.translation_of_params", new Object[]
4705               { this.getTitle(), codeTable.getId() });
4706       af.setTitle(newTitle);
4707       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4708       {
4709         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4710         viewport.openSplitFrame(af, new Alignment(seqs));
4711       }
4712       else
4713       {
4714         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4715                 DEFAULT_HEIGHT);
4716       }
4717     }
4718   }
4719
4720   /**
4721    * Set the file format
4722    *
4723    * @param format
4724    */
4725   public void setFileFormat(FileFormatI format)
4726   {
4727     this.currentFileFormat = format;
4728   }
4729
4730   /**
4731    * Try to load a features file onto the alignment.
4732    *
4733    * @param file
4734    *          contents or path to retrieve file or a File object
4735    * @param sourceType
4736    *          access mode of file (see jalview.io.AlignFile)
4737    * @return true if features file was parsed correctly.
4738    */
4739   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4740   {
4741     // BH 2018
4742     return avc.parseFeaturesFile(file, sourceType,
4743             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4744
4745   }
4746
4747   @Override
4748   public void refreshFeatureUI(boolean enableIfNecessary)
4749   {
4750     // note - currently this is only still here rather than in the controller
4751     // because of the featureSettings hard reference that is yet to be
4752     // abstracted
4753     if (enableIfNecessary)
4754     {
4755       viewport.setShowSequenceFeatures(true);
4756       showSeqFeatures.setSelected(true);
4757     }
4758
4759   }
4760
4761   @Override
4762   public void dragEnter(DropTargetDragEvent evt)
4763   {
4764   }
4765
4766   @Override
4767   public void dragExit(DropTargetEvent evt)
4768   {
4769   }
4770
4771   @Override
4772   public void dragOver(DropTargetDragEvent evt)
4773   {
4774   }
4775
4776   @Override
4777   public void dropActionChanged(DropTargetDragEvent evt)
4778   {
4779   }
4780
4781   @Override
4782   public void drop(DropTargetDropEvent evt)
4783   {
4784     // JAL-1552 - acceptDrop required before getTransferable call for
4785     // Java's Transferable for native dnd
4786     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4787     Transferable t = evt.getTransferable();
4788
4789     final AlignFrame thisaf = this;
4790     final List<Object> files = new ArrayList<>();
4791     List<DataSourceType> protocols = new ArrayList<>();
4792
4793     try
4794     {
4795       Desktop.transferFromDropTarget(files, protocols, evt, t);
4796     } catch (Exception e)
4797     {
4798       e.printStackTrace();
4799     }
4800     if (files != null)
4801     {
4802       new Thread(new Runnable()
4803       {
4804         @Override
4805         public void run()
4806         {
4807           try
4808           {
4809             // check to see if any of these files have names matching sequences
4810             // in
4811             // the alignment
4812             SequenceIdMatcher idm = new SequenceIdMatcher(
4813                     viewport.getAlignment().getSequencesArray());
4814             /**
4815              * Object[] { String,SequenceI}
4816              */
4817             ArrayList<Object[]> filesmatched = new ArrayList<>();
4818             ArrayList<Object> filesnotmatched = new ArrayList<>();
4819             for (int i = 0; i < files.size(); i++)
4820             {
4821               // BH 2018
4822               Object file = files.get(i);
4823               String fileName = file.toString();
4824               String pdbfn = "";
4825               DataSourceType protocol = (file instanceof File
4826                       ? DataSourceType.FILE
4827                       : FormatAdapter.checkProtocol(fileName));
4828               if (protocol == DataSourceType.FILE)
4829               {
4830                 File fl;
4831                 if (file instanceof File)
4832                 {
4833                   fl = (File) file;
4834                   Platform.cacheFileData(fl);
4835                 }
4836                 else
4837                 {
4838                   fl = new File(fileName);
4839                 }
4840                 pdbfn = fl.getName();
4841               }
4842               else if (protocol == DataSourceType.URL)
4843               {
4844                 URL url = new URL(fileName);
4845                 pdbfn = url.getFile();
4846               }
4847               if (pdbfn.length() > 0)
4848               {
4849                 // attempt to find a match in the alignment
4850                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4851                 int l = 0, c = pdbfn.indexOf(".");
4852                 while (mtch == null && c != -1)
4853                 {
4854                   do
4855                   {
4856                     l = c;
4857                   } while ((c = pdbfn.indexOf(".", l)) > l);
4858                   if (l > -1)
4859                   {
4860                     pdbfn = pdbfn.substring(0, l);
4861                   }
4862                   mtch = idm.findAllIdMatches(pdbfn);
4863                 }
4864                 if (mtch != null)
4865                 {
4866                   FileFormatI type;
4867                   try
4868                   {
4869                     type = new IdentifyFile().identify(file, protocol);
4870                   } catch (Exception ex)
4871                   {
4872                     type = null;
4873                   }
4874                   if (type != null && type.isStructureFile())
4875                   {
4876                     filesmatched.add(new Object[] { file, protocol, mtch });
4877                     continue;
4878                   }
4879                 }
4880                 // File wasn't named like one of the sequences or wasn't a PDB
4881                 // file.
