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.PrintWriter;
  53 import java.net.URL;
  54 import java.util.ArrayList;
  55 import java.util.Arrays;
  56 import java.util.Deque;
  57 import java.util.Enumeration;
  58 import java.util.Hashtable;
  59 import java.util.List;
  60 import java.util.Locale;
  61 import java.util.Vector;
  62 import java.util.concurrent.Callable;
  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.vcf.VCFLoader;
 145 import jalview.jbgui.GAlignFrame;
 146 import jalview.project.Jalview2XML;
 147 import jalview.schemes.ColourSchemeI;
 148 import jalview.schemes.ColourSchemes;
 149 import jalview.schemes.ResidueColourScheme;
 150 import jalview.schemes.TCoffeeColourScheme;
 151 import jalview.util.HttpUtils;
 152 import jalview.util.ImageMaker.TYPE;
 153 import jalview.util.MessageManager;
 154 import jalview.util.Platform;
 155 import jalview.viewmodel.AlignmentViewport;
 156 import jalview.viewmodel.ViewportRanges;
 157 import jalview.ws.DBRefFetcher;
 158 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 159 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 160 import jalview.ws.jws1.Discoverer;
 161 import jalview.ws.jws2.Jws2Discoverer;
 162 import jalview.ws.jws2.jabaws2.Jws2Instance;
 163 import jalview.ws.seqfetcher.DbSourceProxy;
 164
 165 /**
 166  * DOCUMENT ME!
 167  *
 168  * @author $author$
 169  * @version $Revision$
 170  */
 171 @SuppressWarnings("serial")
 172 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 173         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 174 {
 175
 176   public static final int DEFAULT_WIDTH = 700;
 177
 178   public static final int DEFAULT_HEIGHT = 500;
 179
 180   /*
 181    * The currently displayed panel (selected tabbed view if more than one)
 182    */
 183   public AlignmentPanel alignPanel;
 184
 185   AlignViewport viewport;
 186
 187   public AlignViewControllerI avc;
 188
 189   List<AlignmentPanel> alignPanels = new ArrayList<>();
 190
 191   /**
 192    * Last format used to load or save alignments in this window
 193    */
 194   FileFormatI currentFileFormat = null;
 195
 196   /**
 197    * Current filename for this alignment
 198    */
 199   String fileName = null;
 200
 201   File fileObject;
 202
 203   /**
 204    * Creates a new AlignFrame object with specific width and height.
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    */
 210   public AlignFrame(AlignmentI al, int width, int height)
 211   {
 212     this(al, null, width, height);
 213   }
 214
 215   /**
 216    * Creates a new AlignFrame object with specific width, height and
 217    * sequenceSetId
 218    *
 219    * @param al
 220    * @param width
 221    * @param height
 222    * @param sequenceSetId
 223    */
 224   public AlignFrame(AlignmentI al, int width, int height,
 225           String sequenceSetId)
 226   {
 227     this(al, null, width, height, sequenceSetId);
 228   }
 229
 230   /**
 231    * Creates a new AlignFrame object with specific width, height and
 232    * sequenceSetId
 233    *
 234    * @param al
 235    * @param width
 236    * @param height
 237    * @param sequenceSetId
 238    * @param viewId
 239    */
 240   public AlignFrame(AlignmentI al, int width, int height,
 241           String sequenceSetId, String viewId)
 242   {
 243     this(al, null, width, height, sequenceSetId, viewId);
 244   }
 245
 246   /**
 247    * new alignment window with hidden columns
 248    *
 249    * @param al
 250    *          AlignmentI
 251    * @param hiddenColumns
 252    *          ColumnSelection or null
 253    * @param width
 254    *          Width of alignment frame
 255    * @param height
 256    *          height of frame.
 257    */
 258   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 259           int height)
 260   {
 261     this(al, hiddenColumns, width, height, null);
 262   }
 263
 264   /**
 265    * Create alignment frame for al with hiddenColumns, a specific width and
 266    * height, and specific sequenceId
 267    *
 268    * @param al
 269    * @param hiddenColumns
 270    * @param width
 271    * @param height
 272    * @param sequenceSetId
 273    *          (may be null)
 274    */
 275   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 276           int height, String sequenceSetId)
 277   {
 278     this(al, hiddenColumns, width, height, sequenceSetId, null);
 279   }
 280
 281   /**
 282    * Create alignment frame for al with hiddenColumns, a specific width and
 283    * height, and specific sequenceId
 284    *
 285    * @param al
 286    * @param hiddenColumns
 287    * @param width
 288    * @param height
 289    * @param sequenceSetId
 290    *          (may be null)
 291    * @param viewId
 292    *          (may be null)
 293    */
 294   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 295           int height, String sequenceSetId, String viewId)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 305
 306     alignPanel = new AlignmentPanel(this, viewport);
 307
 308     addAlignmentPanel(alignPanel, true);
 309     init();
 310   }
 311
 312   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 313           HiddenColumns hiddenColumns, int width, int height)
 314   {
 315     setSize(width, height);
 316
 317     if (al.getDataset() == null)
 318     {
 319       al.setDataset(null);
 320     }
 321
 322     viewport = new AlignViewport(al, hiddenColumns);
 323
 324     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 325     {
 326       viewport.hideSequence(hiddenSeqs);
 327     }
 328     alignPanel = new AlignmentPanel(this, viewport);
 329     addAlignmentPanel(alignPanel, true);
 330     init();
 331   }
 332
 333   /**
 334    * Make a new AlignFrame from existing alignmentPanels
 335    *
 336    * @param ap
 337    *          AlignmentPanel
 338    * @param av
 339    *          AlignViewport
 340    */
 341   public AlignFrame(AlignmentPanel ap)
 342   {
 343     viewport = ap.av;
 344     alignPanel = ap;
 345     addAlignmentPanel(ap, false);
 346     init();
 347   }
 348
 349   /**
 350    * initalise the alignframe from the underlying viewport data and the
 351    * configurations
 352    */
 353   void init()
 354   {
 355     setFrameIcon(null);
 356
 357     // setBackground(Color.white); // BH 2019
 358
 359     if (!Jalview.isHeadlessMode())
 360     {
 361       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 362     }
 363
 364     avc = new jalview.controller.AlignViewController(this, viewport,
 365             alignPanel);
 366     if (viewport.getAlignmentConservationAnnotation() == null)
 367     {
 368       // BLOSUM62Colour.setEnabled(false);
 369       conservationMenuItem.setEnabled(false);
 370       modifyConservation.setEnabled(false);
 371       // PIDColour.setEnabled(false);
 372       // abovePIDThreshold.setEnabled(false);
 373       // modifyPID.setEnabled(false);
 374     }
 375
 376     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 377
 378     if (sortby.equals("Id"))
 379     {
 380       sortIDMenuItem_actionPerformed(null);
 381     }
 382     else if (sortby.equals("Pairwise Identity"))
 383     {
 384       sortPairwiseMenuItem_actionPerformed(null);
 385     }
 386
 387     this.alignPanel.av
 388             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 389
 390     setMenusFromViewport(viewport);
 391     buildSortByAnnotationScoresMenu();
 392     calculateTree.addActionListener(new ActionListener()
 393     {
 394
 395       @Override
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         openTreePcaDialog();
 399       }
 400     });
 401     buildColourMenu();
 402
 403     if (Desktop.desktop != null)
 404     {
 405       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 406       if (!Platform.isJS())
 407       {
 408         addServiceListeners();
 409       }
 410       setGUINucleotide();
 411     }
 412
 413     if (viewport.getWrapAlignment())
 414     {
 415       wrapMenuItem_actionPerformed(null);
 416     }
 417
 418     if (Cache.getDefault("SHOW_OVERVIEW", false))
 419     {
 420       this.overviewMenuItem_actionPerformed(null);
 421     }
 422
 423     addKeyListener();
 424
 425     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 426     final List<AlignmentPanel> origview = new ArrayList<>();
 427     final String menuLabel = MessageManager
 428             .getString("label.copy_format_from");
 429     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 430             new ViewSetProvider()
 431             {
 432
 433               @Override
 434               public AlignmentPanel[] getAllAlignmentPanels()
 435               {
 436                 origview.clear();
 437                 origview.add(alignPanel);
 438                 // make an array of all alignment panels except for this one
 439                 List<AlignmentPanel> aps = new ArrayList<>(
 440                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 441                 aps.remove(AlignFrame.this.alignPanel);
 442                 return aps.toArray(new AlignmentPanel[aps.size()]);
 443               }
 444             }, selviews, new ItemListener()
 445             {
 446
 447               @Override
 448               public void itemStateChanged(ItemEvent e)
 449               {
 450                 if (origview.size() > 0)
 451                 {
 452                   final AlignmentPanel ap = origview.get(0);
 453
 454                   /*
 455                    * Copy the ViewStyle of the selected panel to 'this one'.
 456                    * Don't change value of 'scaleProteinAsCdna' unless copying
 457                    * from a SplitFrame.
 458                    */
 459                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 460                           .getViewStyle();
 461                   boolean fromSplitFrame = selviews.get(0)
 462                           .getAlignViewport().getCodingComplement() != null;
 463                   if (!fromSplitFrame)
 464                   {
 465                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 466                             .getViewStyle().isScaleProteinAsCdna());
 467                   }
 468                   ap.getAlignViewport().setViewStyle(vs);
 469
 470                   /*
 471                    * Also rescale ViewStyle of SplitFrame complement if there is
 472                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 473                    * the whole ViewStyle (allow cDNA protein to have different
 474                    * fonts)
 475                    */
 476                   AlignViewportI complement = ap.getAlignViewport()
 477                           .getCodingComplement();
 478                   if (complement != null && vs.isScaleProteinAsCdna())
 479                   {
 480                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 481                     ((SplitFrame) af.getSplitViewContainer())
 482                             .adjustLayout();
 483                     af.setMenusForViewport();
 484                   }
 485
 486                   ap.updateLayout();
 487                   ap.setSelected(true);
 488                   ap.alignFrame.setMenusForViewport();
 489
 490                 }
 491               }
 492             });
 493     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 494             .indexOf("devel") > -1
 495             || Cache.getDefault("VERSION", "DEVELOPMENT")
 496                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 497     {
 498       formatMenu.add(vsel);
 499     }
 500     addFocusListener(new FocusAdapter()
 501     {
 502       @Override
 503       public void focusGained(FocusEvent e)
 504       {
 505         Jalview.setCurrentAlignFrame(AlignFrame.this);
 506       }
 507     });
 508
 509   }
 510
 511   /**
 512    * Change the filename and format for the alignment, and enable the 'reload'
 513    * button functionality.
 514    *
 515    * @param file
 516    *          valid filename
 517    * @param format
 518    *          format of file
 519    */
 520   public void setFileName(String file, FileFormatI format)
 521   {
 522     fileName = file;
 523     setFileFormat(format);
 524     reload.setEnabled(true);
 525   }
 526
 527   /**
 528    * JavaScript will have this, maybe others. More dependable than a file name
 529    * and maintains a reference to the actual bytes loaded.
 530    *
 531    * @param file
 532    */
 533   public void setFileObject(File file)
 534   {
 535     this.fileObject = file;
 536   }
 537
 538   /**
 539    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 540    * events
 541    */
 542   void addKeyListener()
 543   {
 544     addKeyListener(new KeyAdapter()
 545     {
 546       @Override
 547       public void keyPressed(KeyEvent evt)
 548       {
 549         if (viewport.cursorMode
 550                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 551                         && evt.getKeyCode() <= KeyEvent.VK_9)
 552                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 553                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 554                 && Character.isDigit(evt.getKeyChar()))
 555         {
 556           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 557         }
 558
 559         switch (evt.getKeyCode())
 560         {
 561
 562         case 27: // escape key
 563           deselectAllSequenceMenuItem_actionPerformed(null);
 564
 565           break;
 566
 567         case KeyEvent.VK_DOWN:
 568           if (evt.isAltDown() || !viewport.cursorMode)
 569           {
 570             moveSelectedSequences(false);
 571           }
 572           if (viewport.cursorMode)
 573           {
 574             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 575           }
 576           break;
 577
 578         case KeyEvent.VK_UP:
 579           if (evt.isAltDown() || !viewport.cursorMode)
 580           {
 581             moveSelectedSequences(true);
 582           }
 583           if (viewport.cursorMode)
 584           {
 585             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 586           }
 587
 588           break;
 589
 590         case KeyEvent.VK_LEFT:
 591           if (evt.isAltDown() || !viewport.cursorMode)
 592           {
 593             slideSequences(false,
 594                     alignPanel.getSeqPanel().getKeyboardNo1());
 595           }
 596           else
 597           {
 598             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 599           }
 600
 601           break;
 602
 603         case KeyEvent.VK_RIGHT:
 604           if (evt.isAltDown() || !viewport.cursorMode)
 605           {
 606             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 607           }
 608           else
 609           {
 610             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 611           }
 612           break;
 613
 614         case KeyEvent.VK_SPACE:
 615           if (viewport.cursorMode)
 616           {
 617             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 618                     || evt.isShiftDown() || evt.isAltDown());
 619           }
 620           break;
 621
 622         // case KeyEvent.VK_A:
 623         // if (viewport.cursorMode)
 624         // {
 625         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 626         // //System.out.println("A");
 627         // }
 628         // break;
 629         /*
 630          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 631          * System.out.println("closing bracket"); } break;
 632          */
 633         case KeyEvent.VK_DELETE:
 634         case KeyEvent.VK_BACK_SPACE:
 635           if (!viewport.cursorMode)
 636           {
 637             cut_actionPerformed();
 638           }
 639           else
 640           {
 641             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 642                     || evt.isShiftDown() || evt.isAltDown());
 643           }
 644
 645           break;
 646
 647         case KeyEvent.VK_S:
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().setCursorRow();
 651           }
 652           break;
 653         case KeyEvent.VK_C:
 654           if (viewport.cursorMode && !evt.isControlDown())
 655           {
 656             alignPanel.getSeqPanel().setCursorColumn();
 657           }
 658           break;
 659         case KeyEvent.VK_P:
 660           if (viewport.cursorMode)
 661           {
 662             alignPanel.getSeqPanel().setCursorPosition();
 663           }
 664           break;
 665
 666         case KeyEvent.VK_ENTER:
 667         case KeyEvent.VK_COMMA:
 668           if (viewport.cursorMode)
 669           {
 670             alignPanel.getSeqPanel().setCursorRowAndColumn();
 671           }
 672           break;
 673
 674         case KeyEvent.VK_Q:
 675           if (viewport.cursorMode)
 676           {
 677             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 678           }
 679           break;
 680         case KeyEvent.VK_M:
 681           if (viewport.cursorMode)
 682           {
 683             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 684           }
 685           break;
 686
 687         case KeyEvent.VK_F2:
 688           viewport.cursorMode = !viewport.cursorMode;
 689           setStatus(MessageManager
 690                   .formatMessage("label.keyboard_editing_mode", new String[]
 691                   { (viewport.cursorMode ? "on" : "off") }));
 692           if (viewport.cursorMode)
 693           {
 694             ViewportRanges ranges = viewport.getRanges();
 695             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 696                     .getStartRes();
 697             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 698                     .getStartSeq();
 699           }
 700           alignPanel.getSeqPanel().seqCanvas.repaint();
 701           break;
 702
 703         case KeyEvent.VK_F1:
 704           try
 705           {
 706             Help.showHelpWindow();
 707           } catch (Exception ex)
 708           {
 709             ex.printStackTrace();
 710           }
 711           break;
 712         case KeyEvent.VK_H:
 713         {
 714           boolean toggleSeqs = !evt.isControlDown();
 715           boolean toggleCols = !evt.isShiftDown();
 716           toggleHiddenRegions(toggleSeqs, toggleCols);
 717           break;
 718         }
 719         case KeyEvent.VK_B:
 720         {
 721           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 722           boolean modifyExisting = true; // always modify, don't clear
 723                                          // evt.isShiftDown();
 724           boolean invertHighlighted = evt.isAltDown();
 725           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 726                   toggleSel);
 727           break;
 728         }
 729         case KeyEvent.VK_PAGE_UP:
 730           viewport.getRanges().pageUp();
 731           break;
 732         case KeyEvent.VK_PAGE_DOWN:
 733           viewport.getRanges().pageDown();
 734           break;
 735         }
 736       }
 737
 738       @Override
 739       public void keyReleased(KeyEvent evt)
 740       {
 741         switch (evt.getKeyCode())
 742         {
 743         case KeyEvent.VK_LEFT:
 744           if (evt.isAltDown() || !viewport.cursorMode)
 745           {
 746             viewport.firePropertyChange("alignment", null,
 747                     viewport.getAlignment().getSequences());
 748           }
 749           break;
 750
 751         case KeyEvent.VK_RIGHT:
 752           if (evt.isAltDown() || !viewport.cursorMode)
 753           {
 754             viewport.firePropertyChange("alignment", null,
 755                     viewport.getAlignment().getSequences());
 756           }
 757           break;
 758         }
 759       }
 760     });
 761   }
 762
 763   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 764   {
 765     ap.alignFrame = this;
 766     avc = new jalview.controller.AlignViewController(this, viewport,
 767             alignPanel);
 768
 769     alignPanels.add(ap);
 770
 771     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 772
 773     int aSize = alignPanels.size();
 774
 775     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 776
 777     if (aSize == 1 && ap.av.getViewName() == null)
 778     {
 779       this.getContentPane().add(ap, BorderLayout.CENTER);
 780     }
 781     else
 782     {
 783       if (aSize == 2)
 784       {
 785         setInitialTabVisible();
 786       }
 787
 788       expandViews.setEnabled(true);
 789       gatherViews.setEnabled(true);
 790       tabbedPane.addTab(ap.av.getViewName(), ap);
 791
 792       ap.setVisible(false);
 793     }
 794
 795     if (newPanel)
 796     {
 797       if (ap.av.isPadGaps())
 798       {
 799         ap.av.getAlignment().padGaps();
 800       }
 801       ap.av.updateConservation(ap);
 802       ap.av.updateConsensus(ap);
 803       ap.av.updateStrucConsensus(ap);
 804     }
 805   }
 806
 807   public void setInitialTabVisible()
 808   {
 809     expandViews.setEnabled(true);
 810     gatherViews.setEnabled(true);
 811     tabbedPane.setVisible(true);
 812     AlignmentPanel first = alignPanels.get(0);
 813     tabbedPane.addTab(first.av.getViewName(), first);
 814     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 815   }
 816
 817   public AlignViewport getViewport()
 818   {
 819     return viewport;
 820   }
 821
 822   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 823   private void addServiceListeners()
 824   {
 825     final java.beans.PropertyChangeListener thisListener;
 826     Desktop.instance.addJalviewPropertyChangeListener("services",
 827             thisListener = new java.beans.PropertyChangeListener()
 828             {
 829               @Override
 830               public void propertyChange(PropertyChangeEvent evt)
 831               {
 832                 // // System.out.println("Discoverer property change.");
 833                 // if (evt.getPropertyName().equals("services"))
 834                 {
 835                   SwingUtilities.invokeLater(new Runnable()
 836                   {
 837
 838                     @Override
 839                     public void run()
 840                     {
 841                       System.err.println(
 842                               "Rebuild WS Menu for service change");
 843                       BuildWebServiceMenu();
 844                     }
 845
 846                   });
 847                 }
 848               }
 849             });
 850     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 851     {
 852       @Override
 853       public void internalFrameClosed(
 854               javax.swing.event.InternalFrameEvent evt)
 855       {
 856         // System.out.println("deregistering discoverer listener");
 857         Desktop.instance.removeJalviewPropertyChangeListener("services",
 858                 thisListener);
 859         closeMenuItem_actionPerformed(true);
 860       }
 861     });
 862     // Finally, build the menu once to get current service state
 863     new Thread(new Runnable()
 864     {
 865       @Override
 866       public void run()
 867       {
 868         BuildWebServiceMenu();
 869       }
 870     }).start();
 871   }
 872
 873   /**
 874    * Configure menu items that vary according to whether the alignment is
 875    * nucleotide or protein
 876    */
 877   public void setGUINucleotide()
 878   {
 879     AlignmentI al = getViewport().getAlignment();
 880     boolean nucleotide = al.isNucleotide();
 881
 882     loadVcf.setVisible(nucleotide);
 883     showTranslation.setVisible(nucleotide);
 884     showReverse.setVisible(nucleotide);
 885     showReverseComplement.setVisible(nucleotide);
 886     conservationMenuItem.setEnabled(!nucleotide);
 887     modifyConservation
 888             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 889     showGroupConservation.setEnabled(!nucleotide);
 890
 891     showComplementMenuItem
 892             .setText(nucleotide ? MessageManager.getString("label.protein")
 893                     : MessageManager.getString("label.nucleotide"));
 894   }
 895
 896   /**
 897    * set up menus for the current viewport. This may be called after any
 898    * operation that affects the data in the current view (selection changed,
 899    * etc) to update the menus to reflect the new state.
