src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenMarkovModel;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.hmmer.HMMAlign;
  67 import jalview.hmmer.HMMBuild;
  68 import jalview.hmmer.HMMERParamStore;
  69 import jalview.hmmer.HMMERPreset;
  70 import jalview.hmmer.HMMSearch;
  71 import jalview.hmmer.HmmerCommand;
  72 import jalview.io.AlignmentProperties;
  73 import jalview.io.AnnotationFile;
  74 import jalview.io.BioJsHTMLOutput;
  75 import jalview.io.DataSourceType;
  76 import jalview.io.FileFormat;
  77 import jalview.io.FileFormatI;
  78 import jalview.io.FileFormats;
  79 import jalview.io.FileLoader;
  80 import jalview.io.FileParse;
  81 import jalview.io.FormatAdapter;
  82 import jalview.io.HtmlSvgOutput;
  83 import jalview.io.IdentifyFile;
  84 import jalview.io.JPredFile;
  85 import jalview.io.JalviewFileChooser;
  86 import jalview.io.JalviewFileView;
  87 import jalview.io.JnetAnnotationMaker;
  88 import jalview.io.NewickFile;
  89 import jalview.io.ScoreMatrixFile;
  90 import jalview.io.TCoffeeScoreFile;
  91 import jalview.io.vcf.VCFLoader;
  92 import jalview.jbgui.GAlignFrame;
  93 import jalview.schemes.ColourSchemeI;
  94 import jalview.schemes.ColourSchemes;
  95 import jalview.schemes.ResidueColourScheme;
  96 import jalview.schemes.TCoffeeColourScheme;
  97 import jalview.util.MessageManager;
  98 import jalview.util.StringUtils;
  99 import jalview.viewmodel.AlignmentViewport;
 100 import jalview.viewmodel.ViewportRanges;
 101 import jalview.ws.DBRefFetcher;
 102 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 103 import jalview.ws.jws1.Discoverer;
 104 import jalview.ws.jws2.Jws2Discoverer;
 105 import jalview.ws.jws2.jabaws2.Jws2Instance;
 106 import jalview.ws.params.ArgumentI;
 107 import jalview.ws.params.ParamDatastoreI;
 108 import jalview.ws.params.WsParamSetI;
 109 import jalview.ws.seqfetcher.DbSourceProxy;
 110
 111 import java.awt.BorderLayout;
 112 import java.awt.Component;
 113 import java.awt.Rectangle;
 114 import java.awt.Toolkit;
 115 import java.awt.datatransfer.Clipboard;
 116 import java.awt.datatransfer.DataFlavor;
 117 import java.awt.datatransfer.StringSelection;
 118 import java.awt.datatransfer.Transferable;
 119 import java.awt.dnd.DnDConstants;
 120 import java.awt.dnd.DropTargetDragEvent;
 121 import java.awt.dnd.DropTargetDropEvent;
 122 import java.awt.dnd.DropTargetEvent;
 123 import java.awt.dnd.DropTargetListener;
 124 import java.awt.event.ActionEvent;
 125 import java.awt.event.ActionListener;
 126 import java.awt.event.FocusAdapter;
 127 import java.awt.event.FocusEvent;
 128 import java.awt.event.ItemEvent;
 129 import java.awt.event.ItemListener;
 130 import java.awt.event.KeyAdapter;
 131 import java.awt.event.KeyEvent;
 132 import java.awt.event.MouseEvent;
 133 import java.awt.print.PageFormat;
 134 import java.awt.print.PrinterJob;
 135 import java.beans.PropertyChangeEvent;
 136 import java.io.File;
 137 import java.io.FileWriter;
 138 import java.io.IOException;
 139 import java.io.PrintWriter;
 140 import java.net.URL;
 141 import java.util.ArrayList;
 142 import java.util.Arrays;
 143 import java.util.Deque;
 144 import java.util.Enumeration;
 145 import java.util.HashMap;
 146 import java.util.Hashtable;
 147 import java.util.List;
 148 import java.util.Map;
 149 import java.util.Scanner;
 150 import java.util.Vector;
 151
 152 import javax.swing.JCheckBoxMenuItem;
 153 import javax.swing.JEditorPane;
 154 import javax.swing.JFileChooser;
 155 import javax.swing.JFrame;
 156 import javax.swing.JInternalFrame;
 157 import javax.swing.JLayeredPane;
 158 import javax.swing.JMenu;
 159 import javax.swing.JMenuItem;
 160 import javax.swing.JOptionPane;
 161 import javax.swing.JScrollPane;
 162 import javax.swing.SwingUtilities;
 163
 164 /**
 165  * DOCUMENT ME!
 166  *
 167  * @author $author$
 168  * @version $Revision$
 169  */
 170 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 171         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 172 {
 173
 174   Map<String, Float> distribution = new HashMap<>(); // temporary
 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    * The selected HMM for this align frame
 190    */
 191   SequenceI selectedHMMSequence;
 192
 193   List<AlignmentPanel> alignPanels = new ArrayList<>();
 194
 195   /**
 196    * Last format used to load or save alignments in this window
 197    */
 198   FileFormatI currentFileFormat = null;
 199
 200   /**
 201    * Current filename for this alignment
 202    */
 203   String fileName = null;
 204
 205
 206   /**
 207    * Creates a new AlignFrame object with specific width and height.
 208    *
 209    * @param al
 210    * @param width
 211    * @param height
 212    */
 213   public AlignFrame(AlignmentI al, int width, int height)
 214   {
 215     this(al, null, width, height);
 216   }
 217
 218   /**
 219    * Creates a new AlignFrame object with specific width, height and
 220    * sequenceSetId
 221    *
 222    * @param al
 223    * @param width
 224    * @param height
 225    * @param sequenceSetId
 226    */
 227   public AlignFrame(AlignmentI al, int width, int height,
 228           String sequenceSetId)
 229   {
 230     this(al, null, width, height, sequenceSetId);
 231   }
 232
 233   /**
 234    * Creates a new AlignFrame object with specific width, height and
 235    * sequenceSetId
 236    *
 237    * @param al
 238    * @param width
 239    * @param height
 240    * @param sequenceSetId
 241    * @param viewId
 242    */
 243   public AlignFrame(AlignmentI al, int width, int height,
 244           String sequenceSetId, String viewId)
 245   {
 246     this(al, null, width, height, sequenceSetId, viewId);
 247   }
 248
 249   /**
 250    * new alignment window with hidden columns
 251    *
 252    * @param al
 253    *          AlignmentI
 254    * @param hiddenColumns
 255    *          ColumnSelection or null
 256    * @param width
 257    *          Width of alignment frame
 258    * @param height
 259    *          height of frame.
 260    */
 261   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 262           int height)
 263   {
 264     this(al, hiddenColumns, width, height, null);
 265   }
 266
 267   /**
 268    * Create alignment frame for al with hiddenColumns, a specific width and
 269    * height, and specific sequenceId
 270    *
 271    * @param al
 272    * @param hiddenColumns
 273    * @param width
 274    * @param height
 275    * @param sequenceSetId
 276    *          (may be null)
 277    */
 278   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 279           int height, String sequenceSetId)
 280   {
 281     this(al, hiddenColumns, width, height, sequenceSetId, null);
 282   }
 283
 284   /**
 285    * Create alignment frame for al with hiddenColumns, a specific width and
 286    * height, and specific sequenceId
 287    *
 288    * @param al
 289    * @param hiddenColumns
 290    * @param width
 291    * @param height
 292    * @param sequenceSetId
 293    *          (may be null)
 294    * @param viewId
 295    *          (may be null)
 296    */
 297   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 298           int height, String sequenceSetId, String viewId)
 299   {
 300     setSize(width, height);
 301
 302     if (al.getDataset() == null)
 303     {
 304       al.setDataset(null);
 305     }
 306
 307     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 308
 309     alignPanel = new AlignmentPanel(this, viewport);
 310
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 316           HiddenColumns hiddenColumns, int width, int height)
 317   {
 318     setSize(width, height);
 319
 320     if (al.getDataset() == null)
 321     {
 322       al.setDataset(null);
 323     }
 324
 325     viewport = new AlignViewport(al, hiddenColumns);
 326
 327     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 328     {
 329       viewport.hideSequence(hiddenSeqs);
 330     }
 331     alignPanel = new AlignmentPanel(this, viewport);
 332     addAlignmentPanel(alignPanel, true);
 333     init();
 334   }
 335
 336   /**
 337    * Make a new AlignFrame from existing alignmentPanels
 338    *
 339    * @param ap
 340    *          AlignmentPanel
 341    * @param av
 342    *          AlignViewport
 343    */
 344   public AlignFrame(AlignmentPanel ap)
 345   {
 346     viewport = ap.av;
 347     alignPanel = ap;
 348     addAlignmentPanel(ap, false);
 349     init();
 350   }
 351
 352   /**
 353    * initalise the alignframe from the underlying viewport data and the
 354    * configurations
 355    */
 356   void init()
 357   {
 358     if (!Jalview.isHeadlessMode())
 359     {
 360       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 361     }
 362
 363     avc = new jalview.controller.AlignViewController(this, viewport,
 364             alignPanel);
 365     if (viewport.getAlignmentConservationAnnotation() == null)
 366     {
 367       // BLOSUM62Colour.setEnabled(false);
 368       conservationMenuItem.setEnabled(false);
 369       modifyConservation.setEnabled(false);
 370       // PIDColour.setEnabled(false);
 371       // abovePIDThreshold.setEnabled(false);
 372       // modifyPID.setEnabled(false);
 373     }
 374
 375     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 376             "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       addServiceListeners();
 407       setGUINucleotide();
 408     }
 409
 410     if (viewport.getWrapAlignment())
 411     {
 412       wrapMenuItem_actionPerformed(null);
 413     }
 414
 415     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 416     {
 417       this.overviewMenuItem_actionPerformed(null);
 418     }
 419
 420     addKeyListener();
 421
 422     final List<AlignmentPanel> selviews = new ArrayList<>();
 423     final List<AlignmentPanel> origview = new ArrayList<>();
 424     final String menuLabel = MessageManager
 425             .getString("label.copy_format_from");
 426     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 427             new ViewSetProvider()
 428             {
 429
 430               @Override
 431               public AlignmentPanel[] getAllAlignmentPanels()
 432               {
 433                 origview.clear();
 434                 origview.add(alignPanel);
 435                 // make an array of all alignment panels except for this one
 436                 List<AlignmentPanel> aps = new ArrayList<>(
 437                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 438                 aps.remove(AlignFrame.this.alignPanel);
 439                 return aps.toArray(new AlignmentPanel[aps.size()]);
 440               }
 441             }, selviews, new ItemListener()
 442             {
 443
 444               @Override
 445               public void itemStateChanged(ItemEvent e)
 446               {
 447                 if (origview.size() > 0)
 448                 {
 449                   final AlignmentPanel ap = origview.get(0);
 450
 451                   /*
 452                    * Copy the ViewStyle of the selected panel to 'this one'.
 453                    * Don't change value of 'scaleProteinAsCdna' unless copying
 454                    * from a SplitFrame.
 455                    */
 456                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 457                           .getViewStyle();
 458                   boolean fromSplitFrame = selviews.get(0)
 459                           .getAlignViewport().getCodingComplement() != null;
 460                   if (!fromSplitFrame)
 461                   {
 462                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 463                             .getViewStyle().isScaleProteinAsCdna());
 464                   }
 465                   ap.getAlignViewport().setViewStyle(vs);
 466
 467                   /*
 468                    * Also rescale ViewStyle of SplitFrame complement if there is
 469                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 470                    * the whole ViewStyle (allow cDNA protein to have different
 471                    * fonts)
 472                    */
 473                   AlignViewportI complement = ap.getAlignViewport()
 474                           .getCodingComplement();
 475                   if (complement != null && vs.isScaleProteinAsCdna())
 476                   {
 477                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 478                     ((SplitFrame) af.getSplitViewContainer())
 479                             .adjustLayout();
 480                     af.setMenusForViewport();
 481                   }
 482
 483                   ap.updateLayout();
 484                   ap.setSelected(true);
 485                   ap.alignFrame.setMenusForViewport();
 486
 487                 }
 488               }
 489             });
 490     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 491             .indexOf("devel") > -1
 492             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 493                     .indexOf("test") > -1)
 494     {
 495       formatMenu.add(vsel);
 496     }
 497     addFocusListener(new FocusAdapter()
 498     {
 499       @Override
 500       public void focusGained(FocusEvent e)
 501       {
 502         Jalview.setCurrentAlignFrame(AlignFrame.this);
 503       }
 504     });
 505
 506   }
 507
 508   /**
 509    * Change the filename and format for the alignment, and enable the 'reload'
 510    * button functionality.