4882                 filesnotmatched.add(file);
4883               }
4884             }
4885             int assocfiles = 0;
4886             if (filesmatched.size() > 0)
4887             {
4888               boolean autoAssociate = Cache
4889                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4890               if (!autoAssociate)
4891               {
4892                 String msg = MessageManager.formatMessage(
4893                         "label.automatically_associate_structure_files_with_sequences_same_name",
4894                         new Object[]
4895                         { Integer.valueOf(filesmatched.size())
4896                                 .toString() });
4897                 String ttl = MessageManager.getString(
4898                         "label.automatically_associate_structure_files_by_name");
4899                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4900                         ttl, JvOptionPane.YES_NO_OPTION);
4901                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4902               }
4903               if (autoAssociate)
4904               {
4905                 for (Object[] fm : filesmatched)
4906                 {
4907                   // try and associate
4908                   // TODO: may want to set a standard ID naming formalism for
4909                   // associating PDB files which have no IDs.
4910                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4911                   {
4912                     PDBEntry pe = new AssociatePdbFileWithSeq()
4913                             .associatePdbWithSeq(fm[0].toString(),
4914                                     (DataSourceType) fm[1], toassoc, false,
4915                                     Desktop.instance);
4916                     if (pe != null)
4917                     {
4918                       jalview.bin.Console.errPrintln("Associated file : "
4919                               + (fm[0].toString()) + " with "
4920                               + toassoc.getDisplayId(true));
4921                       assocfiles++;
4922                     }
4923                   }
4924                   // TODO: do we need to update overview ? only if features are
4925                   // shown I guess
4926                   alignPanel.paintAlignment(true, false);
4927                 }
4928               }
4929               else
4930               {
4931                 /*
4932                  * add declined structures as sequences
4933                  */
4934                 for (Object[] o : filesmatched)
4935                 {
4936                   filesnotmatched.add(o[0]);
4937                 }
4938               }
4939             }
4940             if (filesnotmatched.size() > 0)
4941             {
4942               if (assocfiles > 0 && (Cache.getDefault(
4943                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4944                       || JvOptionPane.showConfirmDialog(thisaf,
4945                               "<html>" + MessageManager.formatMessage(
4946                                       "label.ignore_unmatched_dropped_files_info",
4947                                       new Object[]
4948                                       { Integer.valueOf(
4949                                               filesnotmatched.size())
4950                                               .toString() })
4951                                       + "</html>",
4952                               MessageManager.getString(
4953                                       "label.ignore_unmatched_dropped_files"),
4954                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4955               {
4956                 return;
4957               }
4958               for (Object fn : filesnotmatched)
4959               {
4960                 loadJalviewDataFile(fn, null, null, null);
4961               }
4962
4963             }
4964           } catch (Exception ex)
4965           {
4966             ex.printStackTrace();
4967           }
4968         }
4969       }).start();
4970     }
4971   }
4972
4973   /**
4974    * Attempt to load a "dropped" file or URL string, by testing in turn for
4975    * <ul>
4976    * <li>an Annotation file</li>
4977    * <li>a JNet file</li>
4978    * <li>a features file</li>
4979    * <li>else try to interpret as an alignment file</li>
4980    * </ul>
4981    *
4982    * @param file
4983    *          either a filename or a URL string.
4984    */
4985   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4986           FileFormatI format, SequenceI assocSeq)
4987   {
4988     // BH 2018 was String file
4989     try
4990     {
4991       if (sourceType == null)
4992       {
4993         sourceType = FormatAdapter.checkProtocol(file);
4994       }
4995       // if the file isn't identified, or not positively identified as some
4996       // other filetype (PFAM is default unidentified alignment file type) then
4997       // try to parse as annotation.
4998       boolean isAnnotation = (format == null
4999               || FileFormat.Pfam.equals(format))
5000                       ? new AnnotationFile().annotateAlignmentView(viewport,
5001                               file, sourceType)
5002                       : false;
5003
5004       if (!isAnnotation)
5005       {
5006         // first see if its a T-COFFEE score file
5007         TCoffeeScoreFile tcf = null;
5008         try
5009         {
5010           tcf = new TCoffeeScoreFile(file, sourceType);
5011           if (tcf.isValid())
5012           {
5013             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5014             {
5015               buildColourMenu();
5016               changeColour(
5017                       new TCoffeeColourScheme(viewport.getAlignment()));
5018               isAnnotation = true;
5019               setStatus(MessageManager.getString(
5020                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
5021             }
5022             else
5023             {
5024               // some problem - if no warning its probable that the ID matching
5025               // process didn't work
5026               JvOptionPane.showMessageDialog(Desktop.desktop,
5027                       tcf.getWarningMessage() == null
5028                               ? MessageManager.getString(
5029                                       "label.check_file_matches_sequence_ids_alignment")
5030                               : tcf.getWarningMessage(),
5031                       MessageManager.getString(
5032                               "label.problem_reading_tcoffee_score_file"),
5033                       JvOptionPane.WARNING_MESSAGE);
5034             }
5035           }
5036           else
5037           {
5038             tcf = null;
5039           }