 900    */
 901   @Override
 902   public void setMenusForViewport()
 903   {
 904     setMenusFromViewport(viewport);
 905   }
 906
 907   /**
 908    * Need to call this method when tabs are selected for multiple views, or when
 909    * loading from Jalview2XML.java
 910    *
 911    * @param av
 912    *          AlignViewport
 913    */
 914   public void setMenusFromViewport(AlignViewport av)
 915   {
 916     padGapsMenuitem.setSelected(av.isPadGaps());
 917     colourTextMenuItem.setSelected(av.isShowColourText());
 918     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 919     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 920     conservationMenuItem.setSelected(av.getConservationSelected());
 921     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 922     seqLimits.setSelected(av.getShowJVSuffix());
 923     idRightAlign.setSelected(av.isRightAlignIds());
 924     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 925     renderGapsMenuItem.setSelected(av.isRenderGaps());
 926     wrapMenuItem.setSelected(av.getWrapAlignment());
 927     scaleAbove.setVisible(av.getWrapAlignment());
 928     scaleLeft.setVisible(av.getWrapAlignment());
 929     scaleRight.setVisible(av.getWrapAlignment());
 930     annotationPanelMenuItem.setState(av.isShowAnnotation());
 931     /*
 932      * Show/hide annotations only enabled if annotation panel is shown
 933      */
 934     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 935     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 936     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 938     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 939     viewTextMenuItem.setSelected(av.getShowText());
 940     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 941     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 942     showGroupConservation.setSelected(av.isShowGroupConservation());
 943     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 944     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 945     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 946
 947     ColourMenuHelper.setColourSelected(colourMenu,
 948             av.getGlobalColourScheme());
 949
 950     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 951     hiddenMarkers.setState(av.getShowHiddenMarkers());
 952     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 953     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 954     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 955     autoCalculate.setSelected(av.autoCalculateConsensus);
 956     sortByTree.setSelected(av.sortByTree);
 957     listenToViewSelections.setSelected(av.followSelection);
 958
 959     showProducts.setEnabled(canShowProducts());
 960     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 961
 962     updateEditMenuBar();
 963   }
 964
 965   /**
 966    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 967    *
 968    * @param b
 969    */
 970   public void setGroovyEnabled(boolean b)
 971   {
 972     runGroovy.setEnabled(b);
 973   }
 974
 975   private IProgressIndicator progressBar;
 976
 977   /*
 978    * (non-Javadoc)
 979    *
 980    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 981    */
 982   @Override
 983   public void setProgressBar(String message, long id)
 984   {
 985     if (!Platform.isHeadless())
 986       progressBar.setProgressBar(message, id);
 987   }
 988
 989   @Override
 990   public void registerHandler(final long id,
 991           final IProgressIndicatorHandler handler)
 992   {
 993     progressBar.registerHandler(id, handler);
 994   }
 995
 996   /**
 997    *
 998    * @return true if any progress bars are still active
 999    */
1000   @Override
1001   public boolean operationInProgress()
1002   {
1003     return progressBar.operationInProgress();
1004   }
1005
1006   /**
1007    * Sets the text of the status bar. Note that setting a null or empty value
1008    * will cause the status bar to be hidden, with possibly undesirable flicker
1009    * of the screen layout.
1010    */
1011   @Override
1012   public void setStatus(String text)
1013   {
1014     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1015   }
1016
1017   /*
1018    * Added so Castor Mapping file can obtain Jalview Version
1019    */
1020   public String getVersion()
1021   {
1022     return Cache.getProperty("VERSION");
1023   }
1024
1025   public FeatureRenderer getFeatureRenderer()
1026   {
1027     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1028   }
1029
1030   @Override
1031   public void fetchSequence_actionPerformed()
1032   {
1033     new SequenceFetcher(this);
1034   }
1035
1036   @Override
1037   public void addFromFile_actionPerformed(ActionEvent e)
1038   {
1039     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1040   }
1041
1042   @Override
1043   public void reload_actionPerformed(ActionEvent e)
1044   {
1045     if (fileName != null)
1046     {
1047       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1048       // originating file's format
1049       // TODO: work out how to recover feature settings for correct view(s) when
1050       // file is reloaded.
1051       if (FileFormat.Jalview.equals(currentFileFormat))
1052       {
1053         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1054         for (int i = 0; i < frames.length; i++)
1055         {
1056           if (frames[i] instanceof AlignFrame && frames[i] != this
1057                   && ((AlignFrame) frames[i]).fileName != null
1058                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1059           {
1060             try
1061             {
1062               frames[i].setSelected(true);
1063               Desktop.instance.closeAssociatedWindows();
1064             } catch (java.beans.PropertyVetoException ex)
1065             {
1066             }
1067           }
1068
1069         }
1070         Desktop.instance.closeAssociatedWindows();
1071
1072         FileLoader loader = new FileLoader();
1073         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1074                 ? DataSourceType.URL
1075                 : DataSourceType.FILE;
1076         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1077       }
1078       else
1079       {
1080         Rectangle bounds = this.getBounds();
1081
1082         FileLoader loader = new FileLoader();
1083
1084         AlignFrame newframe = null;
1085
1086         if (fileObject == null)
1087         {
1088
1089           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1090                   fileName) ? DataSourceType.URL : DataSourceType.FILE;
1091           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1092                   currentFileFormat);
1093         }
1094         else
1095         {
1096           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1097                   DataSourceType.FILE, currentFileFormat);
1098         }
1099
1100         newframe.setBounds(bounds);
1101         if (featureSettings != null && featureSettings.isShowing())
1102         {
1103           final Rectangle fspos = featureSettings.frame.getBounds();
1104           // TODO: need a 'show feature settings' function that takes bounds -
1105           // need to refactor Desktop.addFrame
1106           newframe.featureSettings_actionPerformed(null);
1107           final FeatureSettings nfs = newframe.featureSettings;
1108           SwingUtilities.invokeLater(new Runnable()
1109           {
1110             @Override
1111             public void run()
1112             {
1113               nfs.frame.setBounds(fspos);
1114             }
1115           });
1116           this.featureSettings.close();
1117           this.featureSettings = null;
1118         }
1119         this.closeMenuItem_actionPerformed(true);
1120       }
1121     }
1122   }
1123
1124   @Override
1125   public void addFromText_actionPerformed(ActionEvent e)
1126   {
1127     Desktop.instance
1128             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1129   }
1130
1131   @Override
1132   public void addFromURL_actionPerformed(ActionEvent e)
1133   {
1134     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1135   }
1136
1137   @Override
1138   public void save_actionPerformed(ActionEvent e)
1139   {
1140     if (fileName == null || (currentFileFormat == null)
1141             || HttpUtils.startsWithHttpOrHttps(fileName))
1142     {
1143       saveAs_actionPerformed();
1144     }
1145     else
1146     {
1147       saveAlignment(fileName, currentFileFormat);
1148     }
1149   }
1150
1151   /**
1152    * Saves the alignment to a file with a name chosen by the user, if necessary
1153    * warning if a file would be overwritten
1154    */
1155   @Override
1156   public void saveAs_actionPerformed()
1157   {
1158     String format = currentFileFormat == null ? null
1159             : currentFileFormat.getName();
1160     JalviewFileChooser chooser = JalviewFileChooser
1161             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1162
1163     chooser.setFileView(new JalviewFileView());
1164     chooser.setDialogTitle(
1165             MessageManager.getString("label.save_alignment_to_file"));
1166     chooser.setToolTipText(MessageManager.getString("action.save"));
1167
1168     int value = chooser.showSaveDialog(this);
1169
1170     if (value != JalviewFileChooser.APPROVE_OPTION)
1171     {
1172       return;
1173     }
1174     currentFileFormat = chooser.getSelectedFormat();
1175     // todo is this (2005) test now obsolete - value is never null?
1176     while (currentFileFormat == null)
1177     {
1178       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1179               MessageManager
1180                       .getString("label.select_file_format_before_saving"),
1181               MessageManager.getString("label.file_format_not_specified"),
1182               JvOptionPane.WARNING_MESSAGE);
1183       currentFileFormat = chooser.getSelectedFormat();
1184       value = chooser.showSaveDialog(this);
1185       if (value != JalviewFileChooser.APPROVE_OPTION)
1186       {
1187         return;
1188       }
1189     }
1190
1191     fileName = chooser.getSelectedFile().getPath();
1192
1193     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1194     Cache.setProperty("LAST_DIRECTORY", fileName);
1195     saveAlignment(fileName, currentFileFormat);
1196   }
1197
1198   boolean lastSaveSuccessful = false;
1199
1200   FileFormatI lastFormatSaved;
1201
1202   String lastFilenameSaved;
1203
1204   /**
1205    * Raise a dialog or status message for the last call to saveAlignment.
1206    *
1207    * @return true if last call to saveAlignment(file, format) was successful.
1208    */
1209   public boolean isSaveAlignmentSuccessful()
1210   {
1211
1212     if (!lastSaveSuccessful)
1213     {
1214       if (!Platform.isHeadless())
1215       {
1216         JvOptionPane.showInternalMessageDialog(this, MessageManager
1217                 .formatMessage("label.couldnt_save_file", new Object[]
1218                 { lastFilenameSaved }),
1219                 MessageManager.getString("label.error_saving_file"),
1220                 JvOptionPane.WARNING_MESSAGE);
1221       }
1222       else
1223       {
1224         Console.error(MessageManager
1225                 .formatMessage("label.couldnt_save_file", new Object[]
1226                 { lastFilenameSaved }));
1227       }
1228     }
1229     else
1230     {
1231
1232       setStatus(MessageManager.formatMessage(
1233               "label.successfully_saved_to_file_in_format", new Object[]
1234               { lastFilenameSaved, lastFormatSaved }));
1235
1236     }
1237     return lastSaveSuccessful;
1238   }
1239
1240   /**
1241    * Saves the alignment to the specified file path, in the specified format,
1242    * which may be an alignment format, or Jalview project format. If the
1243    * alignment has hidden regions, or the format is one capable of including
1244    * non-sequence data (features, annotations, groups), then the user may be
1245    * prompted to specify what to include in the output.
1246    *
1247    * @param file
1248    * @param format
1249    */
1250   public void saveAlignment(String file, FileFormatI format)
1251   {
1252     lastSaveSuccessful = true;
1253     lastFilenameSaved = file;
1254     lastFormatSaved = format;
1255
1256     if (FileFormat.Jalview.equals(format))
1257     {
1258       String shortName = title;
1259       if (shortName.indexOf(File.separatorChar) > -1)
1260       {
1261         shortName = shortName
1262                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1263       }
1264       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1265               shortName);
1266
1267       Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1268       if (lastSaveSuccessful)
1269       {
1270         this.getViewport().setSavedUpToDate(true);
1271       }
1272
1273       statusBar.setText(MessageManager.formatMessage(
1274               "label.successfully_saved_to_file_in_format", new Object[]
1275               { file, format }));
1276
1277       return;
1278     }
1279
1280     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1281     Callable<Void> cancelAction = () -> {
1282       lastSaveSuccessful = false;
1283       return null;
1284     };
1285     Callable<Void> outputAction = () -> {
1286       // todo defer this to inside formatSequences (or later)
1287       AlignmentExportData exportData = viewport.getAlignExportData(options);
1288       String output = new FormatAdapter(alignPanel, options)
1289               .formatSequences(format, exportData.getAlignment(),
1290                       exportData.getOmitHidden(),
1291                       exportData.getStartEndPostions(),
1292                       viewport.getAlignment().getHiddenColumns());
1293       if (output == null)
1294       {
1295         lastSaveSuccessful = false;
1296       }
1297       else
1298       {
1299         // create backupfiles object and get new temp filename destination
1300         boolean doBackup = BackupFiles.getEnabled();
1301         BackupFiles backupfiles = null;
1302         if (doBackup)
1303         {
1304           Console.trace("ALIGNFRAME making backupfiles object for " + file);
1305           backupfiles = new BackupFiles(file);
1306         }
1307         try
1308         {
1309           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1310                   : file;
1311           Console.trace("ALIGNFRAME setting PrintWriter");
1312           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1313
1314           if (backupfiles != null)
1315           {
1316             Console.trace("ALIGNFRAME about to write to temp file "
1317                     + backupfiles.getTempFilePath());
1318           }
1319
1320           out.print(output);
1321           Console.trace("ALIGNFRAME about to close file");
1322           out.close();
1323           Console.trace("ALIGNFRAME closed file");
1324           AlignFrame.this.setTitle(file);
1325           statusBar.setText(MessageManager.formatMessage(
1326                   "label.successfully_saved_to_file_in_format", new Object[]
1327                   { fileName, format.getName() }));
1328           lastSaveSuccessful = true;
1329         } catch (IOException e)
1330         {
1331           lastSaveSuccessful = false;
1332           Console.error(
1333                   "ALIGNFRAME Something happened writing the temp file");
1334           Console.error(e.getMessage());
1335           Console.debug(Cache.getStackTraceString(e));
1336         } catch (Exception ex)
1337         {
1338           lastSaveSuccessful = false;
1339           Console.error(
1340                   "ALIGNFRAME Something unexpected happened writing the temp file");
1341           Console.error(ex.getMessage());
1342           Console.debug(Cache.getStackTraceString(ex));
1343         }
1344
1345         if (doBackup)
1346         {
1347           backupfiles.setWriteSuccess(lastSaveSuccessful);
1348           Console.debug("ALIGNFRAME writing temp file was "
1349                   + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1350           // do the backup file roll and rename the temp file to actual file
1351           Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1352           lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1353           Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1354                   + (lastSaveSuccessful ? "" : "un") + "successfully");
1355         }
1356
1357         Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1358         if (lastSaveSuccessful)
1359         {
1360           AlignFrame.this.getViewport().setSavedUpToDate(true);
1361         }
1362       }
1363       return null;
1364     };
1365
1366     /*
1367      * show dialog with export options if applicable; else just do it
1368      */
1369     if (AlignExportOptions.isNeeded(viewport, format))
1370     {
1371       AlignExportOptions choices = new AlignExportOptions(
1372               alignPanel.getAlignViewport(), format, options);
1373       choices.setResponseAction(0, outputAction);
1374       choices.setResponseAction(1, cancelAction);
1375       choices.showDialog();
1376     }
1377     else
1378     {
1379       try
1380       {
1381         outputAction.call();
1382       } catch (Exception e)
1383       {
1384         // TODO Auto-generated catch block
1385         e.printStackTrace();
1386       }
1387     }
1388   }
1389
1390   /**
1391    * Outputs the alignment to textbox in the requested format, if necessary
1392    * first prompting the user for whether to include hidden regions or
1393    * non-sequence data
1394    *
1395    * @param fileFormatName
1396    */
1397   @Override
1398   protected void outputText_actionPerformed(String fileFormatName)
1399   {
1400     FileFormatI fileFormat = FileFormats.getInstance()
1401             .forName(fileFormatName);
1402     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1403     Callable<Void> outputAction = () -> {
1404       // todo defer this to inside formatSequences (or later)
1405       AlignmentExportData exportData = viewport.getAlignExportData(options);
1406       CutAndPasteTransfer cap = new CutAndPasteTransfer();
1407       cap.setForInput(null);
1408       try
1409       {
1410         FileFormatI format = fileFormat;
1411         cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
1412                 format, exportData.getAlignment(),
1413                 exportData.getOmitHidden(),
1414                 exportData.getStartEndPostions(),
1415                 viewport.getAlignment().getHiddenColumns()));
1416         Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1417                 "label.alignment_output_command", new Object[]
1418                 { fileFormat.getName() }), 600, 500);
1419       } catch (OutOfMemoryError oom)
1420       {
1421         new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1422                 oom);
1423         cap.dispose();
1424       }
1425       return null;
1426     };
1427
1428     /*
1429      * show dialog with export options if applicable; else just do it
1430      */
1431     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1432     {
1433       AlignExportOptions choices = new AlignExportOptions(
1434               alignPanel.getAlignViewport(), fileFormat, options);
1435       choices.setResponseAction(0, outputAction);
1436       choices.showDialog();
1437     }
1438     else
1439     {
1440       try
1441       {
1442         outputAction.call();
1443       } catch (Exception e)
1444       {
1445         e.printStackTrace();
1446       }
1447     }
1448   }
1449
1450   /**
1451    * DOCUMENT ME!
1452    *
1453    * @param e
1454    *          DOCUMENT ME!
1455    */
1456   @Override
1457   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1458   {
1459     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1460     htmlSVG.exportHTML(null);
1461   }
1462
1463   @Override
1464   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1465   {
1466     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1467     bjs.exportHTML(null);
1468   }
1469
1470   public void createImageMap(File file, String image)
1471   {
1472     alignPanel.makePNGImageMap(file, image);
1473   }
1474
1475   /**
1476    * Creates a PNG image of the alignment and writes it to the given file. If
1477    * the file is null, the user is prompted to choose a file.
1478    *
1479    * @param f
1480    */
1481   @Override
1482   public void createPNG(File f)
1483   {
1484     createPNG(f, null, 0.0f, 0, 0);
1485   }
1486
1487   public void createPNG(File f, String renderer, float bitmapscale,
1488           int bitmapwidth, int bitmapheight)
1489   {
1490     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, bitmapscale,
1491             bitmapwidth, bitmapheight);
1492   }
1493
1494   /**
1495    * Creates an EPS image of the alignment and writes it to the given file. If
1496    * the file is null, the user is prompted to choose a file.
1497    *
1498    * @param f
1499    */
1500   @Override
1501   public void createEPS(File f)
1502   {
1503     createEPS(f, null);
1504   }
1505
1506   public void createEPS(File f, String renderer)
1507   {
1508     alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
1509   }
1510
1511   /**
1512    * Creates an SVG image of the alignment and writes it to the given file. If
1513    * the file is null, the user is prompted to choose a file.
1514    *
1515    * @param f
1516    */
1517   @Override
1518   public void createSVG(File f)
1519   {
1520     createSVG(f, null);
1521   }
1522
1523   public void createSVG(File f, String renderer)
1524   {
1525     alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
1526   }
1527
1528   @Override
1529   public void pageSetup_actionPerformed(ActionEvent e)
1530   {
1531     PrinterJob printJob = PrinterJob.getPrinterJob();
1532     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1533   }
1534
1535   /**
1536    * DOCUMENT ME!
1537    *
1538    * @param e
1539    *          DOCUMENT ME!
1540    */
1541   @Override
1542   public void printMenuItem_actionPerformed(ActionEvent e)
1543   {
1544     // Putting in a thread avoids Swing painting problems
1545     PrintThread thread = new PrintThread(alignPanel);
1546     thread.start();
1547   }
1548
1549   @Override
1550   public void exportFeatures_actionPerformed(ActionEvent e)
1551   {
1552     new AnnotationExporter(alignPanel).exportFeatures();
1553   }
1554
1555   @Override
1556   public void exportAnnotations_actionPerformed(ActionEvent e)
1557   {
1558     new AnnotationExporter(alignPanel).exportAnnotations();
1559   }
1560
1561   @Override
1562   public void associatedData_actionPerformed(ActionEvent e)
1563   {
1564     final JalviewFileChooser chooser = new JalviewFileChooser(
1565             Cache.getProperty("LAST_DIRECTORY"));
1566     chooser.setFileView(new JalviewFileView());
1567     String tooltip = MessageManager
1568             .getString("label.load_jalview_annotations");
1569     chooser.setDialogTitle(tooltip);
1570     chooser.setToolTipText(tooltip);
1571     chooser.setResponseHandler(0, () -> {
1572       String choice = chooser.getSelectedFile().getPath();
1573       Cache.setProperty("LAST_DIRECTORY", choice);
1574       loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1575       return null;
1576     });
1577
1578     chooser.showOpenDialog(this);
1579   }
1580
1581   /**
1582    * Close the current view or all views in the alignment frame. If the frame
1583    * only contains one view then the alignment will be removed from memory.