 511    *
 512    * @param file
 513    *          valid filename
 514    * @param format
 515    *          format of file
 516    */
 517   public void setFileName(String file, FileFormatI format)
 518   {
 519     fileName = file;
 520     setFileFormat(format);
 521     reload.setEnabled(true);
 522   }
 523
 524   /**
 525    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 526    * events
 527    */
 528   void addKeyListener()
 529   {
 530     addKeyListener(new KeyAdapter()
 531     {
 532       @Override
 533       public void keyPressed(KeyEvent evt)
 534       {
 535         if (viewport.cursorMode
 536                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 537                         && evt.getKeyCode() <= KeyEvent.VK_9)
 538                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 539                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 540                 && Character.isDigit(evt.getKeyChar()))
 541         {
 542           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 543         }
 544
 545         switch (evt.getKeyCode())
 546         {
 547
 548         case 27: // escape key
 549           deselectAllSequenceMenuItem_actionPerformed(null);
 550
 551           break;
 552
 553         case KeyEvent.VK_DOWN:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555           {
 556             moveSelectedSequences(false);
 557           }
 558           if (viewport.cursorMode)
 559           {
 560             alignPanel.getSeqPanel().moveCursor(0, 1);
 561           }
 562           break;
 563
 564         case KeyEvent.VK_UP:
 565           if (evt.isAltDown() || !viewport.cursorMode)
 566           {
 567             moveSelectedSequences(true);
 568           }
 569           if (viewport.cursorMode)
 570           {
 571             alignPanel.getSeqPanel().moveCursor(0, -1);
 572           }
 573
 574           break;
 575
 576         case KeyEvent.VK_LEFT:
 577           if (evt.isAltDown() || !viewport.cursorMode)
 578           {
 579             slideSequences(false,
 580                     alignPanel.getSeqPanel().getKeyboardNo1());
 581           }
 582           else
 583           {
 584             alignPanel.getSeqPanel().moveCursor(-1, 0);
 585           }
 586
 587           break;
 588
 589         case KeyEvent.VK_RIGHT:
 590           if (evt.isAltDown() || !viewport.cursorMode)
 591           {
 592             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 593           }
 594           else
 595           {
 596             alignPanel.getSeqPanel().moveCursor(1, 0);
 597           }
 598           break;
 599
 600         case KeyEvent.VK_SPACE:
 601           if (viewport.cursorMode)
 602           {
 603             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 604                     || evt.isShiftDown() || evt.isAltDown());
 605           }
 606           break;
 607
 608         // case KeyEvent.VK_A:
 609         // if (viewport.cursorMode)
 610         // {
 611         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 612         // //System.out.println("A");
 613         // }
 614         // break;
 615         /*
 616          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 617          * System.out.println("closing bracket"); } break;
 618          */
 619         case KeyEvent.VK_DELETE:
 620         case KeyEvent.VK_BACK_SPACE:
 621           if (!viewport.cursorMode)
 622           {
 623             cut_actionPerformed(null);
 624           }
 625           else
 626           {
 627             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 628                     || evt.isShiftDown() || evt.isAltDown());
 629           }
 630
 631           break;
 632
 633         case KeyEvent.VK_S:
 634           if (viewport.cursorMode)
 635           {
 636             alignPanel.getSeqPanel().setCursorRow();
 637           }
 638           break;
 639         case KeyEvent.VK_C:
 640           if (viewport.cursorMode && !evt.isControlDown())
 641           {
 642             alignPanel.getSeqPanel().setCursorColumn();
 643           }
 644           break;
 645         case KeyEvent.VK_P:
 646           if (viewport.cursorMode)
 647           {
 648             alignPanel.getSeqPanel().setCursorPosition();
 649           }
 650           break;
 651
 652         case KeyEvent.VK_ENTER:
 653         case KeyEvent.VK_COMMA:
 654           if (viewport.cursorMode)
 655           {
 656             alignPanel.getSeqPanel().setCursorRowAndColumn();
 657           }
 658           break;
 659
 660         case KeyEvent.VK_Q:
 661           if (viewport.cursorMode)
 662           {
 663             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 664           }
 665           break;
 666         case KeyEvent.VK_M:
 667           if (viewport.cursorMode)
 668           {
 669             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 670           }
 671           break;
 672
 673         case KeyEvent.VK_F2:
 674           viewport.cursorMode = !viewport.cursorMode;
 675           statusBar.setText(MessageManager
 676                   .formatMessage("label.keyboard_editing_mode", new String[]
 677                   { (viewport.cursorMode ? "on" : "off") }));
 678           if (viewport.cursorMode)
 679           {
 680             ViewportRanges ranges = viewport.getRanges();
 681             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 682                     .getStartRes();
 683             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 684                     .getStartSeq();
 685           }
 686           alignPanel.getSeqPanel().seqCanvas.repaint();
 687           break;
 688
 689         case KeyEvent.VK_F1:
 690           try
 691           {
 692             Help.showHelpWindow();
 693           } catch (Exception ex)
 694           {
 695             ex.printStackTrace();
 696           }
 697           break;
 698         case KeyEvent.VK_H:
 699         {
 700           boolean toggleSeqs = !evt.isControlDown();
 701           boolean toggleCols = !evt.isShiftDown();
 702           toggleHiddenRegions(toggleSeqs, toggleCols);
 703           break;
 704         }
 705         case KeyEvent.VK_B:
 706         {
 707           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 708           boolean modifyExisting = true; // always modify, don't clear
 709                                          // evt.isShiftDown();
 710           boolean invertHighlighted = evt.isAltDown();
 711           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 712                   toggleSel);
 713           break;
 714         }
 715         case KeyEvent.VK_PAGE_UP:
 716           viewport.getRanges().pageUp();
 717           break;
 718         case KeyEvent.VK_PAGE_DOWN:
 719           viewport.getRanges().pageDown();
 720           break;
 721         }
 722       }
 723
 724       @Override
 725       public void keyReleased(KeyEvent evt)
 726       {
 727         switch (evt.getKeyCode())
 728         {
 729         case KeyEvent.VK_LEFT:
 730           if (evt.isAltDown() || !viewport.cursorMode)
 731           {
 732             viewport.firePropertyChange("alignment", null,
 733                     viewport.getAlignment().getSequences());
 734           }
 735           break;
 736
 737         case KeyEvent.VK_RIGHT:
 738           if (evt.isAltDown() || !viewport.cursorMode)
 739           {
 740             viewport.firePropertyChange("alignment", null,
 741                     viewport.getAlignment().getSequences());
 742           }
 743           break;
 744         }
 745       }
 746     });
 747   }
 748
 749   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 750   {
 751     ap.alignFrame = this;
 752     avc = new jalview.controller.AlignViewController(this, viewport,
 753             alignPanel);
 754
 755     alignPanels.add(ap);
 756
 757     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 758
 759     int aSize = alignPanels.size();
 760
 761     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 762
 763     if (aSize == 1 && ap.av.viewName == null)
 764     {
 765       this.getContentPane().add(ap, BorderLayout.CENTER);
 766     }
 767     else
 768     {
 769       if (aSize == 2)
 770       {
 771         setInitialTabVisible();
 772       }
 773
 774       expandViews.setEnabled(true);
 775       gatherViews.setEnabled(true);
 776       tabbedPane.addTab(ap.av.viewName, ap);
 777
 778       ap.setVisible(false);
 779     }
 780
 781     if (newPanel)
 782     {
 783       if (ap.av.isPadGaps())
 784       {
 785         ap.av.getAlignment().padGaps();
 786       }
 787       ap.av.updateConservation(ap);
 788       ap.av.updateConsensus(ap);
 789       ap.av.updateStrucConsensus(ap);
 790       ap.av.updateInformation(ap);
 791     }
 792   }
 793
 794   public void setInitialTabVisible()
 795   {
 796     expandViews.setEnabled(true);
 797     gatherViews.setEnabled(true);
 798     tabbedPane.setVisible(true);
 799     AlignmentPanel first = alignPanels.get(0);
 800     tabbedPane.addTab(first.av.viewName, first);
 801     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 802   }
 803
 804   public AlignViewport getViewport()
 805   {
 806     return viewport;
 807   }
 808
 809   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 810   private void addServiceListeners()
 811   {
 812     final java.beans.PropertyChangeListener thisListener;
 813     Desktop.instance.addJalviewPropertyChangeListener("services",
 814             thisListener = new java.beans.PropertyChangeListener()
 815             {
 816               @Override
 817               public void propertyChange(PropertyChangeEvent evt)
 818               {
 819                 // // System.out.println("Discoverer property change.");
 820                 // if (evt.getPropertyName().equals("services"))
 821                 {
 822                   SwingUtilities.invokeLater(new Runnable()
 823                   {
 824
 825                     @Override
 826                     public void run()
 827                     {
 828                       System.err.println(
 829                               "Rebuild WS Menu for service change");
 830                       BuildWebServiceMenu();
 831                     }
 832
 833                   });
 834                 }
 835               }
 836             });
 837     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 838     {
 839       @Override
 840       public void internalFrameClosed(
 841               javax.swing.event.InternalFrameEvent evt)
 842       {
 843         // System.out.println("deregistering discoverer listener");
 844         Desktop.instance.removeJalviewPropertyChangeListener("services",
 845                 thisListener);
 846         closeMenuItem_actionPerformed(true);
 847       };
 848     });
 849     // Finally, build the menu once to get current service state
 850     new Thread(new Runnable()
 851     {
 852       @Override
 853       public void run()
 854       {
 855         BuildWebServiceMenu();
 856       }
 857     }).start();
 858   }
 859
 860   /**
 861    * Configure menu items that vary according to whether the alignment is
 862    * nucleotide or protein
 863    */
 864   public void setGUINucleotide()
 865   {
 866     AlignmentI al = getViewport().getAlignment();
 867     boolean nucleotide = al.isNucleotide();
 868
 869     loadVcf.setVisible(nucleotide);
 870     showTranslation.setVisible(nucleotide);
 871     showReverse.setVisible(nucleotide);
 872     showReverseComplement.setVisible(nucleotide);
 873     conservationMenuItem.setEnabled(!nucleotide);
 874     modifyConservation
 875             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 876     showGroupConservation.setEnabled(!nucleotide);
 877
 878     showComplementMenuItem
 879             .setText(nucleotide ? MessageManager.getString("label.protein")
 880                     : MessageManager.getString("label.nucleotide"));
 881   }
 882
 883   /**
 884    * set up menus for the current viewport. This may be called after any
 885    * operation that affects the data in the current view (selection changed,
 886    * etc) to update the menus to reflect the new state.
 887    */
 888   @Override
 889   public void setMenusForViewport()
 890   {
 891     setMenusFromViewport(viewport);
 892   }
 893
 894   /**
 895    * Need to call this method when tabs are selected for multiple views, or when
 896    * loading from Jalview2XML.java
 897    *
 898    * @param av
 899    *          AlignViewport
 900    */
 901   void setMenusFromViewport(AlignViewport av)
 902   {
 903     padGapsMenuitem.setSelected(av.isPadGaps());
 904     colourTextMenuItem.setSelected(av.isShowColourText());
 905     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 906     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 907     conservationMenuItem.setSelected(av.getConservationSelected());
 908     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 909     seqLimits.setSelected(av.getShowJVSuffix());
 910     idRightAlign.setSelected(av.isRightAlignIds());
 911     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 912     renderGapsMenuItem.setSelected(av.isRenderGaps());
 913     wrapMenuItem.setSelected(av.getWrapAlignment());
 914     scaleAbove.setVisible(av.getWrapAlignment());
 915     scaleLeft.setVisible(av.getWrapAlignment());
 916     scaleRight.setVisible(av.getWrapAlignment());
 917     annotationPanelMenuItem.setState(av.isShowAnnotation());
 918     /*
 919      * Show/hide annotations only enabled if annotation panel is shown
 920      */
 921     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 922     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 923     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 924     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 925     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 926     viewTextMenuItem.setSelected(av.getShowText());
 927     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 928     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 929     showGroupConservation.setSelected(av.isShowGroupConservation());
 930     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 931     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 932     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 933     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 934     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 935     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 936
 937     ColourMenuHelper.setColourSelected(colourMenu,
 938             av.getGlobalColourScheme());
 939
 940     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 941     hiddenMarkers.setState(av.getShowHiddenMarkers());
 942     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 943     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 944     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 945     autoCalculate.setSelected(av.autoCalculateConsensus);
 946     sortByTree.setSelected(av.sortByTree);
 947     listenToViewSelections.setSelected(av.followSelection);
 948
 949     showProducts.setEnabled(canShowProducts());
 950     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 951
 952     updateEditMenuBar();
 953   }
 954
 955   /**
 956    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 957    *
 958    * @param b
 959    */
 960   public void setGroovyEnabled(boolean b)
 961   {
 962     runGroovy.setEnabled(b);
 963   }
 964
 965   private IProgressIndicator progressBar;
 966
 967   /*
 968    * (non-Javadoc)
 969    *
 970    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 971    */
 972   @Override
 973   public void setProgressBar(String message, long id)
 974   {
 975     progressBar.setProgressBar(message, id);
 976   }
 977
 978   @Override
 979   public void registerHandler(final long id,
 980           final IProgressIndicatorHandler handler)
 981   {
 982     progressBar.registerHandler(id, handler);
 983   }
 984
 985   /**
 986    *
 987    * @return true if any progress bars are still active
 988    */
 989   @Override
 990   public boolean operationInProgress()
 991   {
 992     return progressBar.operationInProgress();
 993   }
 994
 995   @Override
 996   public void setStatus(String text)
 997   {
 998     statusBar.setText(text);
 999   }
1000
1001   /*
1002    * Added so Castor Mapping file can obtain Jalview Version
1003    */
1004   public String getVersion()
1005   {
1006     return jalview.bin.Cache.getProperty("VERSION");
1007   }
1008
1009   public FeatureRenderer getFeatureRenderer()
1010   {
1011     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1012   }
1013
1014   @Override
1015   public void fetchSequence_actionPerformed(ActionEvent e)
1016   {
1017     new jalview.gui.SequenceFetcher(this);
1018   }
1019
1020   @Override
1021   public void addFromFile_actionPerformed(ActionEvent e)
1022   {
1023     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1024   }
1025
1026   @Override
1027   public void hmmBuildSettings_actionPerformed()
1028   {
1029     if (!(alignmentIsSufficient(1)))
1030     {
1031       return;
1032     }
1033     WsParamSetI set = new HMMERPreset();
1034     List<ArgumentI> args = new ArrayList<>();
1035     ParamDatastoreI store = new HMMERParamStore("hmmbuild");
1036     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1037             args);
1038     if (params.showRunDialog())
1039     {
1040       new Thread(new HMMBuild(this, params.getJobParams())).start();
1041     }
1042     alignPanel.repaint();
1043
1044   }
1045
1046   @Override
1047   public void hmmAlignSettings_actionPerformed()
1048   {
1049     if (!(checkForHMM() && alignmentIsSufficient(2)))
1050     {
1051       return;
1052     }
1053     WsParamSetI set = new HMMERPreset();
1054     List<ArgumentI> args = new ArrayList<>();
1055     ParamDatastoreI store = new HMMERParamStore("hmmalign");
1056     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1057             args);
1058     if (params.showRunDialog())
1059     {
1060       new Thread(new HMMAlign(this, params.getJobParams()))
1061             .start();
1062     }
1063     alignPanel.repaint();
1064   }
1065
1066   @Override
1067   public void hmmSearchSettings_actionPerformed()
1068   {
1069     if (!checkForHMM())
1070     {
1071       return;
1072     }
1073     WsParamSetI set = new HMMERPreset();
1074     List<ArgumentI> args = new ArrayList<>();
1075     ParamDatastoreI store = new HMMERParamStore("hmmsearch");
1076     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1077             args);
1078     if (params.showRunDialog())
1079     {
1080       new Thread(new HMMSearch(this, params.getJobParams()))
1081             .start();
1082     }
1083     alignPanel.repaint();
1084   }
1085
1086   @Override
1087   public void hmmBuildRun_actionPerformed()
1088   {
1089     if (!alignmentIsSufficient(1))
1090     {
1091       return;
1092     }
1093     new Thread(new HMMBuild(this, null))
1094             .start();
1095   }
1096
1097   @Override
1098   public void hmmAlignRun_actionPerformed()
1099   {
1100     if (!(checkForHMM() && alignmentIsSufficient(2)))
1101     {
1102       return;
1103     }
1104     new Thread(new HMMAlign(this, null)).start();
1105   }
1106
1107   @Override
1108   public void hmmSearchRun_actionPerformed()
1109   {
1110     if (!checkForHMM())
1111     {
1112       return;
1113     }
1114     new Thread(new HMMSearch(this, null)).start();
1115   }
1116
1117   /**
1118    * Checks if the frame has a selected hidden Markov model
1119    *
1120    * @return
1121    */
1122   private boolean checkForHMM()
1123   {
1124     if (getSelectedHMM() == null)
1125     {
1126       JOptionPane.showMessageDialog(this,
1127               MessageManager.getString("warn.no_selected_hmm"));
1128       return false;
1129     }
1130     return true;
1131   }
1132
1133   /**
1134    * Checks if the alignment contains the required number of sequences.