5040         } catch (Exception x)
5041         {
5042           Console.debug(
5043                   "Exception when processing data source as T-COFFEE score file",
5044                   x);
5045           tcf = null;
5046         }
5047         if (tcf == null)
5048         {
5049           // try to see if its a JNet 'concise' style annotation file *before*
5050           // we
5051           // try to parse it as a features file
5052           if (format == null)
5053           {
5054             format = new IdentifyFile().identify(file, sourceType);
5055           }
5056           if (FileFormat.ScoreMatrix == format)
5057           {
5058             ScoreMatrixFile sm = new ScoreMatrixFile(
5059                     new FileParse(file, sourceType));
5060             sm.parse();
5061             // todo: i18n this message
5062             setStatus(MessageManager.formatMessage(
5063                     "label.successfully_loaded_matrix",
5064                     sm.getMatrixName()));
5065           }
5066           else if (FileFormat.Jnet.equals(format))
5067           {
5068             JPredFile predictions = new JPredFile(file, sourceType);
5069             new JnetAnnotationMaker();
5070             JnetAnnotationMaker.add_annotation(predictions,
5071                     viewport.getAlignment(), 0, false);
5072             viewport.getAlignment().setupJPredAlignment();
5073             isAnnotation = true;
5074           }
5075           // else if (IdentifyFile.FeaturesFile.equals(format))
5076           else if (FileFormat.Features.equals(format))
5077           {
5078             if (parseFeaturesFile(file, sourceType))
5079             {
5080               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
5081               if (splitFrame != null)
5082               {
5083                 splitFrame.repaint();
5084               }
5085               else
5086               {
5087                 alignPanel.paintAlignment(true, true);
5088               }
5089             }
5090           }
5091           else
5092           {
5093             new FileLoader().LoadFile(viewport, file, sourceType, format);
5094           }
5095         }
5096       }
5097       if (isAnnotation)
5098       {
5099
5100         alignPanel.adjustAnnotationHeight();
5101         viewport.updateSequenceIdColours();
5102         buildSortByAnnotationScoresMenu();
5103         alignPanel.paintAlignment(true, true);
5104       }
5105     } catch (Exception ex)
5106     {
5107       ex.printStackTrace();
5108     } catch (OutOfMemoryError oom)
5109     {
5110       try
5111       {
5112         System.gc();
5113       } catch (Exception x)
5114       {
5115       }
5116       new OOMWarning(
5117               "loading data "
5118                       + (sourceType != null
5119                               ? (sourceType == DataSourceType.PASTE
5120                                       ? "from clipboard."
5121                                       : "using " + sourceType + " from "
5122                                               + file)
5123                               : ".")
5124                       + (format != null
5125                               ? "(parsing as '" + format + "' file)"
5126                               : ""),
5127               oom, Desktop.desktop);
5128     }
5129   }
5130
5131   /**
5132    * Method invoked by the ChangeListener on the tabbed pane, in other words
5133    * when a different tabbed pane is selected by the user or programmatically.
5134    */
5135   @Override
5136   public void tabSelectionChanged(int index)
5137   {
5138     if (index > -1)
5139     {
5140       /*
5141        * update current Overview window title (if there is one)
5142        * to add view name "Original" if necessary
5143        */
5144       alignPanel.setOverviewTitle(this);
5145
5146       /*
5147        * switch panels and set Overview title (if there is one
5148        * because it was opened automatically)
5149        */
5150       alignPanel = alignPanels.get(index);
5151       alignPanel.setOverviewTitle(this);
5152
5153       viewport = alignPanel.av;
5154       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5155       setMenusFromViewport(viewport);
5156       if (featureSettings != null && featureSettings.isOpen()
5157               && featureSettings.fr.getViewport() != viewport)
5158       {
5159         if (viewport.isShowSequenceFeatures())
5160         {
5161           // refresh the featureSettings to reflect UI change
5162           showFeatureSettingsUI();
5163         }
5164         else
5165         {
5166           // close feature settings for this view.
5167           featureSettings.close();
5168         }
5169       }
5170
5171     }
5172
5173     /*
5174      * 'focus' any colour slider that is open to the selected viewport
5175      */
5176     if (viewport.getConservationSelected())
5177     {
5178       SliderPanel.setConservationSlider(alignPanel,
5179               viewport.getResidueShading(), alignPanel.getViewName());
5180     }
5181     else
5182     {
5183       SliderPanel.hideConservationSlider();
5184     }
5185     if (viewport.getAbovePIDThreshold())
5186     {
5187       SliderPanel.setPIDSliderSource(alignPanel,
5188               viewport.getResidueShading(), alignPanel.getViewName());
5189     }
5190     else
5191     {
5192       SliderPanel.hidePIDSlider();
5193     }
5194
5195     /*
5196      * If there is a frame linked to this one in a SplitPane, switch it to the
5197      * same view tab index. No infinite recursion of calls should happen, since
5198      * tabSelectionChanged() should not get invoked on setting the selected
5199      * index to an unchanged value. Guard against setting an invalid index
5200      * before the new view peer tab has been created.
5201      */
5202     final AlignViewportI peer = viewport.getCodingComplement();
5203     if (peer != null)
5204     {
5205       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5206               .getAlignPanel().alignFrame;
5207       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5208       {
5209         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5210       }
5211     }
5212   }
5213
5214   /**
5215    * On right mouse click on view tab, prompt for and set new view name.
5216    */
5217   @Override
5218   public void tabbedPane_mousePressed(MouseEvent e)
5219   {
5220     if (e.isPopupTrigger())
5221     {
5222       String msg = MessageManager.getString("label.enter_view_name");
5223       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5224       String reply = JvOptionPane.showInputDialog(msg, ttl);
5225
5226       if (reply != null)
5227       {
5228         viewport.setViewName(reply);
5229         // TODO warn if reply is in getExistingViewNames()?