1584    *
1585    * @param closeAllTabs
1586    */
1587   @Override
1588   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1589   {
1590     if (alignPanels != null && alignPanels.size() < 2)
1591     {
1592       closeAllTabs = true;
1593     }
1594
1595     try
1596     {
1597       if (alignPanels != null)
1598       {
1599         if (closeAllTabs)
1600         {
1601           if (this.isClosed())
1602           {
1603             // really close all the windows - otherwise wait till
1604             // setClosed(true) is called
1605             for (int i = 0; i < alignPanels.size(); i++)
1606             {
1607               AlignmentPanel ap = alignPanels.get(i);
1608               ap.closePanel();
1609             }
1610           }
1611         }
1612         else
1613         {
1614           closeView(alignPanel);
1615         }
1616       }
1617       if (closeAllTabs)
1618       {
1619         if (featureSettings != null && featureSettings.isOpen())
1620         {
1621           featureSettings.close();
1622           featureSettings = null;
1623         }
1624         /*
1625          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1626          * be called recursively, with the frame now in 'closed' state
1627          */
1628         this.setClosed(true);
1629       }
1630     } catch (Exception ex)
1631     {
1632       ex.printStackTrace();
1633     }
1634   }
1635
1636   /**
1637    * Close the specified panel and close up tabs appropriately.
1638    *
1639    * @param panelToClose
1640    */
1641   public void closeView(AlignmentPanel panelToClose)
1642   {
1643     int index = tabbedPane.getSelectedIndex();
1644     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1645     alignPanels.remove(panelToClose);
1646     panelToClose.closePanel();
1647     panelToClose = null;
1648
1649     tabbedPane.removeTabAt(closedindex);
1650     tabbedPane.validate();
1651
1652     if (index > closedindex || index == tabbedPane.getTabCount())
1653     {
1654       // modify currently selected tab index if necessary.
1655       index--;
1656     }
1657
1658     this.tabSelectionChanged(index);
1659   }
1660
1661   /**
1662    * DOCUMENT ME!
1663    */
1664   void updateEditMenuBar()
1665   {
1666
1667     if (viewport.getHistoryList().size() > 0)
1668     {
1669       undoMenuItem.setEnabled(true);
1670       CommandI command = viewport.getHistoryList().peek();
1671       undoMenuItem.setText(MessageManager
1672               .formatMessage("label.undo_command", new Object[]
1673               { command.getDescription() }));
1674     }
1675     else
1676     {
1677       undoMenuItem.setEnabled(false);
1678       undoMenuItem.setText(MessageManager.getString("action.undo"));
1679     }
1680
1681     if (viewport.getRedoList().size() > 0)
1682     {
1683       redoMenuItem.setEnabled(true);
1684
1685       CommandI command = viewport.getRedoList().peek();
1686       redoMenuItem.setText(MessageManager
1687               .formatMessage("label.redo_command", new Object[]
1688               { command.getDescription() }));
1689     }
1690     else
1691     {
1692       redoMenuItem.setEnabled(false);
1693       redoMenuItem.setText(MessageManager.getString("action.redo"));
1694     }
1695   }
1696
1697   @Override
1698   public void addHistoryItem(CommandI command)
1699   {
1700     if (command.getSize() > 0)
1701     {
1702       viewport.addToHistoryList(command);
1703       viewport.clearRedoList();
1704       updateEditMenuBar();
1705       viewport.updateHiddenColumns();
1706       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1707       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1708       // viewport.getColumnSelection()
1709       // .getHiddenColumns().size() > 0);
1710     }
1711   }
1712
1713   /**
1714    *
1715    * @return alignment objects for all views
1716    */
1717   AlignmentI[] getViewAlignments()
1718   {
1719     if (alignPanels != null)
1720     {
1721       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1722       int i = 0;
1723       for (AlignmentPanel ap : alignPanels)
1724       {
1725         als[i++] = ap.av.getAlignment();
1726       }
1727       return als;
1728     }
1729     if (viewport != null)
1730     {
1731       return new AlignmentI[] { viewport.getAlignment() };
1732     }
1733     return null;
1734   }
1735
1736   /**
1737    * DOCUMENT ME!
1738    *
1739    * @param e
1740    *          DOCUMENT ME!
1741    */
1742   @Override
1743   protected void undoMenuItem_actionPerformed(ActionEvent e)
1744   {
1745     if (viewport.getHistoryList().isEmpty())
1746     {
1747       return;
1748     }
1749     CommandI command = viewport.getHistoryList().pop();
1750     viewport.addToRedoList(command);
1751     command.undoCommand(getViewAlignments());
1752
1753     AlignmentViewport originalSource = getOriginatingSource(command);
1754     updateEditMenuBar();
1755
1756     if (originalSource != null)
1757     {
1758       if (originalSource != viewport)
1759       {
1760         Console.warn(
1761                 "Implementation worry: mismatch of viewport origin for undo");
1762       }
1763       originalSource.updateHiddenColumns();
1764       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1765       // null
1766       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1767       // viewport.getColumnSelection()
1768       // .getHiddenColumns().size() > 0);
1769       originalSource.firePropertyChange("alignment", null,
1770               originalSource.getAlignment().getSequences());
1771     }
1772   }
1773
1774   /**
1775    * DOCUMENT ME!
1776    *
1777    * @param e
1778    *          DOCUMENT ME!
1779    */
1780   @Override
1781   protected void redoMenuItem_actionPerformed(ActionEvent e)
1782   {
1783     if (viewport.getRedoList().size() < 1)
1784     {
1785       return;
1786     }
1787
1788     CommandI command = viewport.getRedoList().pop();
1789     viewport.addToHistoryList(command);
1790     command.doCommand(getViewAlignments());
1791
1792     AlignmentViewport originalSource = getOriginatingSource(command);
1793     updateEditMenuBar();
1794
1795     if (originalSource != null)
1796     {
1797
1798       if (originalSource != viewport)
1799       {
1800         Console.warn(
1801                 "Implementation worry: mismatch of viewport origin for redo");
1802       }
1803       originalSource.updateHiddenColumns();
1804       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1805       // null
1806       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1807       // viewport.getColumnSelection()
1808       // .getHiddenColumns().size() > 0);
1809       originalSource.firePropertyChange("alignment", null,
1810               originalSource.getAlignment().getSequences());
1811     }
1812   }
1813
1814   AlignmentViewport getOriginatingSource(CommandI command)
1815   {
1816     AlignmentViewport originalSource = null;
1817     // For sequence removal and addition, we need to fire
1818     // the property change event FROM the viewport where the
1819     // original alignment was altered
1820     AlignmentI al = null;
1821     if (command instanceof EditCommand)
1822     {
1823       EditCommand editCommand = (EditCommand) command;
1824       al = editCommand.getAlignment();
1825       List<Component> comps = PaintRefresher.components
1826               .get(viewport.getSequenceSetId());
1827
1828       for (Component comp : comps)
1829       {
1830         if (comp instanceof AlignmentPanel)
1831         {
1832           if (al == ((AlignmentPanel) comp).av.getAlignment())
1833           {
1834             originalSource = ((AlignmentPanel) comp).av;
1835             break;
1836           }
1837         }
1838       }
1839     }
1840
1841     if (originalSource == null)
1842     {
1843       // The original view is closed, we must validate
1844       // the current view against the closed view first
1845       if (al != null)
1846       {
1847         PaintRefresher.validateSequences(al, viewport.getAlignment());
1848       }
1849
1850       originalSource = viewport;
1851     }
1852
1853     return originalSource;
1854   }
1855
1856   /**
1857    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1858    * or the sequence under cursor in keyboard mode
1859    *
1860    * @param up
1861    *          or down (if !up)
1862    */
1863   public void moveSelectedSequences(boolean up)
1864   {
1865     SequenceGroup sg = viewport.getSelectionGroup();
1866
1867     if (sg == null)
1868     {
1869       if (viewport.cursorMode)
1870       {
1871         sg = new SequenceGroup();
1872         sg.addSequence(viewport.getAlignment().getSequenceAt(
1873                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1874       }
1875       else
1876       {
1877         return;
1878       }
1879     }
1880
1881     if (sg.getSize() < 1)
1882     {
1883       return;
1884     }
1885
1886     // TODO: JAL-3733 - add an event to the undo buffer for this !
1887
1888     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1889             viewport.getHiddenRepSequences(), up);
1890     alignPanel.paintAlignment(true, false);
1891   }
1892
1893   synchronized void slideSequences(boolean right, int size)
1894   {
1895     List<SequenceI> sg = new ArrayList<>();
1896     if (viewport.cursorMode)
1897     {
1898       sg.add(viewport.getAlignment()
1899               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1900     }
1901     else if (viewport.getSelectionGroup() != null
1902             && viewport.getSelectionGroup().getSize() != viewport
1903                     .getAlignment().getHeight())
1904     {
1905       sg = viewport.getSelectionGroup()
1906               .getSequences(viewport.getHiddenRepSequences());
1907     }
1908
1909     if (sg.size() < 1)
1910     {
1911       return;
1912     }
1913
1914     List<SequenceI> invertGroup = new ArrayList<>();
1915
1916     for (SequenceI seq : viewport.getAlignment().getSequences())
1917     {
1918       if (!sg.contains(seq))
1919       {
1920         invertGroup.add(seq);
1921       }
1922     }
1923
1924     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1925
1926     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1927     for (int i = 0; i < invertGroup.size(); i++)
1928     {
1929       seqs2[i] = invertGroup.get(i);
1930     }
1931
1932     SlideSequencesCommand ssc;
1933     if (right)
1934     {
1935       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1936               viewport.getGapCharacter());
1937     }
1938     else
1939     {
1940       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1941               viewport.getGapCharacter());
1942     }
1943
1944     int groupAdjustment = 0;
1945     if (ssc.getGapsInsertedBegin() && right)
1946     {
1947       if (viewport.cursorMode)
1948       {
1949         alignPanel.getSeqPanel().moveCursor(size, 0);
1950       }
1951       else
1952       {
1953         groupAdjustment = size;
1954       }
1955     }
1956     else if (!ssc.getGapsInsertedBegin() && !right)
1957     {
1958       if (viewport.cursorMode)
1959       {
1960         alignPanel.getSeqPanel().moveCursor(-size, 0);
1961       }
1962       else
1963       {
1964         groupAdjustment = -size;
1965       }
1966     }
1967
1968     if (groupAdjustment != 0)
1969     {
1970       viewport.getSelectionGroup().setStartRes(
1971               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1972       viewport.getSelectionGroup().setEndRes(
1973               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1974     }
1975
1976     /*
1977      * just extend the last slide command if compatible; but not if in
1978      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1979      */
1980     boolean appendHistoryItem = false;
1981     Deque<CommandI> historyList = viewport.getHistoryList();
1982     boolean inSplitFrame = getSplitViewContainer() != null;
1983     if (!inSplitFrame && historyList != null && historyList.size() > 0
1984             && historyList.peek() instanceof SlideSequencesCommand)
1985     {
1986       appendHistoryItem = ssc.appendSlideCommand(
1987               (SlideSequencesCommand) historyList.peek());
1988     }
1989
1990     if (!appendHistoryItem)
1991     {
1992       addHistoryItem(ssc);
1993     }
1994
1995     repaint();
1996   }
1997
1998   /**
1999    * DOCUMENT ME!
2000    *
2001    * @param e
2002    *          DOCUMENT ME!
2003    */
2004   @Override
2005   protected void copy_actionPerformed()
2006   {
2007     if (viewport.getSelectionGroup() == null)
2008     {
2009       return;
2010     }
2011     // TODO: preserve the ordering of displayed alignment annotation in any
2012     // internal paste (particularly sequence associated annotation)
2013     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2014     String[] omitHidden = null;
2015
2016     if (viewport.hasHiddenColumns())
2017     {
2018       omitHidden = viewport.getViewAsString(true);
2019     }
2020
2021     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2022             seqs, omitHidden, null);
2023
2024     StringSelection ss = new StringSelection(output);
2025
2026     try
2027     {
2028       jalview.gui.Desktop.internalCopy = true;
2029       // Its really worth setting the clipboard contents
2030       // to empty before setting the large StringSelection!!
2031       Toolkit.getDefaultToolkit().getSystemClipboard()
2032               .setContents(new StringSelection(""), null);
2033
2034       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2035               Desktop.instance);
2036     } catch (OutOfMemoryError er)
2037     {
2038       new OOMWarning("copying region", er);
2039       return;
2040     }
2041
2042     HiddenColumns hiddenColumns = null;
2043     if (viewport.hasHiddenColumns())
2044     {
2045       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2046       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2047
2048       // create new HiddenColumns object with copy of hidden regions
2049       // between startRes and endRes, offset by startRes
2050       hiddenColumns = new HiddenColumns(
2051               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2052               hiddenCutoff, hiddenOffset);
2053     }
2054
2055     Desktop.jalviewClipboard = new Object[] { seqs,
2056         viewport.getAlignment().getDataset(), hiddenColumns };
2057     setStatus(MessageManager.formatMessage(
2058             "label.copied_sequences_to_clipboard", new Object[]
2059             { Integer.valueOf(seqs.length).toString() }));
2060   }
2061
2062   /**
2063    * DOCUMENT ME!
2064    *
2065    * @param e
2066    *          DOCUMENT ME!
2067    */
2068   @Override
2069   protected void pasteNew_actionPerformed(ActionEvent e)
2070   {
2071     paste(true);
2072   }
2073
2074   /**
2075    * DOCUMENT ME!
2076    *
2077    * @param e
2078    *          DOCUMENT ME!
2079    */
2080   @Override
2081   protected void pasteThis_actionPerformed(ActionEvent e)
2082   {
2083     paste(false);
2084   }
2085
2086   /**
2087    * Paste contents of Jalview clipboard
2088    *
2089    * @param newAlignment
2090    *          true to paste to a new alignment, otherwise add to this.
2091    */
2092   void paste(boolean newAlignment)
2093   {
2094     boolean externalPaste = true;
2095     try
2096     {
2097       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2098       Transferable contents = c.getContents(this);
2099
2100       if (contents == null)
2101       {
2102         return;
2103       }
2104
2105       String str;
2106       FileFormatI format;
2107       try
2108       {
2109         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2110         if (str.length() < 1)
2111         {
2112           return;
2113         }
2114
2115         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2116
2117       } catch (OutOfMemoryError er)
2118       {
2119         new OOMWarning("Out of memory pasting sequences!!", er);
2120         return;
2121       }
2122
2123       SequenceI[] sequences;
2124       boolean annotationAdded = false;
2125       AlignmentI alignment = null;
2126
2127       if (Desktop.jalviewClipboard != null)
2128       {
2129         // The clipboard was filled from within Jalview, we must use the
2130         // sequences
2131         // And dataset from the copied alignment
2132         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2133         // be doubly sure that we create *new* sequence objects.
2134         sequences = new SequenceI[newseq.length];
2135         for (int i = 0; i < newseq.length; i++)
2136         {
2137           sequences[i] = new Sequence(newseq[i]);
2138         }
2139         alignment = new Alignment(sequences);
2140         externalPaste = false;
2141       }
2142       else
2143       {
2144         // parse the clipboard as an alignment.
2145         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2146                 format);
2147         sequences = alignment.getSequencesArray();
2148       }
2149
2150       int alwidth = 0;
2151       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2152       int fgroup = -1;
2153
2154       if (newAlignment)
2155       {
2156
2157         if (Desktop.jalviewClipboard != null)
2158         {
2159           // dataset is inherited
2160           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2161         }
2162         else
2163         {
2164           // new dataset is constructed
2165           alignment.setDataset(null);
2166         }
2167         alwidth = alignment.getWidth() + 1;
2168       }
2169       else
2170       {
2171         AlignmentI pastedal = alignment; // preserve pasted alignment object
2172         // Add pasted sequences and dataset into existing alignment.
2173         alignment = viewport.getAlignment();
2174         alwidth = alignment.getWidth() + 1;
2175         // decide if we need to import sequences from an existing dataset
2176         boolean importDs = Desktop.jalviewClipboard != null
2177                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2178         // importDs==true instructs us to copy over new dataset sequences from
2179         // an existing alignment
2180         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2181                                                                       // create
2182         // minimum dataset set
2183
2184         for (int i = 0; i < sequences.length; i++)
2185         {
2186           if (importDs)
2187           {
2188             newDs.addElement(null);
2189           }
2190           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2191           // paste
2192           if (importDs && ds != null)
2193           {
2194             if (!newDs.contains(ds))
2195             {
2196               newDs.setElementAt(ds, i);
2197               ds = new Sequence(ds);
2198               // update with new dataset sequence
2199               sequences[i].setDatasetSequence(ds);
2200             }
2201             else
2202             {
2203               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2204             }
2205           }
2206           else
2207           {
2208             // copy and derive new dataset sequence
2209             sequences[i] = sequences[i].deriveSequence();
2210             alignment.getDataset()
2211                     .addSequence(sequences[i].getDatasetSequence());
2212             // TODO: avoid creation of duplicate dataset sequences with a
2213             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2214           }
2215           alignment.addSequence(sequences[i]); // merges dataset
2216         }
2217         if (newDs != null)
2218         {
2219           newDs.clear(); // tidy up
2220         }
2221         if (alignment.getAlignmentAnnotation() != null)
2222         {
2223           for (AlignmentAnnotation alan : alignment
2224                   .getAlignmentAnnotation())
2225           {
2226             if (alan.graphGroup > fgroup)
2227             {
2228               fgroup = alan.graphGroup;
2229             }
2230           }
2231         }
2232         if (pastedal.getAlignmentAnnotation() != null)
2233         {
2234           // Add any annotation attached to alignment.
2235           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2236           for (int i = 0; i < alann.length; i++)
2237           {
2238             annotationAdded = true;
2239             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2240             {
2241               AlignmentAnnotation newann = new AlignmentAnnotation(
2242                       alann[i]);
2243               if (newann.graphGroup > -1)
2244               {
2245                 if (newGraphGroups.size() <= newann.graphGroup
2246                         || newGraphGroups.get(newann.graphGroup) == null)
2247                 {
2248                   for (int q = newGraphGroups
2249                           .size(); q <= newann.graphGroup; q++)
2250                   {
2251                     newGraphGroups.add(q, null);
2252                   }
2253                   newGraphGroups.set(newann.graphGroup,
2254                           Integer.valueOf(++fgroup));
2255                 }
2256                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2257                         .intValue();
2258               }
2259
2260               newann.padAnnotation(alwidth);
2261               alignment.addAnnotation(newann);
2262             }
2263           }
2264         }
2265       }
2266       if (!newAlignment)
2267       {
2268         // /////
2269         // ADD HISTORY ITEM
2270         //
2271         addHistoryItem(new EditCommand(
2272                 MessageManager.getString("label.add_sequences"),
2273                 Action.PASTE, sequences, 0, alignment.getWidth(),
2274                 alignment));
2275       }
2276       // Add any annotations attached to sequences
2277       for (int i = 0; i < sequences.length; i++)
2278       {
2279         if (sequences[i].getAnnotation() != null)
2280         {
2281           AlignmentAnnotation newann;
2282           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2283           {
2284             annotationAdded = true;
2285             newann = sequences[i].getAnnotation()[a];
2286             newann.adjustForAlignment();
2287             newann.padAnnotation(alwidth);
2288             if (newann.graphGroup > -1)
2289             {
2290               if (newann.graphGroup > -1)
2291               {
2292                 if (newGraphGroups.size() <= newann.graphGroup
2293                         || newGraphGroups.get(newann.graphGroup) == null)
2294                 {
2295                   for (int q = newGraphGroups
2296                           .size(); q <= newann.graphGroup; q++)
2297                   {
2298                     newGraphGroups.add(q, null);
2299                   }
2300                   newGraphGroups.set(newann.graphGroup,
2301                           Integer.valueOf(++fgroup));
2302                 }
2303                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2304                         .intValue();
2305               }
2306             }
2307             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2308             // was
2309             // duplicated
2310             // earlier
2311             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2312                     a);
2313           }
2314         }
2315       }
2316       if (!newAlignment)
2317       {
2318
2319         // propagate alignment changed.
2320         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2321         if (annotationAdded)
2322         {
2323           // Duplicate sequence annotation in all views.