1135    *
1136    * @param required
1137    * @return
1138    */
1139   public boolean alignmentIsSufficient(int required)
1140   {
1141     if (getViewport().getAlignment().getSequences().size() < required)
1142     {
1143       JOptionPane.showMessageDialog(this,
1144               MessageManager.getString("warn.not_enough_sequences"));
1145       return false;
1146     }
1147     return true;
1148   }
1149
1150   @Override
1151   public void addDatabase_actionPerformed() throws IOException
1152   {
1153     if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
1154     {
1155       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1156       Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
1157     }
1158
1159     String path = openFileChooser(false);
1160     if (new File(path).exists())
1161     {
1162       IdentifyFile identifier = new IdentifyFile();
1163       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1164       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1165               || format == FileFormat.Pfam)
1166       {
1167         String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
1168         String currentDbPaths = Cache
1169                 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
1170         currentDbPaths += " " + path;
1171
1172         String fileName = StringUtils.getLastToken(path, File.separator);
1173         Scanner scanner = new Scanner(fileName).useDelimiter(".");
1174         String name = scanner.next();
1175         scanner.close();
1176         currentDbs += " " + path; // TODO remove path from file name
1177         scanner.close();
1178
1179         Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
1180         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1181       }
1182       else
1183       {
1184         JOptionPane.showMessageDialog(this,
1185                 MessageManager.getString("warn.invalid_format"));
1186       }
1187     }
1188     else
1189     {
1190       JOptionPane.showMessageDialog(this,
1191               MessageManager.getString("warn.not_enough_sequences"));
1192     }
1193   }
1194
1195   /**
1196    * Opens a file chooser
1197    *
1198    * @param forFolder
1199    * @return
1200    */
1201   protected String openFileChooser(boolean forFolder)
1202   {
1203     String choice = null;
1204     JFileChooser chooser = new JFileChooser();
1205     if (forFolder)
1206     {
1207       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1208     }
1209     chooser.setDialogTitle(
1210             MessageManager.getString("label.open_local_file"));
1211     chooser.setToolTipText(MessageManager.getString("action.open"));
1212
1213     int value = chooser.showOpenDialog(this);
1214
1215     if (value == JFileChooser.APPROVE_OPTION)
1216     {
1217       choice = chooser.getSelectedFile().getPath();
1218     }
1219     return choice;
1220   }
1221
1222   @Override
1223   public void reload_actionPerformed(ActionEvent e)
1224   {
1225     if (fileName != null)
1226     {
1227       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1228       // originating file's format
1229       // TODO: work out how to recover feature settings for correct view(s) when
1230       // file is reloaded.
1231       if (FileFormat.Jalview.equals(currentFileFormat))
1232       {
1233         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1234         for (int i = 0; i < frames.length; i++)
1235         {
1236           if (frames[i] instanceof AlignFrame && frames[i] != this
1237                   && ((AlignFrame) frames[i]).fileName != null
1238                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1239           {
1240             try
1241             {
1242               frames[i].setSelected(true);
1243               Desktop.instance.closeAssociatedWindows();
1244             } catch (java.beans.PropertyVetoException ex)
1245             {
1246             }
1247           }
1248
1249         }
1250         Desktop.instance.closeAssociatedWindows();
1251
1252         FileLoader loader = new FileLoader();
1253         DataSourceType protocol = fileName.startsWith("http:")
1254                 ? DataSourceType.URL
1255                 : DataSourceType.FILE;
1256         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1257       }
1258       else
1259       {
1260         Rectangle bounds = this.getBounds();
1261
1262         FileLoader loader = new FileLoader();
1263         DataSourceType protocol = fileName.startsWith("http:")
1264                 ? DataSourceType.URL
1265                 : DataSourceType.FILE;
1266         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1267                 protocol, currentFileFormat);
1268
1269         newframe.setBounds(bounds);
1270         if (featureSettings != null && featureSettings.isShowing())
1271         {
1272           final Rectangle fspos = featureSettings.frame.getBounds();
1273           // TODO: need a 'show feature settings' function that takes bounds -
1274           // need to refactor Desktop.addFrame
1275           newframe.featureSettings_actionPerformed(null);
1276           final FeatureSettings nfs = newframe.featureSettings;
1277           SwingUtilities.invokeLater(new Runnable()
1278           {
1279             @Override
1280             public void run()
1281             {
1282               nfs.frame.setBounds(fspos);
1283             }
1284           });
1285           this.featureSettings.close();
1286           this.featureSettings = null;
1287         }
1288         this.closeMenuItem_actionPerformed(true);
1289       }
1290     }
1291   }
1292
1293   @Override
1294   public void addFromText_actionPerformed(ActionEvent e)
1295   {
1296     Desktop.instance
1297             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1298   }
1299
1300   @Override
1301   public void addFromURL_actionPerformed(ActionEvent e)
1302   {
1303     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1304   }
1305
1306   @Override
1307   public void save_actionPerformed(ActionEvent e)
1308   {
1309     if (fileName == null || (currentFileFormat == null)
1310             || fileName.startsWith("http"))
1311     {
1312       saveAs_actionPerformed(null);
1313     }
1314     else
1315     {
1316       saveAlignment(fileName, currentFileFormat);
1317     }
1318   }
1319
1320   /**
1321    * DOCUMENT ME!
1322    *
1323    * @param e
1324    *          DOCUMENT ME!
1325    */
1326   @Override
1327   public void saveAs_actionPerformed(ActionEvent e)
1328   {
1329     String format = currentFileFormat == null ? null
1330             : currentFileFormat.getName();
1331     JalviewFileChooser chooser = JalviewFileChooser
1332             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1333
1334     chooser.setFileView(new JalviewFileView());
1335     chooser.setDialogTitle(
1336             MessageManager.getString("label.save_alignment_to_file"));
1337     chooser.setToolTipText(MessageManager.getString("action.save"));
1338
1339     int value = chooser.showSaveDialog(this);
1340
1341     if (value == JalviewFileChooser.APPROVE_OPTION)
1342     {
1343       currentFileFormat = chooser.getSelectedFormat();
1344       while (currentFileFormat == null)
1345       {
1346         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1347                 MessageManager.getString(
1348                         "label.select_file_format_before_saving"),
1349                 MessageManager.getString("label.file_format_not_specified"),
1350                 JvOptionPane.WARNING_MESSAGE);
1351         currentFileFormat = chooser.getSelectedFormat();
1352         value = chooser.showSaveDialog(this);
1353         if (value != JalviewFileChooser.APPROVE_OPTION)
1354         {
1355           return;
1356         }
1357       }
1358
1359       fileName = chooser.getSelectedFile().getPath();
1360
1361       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1362
1363       Cache.setProperty("LAST_DIRECTORY", fileName);
1364       saveAlignment(fileName, currentFileFormat);
1365     }
1366   }
1367
1368   public boolean saveAlignment(String file, FileFormatI format)
1369   {
1370     boolean success = true;
1371
1372     if (FileFormat.Jalview.equals(format))
1373     {
1374       String shortName = title;
1375
1376       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1377       {
1378         shortName = shortName.substring(
1379                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1380       }
1381
1382       success = new Jalview2XML().saveAlignment(this, file, shortName);
1383
1384       statusBar.setText(MessageManager.formatMessage(
1385               "label.successfully_saved_to_file_in_format", new Object[]
1386               { fileName, format }));
1387
1388     }
1389     else
1390     {
1391       AlignmentExportData exportData = getAlignmentForExport(format,
1392               viewport, null);
1393       if (exportData.getSettings().isCancelled())
1394       {
1395         return false;
1396       }
1397       FormatAdapter f = new FormatAdapter(alignPanel,
1398               exportData.getSettings());
1399       String output = f.formatSequences(format, exportData.getAlignment(), // class
1400                                                                            // cast
1401                                                                            // exceptions
1402                                                                            // will
1403               // occur in the distant future
1404               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1405               f.getCacheSuffixDefault(format),
1406               viewport.getAlignment().getHiddenColumns());
1407
1408       if (output == null)
1409       {
1410         success = false;
1411       }
1412       else
1413       {
1414         try
1415         {
1416           PrintWriter out = new PrintWriter(new FileWriter(file));
1417
1418           out.print(output);
1419           out.close();
1420           this.setTitle(file);
1421           statusBar.setText(MessageManager.formatMessage(
1422                   "label.successfully_saved_to_file_in_format", new Object[]
1423                   { fileName, format.getName() }));
1424         } catch (Exception ex)
1425         {
1426           success = false;
1427           ex.printStackTrace();
1428         }
1429       }
1430     }
1431
1432     if (!success)
1433     {
1434       JvOptionPane.showInternalMessageDialog(this, MessageManager
1435               .formatMessage("label.couldnt_save_file", new Object[]
1436               { fileName }),
1437               MessageManager.getString("label.error_saving_file"),
1438               JvOptionPane.WARNING_MESSAGE);
1439     }
1440
1441     return success;
1442   }
1443
1444   private void warningMessage(String warning, String title)
1445   {
1446     if (new jalview.util.Platform().isHeadless())
1447     {
1448       System.err.println("Warning: " + title + "\nWarning: " + warning);
1449
1450     }
1451     else
1452     {
1453       JvOptionPane.showInternalMessageDialog(this, warning, title,
1454               JvOptionPane.WARNING_MESSAGE);
1455     }
1456     return;
1457   }
1458
1459   /**
1460    * DOCUMENT ME!
1461    *
1462    * @param e
1463    *          DOCUMENT ME!
1464    */
1465   @Override
1466   protected void outputText_actionPerformed(ActionEvent e)
1467   {
1468     FileFormatI fileFormat = FileFormats.getInstance()
1469             .forName(e.getActionCommand());
1470     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1471             viewport, null);
1472     if (exportData.getSettings().isCancelled())
1473     {
1474       return;
1475     }
1476     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1477     cap.setForInput(null);
1478     try
1479     {
1480       FileFormatI format = fileFormat;
1481       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1482               .formatSequences(format, exportData.getAlignment(),
1483                       exportData.getOmitHidden(),
1484                       exportData.getStartEndPostions(),
1485                       viewport.getAlignment().getHiddenColumns()));
1486       Desktop.addInternalFrame(cap, MessageManager
1487               .formatMessage("label.alignment_output_command", new Object[]
1488               { e.getActionCommand() }), 600, 500);
1489     } catch (OutOfMemoryError oom)
1490     {
1491       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1492               oom);
1493       cap.dispose();
1494     }
1495
1496   }
1497
1498   public static AlignmentExportData getAlignmentForExport(
1499           FileFormatI format, AlignViewportI viewport,
1500           AlignExportSettingI exportSettings)
1501   {
1502     AlignmentI alignmentToExport = null;
1503     AlignExportSettingI settings = exportSettings;
1504     String[] omitHidden = null;
1505
1506     HiddenSequences hiddenSeqs = viewport.getAlignment()
1507             .getHiddenSequences();
1508
1509     alignmentToExport = viewport.getAlignment();
1510
1511     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1512     if (settings == null)
1513     {
1514       settings = new AlignExportSettings(hasHiddenSeqs,
1515               viewport.hasHiddenColumns(), format);
1516     }
1517     // settings.isExportAnnotations();
1518
1519     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1520     {
1521       omitHidden = viewport.getViewAsString(false,
1522               settings.isExportHiddenSequences());
1523     }
1524
1525     int[] alignmentStartEnd = new int[2];
1526     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1527     {
1528       alignmentToExport = hiddenSeqs.getFullAlignment();
1529     }
1530     else
1531     {
1532       alignmentToExport = viewport.getAlignment();
1533     }
1534     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1535             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1536     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1537             omitHidden, alignmentStartEnd, settings);
1538     return ed;
1539   }
1540
1541   /**
1542    * DOCUMENT ME!
1543    *
1544    * @param e
1545    *          DOCUMENT ME!
1546    */
1547   @Override
1548   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1549   {
1550     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1551     htmlSVG.exportHTML(null);
1552   }
1553
1554   @Override
1555   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1556   {
1557     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1558     bjs.exportHTML(null);
1559   }
1560
1561   public void createImageMap(File file, String image)
1562   {
1563     alignPanel.makePNGImageMap(file, image);
1564   }
1565
1566   /**
1567    * DOCUMENT ME!