5230         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5231       }
5232     }
5233   }
5234
5235   public AlignViewport getCurrentView()
5236   {
5237     return viewport;
5238   }
5239
5240   /**
5241    * Open the dialog for regex description parsing.
5242    */
5243   @Override
5244   protected void extractScores_actionPerformed(ActionEvent e)
5245   {
5246     ParseProperties pp = new jalview.analysis.ParseProperties(
5247             viewport.getAlignment());
5248     // TODO: verify regex and introduce GUI dialog for version 2.5
5249     // if (pp.getScoresFromDescription("col", "score column ",
5250     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5251     // true)>0)
5252     if (pp.getScoresFromDescription("description column",
5253             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5254     {
5255       buildSortByAnnotationScoresMenu();
5256     }
5257   }
5258
5259   /*
5260    * (non-Javadoc)
5261    *
5262    * @see
5263    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5264    * )
5265    */
5266   @Override
5267   protected void showDbRefs_actionPerformed(ActionEvent e)
5268   {
5269     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5270   }
5271
5272   /*
5273    * (non-Javadoc)
5274    *
5275    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5276    * ActionEvent)
5277    */
5278   @Override
5279   protected void showNpFeats_actionPerformed(ActionEvent e)
5280   {
5281     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5282   }
5283
5284   /**
5285    * find the viewport amongst the tabs in this alignment frame and close that
5286    * tab
5287    *
5288    * @param av
5289    */
5290   public boolean closeView(AlignViewportI av)
5291   {
5292     if (viewport == av)
5293     {
5294       this.closeMenuItem_actionPerformed(false);
5295       return true;
5296     }
5297     Component[] comp = tabbedPane.getComponents();
5298     for (int i = 0; comp != null && i < comp.length; i++)
5299     {
5300       if (comp[i] instanceof AlignmentPanel)
5301       {
5302         if (((AlignmentPanel) comp[i]).av == av)
5303         {
5304           // close the view.
5305           closeView((AlignmentPanel) comp[i]);
5306           return true;
5307         }
5308       }
5309     }
5310     return false;
5311   }
5312
5313   protected void build_fetchdbmenu(JMenu webService)
5314   {
5315     // Temporary hack - DBRef Fetcher always top level ws entry.
5316     // TODO We probably want to store a sequence database checklist in
5317     // preferences and have checkboxes.. rather than individual sources selected
5318     // here
5319     final JMenu rfetch = new JMenu(
5320             MessageManager.getString("action.fetch_db_references"));
5321     rfetch.setToolTipText(MessageManager.getString(
5322             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5323     webService.add(rfetch);
5324
5325     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5326             MessageManager.getString("option.trim_retrieved_seqs"));
5327     trimrs.setToolTipText(
5328             MessageManager.getString("label.trim_retrieved_sequences"));
5329     trimrs.setSelected(
5330             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5331     trimrs.addActionListener(new ActionListener()
5332     {
5333       @Override
5334       public void actionPerformed(ActionEvent e)
5335       {
5336         trimrs.setSelected(trimrs.isSelected());
5337         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5338                 Boolean.valueOf(trimrs.isSelected()).toString());
5339       }
5340     });
5341     rfetch.add(trimrs);
5342     JMenuItem fetchr = new JMenuItem(
5343             MessageManager.getString("label.standard_databases"));
5344     fetchr.setToolTipText(
5345             MessageManager.getString("label.fetch_embl_uniprot"));
5346     fetchr.addActionListener(new ActionListener()
5347     {
5348
5349       @Override
5350       public void actionPerformed(ActionEvent e)
5351       {
5352         new Thread(new Runnable()
5353         {
5354           @Override
5355           public void run()
5356           {
5357             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5358                     .getAlignment().isNucleotide();
5359             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5360                     alignPanel.av.getSequenceSelection(),
5361                     alignPanel.alignFrame, null,
5362                     alignPanel.alignFrame.featureSettings, isNucleotide);
5363             dbRefFetcher.addListener(new FetchFinishedListenerI()
5364             {
5365               @Override
5366               public void finished()
5367               {
5368
5369                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5370                         .getFeatureSettingsModels())
5371                 {
5372
5373                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5374                 }
5375                 AlignFrame.this.setMenusForViewport();
5376               }
5377             });
5378             dbRefFetcher.fetchDBRefs(false);
5379           }
5380         }).start();
5381
5382       }
5383
5384     });
5385     rfetch.add(fetchr);
5386     new Thread(new Runnable()
5387     {
5388       @Override
5389       public void run()
5390       {
5391         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5392                 .getSequenceFetcherSingleton();
5393         javax.swing.SwingUtilities.invokeLater(new Runnable()
5394         {
5395           @Override
5396           public void run()
5397           {
5398             String[] dbclasses = sf.getNonAlignmentSources();
5399             List<DbSourceProxy> otherdb;
5400             JMenu dfetch = new JMenu();
5401             JMenu ifetch = new JMenu();
5402             JMenuItem fetchr = null;
5403             int comp = 0, icomp = 0, mcomp = 15;
5404             String mname = null;
5405             int dbi = 0;
5406             for (String dbclass : dbclasses)
5407             {
5408               otherdb = sf.getSourceProxy(dbclass);
5409               // add a single entry for this class, or submenu allowing 'fetch
5410               // all' or pick one