2324           AlignmentI[] alview = this.getViewAlignments();
2325           for (int i = 0; i < sequences.length; i++)
2326           {
2327             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2328             if (sann == null)
2329             {
2330               continue;
2331             }
2332             for (int avnum = 0; avnum < alview.length; avnum++)
2333             {
2334               if (alview[avnum] != alignment)
2335               {
2336                 // duplicate in a view other than the one with input focus
2337                 int avwidth = alview[avnum].getWidth() + 1;
2338                 // this relies on sann being preserved after we
2339                 // modify the sequence's annotation array for each duplication
2340                 for (int a = 0; a < sann.length; a++)
2341                 {
2342                   AlignmentAnnotation newann = new AlignmentAnnotation(
2343                           sann[a]);
2344                   sequences[i].addAlignmentAnnotation(newann);
2345                   newann.padAnnotation(avwidth);
2346                   alview[avnum].addAnnotation(newann); // annotation was
2347                   // duplicated earlier
2348                   // TODO JAL-1145 graphGroups are not updated for sequence
2349                   // annotation added to several views. This may cause
2350                   // strangeness
2351                   alview[avnum].setAnnotationIndex(newann, a);
2352                 }
2353               }
2354             }
2355           }
2356           buildSortByAnnotationScoresMenu();
2357         }
2358         viewport.firePropertyChange("alignment", null,
2359                 alignment.getSequences());
2360         if (alignPanels != null)
2361         {
2362           for (AlignmentPanel ap : alignPanels)
2363           {
2364             ap.validateAnnotationDimensions(false);
2365           }
2366         }
2367         else
2368         {
2369           alignPanel.validateAnnotationDimensions(false);
2370         }
2371
2372       }
2373       else
2374       {
2375         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2376                 DEFAULT_HEIGHT);
2377         String newtitle = new String("Copied sequences");
2378
2379         if (Desktop.jalviewClipboard != null
2380                 && Desktop.jalviewClipboard[2] != null)
2381         {
2382           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2383           af.viewport.setHiddenColumns(hc);
2384         }
2385
2386         // >>>This is a fix for the moment, until a better solution is
2387         // found!!<<<
2388         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2389                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2390                         .getFeatureRenderer());
2391
2392         // TODO: maintain provenance of an alignment, rather than just make the
2393         // title a concatenation of operations.
2394         if (!externalPaste)
2395         {
2396           if (title.startsWith("Copied sequences"))
2397           {
2398             newtitle = title;
2399           }
2400           else
2401           {
2402             newtitle = newtitle.concat("- from " + title);
2403           }
2404         }
2405         else
2406         {
2407           newtitle = new String("Pasted sequences");
2408         }
2409
2410         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2411                 DEFAULT_HEIGHT);
2412
2413       }
2414
2415     } catch (Exception ex)
2416     {
2417       ex.printStackTrace();
2418       System.out.println("Exception whilst pasting: " + ex);
2419       // could be anything being pasted in here
2420     }
2421
2422   }
2423
2424   @Override
2425   protected void expand_newalign(ActionEvent e)
2426   {
2427     try
2428     {
2429       AlignmentI alignment = AlignmentUtils
2430               .expandContext(getViewport().getAlignment(), -1);
2431       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2432               DEFAULT_HEIGHT);
2433       String newtitle = new String("Flanking alignment");
2434
2435       if (Desktop.jalviewClipboard != null
2436               && Desktop.jalviewClipboard[2] != null)
2437       {
2438         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2439         af.viewport.setHiddenColumns(hc);
2440       }
2441
2442       // >>>This is a fix for the moment, until a better solution is
2443       // found!!<<<
2444       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2445               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2446                       .getFeatureRenderer());
2447
2448       // TODO: maintain provenance of an alignment, rather than just make the
2449       // title a concatenation of operations.
2450       {
2451         if (title.startsWith("Copied sequences"))
2452         {
2453           newtitle = title;
2454         }
2455         else
2456         {
2457           newtitle = newtitle.concat("- from " + title);
2458         }
2459       }
2460
2461       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2462
2463     } catch (Exception ex)
2464     {
2465       ex.printStackTrace();
2466       System.out.println("Exception whilst pasting: " + ex);
2467       // could be anything being pasted in here
2468     } catch (OutOfMemoryError oom)
2469     {
2470       new OOMWarning("Viewing flanking region of alignment", oom);
2471     }
2472   }
2473
2474   /**
2475    * Action Cut (delete and copy) the selected region
2476    */
2477   @Override
2478   protected void cut_actionPerformed()
2479   {
2480     copy_actionPerformed();
2481     delete_actionPerformed();
2482   }
2483
2484   /**
2485    * Performs menu option to Delete the currently selected region
2486    */
2487   @Override
2488   protected void delete_actionPerformed()
2489   {
2490
2491     SequenceGroup sg = viewport.getSelectionGroup();
2492     if (sg == null)
2493     {
2494       return;
2495     }
2496
2497     Callable okAction = () -> {
2498       SequenceI[] cut = sg.getSequences()
2499               .toArray(new SequenceI[sg.getSize()]);
2500
2501       addHistoryItem(new EditCommand(
2502               MessageManager.getString("label.cut_sequences"), Action.CUT,
2503               cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2504               viewport.getAlignment()));
2505
2506       viewport.setSelectionGroup(null);
2507       viewport.sendSelection();
2508       viewport.getAlignment().deleteGroup(sg);
2509
2510       viewport.firePropertyChange("alignment", null,
2511               viewport.getAlignment().getSequences());
2512       if (viewport.getAlignment().getHeight() < 1)
2513       {
2514         try
2515         {
2516           AlignFrame.this.setClosed(true);
2517         } catch (Exception ex)
2518         {
2519         }
2520       }
2521       return null;
2522     };
2523
2524     /*
2525      * If the cut affects all sequences, prompt for confirmation
2526      */
2527     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2528             .getHeight();
2529     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2530             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2531     if (wholeHeight && wholeWidth)
2532     {
2533       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2534       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2535       Object[] options = new Object[] {
2536           MessageManager.getString("action.ok"),
2537           MessageManager.getString("action.cancel") };
2538       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2539               MessageManager.getString("label.delete_all"),
2540               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2541               options, options[0]);
2542     }
2543     else
2544     {
2545       try
2546       {
2547         okAction.call();
2548       } catch (Exception e)
2549       {
2550         e.printStackTrace();
2551       }
2552     }
2553   }
2554
2555   /**
2556    * DOCUMENT ME!
2557    *
2558    * @param e
2559    *          DOCUMENT ME!
2560    */
2561   @Override
2562   protected void deleteGroups_actionPerformed(ActionEvent e)
2563   {
2564     if (avc.deleteGroups())
2565     {
2566       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2567       alignPanel.updateAnnotation();
2568       alignPanel.paintAlignment(true, true);
2569     }
2570   }
2571
2572   /**
2573    * DOCUMENT ME!
2574    *
2575    * @param e
2576    *          DOCUMENT ME!
2577    */
2578   @Override
2579   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2580   {
2581     SequenceGroup sg = new SequenceGroup(
2582             viewport.getAlignment().getSequences());
2583
2584     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2585     viewport.setSelectionGroup(sg);
2586     viewport.isSelectionGroupChanged(true);
2587     viewport.sendSelection();
2588     // JAL-2034 - should delegate to
2589     // alignPanel to decide if overview needs
2590     // updating.
2591     alignPanel.paintAlignment(false, false);
2592     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2593   }
2594
2595   /**
2596    * DOCUMENT ME!
2597    *
2598    * @param e
2599    *          DOCUMENT ME!
2600    */
2601   @Override
2602   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2603   {
2604     if (viewport.cursorMode)
2605     {
2606       alignPanel.getSeqPanel().keyboardNo1 = null;
2607       alignPanel.getSeqPanel().keyboardNo2 = null;
2608     }
2609     viewport.setSelectionGroup(null);
2610     viewport.getColumnSelection().clear();
2611     viewport.setSearchResults(null);
2612     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2613     // JAL-2034 - should delegate to
2614     // alignPanel to decide if overview needs
2615     // updating.
2616     alignPanel.paintAlignment(false, false);
2617     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2618     viewport.sendSelection();
2619   }
2620
2621   /**
2622    * DOCUMENT ME!
2623    *
2624    * @param e
2625    *          DOCUMENT ME!
2626    */
2627   @Override
2628   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2629   {
2630     SequenceGroup sg = viewport.getSelectionGroup();
2631
2632     if (sg == null)
2633     {
2634       selectAllSequenceMenuItem_actionPerformed(null);
2635
2636       return;
2637     }
2638
2639     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2640     {
2641       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2642     }
2643     // JAL-2034 - should delegate to
2644     // alignPanel to decide if overview needs
2645     // updating.
2646
2647     alignPanel.paintAlignment(true, false);
2648     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2649     viewport.sendSelection();
2650   }
2651
2652   @Override
2653   public void invertColSel_actionPerformed(ActionEvent e)
2654   {
2655     viewport.invertColumnSelection();
2656     alignPanel.paintAlignment(true, false);
2657     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2658     viewport.sendSelection();
2659   }
2660
2661   /**
2662    * DOCUMENT ME!
2663    *
2664    * @param e
2665    *          DOCUMENT ME!
2666    */
2667   @Override
2668   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2669   {
2670     trimAlignment(true);
2671   }
2672
2673   /**
2674    * DOCUMENT ME!
2675    *
2676    * @param e
2677    *          DOCUMENT ME!
2678    */
2679   @Override
2680   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2681   {
2682     trimAlignment(false);
2683   }
2684
2685   void trimAlignment(boolean trimLeft)
2686   {
2687     ColumnSelection colSel = viewport.getColumnSelection();
2688     int column;
2689
2690     if (!colSel.isEmpty())
2691     {
2692       if (trimLeft)
2693       {
2694         column = colSel.getMin();
2695       }
2696       else
2697       {
2698         column = colSel.getMax();
2699       }
2700
2701       SequenceI[] seqs;
2702       if (viewport.getSelectionGroup() != null)
2703       {
2704         seqs = viewport.getSelectionGroup()
2705                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2706       }
2707       else
2708       {
2709         seqs = viewport.getAlignment().getSequencesArray();
2710       }
2711
2712       TrimRegionCommand trimRegion;
2713       if (trimLeft)
2714       {
2715         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2716                 column, viewport.getAlignment());
2717         viewport.getRanges().setStartRes(0);
2718       }
2719       else
2720       {
2721         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2722                 column, viewport.getAlignment());
2723       }
2724
2725       setStatus(MessageManager.formatMessage("label.removed_columns",
2726               new String[]
2727               { Integer.valueOf(trimRegion.getSize()).toString() }));
2728
2729       addHistoryItem(trimRegion);
2730
2731       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2732       {
2733         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2734                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2735         {
2736           viewport.getAlignment().deleteGroup(sg);
2737         }
2738       }
2739
2740       viewport.firePropertyChange("alignment", null,
2741               viewport.getAlignment().getSequences());
2742     }
2743   }
2744
2745   /**
2746    * DOCUMENT ME!
2747    *
2748    * @param e
2749    *          DOCUMENT ME!
2750    */
2751   @Override
2752   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2753   {
2754     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2755
2756     SequenceI[] seqs;
2757     if (viewport.getSelectionGroup() != null)
2758     {
2759       seqs = viewport.getSelectionGroup()
2760               .getSequencesAsArray(viewport.getHiddenRepSequences());
2761       start = viewport.getSelectionGroup().getStartRes();
2762       end = viewport.getSelectionGroup().getEndRes();
2763     }
2764     else
2765     {
2766       seqs = viewport.getAlignment().getSequencesArray();
2767     }
2768
2769     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2770             "Remove Gapped Columns", seqs, start, end,
2771             viewport.getAlignment());
2772
2773     addHistoryItem(removeGapCols);
2774
2775     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2776             new Object[]
2777             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2778
2779     // This is to maintain viewport position on first residue
2780     // of first sequence
2781     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2782     ViewportRanges ranges = viewport.getRanges();
2783     int startRes = seq.findPosition(ranges.getStartRes());
2784     // ShiftList shifts;
2785     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2786     // edit.alColumnChanges=shifts.getInverse();
2787     // if (viewport.hasHiddenColumns)
2788     // viewport.getColumnSelection().compensateForEdits(shifts);
2789     ranges.setStartRes(seq.findIndex(startRes) - 1);
2790     viewport.firePropertyChange("alignment", null,
2791             viewport.getAlignment().getSequences());
2792
2793   }
2794
2795   /**
2796    * DOCUMENT ME!
2797    *
2798    * @param e
2799    *          DOCUMENT ME!
2800    */
2801   @Override
2802   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2803   {
2804     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2805
2806     SequenceI[] seqs;
2807     if (viewport.getSelectionGroup() != null)
2808     {
2809       seqs = viewport.getSelectionGroup()
2810               .getSequencesAsArray(viewport.getHiddenRepSequences());
2811       start = viewport.getSelectionGroup().getStartRes();
2812       end = viewport.getSelectionGroup().getEndRes();
2813     }
2814     else
2815     {
2816       seqs = viewport.getAlignment().getSequencesArray();
2817     }
2818
2819     // This is to maintain viewport position on first residue
2820     // of first sequence
2821     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2822     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2823
2824     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2825             viewport.getAlignment()));
2826
2827     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2828
2829     viewport.firePropertyChange("alignment", null,
2830             viewport.getAlignment().getSequences());
2831
2832   }
2833
2834   /**
2835    * DOCUMENT ME!
2836    *
2837    * @param e
2838    *          DOCUMENT ME!
2839    */
2840   @Override
2841   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2842   {
2843     viewport.setPadGaps(padGapsMenuitem.isSelected());
2844     viewport.firePropertyChange("alignment", null,
2845             viewport.getAlignment().getSequences());
2846   }
2847
2848   /**
2849    * Opens a Finder dialog
2850    *
2851    * @param e
2852    */
2853   @Override
2854   public void findMenuItem_actionPerformed(ActionEvent e)
2855   {
2856     new Finder(alignPanel, false, null);
2857   }
2858
2859   /**
2860    * Create a new view of the current alignment.
2861    */
2862   @Override
2863   public void newView_actionPerformed(ActionEvent e)
2864   {
2865     newView(null, true);
2866   }
2867
2868   /**
2869    * Creates and shows a new view of the current alignment.
2870    *
2871    * @param viewTitle
2872    *          title of newly created view; if null, one will be generated
2873    * @param copyAnnotation
2874    *          if true then duplicate all annnotation, groups and settings
2875    * @return new alignment panel, already displayed.
2876    */
2877   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2878   {
2879     /*
2880      * Create a new AlignmentPanel (with its own, new Viewport)
2881      */
2882     AlignmentPanel newap = new jalview.project.Jalview2XML()
2883             .copyAlignPanel(alignPanel);
2884     if (!copyAnnotation)
2885     {
2886       /*
2887        * remove all groups and annotation except for the automatic stuff
2888        */
2889       newap.av.getAlignment().deleteAllGroups();
2890       newap.av.getAlignment().deleteAllAnnotations(false);
2891     }
2892
2893     newap.av.setGatherViewsHere(false);
2894
2895     if (viewport.getViewName() == null)
2896     {
2897       viewport.setViewName(
2898               MessageManager.getString("label.view_name_original"));
2899     }
2900
2901     /*
2902      * Views share the same edits undo and redo stacks
2903      */
2904     newap.av.setHistoryList(viewport.getHistoryList());
2905     newap.av.setRedoList(viewport.getRedoList());
2906
2907     /*
2908      * copy any visualisation settings that are not saved in the project
2909      */
2910     newap.av.setColourAppliesToAllGroups(
2911             viewport.getColourAppliesToAllGroups());
2912
2913     /*
2914      * Views share the same mappings; need to deregister any new mappings
2915      * created by copyAlignPanel, and register the new reference to the shared
2916      * mappings
2917      */
2918     newap.av.replaceMappings(viewport.getAlignment());
2919
2920     /*
2921      * start up cDNA consensus (if applicable) now mappings are in place
2922      */
2923     if (newap.av.initComplementConsensus())
2924     {
2925       newap.refresh(true); // adjust layout of annotations
2926     }
2927
2928     newap.av.setViewName(getNewViewName(viewTitle));
2929
2930     addAlignmentPanel(newap, true);
2931     newap.alignmentChanged();
2932
2933     if (alignPanels.size() == 2)
2934     {
2935       viewport.setGatherViewsHere(true);
2936     }
2937     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2938
2939     return newap;
2940   }
2941
2942   /**
2943    * Make a new name for the view, ensuring it is unique within the current
2944    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2945    * these now use viewId. Unique view names are still desirable for usability.)
2946    *
2947    * @param viewTitle
2948    * @return
2949    */
2950   protected String getNewViewName(String viewTitle)
2951   {
2952     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2953     boolean addFirstIndex = false;
2954     if (viewTitle == null || viewTitle.trim().length() == 0)
2955     {
2956       viewTitle = MessageManager.getString("action.view");
2957       addFirstIndex = true;
2958     }
2959     else
2960     {
2961       index = 1;// we count from 1 if given a specific name
2962     }
2963     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2964
2965     List<Component> comps = PaintRefresher.components
2966             .get(viewport.getSequenceSetId());
2967
2968     List<String> existingNames = getExistingViewNames(comps);
2969
2970     while (existingNames.contains(newViewName))
2971     {
2972       newViewName = viewTitle + " " + (++index);
2973     }
2974     return newViewName;
2975   }
2976
2977   /**
2978    * Returns a list of distinct view names found in the given list of
2979    * components. View names are held on the viewport of an AlignmentPanel.
2980    *
2981    * @param comps
2982    * @return
2983    */
2984   protected List<String> getExistingViewNames(List<Component> comps)
2985   {
2986     List<String> existingNames = new ArrayList<>();
2987     for (Component comp : comps)
2988     {
2989       if (comp instanceof AlignmentPanel)
2990       {
2991         AlignmentPanel ap = (AlignmentPanel) comp;
2992         if (!existingNames.contains(ap.av.getViewName()))
2993         {
2994           existingNames.add(ap.av.getViewName());
2995         }
2996       }
2997     }
2998     return existingNames;
2999   }
3000
3001   /**
3002    * Explode tabbed views into separate windows.
3003    */
3004   @Override
3005   public void expandViews_actionPerformed(ActionEvent e)
3006   {
3007     Desktop.explodeViews(this);
3008   }
3009
3010   /**
3011    * Gather views in separate windows back into a tabbed presentation.
3012    */
3013   @Override
3014   public void gatherViews_actionPerformed(ActionEvent e)
3015   {
3016     Desktop.instance.gatherViews(this);
3017   }
3018
3019   /**
3020    * DOCUMENT ME!
3021    *
3022    * @param e
3023    *          DOCUMENT ME!
3024    */
3025   @Override
3026   public void font_actionPerformed(ActionEvent e)
3027   {
3028     new FontChooser(alignPanel);
3029   }
3030
3031   /**
3032    * DOCUMENT ME!
3033    *
3034    * @param e
3035    *          DOCUMENT ME!
3036    */
3037   @Override
3038   protected void seqLimit_actionPerformed(ActionEvent e)
3039   {
3040     viewport.setShowJVSuffix(seqLimits.isSelected());
3041
3042     alignPanel.getIdPanel().getIdCanvas()
3043             .setPreferredSize(alignPanel.calculateIdWidth());
3044     alignPanel.paintAlignment(true, false);
3045   }
3046
3047   @Override
3048   public void idRightAlign_actionPerformed(ActionEvent e)
3049   {
3050     viewport.setRightAlignIds(idRightAlign.isSelected());
3051     alignPanel.paintAlignment(false, false);
3052   }
3053
3054   @Override
3055   public void centreColumnLabels_actionPerformed(ActionEvent e)
3056   {
3057     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3058     alignPanel.paintAlignment(false, false);
3059   }
3060
3061   /*
3062    * (non-Javadoc)
3063    *
3064    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3065    */
3066   @Override
3067   protected void followHighlight_actionPerformed()
3068   {
3069     /*
3070      * Set the 'follow' flag on the Viewport (and scroll to position if now
3071      * true).
3072      */
3073     final boolean state = this.followHighlightMenuItem.getState();
3074     viewport.setFollowHighlight(state);
3075     if (state)
3076     {
3077       alignPanel.scrollToPosition(viewport.getSearchResults());
3078     }
3079   }
3080
3081   /**
3082    * DOCUMENT ME!
3083    *
3084    * @param e
3085    *          DOCUMENT ME!
3086    */
3087   @Override
3088   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setColourText(colourTextMenuItem.isSelected());
3091     alignPanel.paintAlignment(false, false);
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   public void wrapMenuItem_actionPerformed(ActionEvent e)
3102   {
3103     scaleAbove.setVisible(wrapMenuItem.isSelected());
3104     scaleLeft.setVisible(wrapMenuItem.isSelected());
3105     scaleRight.setVisible(wrapMenuItem.isSelected());
3106     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3107     alignPanel.updateLayout();
3108   }
3109
3110   @Override
3111   public void showAllSeqs_actionPerformed(ActionEvent e)
3112   {
3113     viewport.showAllHiddenSeqs();
3114   }
3115
3116   @Override
3117   public void showAllColumns_actionPerformed(ActionEvent e)
3118   {
3119     viewport.showAllHiddenColumns();
3120     alignPanel.paintAlignment(true, true);
3121     viewport.sendSelection();
3122   }
3123
3124   @Override
3125   public void hideSelSequences_actionPerformed(ActionEvent e)
3126   {
3127     viewport.hideAllSelectedSeqs();
3128   }
3129
3130   /**
3131    * called by key handler and the hide all/show all menu items
3132    *
3133    * @param toggleSeqs
3134    * @param toggleCols
3135    */
3136   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3137   {
3138
3139     boolean hide = false;
3140     SequenceGroup sg = viewport.getSelectionGroup();
3141     if (!toggleSeqs && !toggleCols)
3142     {
3143       // Hide everything by the current selection - this is a hack - we do the
3144       // invert and then hide
3145       // first check that there will be visible columns after the invert.