1568    *
1569    * @param e
1570    *          DOCUMENT ME!
1571    */
1572   @Override
1573   public void createPNG(File f)
1574   {
1575     alignPanel.makePNG(f);
1576   }
1577
1578   /**
1579    * DOCUMENT ME!
1580    *
1581    * @param e
1582    *          DOCUMENT ME!
1583    */
1584   @Override
1585   public void createEPS(File f)
1586   {
1587     alignPanel.makeEPS(f);
1588   }
1589
1590   @Override
1591   public void createSVG(File f)
1592   {
1593     alignPanel.makeSVG(f);
1594   }
1595
1596   @Override
1597   public void pageSetup_actionPerformed(ActionEvent e)
1598   {
1599     PrinterJob printJob = PrinterJob.getPrinterJob();
1600     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1601   }
1602
1603   /**
1604    * DOCUMENT ME!
1605    *
1606    * @param e
1607    *          DOCUMENT ME!
1608    */
1609   @Override
1610   public void printMenuItem_actionPerformed(ActionEvent e)
1611   {
1612     // Putting in a thread avoids Swing painting problems
1613     PrintThread thread = new PrintThread(alignPanel);
1614     thread.start();
1615   }
1616
1617   @Override
1618   public void exportFeatures_actionPerformed(ActionEvent e)
1619   {
1620     new AnnotationExporter(alignPanel).exportFeatures();
1621   }
1622
1623   @Override
1624   public void exportAnnotations_actionPerformed(ActionEvent e)
1625   {
1626     new AnnotationExporter(alignPanel).exportAnnotations();
1627   }
1628
1629   @Override
1630   public void associatedData_actionPerformed(ActionEvent e)
1631           throws IOException, InterruptedException
1632   {
1633     // Pick the tree file
1634     JalviewFileChooser chooser = new JalviewFileChooser(
1635             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1636     chooser.setFileView(new JalviewFileView());
1637     chooser.setDialogTitle(
1638             MessageManager.getString("label.load_jalview_annotations"));
1639     chooser.setToolTipText(
1640             MessageManager.getString("label.load_jalview_annotations"));
1641
1642     int value = chooser.showOpenDialog(null);
1643
1644     if (value == JalviewFileChooser.APPROVE_OPTION)
1645     {
1646       String choice = chooser.getSelectedFile().getPath();
1647       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1648       loadJalviewDataFile(choice, null, null, null);
1649     }
1650
1651   }
1652
1653   /**
1654    * Close the current view or all views in the alignment frame. If the frame
1655    * only contains one view then the alignment will be removed from memory.
1656    *
1657    * @param closeAllTabs
1658    */
1659   @Override
1660   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1661   {
1662     if (alignPanels != null && alignPanels.size() < 2)
1663     {
1664       closeAllTabs = true;
1665     }
1666
1667     try
1668     {
1669       if (alignPanels != null)
1670       {
1671         if (closeAllTabs)
1672         {
1673           if (this.isClosed())
1674           {
1675             // really close all the windows - otherwise wait till
1676             // setClosed(true) is called
1677             for (int i = 0; i < alignPanels.size(); i++)
1678             {
1679               AlignmentPanel ap = alignPanels.get(i);
1680               ap.closePanel();
1681             }
1682           }
1683         }
1684         else
1685         {
1686           closeView(alignPanel);
1687         }
1688       }
1689
1690       if (closeAllTabs)
1691       {
1692         /*
1693          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1694          * be called recursively, with the frame now in 'closed' state
1695          */
1696         this.setClosed(true);
1697       }
1698     } catch (Exception ex)
1699     {
1700       ex.printStackTrace();
1701     }
1702   }
1703
1704   /**
1705    * Close the specified panel and close up tabs appropriately.
1706    *
1707    * @param panelToClose
1708    */
1709   public void closeView(AlignmentPanel panelToClose)
1710   {
1711     int index = tabbedPane.getSelectedIndex();
1712     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1713     alignPanels.remove(panelToClose);
1714     panelToClose.closePanel();
1715     panelToClose = null;
1716
1717     tabbedPane.removeTabAt(closedindex);
1718     tabbedPane.validate();
1719
1720     if (index > closedindex || index == tabbedPane.getTabCount())
1721     {
1722       // modify currently selected tab index if necessary.
1723       index--;
1724     }
1725
1726     this.tabSelectionChanged(index);
1727   }
1728
1729   /**
1730    * DOCUMENT ME!
1731    */
1732   void updateEditMenuBar()
1733   {
1734
1735     if (viewport.getHistoryList().size() > 0)
1736     {
1737       undoMenuItem.setEnabled(true);
1738       CommandI command = viewport.getHistoryList().peek();
1739       undoMenuItem.setText(MessageManager
1740               .formatMessage("label.undo_command", new Object[]
1741               { command.getDescription() }));
1742     }
1743     else
1744     {
1745       undoMenuItem.setEnabled(false);
1746       undoMenuItem.setText(MessageManager.getString("action.undo"));
1747     }
1748
1749     if (viewport.getRedoList().size() > 0)
1750     {
1751       redoMenuItem.setEnabled(true);
1752
1753       CommandI command = viewport.getRedoList().peek();
1754       redoMenuItem.setText(MessageManager
1755               .formatMessage("label.redo_command", new Object[]
1756               { command.getDescription() }));
1757     }
1758     else
1759     {
1760       redoMenuItem.setEnabled(false);
1761       redoMenuItem.setText(MessageManager.getString("action.redo"));
1762     }
1763   }
1764
1765   @Override
1766   public void addHistoryItem(CommandI command)
1767   {
1768     if (command.getSize() > 0)
1769     {
1770       viewport.addToHistoryList(command);
1771       viewport.clearRedoList();
1772       updateEditMenuBar();
1773       viewport.updateHiddenColumns();
1774       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1775       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1776       // viewport.getColumnSelection()
1777       // .getHiddenColumns().size() > 0);
1778     }
1779   }
1780
1781   /**
1782    *
1783    * @return alignment objects for all views
1784    */
1785   AlignmentI[] getViewAlignments()
1786   {
1787     if (alignPanels != null)
1788     {
1789       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1790       int i = 0;
1791       for (AlignmentPanel ap : alignPanels)
1792       {
1793         als[i++] = ap.av.getAlignment();
1794       }
1795       return als;
1796     }
1797     if (viewport != null)
1798     {
1799       return new AlignmentI[] { viewport.getAlignment() };
1800     }
1801     return null;
1802   }
1803
1804   /**
1805    * DOCUMENT ME!
1806    *
1807    * @param e
1808    *          DOCUMENT ME!
1809    */
1810   @Override
1811   protected void undoMenuItem_actionPerformed(ActionEvent e)
1812   {
1813     if (viewport.getHistoryList().isEmpty())
1814     {
1815       return;
1816     }
1817     CommandI command = viewport.getHistoryList().pop();
1818     viewport.addToRedoList(command);
1819     command.undoCommand(getViewAlignments());
1820
1821     AlignmentViewport originalSource = getOriginatingSource(command);
1822     updateEditMenuBar();
1823
1824     if (originalSource != null)
1825     {
1826       if (originalSource != viewport)
1827       {
1828         Cache.log.warn(
1829                 "Implementation worry: mismatch of viewport origin for undo");
1830       }
1831       originalSource.updateHiddenColumns();
1832       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1833       // null
1834       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1835       // viewport.getColumnSelection()
1836       // .getHiddenColumns().size() > 0);
1837       originalSource.firePropertyChange("alignment", null,
1838               originalSource.getAlignment().getSequences());
1839     }
1840   }
1841
1842   /**
1843    * DOCUMENT ME!
1844    *
1845    * @param e
1846    *          DOCUMENT ME!
1847    */
1848   @Override
1849   protected void redoMenuItem_actionPerformed(ActionEvent e)
1850   {
1851     if (viewport.getRedoList().size() < 1)
1852     {
1853       return;
1854     }
1855
1856     CommandI command = viewport.getRedoList().pop();
1857     viewport.addToHistoryList(command);
1858     command.doCommand(getViewAlignments());
1859
1860     AlignmentViewport originalSource = getOriginatingSource(command);
1861     updateEditMenuBar();
1862
1863     if (originalSource != null)
1864     {
1865
1866       if (originalSource != viewport)
1867       {
1868         Cache.log.warn(
1869                 "Implementation worry: mismatch of viewport origin for redo");
1870       }
1871       originalSource.updateHiddenColumns();
1872       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1873       // null
1874       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1875       // viewport.getColumnSelection()
1876       // .getHiddenColumns().size() > 0);
1877       originalSource.firePropertyChange("alignment", null,
1878               originalSource.getAlignment().getSequences());
1879     }
1880   }
1881
1882   AlignmentViewport getOriginatingSource(CommandI command)
1883   {
1884     AlignmentViewport originalSource = null;
1885     // For sequence removal and addition, we need to fire
1886     // the property change event FROM the viewport where the
1887     // original alignment was altered
1888     AlignmentI al = null;
1889     if (command instanceof EditCommand)
1890     {
1891       EditCommand editCommand = (EditCommand) command;
1892       al = editCommand.getAlignment();
1893       List<Component> comps = PaintRefresher.components
1894               .get(viewport.getSequenceSetId());
1895
1896       for (Component comp : comps)
1897       {
1898         if (comp instanceof AlignmentPanel)
1899         {
1900           if (al == ((AlignmentPanel) comp).av.getAlignment())
1901           {
1902             originalSource = ((AlignmentPanel) comp).av;
1903             break;
1904           }
1905         }
1906       }
1907     }
1908
1909     if (originalSource == null)
1910     {
1911       // The original view is closed, we must validate
1912       // the current view against the closed view first
1913       if (al != null)
1914       {
1915         PaintRefresher.validateSequences(al, viewport.getAlignment());
1916       }
1917
1918       originalSource = viewport;
1919     }
1920
1921     return originalSource;
1922   }
1923
1924   /**
1925    * DOCUMENT ME!
1926    *
1927    * @param up
1928    *          DOCUMENT ME!
1929    */
1930   public void moveSelectedSequences(boolean up)
1931   {
1932     SequenceGroup sg = viewport.getSelectionGroup();
1933
1934     if (sg == null)
1935     {
1936       return;
1937     }
1938     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1939             viewport.getHiddenRepSequences(), up);
1940     alignPanel.paintAlignment(true, false);
1941   }
1942
1943   synchronized void slideSequences(boolean right, int size)
1944   {
1945     List<SequenceI> sg = new ArrayList<>();
1946     if (viewport.cursorMode)
1947     {
1948       sg.add(viewport.getAlignment()
1949               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1950     }
1951     else if (viewport.getSelectionGroup() != null
1952             && viewport.getSelectionGroup().getSize() != viewport
1953                     .getAlignment().getHeight())
1954     {
1955       sg = viewport.getSelectionGroup()
1956               .getSequences(viewport.getHiddenRepSequences());
1957     }
1958
1959     if (sg.size() < 1)
1960     {
1961       return;
1962     }
1963
1964     List<SequenceI> invertGroup = new ArrayList<>();
1965
1966     for (SequenceI seq : viewport.getAlignment().getSequences())
1967     {
1968       if (!sg.contains(seq))
1969       {
1970         invertGroup.add(seq);
1971       }
1972     }
1973
1974     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1975
1976     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1977     for (int i = 0; i < invertGroup.size(); i++)
1978     {
1979       seqs2[i] = invertGroup.get(i);
1980     }
1981
1982     SlideSequencesCommand ssc;
1983     if (right)
1984     {
1985       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1986               viewport.getGapCharacter());
1987     }
1988     else
1989     {
1990       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1991               viewport.getGapCharacter());
1992     }
1993
1994     int groupAdjustment = 0;
1995     if (ssc.getGapsInsertedBegin() && right)
1996     {
1997       if (viewport.cursorMode)
1998       {
1999         alignPanel.getSeqPanel().moveCursor(size, 0);
2000       }
2001       else
2002       {
2003         groupAdjustment = size;
2004       }
2005     }
2006     else if (!ssc.getGapsInsertedBegin() && !right)
2007     {
2008       if (viewport.cursorMode)
2009       {
2010         alignPanel.getSeqPanel().moveCursor(-size, 0);
2011       }
2012       else
2013       {
2014         groupAdjustment = -size;
2015       }
2016     }
2017
2018     if (groupAdjustment != 0)
2019     {
2020       viewport.getSelectionGroup().setStartRes(
2021               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2022       viewport.getSelectionGroup().setEndRes(
2023               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2024     }
2025
2026     /*
2027      * just extend the last slide command if compatible; but not if in
2028      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2029      */
2030     boolean appendHistoryItem = false;
2031     Deque<CommandI> historyList = viewport.getHistoryList();
2032     boolean inSplitFrame = getSplitViewContainer() != null;
2033     if (!inSplitFrame && historyList != null && historyList.size() > 0
2034             && historyList.peek() instanceof SlideSequencesCommand)
2035     {
2036       appendHistoryItem = ssc.appendSlideCommand(
2037               (SlideSequencesCommand) historyList.peek());
2038     }
2039
2040     if (!appendHistoryItem)
2041     {
2042       addHistoryItem(ssc);
2043     }
2044
2045     repaint();
2046   }
2047
2048   /**
2049    * DOCUMENT ME!
2050    *
2051    * @param e
2052    *          DOCUMENT ME!
2053    */
2054   @Override
2055   protected void copy_actionPerformed(ActionEvent e)
2056   {
2057     System.gc();
2058     if (viewport.getSelectionGroup() == null)
2059     {
2060       return;
2061     }
2062     // TODO: preserve the ordering of displayed alignment annotation in any
2063     // internal paste (particularly sequence associated annotation)
2064     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2065     String[] omitHidden = null;
2066
2067     if (viewport.hasHiddenColumns())
2068     {
2069       omitHidden = viewport.getViewAsString(true);
2070     }
2071
2072     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2073             seqs, omitHidden, null);
2074
2075     StringSelection ss = new StringSelection(output);
2076
2077     try
2078     {
2079       jalview.gui.Desktop.internalCopy = true;
2080       // Its really worth setting the clipboard contents
2081       // to empty before setting the large StringSelection!!