5411               if (otherdb == null || otherdb.size() < 1)
5412               {
5413                 continue;
5414               }
5415               if (mname == null)
5416               {
5417                 mname = "From " + dbclass;
5418               }
5419               if (otherdb.size() == 1)
5420               {
5421                 final DbSourceProxy[] dassource = otherdb
5422                         .toArray(new DbSourceProxy[0]);
5423                 DbSourceProxy src = otherdb.get(0);
5424                 fetchr = new JMenuItem(src.getDbSource());
5425                 fetchr.addActionListener(new ActionListener()
5426                 {
5427
5428                   @Override
5429                   public void actionPerformed(ActionEvent e)
5430                   {
5431                     new Thread(new Runnable()
5432                     {
5433
5434                       @Override
5435                       public void run()
5436                       {
5437                         boolean isNucleotide = alignPanel.alignFrame
5438                                 .getViewport().getAlignment()
5439                                 .isNucleotide();
5440                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5441                                 alignPanel.av.getSequenceSelection(),
5442                                 alignPanel.alignFrame, dassource,
5443                                 alignPanel.alignFrame.featureSettings,
5444                                 isNucleotide);
5445                         dbRefFetcher
5446                                 .addListener(new FetchFinishedListenerI()
5447                                 {
5448                                   @Override
5449                                   public void finished()
5450                                   {
5451                                     FeatureSettingsModelI srcSettings = dassource[0]
5452                                             .getFeatureColourScheme();
5453                                     alignPanel.av.mergeFeaturesStyle(
5454                                             srcSettings);
5455                                     AlignFrame.this.setMenusForViewport();
5456                                   }
5457                                 });
5458                         dbRefFetcher.fetchDBRefs(false);
5459                       }
5460                     }).start();
5461                   }
5462
5463                 });
5464                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5465                         MessageManager.formatMessage(
5466                                 "label.fetch_retrieve_from", new Object[]
5467                                 { src.getDbName() })));
5468                 dfetch.add(fetchr);
5469                 comp++;
5470               }
5471               else
5472               {
5473                 final DbSourceProxy[] dassource = otherdb
5474                         .toArray(new DbSourceProxy[0]);
5475                 // fetch all entry
5476                 DbSourceProxy src = otherdb.get(0);
5477                 fetchr = new JMenuItem(MessageManager
5478                         .formatMessage("label.fetch_all_param", new Object[]
5479                         { src.getDbSource() }));
5480                 fetchr.addActionListener(new ActionListener()
5481                 {
5482                   @Override
5483                   public void actionPerformed(ActionEvent e)
5484                   {
5485                     new Thread(new Runnable()
5486                     {
5487
5488                       @Override
5489                       public void run()
5490                       {
5491                         boolean isNucleotide = alignPanel.alignFrame
5492                                 .getViewport().getAlignment()
5493                                 .isNucleotide();
5494                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5495                                 alignPanel.av.getSequenceSelection(),
5496                                 alignPanel.alignFrame, dassource,
5497                                 alignPanel.alignFrame.featureSettings,
5498                                 isNucleotide);
5499                         dbRefFetcher
5500                                 .addListener(new FetchFinishedListenerI()
5501                                 {
5502                                   @Override
5503                                   public void finished()
5504                                   {
5505                                     AlignFrame.this.setMenusForViewport();
5506                                   }
5507                                 });
5508                         dbRefFetcher.fetchDBRefs(false);
5509                       }
5510                     }).start();
5511                   }
5512                 });
5513
5514                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5515                         MessageManager.formatMessage(
5516                                 "label.fetch_retrieve_from_all_sources",
5517                                 new Object[]
5518                                 { Integer.valueOf(otherdb.size())
5519                                         .toString(),
5520                                     src.getDbSource(), src.getDbName() })));
5521                 dfetch.add(fetchr);
5522                 comp++;
5523                 // and then build the rest of the individual menus
5524                 ifetch = new JMenu(MessageManager.formatMessage(
5525                         "label.source_from_db_source", new Object[]
5526                         { src.getDbSource() }));
5527                 icomp = 0;
5528                 String imname = null;
5529                 int i = 0;
5530                 for (DbSourceProxy sproxy : otherdb)
5531                 {
5532                   String dbname = sproxy.getDbName();
5533                   String sname = dbname.length() > 5
5534                           ? dbname.substring(0, 5) + "..."
5535                           : dbname;
5536                   String msname = dbname.length() > 10
5537                           ? dbname.substring(0, 10) + "..."