3146       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3147               && sg.getStartRes() <= sg.getEndRes()))
3148       {
3149         // now invert the sequence set, if required - empty selection implies
3150         // that no hiding is required.
3151         if (sg != null)
3152         {
3153           invertSequenceMenuItem_actionPerformed(null);
3154           sg = viewport.getSelectionGroup();
3155           toggleSeqs = true;
3156
3157         }
3158         viewport.expandColSelection(sg, true);
3159         // finally invert the column selection and get the new sequence
3160         // selection.
3161         invertColSel_actionPerformed(null);
3162         toggleCols = true;
3163       }
3164     }
3165
3166     if (toggleSeqs)
3167     {
3168       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3169       {
3170         hideSelSequences_actionPerformed(null);
3171         hide = true;
3172       }
3173       else if (!(toggleCols && viewport.hasSelectedColumns()))
3174       {
3175         showAllSeqs_actionPerformed(null);
3176       }
3177     }
3178
3179     if (toggleCols)
3180     {
3181       if (viewport.hasSelectedColumns())
3182       {
3183         hideSelColumns_actionPerformed(null);
3184         if (!toggleSeqs)
3185         {
3186           viewport.setSelectionGroup(sg);
3187         }
3188       }
3189       else if (!hide)
3190       {
3191         showAllColumns_actionPerformed(null);
3192       }
3193     }
3194   }
3195
3196   /*
3197    * (non-Javadoc)
3198    *
3199    * @see
3200    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3201    * event.ActionEvent)
3202    */
3203   @Override
3204   public void hideAllButSelection_actionPerformed(ActionEvent e)
3205   {
3206     toggleHiddenRegions(false, false);
3207     viewport.sendSelection();
3208   }
3209
3210   /*
3211    * (non-Javadoc)
3212    *
3213    * @see
3214    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3215    * .ActionEvent)
3216    */
3217   @Override
3218   public void hideAllSelection_actionPerformed(ActionEvent e)
3219   {
3220     SequenceGroup sg = viewport.getSelectionGroup();
3221     viewport.expandColSelection(sg, false);
3222     viewport.hideAllSelectedSeqs();
3223     viewport.hideSelectedColumns();
3224     alignPanel.updateLayout();
3225     alignPanel.paintAlignment(true, true);
3226     viewport.sendSelection();
3227   }
3228
3229   /*
3230    * (non-Javadoc)
3231    *
3232    * @see
3233    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3234    * ActionEvent)
3235    */
3236   @Override
3237   public void showAllhidden_actionPerformed(ActionEvent e)
3238   {
3239     viewport.showAllHiddenColumns();
3240     viewport.showAllHiddenSeqs();
3241     alignPanel.paintAlignment(true, true);
3242     viewport.sendSelection();
3243   }
3244
3245   @Override
3246   public void hideSelColumns_actionPerformed(ActionEvent e)
3247   {
3248     viewport.hideSelectedColumns();
3249     alignPanel.updateLayout();
3250     alignPanel.paintAlignment(true, true);
3251     viewport.sendSelection();
3252   }
3253
3254   @Override
3255   public void hiddenMarkers_actionPerformed(ActionEvent e)
3256   {
3257     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3258     repaint();
3259   }
3260
3261   /**
3262    * DOCUMENT ME!
3263    *
3264    * @param e
3265    *          DOCUMENT ME!
3266    */
3267   @Override
3268   protected void scaleAbove_actionPerformed(ActionEvent e)
3269   {
3270     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3271     alignPanel.updateLayout();
3272     alignPanel.paintAlignment(true, false);
3273   }
3274
3275   /**
3276    * DOCUMENT ME!
3277    *
3278    * @param e
3279    *          DOCUMENT ME!
3280    */
3281   @Override
3282   protected void scaleLeft_actionPerformed(ActionEvent e)
3283   {
3284     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3285     alignPanel.updateLayout();
3286     alignPanel.paintAlignment(true, false);
3287   }
3288
3289   /**
3290    * DOCUMENT ME!
3291    *
3292    * @param e
3293    *          DOCUMENT ME!
3294    */
3295   @Override
3296   protected void scaleRight_actionPerformed(ActionEvent e)
3297   {
3298     viewport.setScaleRightWrapped(scaleRight.isSelected());
3299     alignPanel.updateLayout();
3300     alignPanel.paintAlignment(true, false);
3301   }
3302
3303   /**
3304    * DOCUMENT ME!
3305    *
3306    * @param e
3307    *          DOCUMENT ME!
3308    */
3309   @Override
3310   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3311   {
3312     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3313     alignPanel.paintAlignment(false, false);
3314   }
3315
3316   /**
3317    * DOCUMENT ME!
3318    *
3319    * @param e
3320    *          DOCUMENT ME!
3321    */
3322   @Override
3323   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3324   {
3325     viewport.setShowText(viewTextMenuItem.isSelected());
3326     alignPanel.paintAlignment(false, false);
3327   }
3328
3329   /**
3330    * DOCUMENT ME!
3331    *
3332    * @param e
3333    *          DOCUMENT ME!
3334    */
3335   @Override
3336   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3337   {
3338     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3339     alignPanel.paintAlignment(false, false);
3340   }
3341
3342   public FeatureSettings featureSettings;
3343
3344   @Override
3345   public FeatureSettingsControllerI getFeatureSettingsUI()
3346   {
3347     return featureSettings;
3348   }
3349
3350   @Override
3351   public void featureSettings_actionPerformed(ActionEvent e)
3352   {
3353     showFeatureSettingsUI();
3354   }
3355
3356   @Override
3357   public FeatureSettingsControllerI showFeatureSettingsUI()
3358   {
3359     if (featureSettings != null)
3360     {
3361       featureSettings.closeOldSettings();
3362       featureSettings = null;
3363     }
3364     if (!showSeqFeatures.isSelected())
3365     {
3366       // make sure features are actually displayed
3367       showSeqFeatures.setSelected(true);
3368       showSeqFeatures_actionPerformed(null);
3369     }
3370     featureSettings = new FeatureSettings(this);
3371     return featureSettings;
3372   }
3373
3374   /**
3375    * Set or clear 'Show Sequence Features'
3376    *
3377    * @param evt
3378    *          DOCUMENT ME!
3379    */
3380   @Override
3381   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3382   {
3383     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3384     alignPanel.paintAlignment(true, true);
3385   }
3386
3387   /**
3388    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3389    * the annotations panel as a whole.
3390    *
3391    * The options to show/hide all annotations should be enabled when the panel
3392    * is shown, and disabled when the panel is hidden.
3393    *
3394    * @param e
3395    */
3396   @Override
3397   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3398   {
3399     final boolean setVisible = annotationPanelMenuItem.isSelected();
3400     viewport.setShowAnnotation(setVisible);
3401     this.showAllSeqAnnotations.setEnabled(setVisible);
3402     this.hideAllSeqAnnotations.setEnabled(setVisible);
3403     this.showAllAlAnnotations.setEnabled(setVisible);
3404     this.hideAllAlAnnotations.setEnabled(setVisible);
3405     alignPanel.updateLayout();
3406   }
3407
3408   @Override
3409   public void alignmentProperties()
3410   {
3411     JComponent pane;
3412     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3413
3414             .formatAsHtml();
3415     String content = MessageManager.formatMessage("label.html_content",
3416             new Object[]
3417             { contents.toString() });
3418     contents = null;
3419
3420     if (Platform.isJS())
3421     {
3422       JLabel textLabel = new JLabel();
3423       textLabel.setText(content);
3424       textLabel.setBackground(Color.WHITE);
3425
3426       pane = new JPanel(new BorderLayout());
3427       ((JPanel) pane).setOpaque(true);
3428       pane.setBackground(Color.WHITE);
3429       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3430     }
3431     else
3432     /**
3433      * Java only
3434      *
3435      * @j2sIgnore
3436      */
3437     {
3438       JEditorPane editPane = new JEditorPane("text/html", "");
3439       editPane.setEditable(false);
3440       editPane.setText(content);
3441       pane = editPane;
3442     }
3443
3444     JInternalFrame frame = new JInternalFrame();
3445
3446     frame.getContentPane().add(new JScrollPane(pane));
3447
3448     Desktop.addInternalFrame(frame, MessageManager
3449             .formatMessage("label.alignment_properties", new Object[]
3450             { getTitle() }), 500, 400);
3451   }
3452
3453   /**
3454    * Opens an Overview panel for the alignment, unless one is open already
3455    *
3456    * @param e
3457    */
3458   @Override
3459   public void overviewMenuItem_actionPerformed(ActionEvent e)
3460   {
3461     boolean showHiddenRegions = Cache
3462             .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
3463     openOverviewPanel(showHiddenRegions);
3464   }
3465
3466   public OverviewPanel openOverviewPanel(boolean showHidden)
3467   {
3468     if (alignPanel.overviewPanel != null)
3469     {
3470       return alignPanel.overviewPanel;
3471     }
3472     JInternalFrame frame = new JInternalFrame();
3473     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
3474             showHidden);
3475     frame.setContentPane(overview);
3476     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
3477             frame.getHeight(), true, true);
3478     frame.setFrameIcon(null);
3479     frame.pack();
3480     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3481     final AlignmentPanel thePanel = this.alignPanel;
3482     frame.addInternalFrameListener(
3483             new javax.swing.event.InternalFrameAdapter()
3484             {
3485               @Override
3486               public void internalFrameClosed(
3487                       javax.swing.event.InternalFrameEvent evt)
3488               {
3489                 overview.dispose();
3490                 thePanel.setOverviewPanel(null);
3491               }
3492             });
3493     if (getKeyListeners().length > 0)
3494     {
3495       frame.addKeyListener(getKeyListeners()[0]);
3496     }
3497
3498     alignPanel.setOverviewPanel(overview);
3499     alignPanel.setOverviewTitle(this);
3500
3501     return overview;
3502   }
3503
3504   @Override
3505   public void textColour_actionPerformed()
3506   {
3507     new TextColourChooser().chooseColour(alignPanel, null);
3508   }
3509
3510   /*
3511    * public void covariationColour_actionPerformed() {
3512    * changeColour(new
3513    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3514    * ()[0])); }
3515    */
3516   @Override
3517   public void annotationColour_actionPerformed()
3518   {
3519     new AnnotationColourChooser(viewport, alignPanel);
3520   }
3521
3522   @Override
3523   public void annotationColumn_actionPerformed(ActionEvent e)
3524   {
3525     new AnnotationColumnChooser(viewport, alignPanel);
3526   }
3527
3528   /**
3529    * Action on the user checking or unchecking the option to apply the selected
3530    * colour scheme to all groups. If unchecked, groups may have their own
3531    * independent colour schemes.
3532    *
3533    * @param selected
3534    */
3535   @Override
3536   public void applyToAllGroups_actionPerformed(boolean selected)
3537   {
3538     viewport.setColourAppliesToAllGroups(selected);
3539   }
3540
3541   /**
3542    * Action on user selecting a colour from the colour menu
3543    *
3544    * @param name
3545    *          the name (not the menu item label!) of the colour scheme
3546    */
3547   @Override
3548   public void changeColour_actionPerformed(String name)
3549   {
3550     /*
3551      * 'User Defined' opens a panel to configure or load a
3552      * user-defined colour scheme
3553      */
3554     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3555     {
3556       new UserDefinedColours(alignPanel);
3557       return;
3558     }
3559
3560     /*
3561      * otherwise set the chosen colour scheme (or null for 'None')
3562      */
3563     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3564             viewport, viewport.getAlignment(),
3565             viewport.getHiddenRepSequences());
3566     changeColour(cs);
3567   }
3568
3569   /**
3570    * Actions on setting or changing the alignment colour scheme
3571    *
3572    * @param cs
3573    */
3574   @Override
3575   public void changeColour(ColourSchemeI cs)
3576   {
3577     // TODO: pull up to controller method
3578     ColourMenuHelper.setColourSelected(colourMenu, cs);
3579
3580     viewport.setGlobalColourScheme(cs);
3581
3582     alignPanel.paintAlignment(true, true);
3583   }
3584
3585   /**
3586    * Show the PID threshold slider panel
3587    */
3588   @Override
3589   protected void modifyPID_actionPerformed()
3590   {
3591     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3592             alignPanel.getViewName());
3593     SliderPanel.showPIDSlider();
3594   }
3595
3596   /**
3597    * Show the Conservation slider panel
3598    */
3599   @Override
3600   protected void modifyConservation_actionPerformed()
3601   {
3602     SliderPanel.setConservationSlider(alignPanel,
3603             viewport.getResidueShading(), alignPanel.getViewName());
3604     SliderPanel.showConservationSlider();
3605   }
3606
3607   /**
3608    * Action on selecting or deselecting (Colour) By Conservation
3609    */
3610   @Override
3611   public void conservationMenuItem_actionPerformed(boolean selected)
3612   {
3613     modifyConservation.setEnabled(selected);
3614     viewport.setConservationSelected(selected);
3615     viewport.getResidueShading().setConservationApplied(selected);
3616
3617     changeColour(viewport.getGlobalColourScheme());
3618     if (selected)
3619     {
3620       modifyConservation_actionPerformed();
3621     }
3622     else
3623     {
3624       SliderPanel.hideConservationSlider();
3625     }
3626   }
3627
3628   /**
3629    * Action on selecting or deselecting (Colour) Above PID Threshold
3630    */
3631   @Override
3632   public void abovePIDThreshold_actionPerformed(boolean selected)
3633   {
3634     modifyPID.setEnabled(selected);
3635     viewport.setAbovePIDThreshold(selected);
3636     if (!selected)
3637     {
3638       viewport.getResidueShading().setThreshold(0,
3639               viewport.isIgnoreGapsConsensus());
3640     }
3641
3642     changeColour(viewport.getGlobalColourScheme());
3643     if (selected)
3644     {
3645       modifyPID_actionPerformed();
3646     }
3647     else
3648     {
3649       SliderPanel.hidePIDSlider();
3650     }
3651   }
3652
3653   /**
3654    * DOCUMENT ME!
3655    *
3656    * @param e
3657    *          DOCUMENT ME!
3658    */
3659   @Override
3660   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3661   {
3662     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3663     AlignmentSorter.sortByPID(viewport.getAlignment(),
3664             viewport.getAlignment().getSequenceAt(0));
3665     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3666             viewport.getAlignment()));
3667     alignPanel.paintAlignment(true, false);
3668   }
3669
3670   /**
3671    * DOCUMENT ME!
3672    *
3673    * @param e
3674    *          DOCUMENT ME!
3675    */
3676   @Override
3677   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3678   {
3679     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3680     AlignmentSorter.sortByID(viewport.getAlignment());
3681     addHistoryItem(
3682             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3683     alignPanel.paintAlignment(true, false);
3684   }
3685
3686   /**
3687    * DOCUMENT ME!
3688    *
3689    * @param e
3690    *          DOCUMENT ME!
3691    */
3692   @Override
3693   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3694   {
3695     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3696     AlignmentSorter.sortByLength(viewport.getAlignment());
3697     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3698             viewport.getAlignment()));
3699     alignPanel.paintAlignment(true, false);
3700   }
3701
3702   /**
3703    * DOCUMENT ME!
3704    *
3705    * @param e
3706    *          DOCUMENT ME!
3707    */
3708   @Override
3709   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3710   {
3711     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3712     AlignmentSorter.sortByGroup(viewport.getAlignment());
3713     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3714             viewport.getAlignment()));
3715
3716     alignPanel.paintAlignment(true, false);
3717   }
3718
3719   /**
3720    * DOCUMENT ME!
3721    *
3722    * @param e
3723    *          DOCUMENT ME!
3724    */
3725   @Override
3726   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3727   {
3728     new RedundancyPanel(alignPanel, this);
3729   }
3730
3731   /**
3732    * DOCUMENT ME!
3733    *
3734    * @param e
3735    *          DOCUMENT ME!
3736    */
3737   @Override
3738   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3739   {
3740     if ((viewport.getSelectionGroup() == null)
3741             || (viewport.getSelectionGroup().getSize() < 2))
3742     {
3743       JvOptionPane.showInternalMessageDialog(this,
3744               MessageManager.getString(
3745                       "label.you_must_select_least_two_sequences"),
3746               MessageManager.getString("label.invalid_selection"),
3747               JvOptionPane.WARNING_MESSAGE);
3748     }
3749     else
3750     {
3751       JInternalFrame frame = new JInternalFrame();
3752       frame.setContentPane(new PairwiseAlignPanel(viewport));
3753       Desktop.addInternalFrame(frame,
3754               MessageManager.getString("action.pairwise_alignment"), 600,
3755               500);
3756     }
3757   }
3758
3759   @Override
3760   public void autoCalculate_actionPerformed(ActionEvent e)
3761   {
3762     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3763     if (viewport.autoCalculateConsensus)
3764     {
3765       viewport.firePropertyChange("alignment", null,
3766               viewport.getAlignment().getSequences());
3767     }
3768   }
3769
3770   @Override
3771   public void sortByTreeOption_actionPerformed(ActionEvent e)
3772   {
3773     viewport.sortByTree = sortByTree.isSelected();
3774   }
3775
3776   @Override
3777   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3778   {
3779     viewport.followSelection = listenToViewSelections.isSelected();
3780   }
3781
3782   /**
3783    * Constructs a tree panel and adds it to the desktop
3784    *
3785    * @param type
3786    *          tree type (NJ or AV)
3787    * @param modelName
3788    *          name of score model used to compute the tree
3789    * @param options
3790    *          parameters for the distance or similarity calculation
3791    */
3792   void newTreePanel(String type, String modelName,
3793           SimilarityParamsI options)
3794   {
3795     String frameTitle = "";
3796     TreePanel tp;
3797
3798     boolean onSelection = false;
3799     if (viewport.getSelectionGroup() != null
3800             && viewport.getSelectionGroup().getSize() > 0)
3801     {
3802       SequenceGroup sg = viewport.getSelectionGroup();
3803
3804       /* Decide if the selection is a column region */
3805       for (SequenceI _s : sg.getSequences())
3806       {
3807         if (_s.getLength() < sg.getEndRes())
3808         {
3809           JvOptionPane.showMessageDialog(Desktop.desktop,
3810                   MessageManager.getString(
3811                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3812                   MessageManager.getString(
3813                           "label.sequences_selection_not_aligned"),
3814                   JvOptionPane.WARNING_MESSAGE);
3815
3816           return;
3817         }
3818       }
3819       onSelection = true;
3820     }
3821     else
3822     {
3823       if (viewport.getAlignment().getHeight() < 2)
3824       {
3825         return;
3826       }
3827     }
3828
3829     tp = new TreePanel(alignPanel, type, modelName, options);
3830     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3831
3832     frameTitle += " from ";
3833
3834     if (viewport.getViewName() != null)
3835     {
3836       frameTitle += viewport.getViewName() + " of ";
3837     }
3838
3839     frameTitle += this.title;
3840
3841     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3842   }
3843
3844   /**
3845    * DOCUMENT ME!
3846    *
3847    * @param title
3848    *          DOCUMENT ME!
3849    * @param order
3850    *          DOCUMENT ME!
3851    */
3852   public void addSortByOrderMenuItem(String title,
3853           final AlignmentOrder order)
3854   {
3855     final JMenuItem item = new JMenuItem(MessageManager
3856             .formatMessage("action.by_title_param", new Object[]
3857             { title }));
3858     sort.add(item);
3859     item.addActionListener(new java.awt.event.ActionListener()
3860     {
3861       @Override
3862       public void actionPerformed(ActionEvent e)
3863       {
3864         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3865
3866         // TODO: JBPNote - have to map order entries to curent SequenceI
3867         // pointers
3868         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3869
3870         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3871                 viewport.getAlignment()));
3872
3873         alignPanel.paintAlignment(true, false);
3874       }
3875     });
3876   }
3877
3878   /**
3879    * Add a new sort by annotation score menu item
3880    *
3881    * @param sort
3882    *          the menu to add the option to
3883    * @param scoreLabel
3884    *          the label used to retrieve scores for each sequence on the
3885    *          alignment
3886    */
3887   public void addSortByAnnotScoreMenuItem(JMenu sort,
3888           final String scoreLabel)
3889   {
3890     final JMenuItem item = new JMenuItem(scoreLabel);
3891     sort.add(item);
3892     item.addActionListener(new java.awt.event.ActionListener()
3893     {
3894       @Override
3895       public void actionPerformed(ActionEvent e)
3896       {
3897         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3898         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3899                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3900         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3901                 viewport.getAlignment()));
3902         alignPanel.paintAlignment(true, false);
3903       }
3904     });
3905   }
3906
3907   /**
3908    * last hash for alignment's annotation array - used to minimise cost of
3909    * rebuild.