2082       Toolkit.getDefaultToolkit().getSystemClipboard()
2083               .setContents(new StringSelection(""), null);
2084
2085       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2086               Desktop.instance);
2087     } catch (OutOfMemoryError er)
2088     {
2089       new OOMWarning("copying region", er);
2090       return;
2091     }
2092
2093     HiddenColumns hiddenColumns = null;
2094     if (viewport.hasHiddenColumns())
2095     {
2096       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2097       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2098
2099       // create new HiddenColumns object with copy of hidden regions
2100       // between startRes and endRes, offset by startRes
2101       hiddenColumns = new HiddenColumns(
2102               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2103               hiddenCutoff, hiddenOffset);
2104     }
2105
2106     Desktop.jalviewClipboard = new Object[] { seqs,
2107         viewport.getAlignment().getDataset(), hiddenColumns };
2108     statusBar.setText(MessageManager.formatMessage(
2109             "label.copied_sequences_to_clipboard", new Object[]
2110             { Integer.valueOf(seqs.length).toString() }));
2111   }
2112
2113   /**
2114    * DOCUMENT ME!
2115    *
2116    * @param e
2117    *          DOCUMENT ME!
2118    * @throws InterruptedException
2119    * @throws IOException
2120    */
2121   @Override
2122   protected void pasteNew_actionPerformed(ActionEvent e)
2123           throws IOException, InterruptedException
2124   {
2125     paste(true);
2126   }
2127
2128   /**
2129    * DOCUMENT ME!
2130    *
2131    * @param e
2132    *          DOCUMENT ME!
2133    * @throws InterruptedException
2134    * @throws IOException
2135    */
2136   @Override
2137   protected void pasteThis_actionPerformed(ActionEvent e)
2138           throws IOException, InterruptedException
2139   {
2140     paste(false);
2141   }
2142
2143   /**
2144    * Paste contents of Jalview clipboard
2145    *
2146    * @param newAlignment
2147    *          true to paste to a new alignment, otherwise add to this.
2148    * @throws InterruptedException
2149    * @throws IOException
2150    */
2151   void paste(boolean newAlignment) throws IOException, InterruptedException
2152   {
2153     boolean externalPaste = true;
2154     try
2155     {
2156       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2157       Transferable contents = c.getContents(this);
2158
2159       if (contents == null)
2160       {
2161         return;
2162       }
2163
2164       String str;
2165       FileFormatI format;
2166       try
2167       {
2168         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2169         if (str.length() < 1)
2170         {
2171           return;
2172         }
2173
2174         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2175
2176       } catch (OutOfMemoryError er)
2177       {
2178         new OOMWarning("Out of memory pasting sequences!!", er);
2179         return;
2180       }
2181
2182       SequenceI[] sequences;
2183       boolean annotationAdded = false;
2184       AlignmentI alignment = null;
2185
2186       if (Desktop.jalviewClipboard != null)
2187       {
2188         // The clipboard was filled from within Jalview, we must use the
2189         // sequences
2190         // And dataset from the copied alignment
2191         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2192         // be doubly sure that we create *new* sequence objects.
2193         sequences = new SequenceI[newseq.length];
2194         for (int i = 0; i < newseq.length; i++)
2195         {
2196           sequences[i] = new Sequence(newseq[i]);
2197         }
2198         alignment = new Alignment(sequences);
2199         externalPaste = false;
2200       }
2201       else
2202       {
2203         // parse the clipboard as an alignment.
2204         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2205                 format);
2206         sequences = alignment.getSequencesArray();
2207       }
2208
2209       int alwidth = 0;
2210       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2211       int fgroup = -1;
2212
2213       if (newAlignment)
2214       {
2215
2216         if (Desktop.jalviewClipboard != null)
2217         {
2218           // dataset is inherited
2219           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2220         }
2221         else
2222         {
2223           // new dataset is constructed
2224           alignment.setDataset(null);
2225         }
2226         alwidth = alignment.getWidth() + 1;
2227       }
2228       else
2229       {
2230         AlignmentI pastedal = alignment; // preserve pasted alignment object
2231         // Add pasted sequences and dataset into existing alignment.
2232         alignment = viewport.getAlignment();
2233         alwidth = alignment.getWidth() + 1;
2234         // decide if we need to import sequences from an existing dataset
2235         boolean importDs = Desktop.jalviewClipboard != null
2236                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2237         // importDs==true instructs us to copy over new dataset sequences from
2238         // an existing alignment
2239         Vector newDs = (importDs) ? new Vector() : null; // used to create
2240         // minimum dataset set
2241
2242         for (int i = 0; i < sequences.length; i++)
2243         {
2244           if (importDs)
2245           {
2246             newDs.addElement(null);
2247           }
2248           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2249           // paste
2250           if (importDs && ds != null)
2251           {
2252             if (!newDs.contains(ds))
2253             {
2254               newDs.setElementAt(ds, i);
2255               ds = new Sequence(ds);
2256               // update with new dataset sequence
2257               sequences[i].setDatasetSequence(ds);
2258             }
2259             else
2260             {
2261               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2262             }
2263           }
2264           else
2265           {
2266             // copy and derive new dataset sequence
2267             sequences[i] = sequences[i].deriveSequence();
2268             alignment.getDataset()
2269                     .addSequence(sequences[i].getDatasetSequence());
2270             // TODO: avoid creation of duplicate dataset sequences with a
2271             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2272           }
2273           alignment.addSequence(sequences[i]); // merges dataset
2274         }
2275         if (newDs != null)
2276         {
2277           newDs.clear(); // tidy up
2278         }
2279         if (alignment.getAlignmentAnnotation() != null)
2280         {
2281           for (AlignmentAnnotation alan : alignment
2282                   .getAlignmentAnnotation())
2283           {
2284             if (alan.graphGroup > fgroup)
2285             {
2286               fgroup = alan.graphGroup;
2287             }
2288           }
2289         }
2290         if (pastedal.getAlignmentAnnotation() != null)
2291         {
2292           // Add any annotation attached to alignment.
2293           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2294           for (int i = 0; i < alann.length; i++)
2295           {
2296             annotationAdded = true;
2297             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2298             {
2299               AlignmentAnnotation newann = new AlignmentAnnotation(
2300                       alann[i]);
2301               if (newann.graphGroup > -1)
2302               {
2303                 if (newGraphGroups.size() <= newann.graphGroup
2304                         || newGraphGroups.get(newann.graphGroup) == null)
2305                 {
2306                   for (int q = newGraphGroups
2307                           .size(); q <= newann.graphGroup; q++)
2308                   {
2309                     newGraphGroups.add(q, null);
2310                   }
2311                   newGraphGroups.set(newann.graphGroup,
2312                           new Integer(++fgroup));
2313                 }
2314                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2315                         .intValue();
2316               }
2317
2318               newann.padAnnotation(alwidth);
2319               alignment.addAnnotation(newann);
2320             }
2321           }
2322         }
2323       }
2324       if (!newAlignment)
2325       {
2326         // /////
2327         // ADD HISTORY ITEM
2328         //
2329         addHistoryItem(new EditCommand(
2330                 MessageManager.getString("label.add_sequences"),
2331                 Action.PASTE, sequences, 0, alignment.getWidth(),
2332                 alignment));
2333       }
2334       // Add any annotations attached to sequences
2335       for (int i = 0; i < sequences.length; i++)
2336       {
2337         if (sequences[i].getAnnotation() != null)
2338         {
2339           AlignmentAnnotation newann;
2340           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2341           {
2342             annotationAdded = true;
2343             newann = sequences[i].getAnnotation()[a];
2344             newann.adjustForAlignment();
2345             newann.padAnnotation(alwidth);
2346             if (newann.graphGroup > -1)
2347             {
2348               if (newann.graphGroup > -1)
2349               {
2350                 if (newGraphGroups.size() <= newann.graphGroup
2351                         || newGraphGroups.get(newann.graphGroup) == null)
2352                 {
2353                   for (int q = newGraphGroups
2354                           .size(); q <= newann.graphGroup; q++)
2355                   {
2356                     newGraphGroups.add(q, null);
2357                   }
2358                   newGraphGroups.set(newann.graphGroup,
2359                           new Integer(++fgroup));
2360                 }
2361                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2362                         .intValue();
2363               }
2364             }
2365             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2366             // was
2367             // duplicated
2368             // earlier
2369             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2370                     a);
2371           }
2372         }
2373       }
2374       if (!newAlignment)
2375       {
2376
2377         // propagate alignment changed.
2378         viewport.getRanges().setEndSeq(alignment.getHeight());
2379         if (annotationAdded)
2380         {
2381           // Duplicate sequence annotation in all views.
2382           AlignmentI[] alview = this.getViewAlignments();
2383           for (int i = 0; i < sequences.length; i++)
2384           {
2385             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2386             if (sann == null)
2387             {
2388               continue;
2389             }
2390             for (int avnum = 0; avnum < alview.length; avnum++)
2391             {
2392               if (alview[avnum] != alignment)
2393               {
2394                 // duplicate in a view other than the one with input focus
2395                 int avwidth = alview[avnum].getWidth() + 1;
2396                 // this relies on sann being preserved after we
2397                 // modify the sequence's annotation array for each duplication
2398                 for (int a = 0; a < sann.length; a++)
2399                 {
2400                   AlignmentAnnotation newann = new AlignmentAnnotation(
2401                           sann[a]);
2402                   sequences[i].addAlignmentAnnotation(newann);
2403                   newann.padAnnotation(avwidth);
2404                   alview[avnum].addAnnotation(newann); // annotation was
2405                   // duplicated earlier
2406                   // TODO JAL-1145 graphGroups are not updated for sequence
2407                   // annotation added to several views. This may cause
2408                   // strangeness
2409                   alview[avnum].setAnnotationIndex(newann, a);
2410                 }
2411               }
2412             }
2413           }
2414           buildSortByAnnotationScoresMenu();
2415         }
2416         viewport.firePropertyChange("alignment", null,
2417                 alignment.getSequences());
2418         if (alignPanels != null)
2419         {
2420           for (AlignmentPanel ap : alignPanels)
2421           {
2422             ap.validateAnnotationDimensions(false);
2423           }
2424         }
2425         else
2426         {
2427           alignPanel.validateAnnotationDimensions(false);
2428         }
2429
2430       }
2431       else
2432       {
2433         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2434                 DEFAULT_HEIGHT);
2435         String newtitle = new String("Copied sequences");
2436
2437         if (Desktop.jalviewClipboard != null
2438                 && Desktop.jalviewClipboard[2] != null)
2439         {
2440           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2441           af.viewport.setHiddenColumns(hc);
2442         }
2443
2444         // >>>This is a fix for the moment, until a better solution is
2445         // found!!<<<
2446         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2447                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2448                         .getFeatureRenderer());
2449
2450         // TODO: maintain provenance of an alignment, rather than just make the
2451         // title a concatenation of operations.
2452         if (!externalPaste)
2453         {
2454           if (title.startsWith("Copied sequences"))
2455           {
2456             newtitle = title;
2457           }
2458           else
2459           {
2460             newtitle = newtitle.concat("- from " + title);
2461           }
2462         }
2463         else
2464         {
2465           newtitle = new String("Pasted sequences");
2466         }
2467
2468         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2469                 DEFAULT_HEIGHT);
2470
2471       }
2472
2473     } catch (Exception ex)
2474     {
2475       ex.printStackTrace();
2476       System.out.println("Exception whilst pasting: " + ex);
2477       // could be anything being pasted in here
2478     }
2479   }
2480
2481   @Override
2482   protected void expand_newalign(ActionEvent e)
2483   {
2484     try
2485     {
2486       AlignmentI alignment = AlignmentUtils
2487               .expandContext(getViewport().getAlignment(), -1);
2488       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2489               DEFAULT_HEIGHT);
2490       String newtitle = new String("Flanking alignment");
2491
2492       if (Desktop.jalviewClipboard != null
2493               && Desktop.jalviewClipboard[2] != null)
2494       {
2495         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2496         af.viewport.setHiddenColumns(hc);
2497       }
2498
2499       // >>>This is a fix for the moment, until a better solution is
2500       // found!!<<<
2501       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2502               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2503                       .getFeatureRenderer());
2504
2505       // TODO: maintain provenance of an alignment, rather than just make the
2506       // title a concatenation of operations.
2507       {
2508         if (title.startsWith("Copied sequences"))
2509         {
2510           newtitle = title;
2511         }
2512         else
2513         {
2514           newtitle = newtitle.concat("- from " + title);
2515         }
2516       }
2517
2518       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2519
2520     } catch (Exception ex)
2521     {
2522       ex.printStackTrace();
2523       System.out.println("Exception whilst pasting: " + ex);
2524       // could be anything being pasted in here
2525     } catch (OutOfMemoryError oom)
2526     {
2527       new OOMWarning("Viewing flanking region of alignment", oom);
2528     }
2529   }
2530
2531   /**
2532    * DOCUMENT ME!
2533    *
2534    * @param e
2535    *          DOCUMENT ME!
2536    */
2537   @Override
2538   protected void cut_actionPerformed(ActionEvent e)
2539   {
2540     copy_actionPerformed(null);
2541     delete_actionPerformed(null);
2542   }
2543
2544   /**
2545    * DOCUMENT ME!
2546    *
2547    * @param e
2548    *          DOCUMENT ME!