5538                           : dbname;
5539                   if (imname == null)
5540                   {
5541                     imname = MessageManager
5542                             .formatMessage("label.from_msname", new Object[]
5543                             { sname });
5544                   }
5545                   fetchr = new JMenuItem(msname);
5546                   final DbSourceProxy[] dassrc = { sproxy };
5547                   fetchr.addActionListener(new ActionListener()
5548                   {
5549
5550                     @Override
5551                     public void actionPerformed(ActionEvent e)
5552                     {
5553                       new Thread(new Runnable()
5554                       {
5555
5556                         @Override
5557                         public void run()
5558                         {
5559                           boolean isNucleotide = alignPanel.alignFrame
5560                                   .getViewport().getAlignment()
5561                                   .isNucleotide();
5562                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5563                                   alignPanel.av.getSequenceSelection(),
5564                                   alignPanel.alignFrame, dassrc,
5565                                   alignPanel.alignFrame.featureSettings,
5566                                   isNucleotide);
5567                           dbRefFetcher
5568                                   .addListener(new FetchFinishedListenerI()
5569                                   {
5570                                     @Override
5571                                     public void finished()
5572                                     {
5573                                       AlignFrame.this.setMenusForViewport();
5574                                     }
5575                                   });
5576                           dbRefFetcher.fetchDBRefs(false);
5577                         }
5578                       }).start();
5579                     }
5580
5581                   });
5582                   fetchr.setToolTipText(
5583                           "<html>" + MessageManager.formatMessage(
5584                                   "label.fetch_retrieve_from", new Object[]
5585                                   { dbname }));
5586                   ifetch.add(fetchr);
5587                   ++i;
5588                   if (++icomp >= mcomp || i == (otherdb.size()))
5589                   {
5590                     ifetch.setText(MessageManager.formatMessage(
5591                             "label.source_to_target", imname, sname));
5592                     dfetch.add(ifetch);
5593                     ifetch = new JMenu();
5594                     imname = null;
5595                     icomp = 0;
5596                     comp++;
5597                   }
5598                 }
5599               }
5600               ++dbi;
5601               if (comp >= mcomp || dbi >= (dbclasses.length))
5602               {
5603                 dfetch.setText(MessageManager.formatMessage(
5604                         "label.source_to_target", mname, dbclass));
5605                 rfetch.add(dfetch);
5606                 dfetch = new JMenu();
5607                 mname = null;
5608                 comp = 0;
5609               }
5610             }
5611           }
5612         });
5613       }
5614     }).start();
5615
5616   }
5617
5618   /**
5619    * Left justify the whole alignment.
5620    */
5621   @Override
5622   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5623   {
5624     AlignmentI al = viewport.getAlignment();
5625     al.justify(false);
5626     viewport.firePropertyChange("alignment", null, al);
5627   }
5628
5629   /**
5630    * Right justify the whole alignment.
5631    */
5632   @Override
5633   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5634   {
5635     AlignmentI al = viewport.getAlignment();
5636     al.justify(true);
5637     viewport.firePropertyChange("alignment", null, al);
5638   }
5639
5640   @Override
5641   public void setShowSeqFeatures(boolean b)
5642   {
5643     showSeqFeatures.setSelected(b);
5644     viewport.setShowSequenceFeatures(b);
5645   }
5646
5647   /*
5648    * (non-Javadoc)
5649    *
5650    * @see
5651    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5652    * awt.event.ActionEvent)
5653    */
5654   @Override
5655   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5656   {
5657     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5658     alignPanel.paintAlignment(false, false);
5659   }
5660
5661   /*
5662    * (non-Javadoc)
5663    *
5664    * @see
5665    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5666    * .ActionEvent)
5667    */
5668   @Override
5669   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5670   {
5671     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5672     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5673
5674   }
5675
5676   /*
5677    * (non-Javadoc)
5678    *
5679    * @see
5680    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5681    * .event.ActionEvent)
5682    */
5683   @Override
5684   protected void showGroupConservation_actionPerformed(ActionEvent e)
5685   {
5686     viewport.setShowGroupConservation(showGroupConservation.getState());
5687     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5688   }
5689
5690   /*
5691    * (non-Javadoc)
5692    *
5693    * @see
5694    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5695    * .event.ActionEvent)
5696    */
5697   @Override
5698   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5699   {
5700     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5701     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5702   }
5703
5704   /*
5705    * (non-Javadoc)
5706    *
5707    * @see
5708    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5709    * .event.ActionEvent)
5710    */
5711   @Override
5712   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5713   {
5714     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5715     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5716   }
5717
5718   @Override
5719   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5720   {
5721     showSequenceLogo.setState(true);
5722     viewport.setShowSequenceLogo(true);
5723     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5724     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5725   }
5726
5727   @Override
5728   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5729   {
5730     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5731   }
5732
5733   /*
5734    * (non-Javadoc)
5735    *
5736    * @see
5737    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5738    * .event.ActionEvent)
5739    */
5740   @Override
5741   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5742   {
5743     if (avc.makeGroupsFromSelection())
5744     {
5745       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5746       alignPanel.updateAnnotation();
5747       alignPanel.paintAlignment(true,
5748               viewport.needToUpdateStructureViews());
5749     }
5750   }
5751
5752   public void clearAlignmentSeqRep()
5753   {
5754     // TODO refactor alignmentseqrep to controller
5755     if (viewport.getAlignment().hasSeqrep())
5756     {
5757       viewport.getAlignment().setSeqrep(null);
5758       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5759       alignPanel.updateAnnotation();
5760       alignPanel.paintAlignment(true, true);
5761     }
5762   }
5763
5764   @Override
5765   protected void createGroup_actionPerformed(ActionEvent e)
5766   {
5767     if (avc.createGroup())
5768     {
5769       if (applyAutoAnnotationSettings.isSelected())
5770       {
5771         alignPanel.updateAnnotation(true, false);
5772       }
5773       alignPanel.alignmentChanged();
5774     }
5775   }
5776
5777   @Override
5778   protected void unGroup_actionPerformed(ActionEvent e)
5779   {
5780     if (avc.unGroup())
5781     {
5782       alignPanel.alignmentChanged();
5783     }
5784   }
5785
5786   /**
5787    * make the given alignmentPanel the currently selected tab
5788    *
5789    * @param alignmentPanel
5790    */
5791   public void setDisplayedView(AlignmentPanel alignmentPanel)
5792   {
5793     if (!viewport.getSequenceSetId()
5794             .equals(alignmentPanel.av.getSequenceSetId()))
5795     {
5796       throw new Error(MessageManager.getString(
5797               "error.implementation_error_cannot_show_view_alignment_frame"));
5798     }
5799     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5800             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5801     {
5802       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5803     }
5804   }
5805
5806   /**
5807    * Action on selection of menu options to Show or Hide annotations.