3910    */
3911   protected int _annotationScoreVectorHash;
3912
3913   /**
3914    * search the alignment and rebuild the sort by annotation score submenu the
3915    * last alignment annotation vector hash is stored to minimize cost of
3916    * rebuilding in subsequence calls.
3917    *
3918    */
3919   @Override
3920   public void buildSortByAnnotationScoresMenu()
3921   {
3922     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3923     {
3924       return;
3925     }
3926
3927     if (viewport.getAlignment().getAlignmentAnnotation()
3928             .hashCode() != _annotationScoreVectorHash)
3929     {
3930       sortByAnnotScore.removeAll();
3931       // almost certainly a quicker way to do this - but we keep it simple
3932       Hashtable<String, String> scoreSorts = new Hashtable<>();
3933       AlignmentAnnotation aann[];
3934       for (SequenceI sqa : viewport.getAlignment().getSequences())
3935       {
3936         aann = sqa.getAnnotation();
3937         for (int i = 0; aann != null && i < aann.length; i++)
3938         {
3939           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3940           {
3941             scoreSorts.put(aann[i].label, aann[i].label);
3942           }
3943         }
3944       }
3945       Enumeration<String> labels = scoreSorts.keys();
3946       while (labels.hasMoreElements())
3947       {
3948         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
3949       }
3950       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3951       scoreSorts.clear();
3952
3953       _annotationScoreVectorHash = viewport.getAlignment()
3954               .getAlignmentAnnotation().hashCode();
3955     }
3956   }
3957
3958   /**
3959    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3960    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3961    * call. Listeners are added to remove the menu item when the treePanel is
3962    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3963    * modified.
3964    */
3965   @Override
3966   public void buildTreeSortMenu()
3967   {
3968     sortByTreeMenu.removeAll();
3969
3970     List<Component> comps = PaintRefresher.components
3971             .get(viewport.getSequenceSetId());
3972     List<TreePanel> treePanels = new ArrayList<>();
3973     for (Component comp : comps)
3974     {
3975       if (comp instanceof TreePanel)
3976       {
3977         treePanels.add((TreePanel) comp);
3978       }
3979     }
3980
3981     if (treePanels.size() < 1)
3982     {
3983       sortByTreeMenu.setVisible(false);
3984       return;
3985     }
3986
3987     sortByTreeMenu.setVisible(true);
3988
3989     for (final TreePanel tp : treePanels)
3990     {
3991       final JMenuItem item = new JMenuItem(tp.getTitle());
3992       item.addActionListener(new java.awt.event.ActionListener()
3993       {
3994         @Override
3995         public void actionPerformed(ActionEvent e)
3996         {
3997           tp.sortByTree_actionPerformed();
3998           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3999
4000         }
4001       });
4002
4003       sortByTreeMenu.add(item);
4004     }
4005   }
4006
4007   public boolean sortBy(AlignmentOrder alorder, String undoname)
4008   {
4009     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4010     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4011     if (undoname != null)
4012     {
4013       addHistoryItem(new OrderCommand(undoname, oldOrder,
4014               viewport.getAlignment()));
4015     }
4016     alignPanel.paintAlignment(true, false);
4017     return true;
4018   }
4019
4020   /**
4021    * Work out whether the whole set of sequences or just the selected set will
4022    * be submitted for multiple alignment.
4023    *
4024    */
4025   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4026   {
4027     // Now, check we have enough sequences
4028     AlignmentView msa = null;
4029
4030     if ((viewport.getSelectionGroup() != null)
4031             && (viewport.getSelectionGroup().getSize() > 1))
4032     {
4033       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4034       // some common interface!
4035       /*
4036        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4037        * SequenceI[sz = seqs.getSize(false)];
4038        *
4039        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4040        * seqs.getSequenceAt(i); }
4041        */
4042       msa = viewport.getAlignmentView(true);
4043     }
4044     else if (viewport.getSelectionGroup() != null
4045             && viewport.getSelectionGroup().getSize() == 1)
4046     {
4047       int option = JvOptionPane.showConfirmDialog(this,
4048               MessageManager.getString("warn.oneseq_msainput_selection"),
4049               MessageManager.getString("label.invalid_selection"),
4050               JvOptionPane.OK_CANCEL_OPTION);
4051       if (option == JvOptionPane.OK_OPTION)
4052       {
4053         msa = viewport.getAlignmentView(false);
4054       }
4055     }
4056     else
4057     {
4058       msa = viewport.getAlignmentView(false);
4059     }
4060     return msa;
4061   }
4062
4063   /**
4064    * Decides what is submitted to a secondary structure prediction service: the
4065    * first sequence in the alignment, or in the current selection, or, if the
4066    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4067    * region or the whole alignment. (where the first sequence in the set is the
4068    * one that the prediction will be for).
4069    */
4070   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4071   {
4072     AlignmentView seqs = null;
4073
4074     if ((viewport.getSelectionGroup() != null)
4075             && (viewport.getSelectionGroup().getSize() > 0))
4076     {
4077       seqs = viewport.getAlignmentView(true);
4078     }
4079     else
4080     {
4081       seqs = viewport.getAlignmentView(false);
4082     }
4083     // limit sequences - JBPNote in future - could spawn multiple prediction
4084     // jobs
4085     // TODO: viewport.getAlignment().isAligned is a global state - the local
4086     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4087     if (!viewport.getAlignment().isAligned(false))
4088     {
4089       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4090       // TODO: if seqs.getSequences().length>1 then should really have warned
4091       // user!
4092
4093     }
4094     return seqs;
4095   }
4096
4097   /**
4098    * DOCUMENT ME!
4099    *
4100    * @param e
4101    *          DOCUMENT ME!
4102    */
4103   @Override
4104   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4105   {
4106     // Pick the tree file
4107     JalviewFileChooser chooser = new JalviewFileChooser(
4108             Cache.getProperty("LAST_DIRECTORY"));
4109     chooser.setFileView(new JalviewFileView());
4110     chooser.setDialogTitle(
4111             MessageManager.getString("label.select_newick_like_tree_file"));
4112     chooser.setToolTipText(
4113             MessageManager.getString("label.load_tree_file"));
4114
4115     chooser.setResponseHandler(0, () -> {
4116       String filePath = chooser.getSelectedFile().getPath();
4117       Cache.setProperty("LAST_DIRECTORY", filePath);
4118       NewickFile fin = null;
4119       try
4120       {
4121         fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4122                 DataSourceType.FILE));
4123         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4124       } catch (Exception ex)
4125       {
4126         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4127                 MessageManager.getString("label.problem_reading_tree_file"),
4128                 JvOptionPane.WARNING_MESSAGE);
4129         ex.printStackTrace();
4130       }
4131       if (fin != null && fin.hasWarningMessage())
4132       {
4133         JvOptionPane.showMessageDialog(Desktop.desktop,
4134                 fin.getWarningMessage(),
4135                 MessageManager
4136                         .getString("label.possible_problem_with_tree_file"),
4137                 JvOptionPane.WARNING_MESSAGE);
4138       }
4139       return null;
4140     });
4141     chooser.showOpenDialog(this);
4142   }
4143
4144   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4145   {
4146     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4147   }
4148
4149   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4150           int h, int x, int y)
4151   {
4152     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4153   }
4154
4155   /**
4156    * Add a treeviewer for the tree extracted from a Newick file object to the
4157    * current alignment view
4158    *
4159    * @param nf
4160    *          the tree
4161    * @param title
4162    *          tree viewer title
4163    * @param input
4164    *          Associated alignment input data (or null)
4165    * @param w
4166    *          width
4167    * @param h
4168    *          height
4169    * @param x
4170    *          position
4171    * @param y
4172    *          position
4173    * @return TreePanel handle
4174    */
4175   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4176           AlignmentView input, int w, int h, int x, int y)
4177   {
4178     TreePanel tp = null;
4179
4180     try
4181     {
4182       nf.parse();
4183
4184       if (nf.getTree() != null)
4185       {
4186         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4187
4188         tp.setSize(w, h);
4189
4190         if (x > 0 && y > 0)
4191         {
4192           tp.setLocation(x, y);
4193         }
4194
4195         Desktop.addInternalFrame(tp, treeTitle, w, h);
4196       }
4197     } catch (Exception ex)
4198     {
4199       ex.printStackTrace();
4200     }
4201
4202     return tp;
4203   }
4204
4205   public void showContactMapTree(AlignmentAnnotation aa,
4206           ContactMatrixI cm)
4207   {
4208     int x = 4, y = 5;
4209     int w = 400, h = 500;
4210
4211     try
4212     {
4213       NewickFile fin = new NewickFile(
4214               new FileParse(cm.getNewick(), DataSourceType.PASTE));
4215       String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree"
4216               + aa.sequenceRef != null
4217                       ? (" for " + aa.sequenceRef.getDisplayId(false))
4218                       : "";
4219
4220       showColumnWiseTree(fin, aa, title, w, h, x, y);
4221     } catch (Throwable xx)
4222     {
4223       Console.error("Unexpected exception showing tree for contact matrix",
4224               xx);
4225     }
4226   }
4227
4228   public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
4229           String treeTitle, int w, int h, int x, int y)
4230   {
4231     try
4232     {
4233       nf.parse();
4234       if (nf.getTree() == null)
4235       {
4236         return null;
4237       }
4238       TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
4239
4240       tp.setSize(w, h);
4241
4242       if (x > 0 && y > 0)
4243       {
4244         tp.setLocation(x, y);
4245       }
4246
4247       Desktop.addInternalFrame(tp, title, w, h);
4248       return tp;
4249     } catch (Throwable xx)
4250     {
4251       Console.error("Unexpected exception showing tree for contact matrix",
4252               xx);
4253     }
4254     return null;
4255   }
4256
4257   private boolean buildingMenu = false;
4258
4259   /**
4260    * Generates menu items and listener event actions for web service clients
4261    *
4262    */
4263   public void BuildWebServiceMenu()
4264   {
4265     while (buildingMenu)
4266     {
4267       try
4268       {
4269         System.err.println("Waiting for building menu to finish.");
4270         Thread.sleep(10);
4271       } catch (Exception e)
4272       {
4273       }
4274     }
4275     final AlignFrame me = this;
4276     buildingMenu = true;
4277     new Thread(new Runnable()
4278     {
4279       @Override
4280       public void run()
4281       {
4282         final List<JMenuItem> legacyItems = new ArrayList<>();
4283         try
4284         {
4285           // System.err.println("Building ws menu again "
4286           // + Thread.currentThread());
4287           // TODO: add support for context dependent disabling of services based
4288           // on
4289           // alignment and current selection
4290           // TODO: add additional serviceHandle parameter to specify abstract
4291           // handler
4292           // class independently of AbstractName
4293           // TODO: add in rediscovery GUI function to restart discoverer
4294           // TODO: group services by location as well as function and/or
4295           // introduce
4296           // object broker mechanism.
4297           final Vector<JMenu> wsmenu = new Vector<>();
4298           final IProgressIndicator af = me;
4299
4300           /*
4301            * do not i18n these strings - they are hard-coded in class
4302            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4303            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4304            */
4305           final JMenu msawsmenu = new JMenu("Alignment");
4306           final JMenu secstrmenu = new JMenu(
4307                   "Secondary Structure Prediction");
4308           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4309           final JMenu analymenu = new JMenu("Analysis");
4310           final JMenu dismenu = new JMenu("Protein Disorder");
4311           // JAL-940 - only show secondary structure prediction services from
4312           // the legacy server
4313           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4314               // &&
4315           Discoverer.services != null && (Discoverer.services.size() > 0))
4316           {
4317             // TODO: refactor to allow list of AbstractName/Handler bindings to
4318             // be
4319             // stored or retrieved from elsewhere
4320             // No MSAWS used any more:
4321             // Vector msaws = null; // (Vector)
4322             // Discoverer.services.get("MsaWS");
4323             Vector<ServiceHandle> secstrpr = Discoverer.services
4324                     .get("SecStrPred");
4325             if (secstrpr != null)
4326             {
4327               // Add any secondary structure prediction services
4328               for (int i = 0, j = secstrpr.size(); i < j; i++)
4329               {
4330                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4331                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4332                         .getServiceClient(sh);
4333                 int p = secstrmenu.getItemCount();
4334                 impl.attachWSMenuEntry(secstrmenu, me);
4335                 int q = secstrmenu.getItemCount();
4336                 for (int litm = p; litm < q; litm++)
4337                 {
4338                   legacyItems.add(secstrmenu.getItem(litm));
4339                 }
4340               }
4341             }
4342           }
4343
4344           // Add all submenus in the order they should appear on the web
4345           // services menu
4346           wsmenu.add(msawsmenu);
4347           wsmenu.add(secstrmenu);
4348           wsmenu.add(dismenu);
4349           wsmenu.add(analymenu);
4350           // No search services yet
4351           // wsmenu.add(seqsrchmenu);
4352
4353           javax.swing.SwingUtilities.invokeLater(new Runnable()
4354           {
4355             @Override
4356             public void run()
4357             {
4358               try
4359               {
4360                 webService.removeAll();
4361                 // first, add discovered services onto the webservices menu
4362                 if (wsmenu.size() > 0)
4363                 {
4364                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4365                   {
4366                     webService.add(wsmenu.get(i));
4367                   }
4368                 }
4369                 else
4370                 {
4371                   webService.add(me.webServiceNoServices);
4372                 }
4373                 // TODO: move into separate menu builder class.
4374                 {
4375                   // logic for 2.11.1.4 is
4376                   // always look to see if there is a discover. if there isn't
4377                   // we can't show any Jws2 services
4378                   // if there are services available, show them - regardless of
4379                   // the 'show JWS2 preference'
4380                   // if the discoverer is running then say so
4381                   // otherwise offer to trigger discovery if 'show JWS2' is not
4382                   // enabled
4383                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4384                   if (jws2servs != null)
4385                   {
4386                     if (jws2servs.hasServices())
4387                     {
4388                       jws2servs.attachWSMenuEntry(webService, me);
4389                       for (Jws2Instance sv : jws2servs.getServices())
4390                       {
4391                         if (sv.description.toLowerCase(Locale.ROOT)
4392                                 .contains("jpred"))
4393                         {
4394                           for (JMenuItem jmi : legacyItems)
4395                           {
4396                             jmi.setVisible(false);
4397                           }
4398                         }
4399                       }
4400                     }
4401
4402                     if (jws2servs.isRunning())
4403                     {
4404                       JMenuItem tm = new JMenuItem(
4405                               "Still discovering JABA Services");
4406                       tm.setEnabled(false);
4407                       webService.add(tm);
4408                     }
4409                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4410                     {
4411                       JMenuItem enableJws2 = new JMenuItem(
4412                               "Discover Web Services");
4413                       enableJws2.setToolTipText(
4414                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4415                       enableJws2.setEnabled(true);
4416                       enableJws2.addActionListener(new ActionListener()
4417                       {
4418
4419                         @Override
4420                         public void actionPerformed(ActionEvent e)
4421                         {
4422                           // start service discoverer, but ignore preference
4423                           Desktop.instance.startServiceDiscovery(false,
4424                                   true);
4425                         }
4426                       });
4427                       webService.add(enableJws2);
4428                     }
4429                   }
4430                 }
4431                 build_urlServiceMenu(me.webService);
4432                 build_fetchdbmenu(webService);
4433                 for (JMenu item : wsmenu)
4434                 {
4435                   if (item.getItemCount() == 0)
4436                   {
4437                     item.setEnabled(false);
4438                   }
4439                   else
4440                   {
4441                     item.setEnabled(true);
4442                   }
4443                 }
4444               } catch (Exception e)
4445               {
4446                 Console.debug(
4447                         "Exception during web service menu building process.",
4448                         e);
4449               }
4450             }
4451           });
4452         } catch (Exception e)
4453         {
4454         }
4455         buildingMenu = false;
4456       }
4457     }).start();
4458
4459   }
4460
4461   /**
4462    * construct any groupURL type service menu entries.
4463    *
4464    * @param webService
4465    */
4466   protected void build_urlServiceMenu(JMenu webService)
4467   {
4468     // TODO: remove this code when 2.7 is released
4469     // DEBUG - alignmentView
4470     /*
4471      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4472      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4473      *
4474      * @Override public void actionPerformed(ActionEvent e) {
4475      * jalview.datamodel.AlignmentView
4476      * .testSelectionViews(af.viewport.getAlignment(),
4477      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4478      *
4479      * }); webService.add(testAlView);
4480      */
4481     // TODO: refactor to RestClient discoverer and merge menu entries for
4482     // rest-style services with other types of analysis/calculation service
4483     // SHmmr test client - still being implemented.
4484     // DEBUG - alignmentView
4485
4486     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4487             .getRestClients())
4488     {
4489       client.attachWSMenuEntry(
4490               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4491               this);
4492     }
4493   }
4494
4495   /**
4496    * Searches the alignment sequences for xRefs and builds the Show
4497    * Cross-References menu (formerly called Show Products), with database
4498    * sources for which cross-references are found (protein sources for a
4499    * nucleotide alignment and vice versa)
4500    *
4501    * @return true if Show Cross-references menu should be enabled
4502    */
4503   public boolean canShowProducts()
4504   {
4505     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4506     AlignmentI dataset = viewport.getAlignment().getDataset();
4507
4508     showProducts.removeAll();
4509     final boolean dna = viewport.getAlignment().isNucleotide();
4510
4511     if (seqs == null || seqs.length == 0)
4512     {
4513       // nothing to see here.
4514       return false;
4515     }
4516
4517     boolean showp = false;
4518     try
4519     {
4520       List<String> ptypes = new CrossRef(seqs, dataset)
4521               .findXrefSourcesForSequences(dna);
4522
4523       for (final String source : ptypes)
4524       {
4525         showp = true;
4526         final AlignFrame af = this;
4527         JMenuItem xtype = new JMenuItem(source);
4528         xtype.addActionListener(new ActionListener()
4529         {
4530           @Override
4531           public void actionPerformed(ActionEvent e)
4532           {
4533             showProductsFor(af.viewport.getSequenceSelection(), dna,
4534                     source);
4535           }
4536         });
4537         showProducts.add(xtype);
4538       }
4539       showProducts.setVisible(showp);
4540       showProducts.setEnabled(showp);
4541     } catch (Exception e)
4542     {
4543       Console.warn(
4544               "canShowProducts threw an exception - please report to help@jalview.org",
4545               e);
4546       return false;
4547     }
4548     return showp;
4549   }
4550
4551   /**
4552    * Finds and displays cross-references for the selected sequences (protein
4553    * products for nucleotide sequences, dna coding sequences for peptides).
4554    *
4555    * @param sel
4556    *          the sequences to show cross-references for
4557    * @param dna
4558    *          true if from a nucleotide alignment (so showing proteins)
4559    * @param source
4560    *          the database to show cross-references for
4561    */
4562   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4563           final String source)
4564   {
4565     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4566             .start();
4567   }
4568
4569   /**
4570    * Construct and display a new frame containing the translation of this
4571    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4572    */
4573   @Override
4574   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4575   {
4576     AlignmentI al = null;
4577     try
4578     {
4579       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4580
4581       al = dna.translateCdna(codeTable);
4582     } catch (Exception ex)
4583     {
4584       Console.error("Exception during translation. Please report this !",
4585               ex);
4586       final String msg = MessageManager.getString(
4587               "label.error_when_translating_sequences_submit_bug_report");
4588       final String errorTitle = MessageManager
4589               .getString("label.implementation_error")
4590               + MessageManager.getString("label.translation_failed");
4591       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4592               JvOptionPane.ERROR_MESSAGE);
4593       return;
4594     }
4595     if (al == null || al.getHeight() == 0)
4596     {
4597       final String msg = MessageManager.getString(
4598               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4599       final String errorTitle = MessageManager
4600               .getString("label.translation_failed");
4601       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4602               JvOptionPane.WARNING_MESSAGE);
4603     }
4604     else
4605     {
4606       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4607       af.setFileFormat(this.currentFileFormat);
4608       final String newTitle = MessageManager
4609               .formatMessage("label.translation_of_params", new Object[]
4610               { this.getTitle(), codeTable.getId() });
4611       af.setTitle(newTitle);
4612       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4613       {
4614         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4615         viewport.openSplitFrame(af, new Alignment(seqs));
4616       }
4617       else
4618       {
4619         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4620                 DEFAULT_HEIGHT);
4621       }
4622     }
4623   }
4624
4625   /**
4626    * Set the file format
4627    *
4628    * @param format
4629    */
4630   public void setFileFormat(FileFormatI format)
4631   {
4632     this.currentFileFormat = format;
4633   }
4634
4635   /**
4636    * Try to load a features file onto the alignment.