2549    */
2550   @Override
2551   protected void delete_actionPerformed(ActionEvent evt)
2552   {
2553
2554     SequenceGroup sg = viewport.getSelectionGroup();
2555     if (sg == null)
2556     {
2557       return;
2558     }
2559
2560     /*
2561      * If the cut affects all sequences, warn, remove highlighted columns
2562      */
2563     if (sg.getSize() == viewport.getAlignment().getHeight())
2564     {
2565       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2566               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2567       if (isEntireAlignWidth)
2568       {
2569         int confirm = JvOptionPane.showConfirmDialog(this,
2570                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2571                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2572                 JvOptionPane.OK_CANCEL_OPTION);
2573
2574         if (confirm == JvOptionPane.CANCEL_OPTION
2575                 || confirm == JvOptionPane.CLOSED_OPTION)
2576         {
2577           return;
2578         }
2579       }
2580       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2581               sg.getEndRes() + 1);
2582     }
2583     SequenceI[] cut = sg.getSequences()
2584             .toArray(new SequenceI[sg.getSize()]);
2585
2586     addHistoryItem(new EditCommand(
2587             MessageManager.getString("label.cut_sequences"), Action.CUT,
2588             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2589             viewport.getAlignment()));
2590
2591     viewport.setSelectionGroup(null);
2592     viewport.sendSelection();
2593     viewport.getAlignment().deleteGroup(sg);
2594
2595     viewport.firePropertyChange("alignment", null,
2596             viewport.getAlignment().getSequences());
2597     if (viewport.getAlignment().getHeight() < 1)
2598     {
2599       try
2600       {
2601         this.setClosed(true);
2602       } catch (Exception ex)
2603       {
2604       }
2605     }
2606   }
2607
2608   /**
2609    * DOCUMENT ME!
2610    *
2611    * @param e
2612    *          DOCUMENT ME!
2613    */
2614   @Override
2615   protected void deleteGroups_actionPerformed(ActionEvent e)
2616   {
2617     if (avc.deleteGroups())
2618     {
2619       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2620       alignPanel.updateAnnotation();
2621       alignPanel.paintAlignment(true, true);
2622     }
2623   }
2624
2625   /**
2626    * DOCUMENT ME!
2627    *
2628    * @param e
2629    *          DOCUMENT ME!
2630    */
2631   @Override
2632   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2633   {
2634     SequenceGroup sg = new SequenceGroup();
2635
2636     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2637     {
2638       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2639     }
2640
2641     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2642     viewport.setSelectionGroup(sg);
2643     viewport.sendSelection();
2644     // JAL-2034 - should delegate to
2645     // alignPanel to decide if overview needs
2646     // updating.
2647     alignPanel.paintAlignment(false, false);
2648     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2649   }
2650
2651   /**
2652    * DOCUMENT ME!
2653    *
2654    * @param e
2655    *          DOCUMENT ME!
2656    */
2657   @Override
2658   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2659   {
2660     if (viewport.cursorMode)
2661     {
2662       alignPanel.getSeqPanel().keyboardNo1 = null;
2663       alignPanel.getSeqPanel().keyboardNo2 = null;
2664     }
2665     viewport.setSelectionGroup(null);
2666     viewport.getColumnSelection().clear();
2667     viewport.setSelectionGroup(null);
2668     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2669     // JAL-2034 - should delegate to
2670     // alignPanel to decide if overview needs
2671     // updating.
2672     alignPanel.paintAlignment(false, false);
2673     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2674     viewport.sendSelection();
2675   }
2676
2677   /**
2678    * DOCUMENT ME!
2679    *
2680    * @param e
2681    *          DOCUMENT ME!
2682    */
2683   @Override
2684   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2685   {
2686     SequenceGroup sg = viewport.getSelectionGroup();
2687
2688     if (sg == null)
2689     {
2690       selectAllSequenceMenuItem_actionPerformed(null);
2691
2692       return;
2693     }
2694
2695     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2696     {
2697       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2698     }
2699     // JAL-2034 - should delegate to
2700     // alignPanel to decide if overview needs
2701     // updating.
2702
2703     alignPanel.paintAlignment(true, false);
2704     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2705     viewport.sendSelection();
2706   }
2707
2708   @Override
2709   public void invertColSel_actionPerformed(ActionEvent e)
2710   {
2711     viewport.invertColumnSelection();
2712     alignPanel.paintAlignment(true, false);
2713     viewport.sendSelection();
2714   }
2715
2716   /**
2717    * DOCUMENT ME!
2718    *
2719    * @param e
2720    *          DOCUMENT ME!
2721    */
2722   @Override
2723   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2724   {
2725     trimAlignment(true);
2726   }
2727
2728   /**
2729    * DOCUMENT ME!
2730    *
2731    * @param e
2732    *          DOCUMENT ME!
2733    */
2734   @Override
2735   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2736   {
2737     trimAlignment(false);
2738   }
2739
2740   void trimAlignment(boolean trimLeft)
2741   {
2742     ColumnSelection colSel = viewport.getColumnSelection();
2743     int column;
2744
2745     if (!colSel.isEmpty())
2746     {
2747       if (trimLeft)
2748       {
2749         column = colSel.getMin();
2750       }
2751       else
2752       {
2753         column = colSel.getMax();
2754       }
2755
2756       SequenceI[] seqs;
2757       if (viewport.getSelectionGroup() != null)
2758       {
2759         seqs = viewport.getSelectionGroup()
2760                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2761       }
2762       else
2763       {
2764         seqs = viewport.getAlignment().getSequencesArray();
2765       }
2766
2767       TrimRegionCommand trimRegion;
2768       if (trimLeft)
2769       {
2770         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2771                 column, viewport.getAlignment());
2772         viewport.getRanges().setStartRes(0);
2773       }
2774       else
2775       {
2776         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2777                 column, viewport.getAlignment());
2778       }
2779
2780       statusBar.setText(MessageManager
2781               .formatMessage("label.removed_columns", new String[]
2782               { Integer.valueOf(trimRegion.getSize()).toString() }));
2783
2784       addHistoryItem(trimRegion);
2785
2786       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2787       {
2788         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2789                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2790         {
2791           viewport.getAlignment().deleteGroup(sg);
2792         }
2793       }
2794
2795       viewport.firePropertyChange("alignment", null,
2796               viewport.getAlignment().getSequences());
2797     }
2798   }
2799
2800   /**
2801    * DOCUMENT ME!
2802    *
2803    * @param e
2804    *          DOCUMENT ME!
2805    */
2806   @Override
2807   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2808   {
2809     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2810
2811     SequenceI[] seqs;
2812     if (viewport.getSelectionGroup() != null)
2813     {
2814       seqs = viewport.getSelectionGroup()
2815               .getSequencesAsArray(viewport.getHiddenRepSequences());
2816       start = viewport.getSelectionGroup().getStartRes();
2817       end = viewport.getSelectionGroup().getEndRes();
2818     }
2819     else
2820     {
2821       seqs = viewport.getAlignment().getSequencesArray();
2822     }
2823
2824     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2825             "Remove Gapped Columns", seqs, start, end,
2826             viewport.getAlignment());
2827
2828     addHistoryItem(removeGapCols);
2829
2830     statusBar.setText(MessageManager
2831             .formatMessage("label.removed_empty_columns", new Object[]
2832             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2833
2834     // This is to maintain viewport position on first residue
2835     // of first sequence
2836     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2837     ViewportRanges ranges = viewport.getRanges();
2838     int startRes = seq.findPosition(ranges.getStartRes());
2839     // ShiftList shifts;
2840     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2841     // edit.alColumnChanges=shifts.getInverse();
2842     // if (viewport.hasHiddenColumns)
2843     // viewport.getColumnSelection().compensateForEdits(shifts);
2844     ranges.setStartRes(seq.findIndex(startRes) - 1);
2845     viewport.firePropertyChange("alignment", null,
2846             viewport.getAlignment().getSequences());
2847
2848   }
2849
2850   /**
2851    * DOCUMENT ME!
2852    *
2853    * @param e
2854    *          DOCUMENT ME!
2855    */
2856   @Override
2857   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2858   {
2859     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2860
2861     SequenceI[] seqs;
2862     if (viewport.getSelectionGroup() != null)
2863     {
2864       seqs = viewport.getSelectionGroup()
2865               .getSequencesAsArray(viewport.getHiddenRepSequences());
2866       start = viewport.getSelectionGroup().getStartRes();
2867       end = viewport.getSelectionGroup().getEndRes();
2868     }
2869     else
2870     {
2871       seqs = viewport.getAlignment().getSequencesArray();
2872     }
2873
2874     // This is to maintain viewport position on first residue
2875     // of first sequence
2876     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2877     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2878
2879     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2880             viewport.getAlignment()));
2881
2882     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2883
2884     viewport.firePropertyChange("alignment", null,
2885             viewport.getAlignment().getSequences());
2886
2887   }
2888
2889   /**
2890    * DOCUMENT ME!
2891    *
2892    * @param e
2893    *          DOCUMENT ME!
2894    */
2895   @Override
2896   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2897   {
2898     viewport.setPadGaps(padGapsMenuitem.isSelected());
2899     viewport.firePropertyChange("alignment", null,
2900             viewport.getAlignment().getSequences());
2901   }
2902
2903   /**
2904    * DOCUMENT ME!
2905    *
2906    * @param e
2907    *          DOCUMENT ME!
2908    */
2909   @Override
2910   public void findMenuItem_actionPerformed(ActionEvent e)
2911   {
2912     new Finder();
2913   }
2914
2915   /**
2916    * Create a new view of the current alignment.
2917    */
2918   @Override
2919   public void newView_actionPerformed(ActionEvent e)
2920   {
2921     newView(null, true);
2922   }
2923
2924   /**
2925    * Creates and shows a new view of the current alignment.
2926    *
2927    * @param viewTitle
2928    *          title of newly created view; if null, one will be generated
2929    * @param copyAnnotation
2930    *          if true then duplicate all annnotation, groups and settings
2931    * @return new alignment panel, already displayed.
2932    */
2933   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2934   {
2935     /*
2936      * Create a new AlignmentPanel (with its own, new Viewport)
2937      */
2938     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2939     if (!copyAnnotation)
2940     {
2941       /*
2942        * remove all groups and annotation except for the automatic stuff
2943        */
2944       newap.av.getAlignment().deleteAllGroups();
2945       newap.av.getAlignment().deleteAllAnnotations(false);
2946     }
2947
2948     newap.av.setGatherViewsHere(false);
2949
2950     if (viewport.viewName == null)
2951     {
2952       viewport.viewName = MessageManager
2953               .getString("label.view_name_original");
2954     }
2955
2956     /*
2957      * Views share the same edits undo and redo stacks
2958      */
2959     newap.av.setHistoryList(viewport.getHistoryList());
2960     newap.av.setRedoList(viewport.getRedoList());
2961
2962     /*
2963      * Views share the same mappings; need to deregister any new mappings
2964      * created by copyAlignPanel, and register the new reference to the shared
2965      * mappings
2966      */
2967     newap.av.replaceMappings(viewport.getAlignment());
2968
2969     /*
2970      * start up cDNA consensus (if applicable) now mappings are in place
2971      */
2972     if (newap.av.initComplementConsensus())
2973     {
2974       newap.refresh(true); // adjust layout of annotations
2975     }
2976
2977     newap.av.viewName = getNewViewName(viewTitle);
2978
2979     addAlignmentPanel(newap, true);
2980     newap.alignmentChanged();
2981
2982     if (alignPanels.size() == 2)
2983     {
2984       viewport.setGatherViewsHere(true);
2985     }
2986     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2987     return newap;
2988   }
2989
2990   /**
2991    * Make a new name for the view, ensuring it is unique within the current
2992    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2993    * these now use viewId. Unique view names are still desirable for usability.)
2994    *
2995    * @param viewTitle
2996    * @return
2997    */
2998   protected String getNewViewName(String viewTitle)
2999   {
3000     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3001     boolean addFirstIndex = false;
3002     if (viewTitle == null || viewTitle.trim().length() == 0)
3003     {
3004       viewTitle = MessageManager.getString("action.view");
3005       addFirstIndex = true;
3006     }
3007     else
3008     {
3009       index = 1;// we count from 1 if given a specific name
3010     }
3011     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3012
3013     List<Component> comps = PaintRefresher.components
3014             .get(viewport.getSequenceSetId());
3015
3016     List<String> existingNames = getExistingViewNames(comps);
3017
3018     while (existingNames.contains(newViewName))
3019     {
3020       newViewName = viewTitle + " " + (++index);
3021     }
3022     return newViewName;
3023   }
3024
3025   /**
3026    * Returns a list of distinct view names found in the given list of
3027    * components. View names are held on the viewport of an AlignmentPanel.
3028    *
3029    * @param comps
3030    * @return
3031    */
3032   protected List<String> getExistingViewNames(List<Component> comps)
3033   {
3034     List<String> existingNames = new ArrayList<>();
3035     for (Component comp : comps)
3036     {
3037       if (comp instanceof AlignmentPanel)
3038       {
3039         AlignmentPanel ap = (AlignmentPanel) comp;
3040         if (!existingNames.contains(ap.av.viewName))
3041         {
3042           existingNames.add(ap.av.viewName);
3043         }
3044       }
3045     }
3046     return existingNames;
3047   }
3048
3049   /**
3050    * Explode tabbed views into separate windows.
3051    */
3052   @Override
3053   public void expandViews_actionPerformed(ActionEvent e)
3054   {
3055     Desktop.explodeViews(this);
3056   }
3057
3058   /**
3059    * Gather views in separate windows back into a tabbed presentation.
3060    */
3061   @Override
3062   public void gatherViews_actionPerformed(ActionEvent e)
3063   {
3064     Desktop.instance.gatherViews(this);
3065   }
3066
3067   /**
3068    * DOCUMENT ME!
3069    *
3070    * @param e
3071    *          DOCUMENT ME!
3072    */
3073   @Override
3074   public void font_actionPerformed(ActionEvent e)
3075   {
3076     new FontChooser(alignPanel);
3077   }
3078
3079   /**
3080    * DOCUMENT ME!
3081    *
3082    * @param e
3083    *          DOCUMENT ME!
3084    */
3085   @Override
3086   protected void seqLimit_actionPerformed(ActionEvent e)
3087   {
3088     viewport.setShowJVSuffix(seqLimits.isSelected());
3089
3090     alignPanel.getIdPanel().getIdCanvas()
3091             .setPreferredSize(alignPanel.calculateIdWidth());
3092     alignPanel.paintAlignment(true, false);
3093   }
3094
3095   @Override
3096   public void idRightAlign_actionPerformed(ActionEvent e)
3097   {
3098     viewport.setRightAlignIds(idRightAlign.isSelected());
3099     alignPanel.paintAlignment(false, false);
3100   }
3101
3102   @Override
3103   public void centreColumnLabels_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3106     alignPanel.paintAlignment(false, false);
3107   }
3108
3109   /*
3110    * (non-Javadoc)
3111    *
3112    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3113    */
3114   @Override
3115   protected void followHighlight_actionPerformed()
3116   {
3117     /*
3118      * Set the 'follow' flag on the Viewport (and scroll to position if now
3119      * true).