5808    *
5809    * @param visible
5810    * @param forSequences
5811    *          update sequence-related annotations
5812    * @param forAlignment
5813    *          update non-sequence-related annotations
5814    */
5815   @Override
5816   public void setAnnotationsVisibility(boolean visible,
5817           boolean forSequences, boolean forAlignment)
5818   {
5819     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5820             .getAlignmentAnnotation();
5821     if (anns == null)
5822     {
5823       return;
5824     }
5825     for (AlignmentAnnotation aa : anns)
5826     {
5827       /*
5828        * don't display non-positional annotations on an alignment
5829        */
5830       if (aa.annotations == null)
5831       {
5832         continue;
5833       }
5834       boolean apply = (aa.sequenceRef == null && forAlignment)
5835               || (aa.sequenceRef != null && forSequences);
5836       if (apply)
5837       {
5838         aa.visible = visible;
5839       }
5840     }
5841     alignPanel.validateAnnotationDimensions(true);
5842     alignPanel.alignmentChanged();
5843   }
5844
5845   /**
5846    * Store selected annotation sort order for the view and repaint.
5847    */
5848   @Override
5849   protected void sortAnnotations_actionPerformed()
5850   {
5851     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5852     this.alignPanel.av
5853             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5854     alignPanel.paintAlignment(false, false);
5855   }
5856
5857   /**
5858    *
5859    * @return alignment panels in this alignment frame
5860    */
5861   public List<? extends AlignmentViewPanel> getAlignPanels()
5862   {
5863     // alignPanels is never null
5864     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5865     return alignPanels;
5866   }
5867
5868   /**
5869    * Open a new alignment window, with the cDNA associated with this (protein)
5870    * alignment, aligned as is the protein.
5871    */
5872   protected void viewAsCdna_actionPerformed()
5873   {
5874     // TODO no longer a menu action - refactor as required
5875     final AlignmentI alignment = getViewport().getAlignment();
5876     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5877     if (mappings == null)
5878     {
5879       return;
5880     }
5881     List<SequenceI> cdnaSeqs = new ArrayList<>();
5882     for (SequenceI aaSeq : alignment.getSequences())
5883     {
5884       for (AlignedCodonFrame acf : mappings)
5885       {
5886         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5887         if (dnaSeq != null)
5888         {
5889           /*
5890            * There is a cDNA mapping for this protein sequence - add to new
5891            * alignment. It will share the same dataset sequence as other mapped
5892            * cDNA (no new mappings need to be created).
5893            */
5894           final Sequence newSeq = new Sequence(dnaSeq);
5895           newSeq.setDatasetSequence(dnaSeq);
5896           cdnaSeqs.add(newSeq);
5897         }
5898       }
5899     }
5900     if (cdnaSeqs.size() == 0)
5901     {
5902       // show a warning dialog no mapped cDNA
5903       return;
5904     }
5905     AlignmentI cdna = new Alignment(
5906             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5907     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5908             AlignFrame.DEFAULT_HEIGHT);
5909     cdna.alignAs(alignment);
5910     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5911             + this.title;
5912     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5913             AlignFrame.DEFAULT_HEIGHT);
5914   }
5915
5916   /**
5917    * Set visibility of dna/protein complement view (available when shown in a
5918    * split frame).
5919    *
5920    * @param show
5921    */
5922   @Override
5923   protected void showComplement_actionPerformed(boolean show)
5924   {
5925     SplitContainerI sf = getSplitViewContainer();
5926     if (sf != null)
5927     {
5928       sf.setComplementVisible(this, show);
5929     }
5930   }
5931
5932   /**
5933    * Generate the reverse (optionally complemented) of the selected sequences,
5934    * and add them to the alignment
5935    */
5936   @Override
5937   protected void showReverse_actionPerformed(boolean complement)
5938   {
5939     AlignmentI al = null;
5940     try
5941     {
5942       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5943       al = dna.reverseCdna(complement);
5944       viewport.addAlignment(al, "");
5945       addHistoryItem(new EditCommand(
5946               MessageManager.getString("label.add_sequences"), Action.PASTE,
5947               al.getSequencesArray(), 0, al.getWidth(),
5948               viewport.getAlignment()));
5949     } catch (Exception ex)
5950     {
5951       jalview.bin.Console.errPrintln(ex.getMessage());
5952       return;
5953     }
5954   }
5955
5956   /**
5957    * Try to run a script in the Groovy console, having first ensured that this
5958    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5959    * be targeted at this alignment.