4637    *
4638    * @param file
4639    *          contents or path to retrieve file or a File object
4640    * @param sourceType
4641    *          access mode of file (see jalview.io.AlignFile)
4642    * @return true if features file was parsed correctly.
4643    */
4644   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4645   {
4646     // BH 2018
4647     return avc.parseFeaturesFile(file, sourceType,
4648             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4649
4650   }
4651
4652   @Override
4653   public void refreshFeatureUI(boolean enableIfNecessary)
4654   {
4655     // note - currently this is only still here rather than in the controller
4656     // because of the featureSettings hard reference that is yet to be
4657     // abstracted
4658     if (enableIfNecessary)
4659     {
4660       viewport.setShowSequenceFeatures(true);
4661       showSeqFeatures.setSelected(true);
4662     }
4663
4664   }
4665
4666   @Override
4667   public void dragEnter(DropTargetDragEvent evt)
4668   {
4669   }
4670
4671   @Override
4672   public void dragExit(DropTargetEvent evt)
4673   {
4674   }
4675
4676   @Override
4677   public void dragOver(DropTargetDragEvent evt)
4678   {
4679   }
4680
4681   @Override
4682   public void dropActionChanged(DropTargetDragEvent evt)
4683   {
4684   }
4685
4686   @Override
4687   public void drop(DropTargetDropEvent evt)
4688   {
4689     // JAL-1552 - acceptDrop required before getTransferable call for
4690     // Java's Transferable for native dnd
4691     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4692     Transferable t = evt.getTransferable();
4693
4694     final AlignFrame thisaf = this;
4695     final List<Object> files = new ArrayList<>();
4696     List<DataSourceType> protocols = new ArrayList<>();
4697
4698     try
4699     {
4700       Desktop.transferFromDropTarget(files, protocols, evt, t);
4701     } catch (Exception e)
4702     {
4703       e.printStackTrace();
4704     }
4705     if (files != null)
4706     {
4707       new Thread(new Runnable()
4708       {
4709         @Override
4710         public void run()
4711         {
4712           try
4713           {
4714             // check to see if any of these files have names matching sequences
4715             // in
4716             // the alignment
4717             SequenceIdMatcher idm = new SequenceIdMatcher(
4718                     viewport.getAlignment().getSequencesArray());
4719             /**
4720              * Object[] { String,SequenceI}
4721              */
4722             ArrayList<Object[]> filesmatched = new ArrayList<>();
4723             ArrayList<Object> filesnotmatched = new ArrayList<>();
4724             for (int i = 0; i < files.size(); i++)
4725             {
4726               // BH 2018
4727               Object file = files.get(i);
4728               String fileName = file.toString();
4729               String pdbfn = "";
4730               DataSourceType protocol = (file instanceof File
4731                       ? DataSourceType.FILE
4732                       : FormatAdapter.checkProtocol(fileName));
4733               if (protocol == DataSourceType.FILE)
4734               {
4735                 File fl;
4736                 if (file instanceof File)
4737                 {
4738                   fl = (File) file;
4739                   Platform.cacheFileData(fl);
4740                 }
4741                 else
4742                 {
4743                   fl = new File(fileName);
4744                 }
4745                 pdbfn = fl.getName();
4746               }
4747               else if (protocol == DataSourceType.URL)
4748               {
4749                 URL url = new URL(fileName);
4750                 pdbfn = url.getFile();
4751               }
4752               if (pdbfn.length() > 0)
4753               {
4754                 // attempt to find a match in the alignment
4755                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4756                 int l = 0, c = pdbfn.indexOf(".");
4757                 while (mtch == null && c != -1)
4758                 {
4759                   do
4760                   {
4761                     l = c;
4762                   } while ((c = pdbfn.indexOf(".", l)) > l);
4763                   if (l > -1)
4764                   {
4765                     pdbfn = pdbfn.substring(0, l);
4766                   }
4767                   mtch = idm.findAllIdMatches(pdbfn);
4768                 }
4769                 if (mtch != null)
4770                 {
4771                   FileFormatI type;
4772                   try
4773                   {
4774                     type = new IdentifyFile().identify(file, protocol);
4775                   } catch (Exception ex)
4776                   {
4777                     type = null;
4778                   }
4779                   if (type != null && type.isStructureFile())
4780                   {
4781                     filesmatched.add(new Object[] { file, protocol, mtch });
4782                     continue;
4783                   }
4784                 }
4785                 // File wasn't named like one of the sequences or wasn't a PDB
4786                 // file.
4787                 filesnotmatched.add(file);
4788               }
4789             }
4790             int assocfiles = 0;
4791             if (filesmatched.size() > 0)
4792             {
4793               boolean autoAssociate = Cache
4794                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4795               if (!autoAssociate)
4796               {
4797                 String msg = MessageManager.formatMessage(
4798                         "label.automatically_associate_structure_files_with_sequences_same_name",
4799                         new Object[]
4800                         { Integer.valueOf(filesmatched.size())
4801                                 .toString() });
4802                 String ttl = MessageManager.getString(
4803                         "label.automatically_associate_structure_files_by_name");
4804                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4805                         ttl, JvOptionPane.YES_NO_OPTION);
4806                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4807               }
4808               if (autoAssociate)
4809               {
4810                 for (Object[] fm : filesmatched)
4811                 {
4812                   // try and associate
4813                   // TODO: may want to set a standard ID naming formalism for
4814                   // associating PDB files which have no IDs.
4815                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4816                   {
4817                     PDBEntry pe = new AssociatePdbFileWithSeq()
4818                             .associatePdbWithSeq(fm[0].toString(),
4819                                     (DataSourceType) fm[1], toassoc, false,
4820                                     Desktop.instance);
4821                     if (pe != null)
4822                     {
4823                       System.err.println("Associated file : "
4824                               + (fm[0].toString()) + " with "
4825                               + toassoc.getDisplayId(true));
4826                       assocfiles++;
4827                     }
4828                   }
4829                   // TODO: do we need to update overview ? only if features are
4830                   // shown I guess
4831                   alignPanel.paintAlignment(true, false);
4832                 }
4833               }
4834               else
4835               {
4836                 /*
4837                  * add declined structures as sequences
4838                  */
4839                 for (Object[] o : filesmatched)
4840                 {
4841                   filesnotmatched.add(o[0]);
4842                 }
4843               }
4844             }
4845             if (filesnotmatched.size() > 0)
4846             {
4847               if (assocfiles > 0 && (Cache.getDefault(
4848                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4849                       || JvOptionPane.showConfirmDialog(thisaf,
4850                               "<html>" + MessageManager.formatMessage(
4851                                       "label.ignore_unmatched_dropped_files_info",
4852                                       new Object[]
4853                                       { Integer.valueOf(
4854                                               filesnotmatched.size())
4855                                               .toString() })
4856                                       + "</html>",
4857                               MessageManager.getString(
4858                                       "label.ignore_unmatched_dropped_files"),
4859                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4860               {
4861                 return;
4862               }
4863               for (Object fn : filesnotmatched)
4864               {
4865                 loadJalviewDataFile(fn, null, null, null);
4866               }
4867
4868             }
4869           } catch (Exception ex)
4870           {
4871             ex.printStackTrace();
4872           }
4873         }
4874       }).start();
4875     }
4876   }
4877
4878   /**
4879    * Attempt to load a "dropped" file or URL string, by testing in turn for
4880    * <ul>
4881    * <li>an Annotation file</li>
4882    * <li>a JNet file</li>
4883    * <li>a features file</li>
4884    * <li>else try to interpret as an alignment file</li>
4885    * </ul>
4886    *
4887    * @param file
4888    *          either a filename or a URL string.
4889    */
4890   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4891           FileFormatI format, SequenceI assocSeq)
4892   {
4893     // BH 2018 was String file
4894     try
4895     {
4896       if (sourceType == null)
4897       {
4898         sourceType = FormatAdapter.checkProtocol(file);
4899       }
4900       // if the file isn't identified, or not positively identified as some
4901       // other filetype (PFAM is default unidentified alignment file type) then
4902       // try to parse as annotation.
4903       boolean isAnnotation = (format == null
4904               || FileFormat.Pfam.equals(format))
4905                       ? new AnnotationFile().annotateAlignmentView(viewport,
4906                               file, sourceType)
4907                       : false;
4908
4909       if (!isAnnotation)
4910       {
4911         // first see if its a T-COFFEE score file
4912         TCoffeeScoreFile tcf = null;
4913         try
4914         {
4915           tcf = new TCoffeeScoreFile(file, sourceType);
4916           if (tcf.isValid())
4917           {
4918             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4919             {
4920               buildColourMenu();
4921               changeColour(
4922                       new TCoffeeColourScheme(viewport.getAlignment()));
4923               isAnnotation = true;
4924               setStatus(MessageManager.getString(
4925                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4926             }
4927             else
4928             {
4929               // some problem - if no warning its probable that the ID matching
4930               // process didn't work
4931               JvOptionPane.showMessageDialog(Desktop.desktop,
4932                       tcf.getWarningMessage() == null
4933                               ? MessageManager.getString(
4934                                       "label.check_file_matches_sequence_ids_alignment")
4935                               : tcf.getWarningMessage(),
4936                       MessageManager.getString(
4937                               "label.problem_reading_tcoffee_score_file"),
4938                       JvOptionPane.WARNING_MESSAGE);
4939             }
4940           }
4941           else
4942           {
4943             tcf = null;
4944           }
4945         } catch (Exception x)
4946         {
4947           Console.debug(
4948                   "Exception when processing data source as T-COFFEE score file",
4949                   x);
4950           tcf = null;
4951         }
4952         if (tcf == null)
4953         {
4954           // try to see if its a JNet 'concise' style annotation file *before*
4955           // we
4956           // try to parse it as a features file
4957           if (format == null)
4958           {
4959             format = new IdentifyFile().identify(file, sourceType);
4960           }
4961           if (FileFormat.ScoreMatrix == format)
4962           {
4963             ScoreMatrixFile sm = new ScoreMatrixFile(
4964                     new FileParse(file, sourceType));
4965             sm.parse();
4966             // todo: i18n this message
4967             setStatus(MessageManager.formatMessage(
4968                     "label.successfully_loaded_matrix",
4969                     sm.getMatrixName()));
4970           }
4971           else if (FileFormat.Jnet.equals(format))
4972           {
4973             JPredFile predictions = new JPredFile(file, sourceType);
4974             new JnetAnnotationMaker();
4975             JnetAnnotationMaker.add_annotation(predictions,
4976                     viewport.getAlignment(), 0, false);
4977             viewport.getAlignment().setupJPredAlignment();
4978             isAnnotation = true;
4979           }
4980           // else if (IdentifyFile.FeaturesFile.equals(format))
4981           else if (FileFormat.Features.equals(format))
4982           {
4983             if (parseFeaturesFile(file, sourceType))
4984             {
4985               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4986               if (splitFrame != null)
4987               {
4988                 splitFrame.repaint();
4989               }
4990               else
4991               {
4992                 alignPanel.paintAlignment(true, true);
4993               }
4994             }
4995           }
4996           else
4997           {
4998             new FileLoader().LoadFile(viewport, file, sourceType, format);
4999           }
5000         }
5001       }
5002       if (isAnnotation)
5003       {
5004
5005         alignPanel.adjustAnnotationHeight();
5006         viewport.updateSequenceIdColours();
5007         buildSortByAnnotationScoresMenu();
5008         alignPanel.paintAlignment(true, true);
5009       }
5010     } catch (Exception ex)
5011     {
5012       ex.printStackTrace();
5013     } catch (OutOfMemoryError oom)
5014     {
5015       try
5016       {
5017         System.gc();
5018       } catch (Exception x)
5019       {
5020       }
5021       new OOMWarning(
5022               "loading data "
5023                       + (sourceType != null
5024                               ? (sourceType == DataSourceType.PASTE
5025                                       ? "from clipboard."
5026                                       : "using " + sourceType + " from "
5027                                               + file)
5028                               : ".")
5029                       + (format != null
5030                               ? "(parsing as '" + format + "' file)"
5031                               : ""),
5032               oom, Desktop.desktop);
5033     }
5034   }
5035
5036   /**
5037    * Method invoked by the ChangeListener on the tabbed pane, in other words
5038    * when a different tabbed pane is selected by the user or programmatically.
5039    */
5040   @Override
5041   public void tabSelectionChanged(int index)
5042   {
5043     if (index > -1)
5044     {
5045       /*
5046        * update current Overview window title (if there is one)
5047        * to add view name "Original" if necessary
5048        */
5049       alignPanel.setOverviewTitle(this);
5050
5051       /*
5052        * switch panels and set Overview title (if there is one
5053        * because it was opened automatically)
5054        */
5055       alignPanel = alignPanels.get(index);
5056       alignPanel.setOverviewTitle(this);
5057
5058       viewport = alignPanel.av;
5059       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5060       setMenusFromViewport(viewport);
5061       if (featureSettings != null && featureSettings.isOpen()
5062               && featureSettings.fr.getViewport() != viewport)
5063       {
5064         if (viewport.isShowSequenceFeatures())
5065         {
5066           // refresh the featureSettings to reflect UI change
5067           showFeatureSettingsUI();
5068         }
5069         else
5070         {
5071           // close feature settings for this view.
5072           featureSettings.close();
5073         }
5074       }
5075
5076     }
5077
5078     /*
5079      * 'focus' any colour slider that is open to the selected viewport
5080      */
5081     if (viewport.getConservationSelected())
5082     {
5083       SliderPanel.setConservationSlider(alignPanel,
5084               viewport.getResidueShading(), alignPanel.getViewName());
5085     }
5086     else
5087     {
5088       SliderPanel.hideConservationSlider();
5089     }
5090     if (viewport.getAbovePIDThreshold())
5091     {
5092       SliderPanel.setPIDSliderSource(alignPanel,
5093               viewport.getResidueShading(), alignPanel.getViewName());
5094     }
5095     else
5096     {
5097       SliderPanel.hidePIDSlider();
5098     }
5099
5100     /*
5101      * If there is a frame linked to this one in a SplitPane, switch it to the
5102      * same view tab index. No infinite recursion of calls should happen, since
5103      * tabSelectionChanged() should not get invoked on setting the selected
5104      * index to an unchanged value. Guard against setting an invalid index
5105      * before the new view peer tab has been created.
5106      */
5107     final AlignViewportI peer = viewport.getCodingComplement();
5108     if (peer != null)
5109     {
5110       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5111               .getAlignPanel().alignFrame;
5112       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5113       {
5114         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5115       }
5116     }
5117   }
5118
5119   /**
5120    * On right mouse click on view tab, prompt for and set new view name.
5121    */
5122   @Override
5123   public void tabbedPane_mousePressed(MouseEvent e)
5124   {
5125     if (e.isPopupTrigger())
5126     {
5127       String msg = MessageManager.getString("label.enter_view_name");
5128       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5129       String reply = JvOptionPane.showInputDialog(msg, ttl);
5130
5131       if (reply != null)
5132       {
5133         viewport.setViewName(reply);
5134         // TODO warn if reply is in getExistingViewNames()?
5135         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5136       }
5137     }
5138   }
5139
5140   public AlignViewport getCurrentView()
5141   {
5142     return viewport;
5143   }
5144
5145   /**
5146    * Open the dialog for regex description parsing.
5147    */
5148   @Override
5149   protected void extractScores_actionPerformed(ActionEvent e)
5150   {
5151     ParseProperties pp = new jalview.analysis.ParseProperties(
5152             viewport.getAlignment());
5153     // TODO: verify regex and introduce GUI dialog for version 2.5
5154     // if (pp.getScoresFromDescription("col", "score column ",
5155     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5156     // true)>0)
5157     if (pp.getScoresFromDescription("description column",
5158             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5159     {
5160       buildSortByAnnotationScoresMenu();
5161     }
5162   }
5163
5164   /*
5165    * (non-Javadoc)
5166    *
5167    * @see
5168    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5169    * )
5170    */
5171   @Override
5172   protected void showDbRefs_actionPerformed(ActionEvent e)
5173   {
5174     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5175   }
5176
5177   /*
5178    * (non-Javadoc)
5179    *
5180    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5181    * ActionEvent)
5182    */
5183   @Override
5184   protected void showNpFeats_actionPerformed(ActionEvent e)
5185   {
5186     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5187   }
5188
5189   /**
5190    * find the viewport amongst the tabs in this alignment frame and close that
5191    * tab
5192    *
5193    * @param av
5194    */
5195   public boolean closeView(AlignViewportI av)
5196   {
5197     if (viewport == av)
5198     {
5199       this.closeMenuItem_actionPerformed(false);
5200       return true;
5201     }
5202     Component[] comp = tabbedPane.getComponents();
5203     for (int i = 0; comp != null && i < comp.length; i++)
5204     {
5205       if (comp[i] instanceof AlignmentPanel)
5206       {
5207         if (((AlignmentPanel) comp[i]).av == av)
5208         {
5209           // close the view.
5210           closeView((AlignmentPanel) comp[i]);
5211           return true;
5212         }
5213       }
5214     }
5215     return false;
5216   }
5217
5218   protected void build_fetchdbmenu(JMenu webService)
5219   {
5220     // Temporary hack - DBRef Fetcher always top level ws entry.