3120      */
3121     final boolean state = this.followHighlightMenuItem.getState();
3122     viewport.setFollowHighlight(state);
3123     if (state)
3124     {
3125       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3126     }
3127   }
3128
3129   /**
3130    * DOCUMENT ME!
3131    *
3132    * @param e
3133    *          DOCUMENT ME!
3134    */
3135   @Override
3136   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3137   {
3138     viewport.setColourText(colourTextMenuItem.isSelected());
3139     alignPanel.paintAlignment(false, false);
3140   }
3141
3142   /**
3143    * DOCUMENT ME!
3144    *
3145    * @param e
3146    *          DOCUMENT ME!
3147    */
3148   @Override
3149   public void wrapMenuItem_actionPerformed(ActionEvent e)
3150   {
3151     scaleAbove.setVisible(wrapMenuItem.isSelected());
3152     scaleLeft.setVisible(wrapMenuItem.isSelected());
3153     scaleRight.setVisible(wrapMenuItem.isSelected());
3154     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3155     alignPanel.updateLayout();
3156   }
3157
3158   @Override
3159   public void showAllSeqs_actionPerformed(ActionEvent e)
3160   {
3161     viewport.showAllHiddenSeqs();
3162   }
3163
3164   @Override
3165   public void showAllColumns_actionPerformed(ActionEvent e)
3166   {
3167     viewport.showAllHiddenColumns();
3168     alignPanel.paintAlignment(true, true);
3169     viewport.sendSelection();
3170   }
3171
3172   @Override
3173   public void hideSelSequences_actionPerformed(ActionEvent e)
3174   {
3175     viewport.hideAllSelectedSeqs();
3176   }
3177
3178   /**
3179    * called by key handler and the hide all/show all menu items
3180    *
3181    * @param toggleSeqs
3182    * @param toggleCols
3183    */
3184   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3185   {
3186
3187     boolean hide = false;
3188     SequenceGroup sg = viewport.getSelectionGroup();
3189     if (!toggleSeqs && !toggleCols)
3190     {
3191       // Hide everything by the current selection - this is a hack - we do the
3192       // invert and then hide
3193       // first check that there will be visible columns after the invert.
3194       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3195               && sg.getStartRes() <= sg.getEndRes()))
3196       {
3197         // now invert the sequence set, if required - empty selection implies
3198         // that no hiding is required.
3199         if (sg != null)
3200         {
3201           invertSequenceMenuItem_actionPerformed(null);
3202           sg = viewport.getSelectionGroup();
3203           toggleSeqs = true;
3204
3205         }
3206         viewport.expandColSelection(sg, true);
3207         // finally invert the column selection and get the new sequence
3208         // selection.
3209         invertColSel_actionPerformed(null);
3210         toggleCols = true;
3211       }
3212     }
3213
3214     if (toggleSeqs)
3215     {
3216       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3217       {
3218         hideSelSequences_actionPerformed(null);
3219         hide = true;
3220       }
3221       else if (!(toggleCols && viewport.hasSelectedColumns()))
3222       {
3223         showAllSeqs_actionPerformed(null);
3224       }
3225     }
3226
3227     if (toggleCols)
3228     {
3229       if (viewport.hasSelectedColumns())
3230       {
3231         hideSelColumns_actionPerformed(null);
3232         if (!toggleSeqs)
3233         {
3234           viewport.setSelectionGroup(sg);
3235         }
3236       }
3237       else if (!hide)
3238       {
3239         showAllColumns_actionPerformed(null);
3240       }
3241     }
3242   }
3243
3244   /*
3245    * (non-Javadoc)
3246    *
3247    * @see
3248    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3249    * event.ActionEvent)
3250    */
3251   @Override
3252   public void hideAllButSelection_actionPerformed(ActionEvent e)
3253   {
3254     toggleHiddenRegions(false, false);
3255     viewport.sendSelection();
3256   }
3257
3258   /*
3259    * (non-Javadoc)
3260    *
3261    * @see
3262    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3263    * .ActionEvent)
3264    */
3265   @Override
3266   public void hideAllSelection_actionPerformed(ActionEvent e)
3267   {
3268     SequenceGroup sg = viewport.getSelectionGroup();
3269     viewport.expandColSelection(sg, false);
3270     viewport.hideAllSelectedSeqs();
3271     viewport.hideSelectedColumns();
3272     alignPanel.paintAlignment(true, true);
3273     viewport.sendSelection();
3274   }
3275
3276   /*
3277    * (non-Javadoc)
3278    *
3279    * @see
3280    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3281    * ActionEvent)
3282    */
3283   @Override
3284   public void showAllhidden_actionPerformed(ActionEvent e)
3285   {
3286     viewport.showAllHiddenColumns();
3287     viewport.showAllHiddenSeqs();
3288     alignPanel.paintAlignment(true, true);
3289     viewport.sendSelection();
3290   }
3291
3292   @Override
3293   public void hideSelColumns_actionPerformed(ActionEvent e)
3294   {
3295     viewport.hideSelectedColumns();
3296     alignPanel.paintAlignment(true, true);
3297     viewport.sendSelection();
3298   }
3299
3300   @Override
3301   public void hiddenMarkers_actionPerformed(ActionEvent e)
3302   {
3303     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3304     repaint();
3305   }
3306
3307   /**
3308    * DOCUMENT ME!
3309    *
3310    * @param e
3311    *          DOCUMENT ME!
3312    */
3313   @Override
3314   protected void scaleAbove_actionPerformed(ActionEvent e)
3315   {
3316     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3317     // TODO: do we actually need to update overview for scale above change ?
3318     alignPanel.paintAlignment(true, false);
3319   }
3320
3321   /**
3322    * DOCUMENT ME!
3323    *
3324    * @param e
3325    *          DOCUMENT ME!
3326    */
3327   @Override
3328   protected void scaleLeft_actionPerformed(ActionEvent e)
3329   {
3330     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3331     alignPanel.paintAlignment(true, false);
3332   }
3333
3334   /**
3335    * DOCUMENT ME!
3336    *
3337    * @param e
3338    *          DOCUMENT ME!
3339    */
3340   @Override
3341   protected void scaleRight_actionPerformed(ActionEvent e)
3342   {
3343     viewport.setScaleRightWrapped(scaleRight.isSelected());
3344     alignPanel.paintAlignment(true, false);
3345   }
3346
3347   /**
3348    * DOCUMENT ME!
3349    *
3350    * @param e
3351    *          DOCUMENT ME!
3352    */
3353   @Override
3354   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3355   {
3356     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3357     alignPanel.paintAlignment(false, false);
3358   }
3359
3360   /**
3361    * DOCUMENT ME!
3362    *
3363    * @param e
3364    *          DOCUMENT ME!
3365    */
3366   @Override
3367   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3368   {
3369     viewport.setShowText(viewTextMenuItem.isSelected());
3370     alignPanel.paintAlignment(false, false);
3371   }
3372
3373   /**
3374    * DOCUMENT ME!
3375    *
3376    * @param e
3377    *          DOCUMENT ME!
3378    */
3379   @Override
3380   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3381   {
3382     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3383     alignPanel.paintAlignment(false, false);
3384   }
3385
3386   public FeatureSettings featureSettings;
3387
3388   @Override
3389   public FeatureSettingsControllerI getFeatureSettingsUI()
3390   {
3391     return featureSettings;
3392   }
3393
3394   @Override
3395   public void featureSettings_actionPerformed(ActionEvent e)
3396   {
3397     if (featureSettings != null)
3398     {
3399       featureSettings.close();
3400       featureSettings = null;
3401     }
3402     if (!showSeqFeatures.isSelected())
3403     {
3404       // make sure features are actually displayed
3405       showSeqFeatures.setSelected(true);
3406       showSeqFeatures_actionPerformed(null);
3407     }
3408     featureSettings = new FeatureSettings(this);
3409   }
3410
3411   /**
3412    * Set or clear 'Show Sequence Features'
3413    *
3414    * @param evt
3415    *          DOCUMENT ME!
3416    */
3417   @Override
3418   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3419   {
3420     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3421     alignPanel.paintAlignment(true, true);
3422   }
3423
3424   /**
3425    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3426    * the annotations panel as a whole.
3427    *
3428    * The options to show/hide all annotations should be enabled when the panel
3429    * is shown, and disabled when the panel is hidden.
3430    *
3431    * @param e
3432    */
3433   @Override
3434   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3435   {
3436     final boolean setVisible = annotationPanelMenuItem.isSelected();
3437     viewport.setShowAnnotation(setVisible);
3438     this.showAllSeqAnnotations.setEnabled(setVisible);
3439     this.hideAllSeqAnnotations.setEnabled(setVisible);
3440     this.showAllAlAnnotations.setEnabled(setVisible);
3441     this.hideAllAlAnnotations.setEnabled(setVisible);
3442     alignPanel.updateLayout();
3443   }
3444
3445   @Override
3446   public void alignmentProperties()
3447   {
3448     JEditorPane editPane = new JEditorPane("text/html", "");
3449     editPane.setEditable(false);
3450     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3451             .formatAsHtml();
3452     editPane.setText(
3453             MessageManager.formatMessage("label.html_content", new Object[]
3454             { contents.toString() }));
3455     JInternalFrame frame = new JInternalFrame();
3456     frame.getContentPane().add(new JScrollPane(editPane));
3457
3458     Desktop.addInternalFrame(frame, MessageManager
3459             .formatMessage("label.alignment_properties", new Object[]
3460             { getTitle() }), 500, 400);
3461   }
3462
3463   /**
3464    * DOCUMENT ME!
3465    *
3466    * @param e
3467    *          DOCUMENT ME!
3468    */
3469   @Override
3470   public void overviewMenuItem_actionPerformed(ActionEvent e)
3471   {
3472     if (alignPanel.overviewPanel != null)
3473     {
3474       return;
3475     }
3476
3477     JInternalFrame frame = new JInternalFrame();
3478     final OverviewPanel overview = new OverviewPanel(alignPanel);
3479     frame.setContentPane(overview);
3480     Desktop.addInternalFrame(frame, MessageManager
3481             .formatMessage("label.overview_params", new Object[]
3482             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3483             true, true);
3484     frame.pack();
3485     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3486     frame.addInternalFrameListener(
3487             new javax.swing.event.InternalFrameAdapter()
3488             {
3489               @Override
3490               public void internalFrameClosed(
3491                       javax.swing.event.InternalFrameEvent evt)
3492               {
3493                 overview.dispose();
3494                 alignPanel.setOverviewPanel(null);
3495               };
3496             });
3497
3498     alignPanel.setOverviewPanel(overview);
3499   }
3500
3501   @Override
3502   public void textColour_actionPerformed()
3503   {
3504     new TextColourChooser().chooseColour(alignPanel, null);
3505   }
3506
3507   /*
3508    * public void covariationColour_actionPerformed() {
3509    * changeColour(new
3510    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3511    * ()[0])); }
3512    */
3513   @Override
3514   public void annotationColour_actionPerformed()
3515   {
3516     new AnnotationColourChooser(viewport, alignPanel);
3517   }
3518
3519   @Override
3520   public void annotationColumn_actionPerformed(ActionEvent e)
3521   {
3522     new AnnotationColumnChooser(viewport, alignPanel);
3523   }
3524
3525   /**
3526    * Action on the user checking or unchecking the option to apply the selected
3527    * colour scheme to all groups. If unchecked, groups may have their own
3528    * independent colour schemes.
3529    *
3530    * @param selected
3531    */
3532   @Override
3533   public void applyToAllGroups_actionPerformed(boolean selected)
3534   {
3535     viewport.setColourAppliesToAllGroups(selected);
3536   }
3537
3538   /**
3539    * Action on user selecting a colour from the colour menu
3540    *
3541    * @param name
3542    *          the name (not the menu item label!) of the colour scheme
3543    */
3544   @Override
3545   public void changeColour_actionPerformed(String name)
3546   {
3547     /*
3548      * 'User Defined' opens a panel to configure or load a
3549      * user-defined colour scheme
3550      */
3551     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3552     {
3553       new UserDefinedColours(alignPanel);
3554       return;
3555     }
3556
3557     /*
3558      * otherwise set the chosen colour scheme (or null for 'None')
3559      */
3560     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3561             viewport.getAlignment(), viewport.getHiddenRepSequences());
3562     changeColour(cs);
3563   }
3564
3565   /**
3566    * Actions on setting or changing the alignment colour scheme
3567    *
3568    * @param cs
3569    */
3570   @Override
3571   public void changeColour(ColourSchemeI cs)
3572   {
3573     // TODO: pull up to controller method
3574     ColourMenuHelper.setColourSelected(colourMenu, cs);
3575
3576     viewport.setGlobalColourScheme(cs);
3577
3578     alignPanel.paintAlignment(true, true);
3579   }
3580
3581   /**
3582    * Show the PID threshold slider panel
3583    */
3584   @Override
3585   protected void modifyPID_actionPerformed()
3586   {
3587     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3588             alignPanel.getViewName());
3589     SliderPanel.showPIDSlider();
3590   }
3591
3592   /**
3593    * Show the Conservation slider panel
3594    */
3595   @Override
3596   protected void modifyConservation_actionPerformed()
3597   {
3598     SliderPanel.setConservationSlider(alignPanel,
3599             viewport.getResidueShading(), alignPanel.getViewName());
3600     SliderPanel.showConservationSlider();
3601   }
3602
3603   /**
3604    * Action on selecting or deselecting (Colour) By Conservation
3605    */
3606   @Override
3607   public void conservationMenuItem_actionPerformed(boolean selected)
3608   {
3609     modifyConservation.setEnabled(selected);
3610     viewport.setConservationSelected(selected);
3611     viewport.getResidueShading().setConservationApplied(selected);
3612
3613     changeColour(viewport.getGlobalColourScheme());
3614     if (selected)
3615     {
3616       modifyConservation_actionPerformed();
3617     }
3618     else
3619     {
3620       SliderPanel.hideConservationSlider();
3621     }
3622   }
3623
3624   /**
3625    * Action on selecting or deselecting (Colour) Above PID Threshold
3626    */
3627   @Override
3628   public void abovePIDThreshold_actionPerformed(boolean selected)
3629   {
3630     modifyPID.setEnabled(selected);
3631     viewport.setAbovePIDThreshold(selected);
3632     if (!selected)
3633     {
3634       viewport.getResidueShading().setThreshold(0,
3635               viewport.isIgnoreGapsConsensus());
3636     }
3637
3638     changeColour(viewport.getGlobalColourScheme());
3639     if (selected)
3640     {
3641       modifyPID_actionPerformed();
3642     }
3643     else
3644     {
3645       SliderPanel.hidePIDSlider();
3646     }
3647   }
3648
3649   /**
3650    * DOCUMENT ME!