5960    */
5961   @Override
5962   protected void runGroovy_actionPerformed()
5963   {
5964     Jalview.setCurrentAlignFrame(this);
5965     groovy.ui.Console console = Desktop.getGroovyConsole();
5966     if (console != null)
5967     {
5968       try
5969       {
5970         console.runScript();
5971       } catch (Exception ex)
5972       {
5973         jalview.bin.Console.errPrintln((ex.toString()));
5974         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5975                 MessageManager.getString("label.couldnt_run_groovy_script"),
5976                 MessageManager.getString("label.groovy_support_failed"),
5977                 JvOptionPane.ERROR_MESSAGE);
5978       }
5979     }
5980     else
5981     {
5982       jalview.bin.Console
5983               .errPrintln("Can't run Groovy script as console not found");
5984     }
5985   }
5986
5987   /**
5988    * Hides columns containing (or not containing) a specified feature, provided
5989    * that would not leave all columns hidden
5990    *
5991    * @param featureType
5992    * @param columnsContaining
5993    * @return
5994    */
5995   public boolean hideFeatureColumns(String featureType,
5996           boolean columnsContaining)
5997   {
5998     boolean notForHiding = avc.markColumnsContainingFeatures(
5999             columnsContaining, false, false, featureType);
6000     if (notForHiding)
6001     {
6002       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6003               false, featureType))
6004       {
6005         getViewport().hideSelectedColumns();
6006         return true;
6007       }
6008     }
6009     return false;
6010   }
6011
6012   @Override
6013   protected void selectHighlightedColumns_actionPerformed(
6014           ActionEvent actionEvent)
6015   {
6016     // include key modifier check in case user selects from menu
6017     avc.markHighlightedColumns(
6018             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
6019             (actionEvent.getModifiers() & (ActionEvent.META_MASK
6020                     | ActionEvent.CTRL_MASK)) != 0);
6021   }
6022
6023   @Override
6024   protected void copyHighlightedColumns_actionPerformed(
6025           ActionEvent actionEvent)
6026   {
6027     avc.copyHighlightedRegionsToClipboard();
6028   }
6029
6030   /**
6031    * Rebuilds the Colour menu, including any user-defined colours which have
6032    * been loaded either on startup or during the session
6033    */
6034   public void buildColourMenu()
6035   {
6036     colourMenu.removeAll();
6037
6038     colourMenu.add(applyToAllGroups);
6039     colourMenu.add(textColour);
6040     colourMenu.addSeparator();
6041
6042     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
6043             viewport.getAlignment(), false);
6044
6045     colourMenu.add(annotationColour);
6046     bg.add(annotationColour);
6047     colourMenu.addSeparator();
6048     colourMenu.add(conservationMenuItem);
6049     colourMenu.add(modifyConservation);
6050     colourMenu.add(abovePIDThreshold);
6051     colourMenu.add(modifyPID);
6052
6053     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
6054     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
6055   }
6056
6057   /**
6058    * Open a dialog (if not already open) that allows the user to select and
6059    * calculate PCA or Tree analysis
6060    */
6061   protected void openTreePcaDialog()
6062   {
6063     if (alignPanel.getCalculationDialog() == null)
6064     {
6065       new CalculationChooser(AlignFrame.this);
6066     }
6067   }
6068
6069   @Override
6070   protected void loadVcf_actionPerformed()
6071   {
6072     JalviewFileChooser chooser = new JalviewFileChooser(
6073             Cache.getProperty("LAST_DIRECTORY"));
6074     chooser.setFileView(new JalviewFileView());
6075     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
6076     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
6077     final AlignFrame us = this;
6078     chooser.setResponseHandler(0, () -> {
6079       String choice = chooser.getSelectedFile().getPath();
6080       Cache.setProperty("LAST_DIRECTORY", choice);
6081       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
6082       new VCFLoader(choice).loadVCF(seqs, us);
6083     });
6084     chooser.showOpenDialog(null);
6085
6086   }
6087
6088   private Rectangle lastFeatureSettingsBounds = null;
6089
6090   @Override
6091   public void setFeatureSettingsGeometry(Rectangle bounds)
6092   {
6093     lastFeatureSettingsBounds = bounds;
6094   }
6095
6096   @Override
6097   public Rectangle getFeatureSettingsGeometry()
6098   {
6099     return lastFeatureSettingsBounds;
6100   }
6101
6102 }
6103
6104 class PrintThread extends Thread
6105 {
6106   AlignmentPanel ap;
6107
6108   public PrintThread(AlignmentPanel ap)
6109   {
6110     this.ap = ap;
6111   }
6112
6113   static PageFormat pf;
6114
6115   @Override
6116   public void run()
6117   {
6118     PrinterJob printJob = PrinterJob.getPrinterJob();
6119
6120     if (pf != null)
6121     {
6122       printJob.setPrintable(ap, pf);
6123     }
6124     else
6125     {
6126       printJob.setPrintable(ap);
6127     }
6128
6129     if (printJob.printDialog())
6130     {
6131       try
6132       {
6133         printJob.print();
6134       } catch (Exception PrintException)
6135       {
6136         PrintException.printStackTrace();
6137       }
6138     }
6139   }
6140 }