5221     // TODO We probably want to store a sequence database checklist in
5222     // preferences and have checkboxes.. rather than individual sources selected
5223     // here
5224     final JMenu rfetch = new JMenu(
5225             MessageManager.getString("action.fetch_db_references"));
5226     rfetch.setToolTipText(MessageManager.getString(
5227             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5228     webService.add(rfetch);
5229
5230     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5231             MessageManager.getString("option.trim_retrieved_seqs"));
5232     trimrs.setToolTipText(
5233             MessageManager.getString("label.trim_retrieved_sequences"));
5234     trimrs.setSelected(
5235             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5236     trimrs.addActionListener(new ActionListener()
5237     {
5238       @Override
5239       public void actionPerformed(ActionEvent e)
5240       {
5241         trimrs.setSelected(trimrs.isSelected());
5242         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5243                 Boolean.valueOf(trimrs.isSelected()).toString());
5244       }
5245     });
5246     rfetch.add(trimrs);
5247     JMenuItem fetchr = new JMenuItem(
5248             MessageManager.getString("label.standard_databases"));
5249     fetchr.setToolTipText(
5250             MessageManager.getString("label.fetch_embl_uniprot"));
5251     fetchr.addActionListener(new ActionListener()
5252     {
5253
5254       @Override
5255       public void actionPerformed(ActionEvent e)
5256       {
5257         new Thread(new Runnable()
5258         {
5259           @Override
5260           public void run()
5261           {
5262             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5263                     .getAlignment().isNucleotide();
5264             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5265                     alignPanel.av.getSequenceSelection(),
5266                     alignPanel.alignFrame, null,
5267                     alignPanel.alignFrame.featureSettings, isNucleotide);
5268             dbRefFetcher.addListener(new FetchFinishedListenerI()
5269             {
5270               @Override
5271               public void finished()
5272               {
5273
5274                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5275                         .getFeatureSettingsModels())
5276                 {
5277
5278                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5279                 }
5280                 AlignFrame.this.setMenusForViewport();
5281               }
5282             });
5283             dbRefFetcher.fetchDBRefs(false);
5284           }
5285         }).start();
5286
5287       }
5288
5289     });
5290     rfetch.add(fetchr);
5291     new Thread(new Runnable()
5292     {
5293       @Override
5294       public void run()
5295       {
5296         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5297                 .getSequenceFetcherSingleton();
5298         javax.swing.SwingUtilities.invokeLater(new Runnable()
5299         {
5300           @Override
5301           public void run()
5302           {
5303             String[] dbclasses = sf.getNonAlignmentSources();
5304             List<DbSourceProxy> otherdb;
5305             JMenu dfetch = new JMenu();
5306             JMenu ifetch = new JMenu();
5307             JMenuItem fetchr = null;
5308             int comp = 0, icomp = 0, mcomp = 15;
5309             String mname = null;
5310             int dbi = 0;
5311             for (String dbclass : dbclasses)
5312             {
5313               otherdb = sf.getSourceProxy(dbclass);
5314               // add a single entry for this class, or submenu allowing 'fetch
5315               // all' or pick one
5316               if (otherdb == null || otherdb.size() < 1)
5317               {
5318                 continue;
5319               }
5320               if (mname == null)
5321               {
5322                 mname = "From " + dbclass;
5323               }
5324               if (otherdb.size() == 1)
5325               {
5326                 final DbSourceProxy[] dassource = otherdb
5327                         .toArray(new DbSourceProxy[0]);
5328                 DbSourceProxy src = otherdb.get(0);
5329                 fetchr = new JMenuItem(src.getDbSource());
5330                 fetchr.addActionListener(new ActionListener()
5331                 {
5332
5333                   @Override
5334                   public void actionPerformed(ActionEvent e)
5335                   {
5336                     new Thread(new Runnable()
5337                     {
5338
5339                       @Override
5340                       public void run()
5341                       {
5342                         boolean isNucleotide = alignPanel.alignFrame
5343                                 .getViewport().getAlignment()
5344                                 .isNucleotide();
5345                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5346                                 alignPanel.av.getSequenceSelection(),
5347                                 alignPanel.alignFrame, dassource,
5348                                 alignPanel.alignFrame.featureSettings,
5349                                 isNucleotide);
5350                         dbRefFetcher
5351                                 .addListener(new FetchFinishedListenerI()
5352                                 {
5353                                   @Override
5354                                   public void finished()
5355                                   {
5356                                     FeatureSettingsModelI srcSettings = dassource[0]
5357                                             .getFeatureColourScheme();
5358                                     alignPanel.av.mergeFeaturesStyle(
5359                                             srcSettings);
5360                                     AlignFrame.this.setMenusForViewport();
5361                                   }
5362                                 });
5363                         dbRefFetcher.fetchDBRefs(false);
5364                       }
5365                     }).start();
5366                   }
5367
5368                 });
5369                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5370                         MessageManager.formatMessage(
5371                                 "label.fetch_retrieve_from", new Object[]
5372                                 { src.getDbName() })));
5373                 dfetch.add(fetchr);
5374                 comp++;
5375               }
5376               else
5377               {
5378                 final DbSourceProxy[] dassource = otherdb
5379                         .toArray(new DbSourceProxy[0]);
5380                 // fetch all entry
5381                 DbSourceProxy src = otherdb.get(0);
5382                 fetchr = new JMenuItem(MessageManager
5383                         .formatMessage("label.fetch_all_param", new Object[]
5384                         { src.getDbSource() }));
5385                 fetchr.addActionListener(new ActionListener()
5386                 {
5387                   @Override
5388                   public void actionPerformed(ActionEvent e)
5389                   {
5390                     new Thread(new Runnable()
5391                     {
5392
5393                       @Override
5394                       public void run()
5395                       {
5396                         boolean isNucleotide = alignPanel.alignFrame
5397                                 .getViewport().getAlignment()
5398                                 .isNucleotide();
5399                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5400                                 alignPanel.av.getSequenceSelection(),
5401                                 alignPanel.alignFrame, dassource,
5402                                 alignPanel.alignFrame.featureSettings,
5403                                 isNucleotide);
5404                         dbRefFetcher
5405                                 .addListener(new FetchFinishedListenerI()
5406                                 {
5407                                   @Override
5408                                   public void finished()
5409                                   {
5410                                     AlignFrame.this.setMenusForViewport();
5411                                   }
5412                                 });
5413                         dbRefFetcher.fetchDBRefs(false);
5414                       }
5415                     }).start();
5416                   }
5417                 });
5418
5419                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5420                         MessageManager.formatMessage(
5421                                 "label.fetch_retrieve_from_all_sources",
5422                                 new Object[]
5423                                 { Integer.valueOf(otherdb.size())
5424                                         .toString(),
5425                                     src.getDbSource(), src.getDbName() })));
5426                 dfetch.add(fetchr);
5427                 comp++;
5428                 // and then build the rest of the individual menus
5429                 ifetch = new JMenu(MessageManager.formatMessage(
5430                         "label.source_from_db_source", new Object[]
5431                         { src.getDbSource() }));
5432                 icomp = 0;
5433                 String imname = null;
5434                 int i = 0;
5435                 for (DbSourceProxy sproxy : otherdb)
5436                 {
5437                   String dbname = sproxy.getDbName();
5438                   String sname = dbname.length() > 5
5439                           ? dbname.substring(0, 5) + "..."
5440                           : dbname;
5441                   String msname = dbname.length() > 10
5442                           ? dbname.substring(0, 10) + "..."
5443                           : dbname;
5444                   if (imname == null)
5445                   {
5446                     imname = MessageManager
5447                             .formatMessage("label.from_msname", new Object[]
5448                             { sname });
5449                   }
5450                   fetchr = new JMenuItem(msname);
5451                   final DbSourceProxy[] dassrc = { sproxy };
5452                   fetchr.addActionListener(new ActionListener()
5453                   {
5454
5455                     @Override
5456                     public void actionPerformed(ActionEvent e)
5457                     {
5458                       new Thread(new Runnable()
5459                       {
5460
5461                         @Override
5462                         public void run()
5463                         {
5464                           boolean isNucleotide = alignPanel.alignFrame
5465                                   .getViewport().getAlignment()
5466                                   .isNucleotide();
5467                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5468                                   alignPanel.av.getSequenceSelection(),
5469                                   alignPanel.alignFrame, dassrc,
5470                                   alignPanel.alignFrame.featureSettings,
5471                                   isNucleotide);
5472                           dbRefFetcher
5473                                   .addListener(new FetchFinishedListenerI()
5474                                   {
5475                                     @Override
5476                                     public void finished()
5477                                     {
5478                                       AlignFrame.this.setMenusForViewport();
5479                                     }
5480                                   });
5481                           dbRefFetcher.fetchDBRefs(false);
5482                         }
5483                       }).start();
5484                     }
5485
5486                   });
5487                   fetchr.setToolTipText(
5488                           "<html>" + MessageManager.formatMessage(
5489                                   "label.fetch_retrieve_from", new Object[]
5490                                   { dbname }));
5491                   ifetch.add(fetchr);
5492                   ++i;
5493                   if (++icomp >= mcomp || i == (otherdb.size()))
5494                   {
5495                     ifetch.setText(MessageManager.formatMessage(
5496                             "label.source_to_target", imname, sname));
5497                     dfetch.add(ifetch);
5498                     ifetch = new JMenu();
5499                     imname = null;
5500                     icomp = 0;
5501                     comp++;
5502                   }
5503                 }
5504               }
5505               ++dbi;
5506               if (comp >= mcomp || dbi >= (dbclasses.length))
5507               {
5508                 dfetch.setText(MessageManager.formatMessage(
5509                         "label.source_to_target", mname, dbclass));
5510                 rfetch.add(dfetch);
5511                 dfetch = new JMenu();
5512                 mname = null;
5513                 comp = 0;
5514               }
5515             }
5516           }
5517         });
5518       }
5519     }).start();
5520
5521   }
5522
5523   /**
5524    * Left justify the whole alignment.
5525    */
5526   @Override
5527   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5528   {
5529     AlignmentI al = viewport.getAlignment();
5530     al.justify(false);
5531     viewport.firePropertyChange("alignment", null, al);
5532   }
5533
5534   /**
5535    * Right justify the whole alignment.
5536    */
5537   @Override
5538   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5539   {
5540     AlignmentI al = viewport.getAlignment();
5541     al.justify(true);
5542     viewport.firePropertyChange("alignment", null, al);
5543   }
5544
5545   @Override
5546   public void setShowSeqFeatures(boolean b)
5547   {
5548     showSeqFeatures.setSelected(b);
5549     viewport.setShowSequenceFeatures(b);
5550   }
5551
5552   /*
5553    * (non-Javadoc)
5554    *
5555    * @see
5556    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5557    * awt.event.ActionEvent)
5558    */
5559   @Override
5560   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5561   {
5562     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5563     alignPanel.paintAlignment(false, false);
5564   }
5565
5566   /*
5567    * (non-Javadoc)
5568    *
5569    * @see
5570    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5571    * .ActionEvent)
5572    */
5573   @Override
5574   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5575   {
5576     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5577     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5578
5579   }
5580
5581   /*
5582    * (non-Javadoc)
5583    *
5584    * @see
5585    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5586    * .event.ActionEvent)
5587    */
5588   @Override
5589   protected void showGroupConservation_actionPerformed(ActionEvent e)
5590   {
5591     viewport.setShowGroupConservation(showGroupConservation.getState());
5592     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5593   }
5594
5595   /*
5596    * (non-Javadoc)
5597    *
5598    * @see
5599    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5600    * .event.ActionEvent)
5601    */
5602   @Override
5603   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5604   {
5605     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5606     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5607   }
5608
5609   /*
5610    * (non-Javadoc)
5611    *
5612    * @see
5613    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5614    * .event.ActionEvent)
5615    */
5616   @Override
5617   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5618   {
5619     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5620     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5621   }
5622
5623   @Override
5624   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5625   {
5626     showSequenceLogo.setState(true);
5627     viewport.setShowSequenceLogo(true);
5628     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5629     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5630   }
5631
5632   @Override
5633   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5634   {
5635     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5636   }
5637
5638   /*
5639    * (non-Javadoc)
5640    *
5641    * @see
5642    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5643    * .event.ActionEvent)
5644    */
5645   @Override
5646   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5647   {
5648     if (avc.makeGroupsFromSelection())
5649     {
5650       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5651       alignPanel.updateAnnotation();
5652       alignPanel.paintAlignment(true,
5653               viewport.needToUpdateStructureViews());
5654     }
5655   }
5656
5657   public void clearAlignmentSeqRep()
5658   {
5659     // TODO refactor alignmentseqrep to controller
5660     if (viewport.getAlignment().hasSeqrep())
5661     {
5662       viewport.getAlignment().setSeqrep(null);
5663       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5664       alignPanel.updateAnnotation();
5665       alignPanel.paintAlignment(true, true);
5666     }
5667   }
5668
5669   @Override
5670   protected void createGroup_actionPerformed(ActionEvent e)
5671   {
5672     if (avc.createGroup())
5673     {
5674       if (applyAutoAnnotationSettings.isSelected())
5675       {
5676         alignPanel.updateAnnotation(true, false);
5677       }
5678       alignPanel.alignmentChanged();
5679     }
5680   }
5681
5682   @Override
5683   protected void unGroup_actionPerformed(ActionEvent e)
5684   {
5685     if (avc.unGroup())
5686     {
5687       alignPanel.alignmentChanged();
5688     }
5689   }
5690
5691   /**
5692    * make the given alignmentPanel the currently selected tab
5693    *
5694    * @param alignmentPanel
5695    */
5696   public void setDisplayedView(AlignmentPanel alignmentPanel)
5697   {
5698     if (!viewport.getSequenceSetId()
5699             .equals(alignmentPanel.av.getSequenceSetId()))
5700     {
5701       throw new Error(MessageManager.getString(
5702               "error.implementation_error_cannot_show_view_alignment_frame"));
5703     }
5704     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5705             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5706     {
5707       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5708     }
5709   }
5710
5711   /**
5712    * Action on selection of menu options to Show or Hide annotations.
5713    *
5714    * @param visible
5715    * @param forSequences
5716    *          update sequence-related annotations
5717    * @param forAlignment
5718    *          update non-sequence-related annotations
5719    */
5720   @Override
5721   public void setAnnotationsVisibility(boolean visible,
5722           boolean forSequences, boolean forAlignment)
5723   {
5724     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5725             .getAlignmentAnnotation();
5726     if (anns == null)
5727     {
5728       return;
5729     }
5730     for (AlignmentAnnotation aa : anns)
5731     {
5732       /*
5733        * don't display non-positional annotations on an alignment
5734        */
5735       if (aa.annotations == null)
5736       {
5737         continue;
5738       }
5739       boolean apply = (aa.sequenceRef == null && forAlignment)
5740               || (aa.sequenceRef != null && forSequences);
5741       if (apply)
5742       {
5743         aa.visible = visible;
5744       }
5745     }
5746     alignPanel.validateAnnotationDimensions(true);
5747     alignPanel.alignmentChanged();
5748   }
5749
5750   /**
5751    * Store selected annotation sort order for the view and repaint.
5752    */
5753   @Override
5754   protected void sortAnnotations_actionPerformed()
5755   {
5756     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5757     this.alignPanel.av
5758             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5759     alignPanel.paintAlignment(false, false);
5760   }
5761
5762   /**
5763    *
5764    * @return alignment panels in this alignment frame
5765    */
5766   public List<? extends AlignmentViewPanel> getAlignPanels()
5767   {
5768     // alignPanels is never null
5769     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5770     return alignPanels;
5771   }
5772
5773   /**
5774    * Open a new alignment window, with the cDNA associated with this (protein)
5775    * alignment, aligned as is the protein.
5776    */
5777   protected void viewAsCdna_actionPerformed()
5778   {
5779     // TODO no longer a menu action - refactor as required
5780     final AlignmentI alignment = getViewport().getAlignment();
5781     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5782     if (mappings == null)
5783     {
5784       return;
5785     }
5786     List<SequenceI> cdnaSeqs = new ArrayList<>();
5787     for (SequenceI aaSeq : alignment.getSequences())
5788     {
5789       for (AlignedCodonFrame acf : mappings)
5790       {
5791         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5792         if (dnaSeq != null)
5793         {
5794           /*
5795            * There is a cDNA mapping for this protein sequence - add to new
5796            * alignment. It will share the same dataset sequence as other mapped
5797            * cDNA (no new mappings need to be created).
5798            */
5799           final Sequence newSeq = new Sequence(dnaSeq);
5800           newSeq.setDatasetSequence(dnaSeq);
5801           cdnaSeqs.add(newSeq);
5802         }
5803       }
5804     }
5805     if (cdnaSeqs.size() == 0)
5806     {
5807       // show a warning dialog no mapped cDNA
5808       return;
5809     }
5810     AlignmentI cdna = new Alignment(
5811             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5812     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5813             AlignFrame.DEFAULT_HEIGHT);
5814     cdna.alignAs(alignment);
5815     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5816             + this.title;
5817     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5818             AlignFrame.DEFAULT_HEIGHT);
5819   }
5820
5821   /**
5822    * Set visibility of dna/protein complement view (available when shown in a
5823    * split frame).
5824    *
5825    * @param show
5826    */
5827   @Override
5828   protected void showComplement_actionPerformed(boolean show)
5829   {
5830     SplitContainerI sf = getSplitViewContainer();
5831     if (sf != null)
5832     {
5833       sf.setComplementVisible(this, show);
5834     }
5835   }
5836
5837   /**
5838    * Generate the reverse (optionally complemented) of the selected sequences,
5839    * and add them to the alignment
5840    */
5841   @Override
5842   protected void showReverse_actionPerformed(boolean complement)
5843   {
5844     AlignmentI al = null;
5845     try
5846     {
5847       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5848       al = dna.reverseCdna(complement);
5849       viewport.addAlignment(al, "");
5850       addHistoryItem(new EditCommand(
5851               MessageManager.getString("label.add_sequences"), Action.PASTE,
5852               al.getSequencesArray(), 0, al.getWidth(),
5853               viewport.getAlignment()));
5854     } catch (Exception ex)
5855     {
5856       System.err.println(ex.getMessage());
5857       return;
5858     }
5859   }
5860
5861   /**
5862    * Try to run a script in the Groovy console, having first ensured that this
5863    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5864    * be targeted at this alignment.
5865    */
5866   @Override
5867   protected void runGroovy_actionPerformed()
5868   {
5869     Jalview.setCurrentAlignFrame(this);
5870     groovy.ui.Console console = Desktop.getGroovyConsole();
5871     if (console != null)
5872     {
5873       try
5874       {
5875         console.runScript();
5876       } catch (Exception ex)
5877       {
5878         System.err.println((ex.toString()));
5879         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5880                 MessageManager.getString("label.couldnt_run_groovy_script"),
5881                 MessageManager.getString("label.groovy_support_failed"),
5882                 JvOptionPane.ERROR_MESSAGE);
5883       }
5884     }
5885     else
5886     {
5887       System.err.println("Can't run Groovy script as console not found");
5888     }
5889   }
5890
5891   /**
5892    * Hides columns containing (or not containing) a specified feature, provided
5893    * that would not leave all columns hidden
5894    *
5895    * @param featureType
5896    * @param columnsContaining
5897    * @return
5898    */
5899   public boolean hideFeatureColumns(String featureType,
5900           boolean columnsContaining)
5901   {
5902     boolean notForHiding = avc.markColumnsContainingFeatures(
5903             columnsContaining, false, false, featureType);
5904     if (notForHiding)
5905     {
5906       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5907               false, featureType))
5908       {
5909         getViewport().hideSelectedColumns();
5910         return true;
5911       }
5912     }
5913     return false;
5914   }
5915
5916   @Override
5917   protected void selectHighlightedColumns_actionPerformed(
5918           ActionEvent actionEvent)
5919   {
5920     // include key modifier check in case user selects from menu
5921     avc.markHighlightedColumns(
5922             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5923             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5924                     | ActionEvent.CTRL_MASK)) != 0);
5925   }
5926
5927   @Override
5928   protected void copyHighlightedColumns_actionPerformed(
5929           ActionEvent actionEvent)
5930   {
5931     avc.copyHighlightedRegionsToClipboard();
5932   }
5933
5934   /**
5935    * Rebuilds the Colour menu, including any user-defined colours which have
5936    * been loaded either on startup or during the session
5937    */
5938   public void buildColourMenu()
5939   {
5940     colourMenu.removeAll();
5941
5942     colourMenu.add(applyToAllGroups);
5943     colourMenu.add(textColour);
5944     colourMenu.addSeparator();
5945
5946     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5947             viewport.getAlignment(), false);
5948
5949     colourMenu.add(annotationColour);
5950     bg.add(annotationColour);
5951     colourMenu.addSeparator();
5952     colourMenu.add(conservationMenuItem);
5953     colourMenu.add(modifyConservation);
5954     colourMenu.add(abovePIDThreshold);
5955     colourMenu.add(modifyPID);
5956
5957     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5958     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5959   }
5960
5961   /**
5962    * Open a dialog (if not already open) that allows the user to select and
5963    * calculate PCA or Tree analysis
5964    */
5965   protected void openTreePcaDialog()
5966   {
5967     if (alignPanel.getCalculationDialog() == null)
5968     {
5969       new CalculationChooser(AlignFrame.this);
5970     }
5971   }
5972
5973   @Override
5974   protected void loadVcf_actionPerformed()
5975   {
5976     JalviewFileChooser chooser = new JalviewFileChooser(
5977             Cache.getProperty("LAST_DIRECTORY"));
5978     chooser.setFileView(new JalviewFileView());
5979     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5980     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5981     final AlignFrame us = this;
5982     chooser.setResponseHandler(0, () -> {
5983       String choice = chooser.getSelectedFile().getPath();
5984       Cache.setProperty("LAST_DIRECTORY", choice);
5985       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5986       new VCFLoader(choice).loadVCF(seqs, us);
5987       return null;
5988     });
5989     chooser.showOpenDialog(null);
5990
5991   }
5992
5993   private Rectangle lastFeatureSettingsBounds = null;
5994
5995   @Override
5996   public void setFeatureSettingsGeometry(Rectangle bounds)
5997   {
5998     lastFeatureSettingsBounds = bounds;
5999   }
6000
6001   @Override
6002   public Rectangle getFeatureSettingsGeometry()
6003   {
6004     return lastFeatureSettingsBounds;
6005   }
6006
6007 }
6008
6009 class PrintThread extends Thread
6010 {
6011   AlignmentPanel ap;
6012
6013   public PrintThread(AlignmentPanel ap)
6014   {
6015     this.ap = ap;
6016   }
6017
6018   static PageFormat pf;
6019
6020   @Override
6021   public void run()
6022   {
6023     PrinterJob printJob = PrinterJob.getPrinterJob();
6024
6025     if (pf != null)
6026     {
6027       printJob.setPrintable(ap, pf);
6028     }
6029     else
6030     {
6031       printJob.setPrintable(ap);
6032     }
6033
6034     if (printJob.printDialog())
6035     {
6036       try
6037       {
6038         printJob.print();
6039       } catch (Exception PrintException)
6040       {
6041         PrintException.printStackTrace();
6042       }
6043     }
6044   }
6045 }