3651    *
3652    * @param e
3653    *          DOCUMENT ME!
3654    */
3655   @Override
3656   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3657   {
3658     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3659     AlignmentSorter.sortByPID(viewport.getAlignment(),
3660             viewport.getAlignment().getSequenceAt(0));
3661     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3662             viewport.getAlignment()));
3663     alignPanel.paintAlignment(true, false);
3664   }
3665
3666   /**
3667    * DOCUMENT ME!
3668    *
3669    * @param e
3670    *          DOCUMENT ME!
3671    */
3672   @Override
3673   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3674   {
3675     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3676     AlignmentSorter.sortByID(viewport.getAlignment());
3677     addHistoryItem(
3678             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3679     alignPanel.paintAlignment(true, false);
3680   }
3681
3682   /**
3683    * DOCUMENT ME!
3684    *
3685    * @param e
3686    *          DOCUMENT ME!
3687    */
3688   @Override
3689   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3690   {
3691     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3692     AlignmentSorter.sortByLength(viewport.getAlignment());
3693     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3694             viewport.getAlignment()));
3695     alignPanel.paintAlignment(true, false);
3696   }
3697
3698   /**
3699    * DOCUMENT ME!
3700    *
3701    * @param e
3702    *          DOCUMENT ME!
3703    */
3704   @Override
3705   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3706   {
3707     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3708     AlignmentSorter.sortByGroup(viewport.getAlignment());
3709     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3710             viewport.getAlignment()));
3711
3712     alignPanel.paintAlignment(true, false);
3713   }
3714
3715   /**
3716    * DOCUMENT ME!
3717    *
3718    * @param e
3719    *          DOCUMENT ME!
3720    */
3721   @Override
3722   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3723   {
3724     new RedundancyPanel(alignPanel, this);
3725   }
3726
3727   /**
3728    * DOCUMENT ME!
3729    *
3730    * @param e
3731    *          DOCUMENT ME!
3732    */
3733   @Override
3734   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3735   {
3736     if ((viewport.getSelectionGroup() == null)
3737             || (viewport.getSelectionGroup().getSize() < 2))
3738     {
3739       JvOptionPane.showInternalMessageDialog(this,
3740               MessageManager.getString(
3741                       "label.you_must_select_least_two_sequences"),
3742               MessageManager.getString("label.invalid_selection"),
3743               JvOptionPane.WARNING_MESSAGE);
3744     }
3745     else
3746     {
3747       JInternalFrame frame = new JInternalFrame();
3748       frame.setContentPane(new PairwiseAlignPanel(viewport));
3749       Desktop.addInternalFrame(frame,
3750               MessageManager.getString("action.pairwise_alignment"), 600,
3751               500);
3752     }
3753   }
3754
3755   @Override
3756   public void autoCalculate_actionPerformed(ActionEvent e)
3757   {
3758     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3759     if (viewport.autoCalculateConsensus)
3760     {
3761       viewport.firePropertyChange("alignment", null,
3762               viewport.getAlignment().getSequences());
3763     }
3764   }
3765
3766   @Override
3767   public void sortByTreeOption_actionPerformed(ActionEvent e)
3768   {
3769     viewport.sortByTree = sortByTree.isSelected();
3770   }
3771
3772   @Override
3773   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3774   {
3775     viewport.followSelection = listenToViewSelections.isSelected();
3776   }
3777
3778   /**
3779    * Constructs a tree panel and adds it to the desktop
3780    *
3781    * @param type
3782    *          tree type (NJ or AV)
3783    * @param modelName
3784    *          name of score model used to compute the tree
3785    * @param options
3786    *          parameters for the distance or similarity calculation
3787    */
3788   void newTreePanel(String type, String modelName,
3789           SimilarityParamsI options)
3790   {
3791     String frameTitle = "";
3792     TreePanel tp;
3793
3794     boolean onSelection = false;
3795     if (viewport.getSelectionGroup() != null
3796             && viewport.getSelectionGroup().getSize() > 0)
3797     {
3798       SequenceGroup sg = viewport.getSelectionGroup();
3799
3800       /* Decide if the selection is a column region */
3801       for (SequenceI _s : sg.getSequences())
3802       {
3803         if (_s.getLength() < sg.getEndRes())
3804         {
3805           JvOptionPane.showMessageDialog(Desktop.desktop,
3806                   MessageManager.getString(
3807                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3808                   MessageManager.getString(
3809                           "label.sequences_selection_not_aligned"),
3810                   JvOptionPane.WARNING_MESSAGE);
3811
3812           return;
3813         }
3814       }
3815       onSelection = true;
3816     }
3817     else
3818     {
3819       if (viewport.getAlignment().getHeight() < 2)
3820       {
3821         return;
3822       }
3823     }
3824
3825     tp = new TreePanel(alignPanel, type, modelName, options);
3826     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3827
3828     frameTitle += " from ";
3829
3830     if (viewport.viewName != null)
3831     {
3832       frameTitle += viewport.viewName + " of ";
3833     }
3834
3835     frameTitle += this.title;
3836
3837     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3838   }
3839
3840   /**
3841    * DOCUMENT ME!
3842    *
3843    * @param title
3844    *          DOCUMENT ME!
3845    * @param order
3846    *          DOCUMENT ME!
3847    */
3848   public void addSortByOrderMenuItem(String title,
3849           final AlignmentOrder order)
3850   {
3851     final JMenuItem item = new JMenuItem(MessageManager
3852             .formatMessage("action.by_title_param", new Object[]
3853             { title }));
3854     sort.add(item);
3855     item.addActionListener(new java.awt.event.ActionListener()
3856     {
3857       @Override
3858       public void actionPerformed(ActionEvent e)
3859       {
3860         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3861
3862         // TODO: JBPNote - have to map order entries to curent SequenceI
3863         // pointers
3864         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3865
3866         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3867                 viewport.getAlignment()));
3868
3869         alignPanel.paintAlignment(true, false);
3870       }
3871     });
3872   }
3873
3874   /**
3875    * Add a new sort by annotation score menu item
3876    *
3877    * @param sort
3878    *          the menu to add the option to
3879    * @param scoreLabel
3880    *          the label used to retrieve scores for each sequence on the
3881    *          alignment
3882    */
3883   public void addSortByAnnotScoreMenuItem(JMenu sort,
3884           final String scoreLabel)
3885   {
3886     final JMenuItem item = new JMenuItem(scoreLabel);
3887     sort.add(item);
3888     item.addActionListener(new java.awt.event.ActionListener()
3889     {
3890       @Override
3891       public void actionPerformed(ActionEvent e)
3892       {
3893         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3894         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3895                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3896         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3897                 viewport.getAlignment()));
3898         alignPanel.paintAlignment(true, false);
3899       }
3900     });
3901   }
3902
3903   /**
3904    * last hash for alignment's annotation array - used to minimise cost of
3905    * rebuild.
3906    */
3907   protected int _annotationScoreVectorHash;
3908
3909   /**
3910    * search the alignment and rebuild the sort by annotation score submenu the
3911    * last alignment annotation vector hash is stored to minimize cost of
3912    * rebuilding in subsequence calls.
3913    *
3914    */
3915   @Override
3916   public void buildSortByAnnotationScoresMenu()
3917   {
3918     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3919     {
3920       return;
3921     }
3922
3923     if (viewport.getAlignment().getAlignmentAnnotation()
3924             .hashCode() != _annotationScoreVectorHash)
3925     {
3926       sortByAnnotScore.removeAll();
3927       // almost certainly a quicker way to do this - but we keep it simple
3928       Hashtable scoreSorts = new Hashtable();
3929       AlignmentAnnotation aann[];
3930       for (SequenceI sqa : viewport.getAlignment().getSequences())
3931       {
3932         aann = sqa.getAnnotation();
3933         for (int i = 0; aann != null && i < aann.length; i++)
3934         {
3935           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3936           {
3937             scoreSorts.put(aann[i].label, aann[i].label);
3938           }
3939         }
3940       }
3941       Enumeration labels = scoreSorts.keys();
3942       while (labels.hasMoreElements())
3943       {
3944         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3945                 (String) labels.nextElement());
3946       }
3947       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3948       scoreSorts.clear();
3949
3950       _annotationScoreVectorHash = viewport.getAlignment()
3951               .getAlignmentAnnotation().hashCode();
3952     }
3953   }
3954
3955   /**
3956    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3957    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3958    * call. Listeners are added to remove the menu item when the treePanel is
3959    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3960    * modified.
3961    */
3962   @Override
3963   public void buildTreeSortMenu()
3964   {
3965     sortByTreeMenu.removeAll();
3966
3967     List<Component> comps = PaintRefresher.components
3968             .get(viewport.getSequenceSetId());
3969     List<TreePanel> treePanels = new ArrayList<>();
3970     for (Component comp : comps)
3971     {
3972       if (comp instanceof TreePanel)
3973       {
3974         treePanels.add((TreePanel) comp);
3975       }
3976     }
3977
3978     if (treePanels.size() < 1)
3979     {
3980       sortByTreeMenu.setVisible(false);
3981       return;
3982     }
3983
3984     sortByTreeMenu.setVisible(true);
3985
3986     for (final TreePanel tp : treePanels)
3987     {
3988       final JMenuItem item = new JMenuItem(tp.getTitle());
3989       item.addActionListener(new java.awt.event.ActionListener()
3990       {
3991         @Override
3992         public void actionPerformed(ActionEvent e)
3993         {
3994           tp.sortByTree_actionPerformed();
3995           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3996
3997         }
3998       });
3999
4000       sortByTreeMenu.add(item);
4001     }
4002   }
4003
4004   public boolean sortBy(AlignmentOrder alorder, String undoname)
4005   {
4006     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4007     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4008     if (undoname != null)
4009     {
4010       addHistoryItem(new OrderCommand(undoname, oldOrder,
4011               viewport.getAlignment()));
4012     }
4013     alignPanel.paintAlignment(true, false);
4014     return true;
4015   }
4016
4017   /**
4018    * Work out whether the whole set of sequences or just the selected set will
4019    * be submitted for multiple alignment.
4020    *
4021    */
4022   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4023   {
4024     // Now, check we have enough sequences
4025     AlignmentView msa = null;
4026
4027     if ((viewport.getSelectionGroup() != null)
4028             && (viewport.getSelectionGroup().getSize() > 1))
4029     {
4030       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4031       // some common interface!
4032       /*
4033        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4034        * SequenceI[sz = seqs.getSize(false)];
4035        *
4036        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4037        * seqs.getSequenceAt(i); }
4038        */
4039       msa = viewport.getAlignmentView(true);
4040     }
4041     else if (viewport.getSelectionGroup() != null
4042             && viewport.getSelectionGroup().getSize() == 1)
4043     {
4044       int option = JvOptionPane.showConfirmDialog(this,
4045               MessageManager.getString("warn.oneseq_msainput_selection"),
4046               MessageManager.getString("label.invalid_selection"),
4047               JvOptionPane.OK_CANCEL_OPTION);
4048       if (option == JvOptionPane.OK_OPTION)
4049       {
4050         msa = viewport.getAlignmentView(false);
4051       }
4052     }
4053     else
4054     {
4055       msa = viewport.getAlignmentView(false);
4056     }
4057     return msa;
4058   }
4059
4060   /**
4061    * Decides what is submitted to a secondary structure prediction service: the
4062    * first sequence in the alignment, or in the current selection, or, if the
4063    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4064    * region or the whole alignment. (where the first sequence in the set is the
4065    * one that the prediction will be for).
4066    */
4067   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4068   {
4069     AlignmentView seqs = null;
4070
4071     if ((viewport.getSelectionGroup() != null)
4072             && (viewport.getSelectionGroup().getSize() > 0))
4073     {
4074       seqs = viewport.getAlignmentView(true);
4075     }
4076     else
4077     {
4078       seqs = viewport.getAlignmentView(false);
4079     }
4080     // limit sequences - JBPNote in future - could spawn multiple prediction
4081     // jobs
4082     // TODO: viewport.getAlignment().isAligned is a global state - the local
4083     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4084     if (!viewport.getAlignment().isAligned(false))
4085     {
4086       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4087       // TODO: if seqs.getSequences().length>1 then should really have warned
4088       // user!
4089
4090     }
4091     return seqs;
4092   }
4093
4094   /**
4095    * DOCUMENT ME!
4096    *
4097    * @param e
4098    *          DOCUMENT ME!
4099    */
4100   @Override
4101   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4102   {
4103     // Pick the tree file
4104     JalviewFileChooser chooser = new JalviewFileChooser(
4105             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4106     chooser.setFileView(new JalviewFileView());
4107     chooser.setDialogTitle(
4108             MessageManager.getString("label.select_newick_like_tree_file"));
4109     chooser.setToolTipText(
4110             MessageManager.getString("label.load_tree_file"));
4111
4112     int value = chooser.showOpenDialog(null);
4113
4114     if (value == JalviewFileChooser.APPROVE_OPTION)
4115     {
4116       String filePath = chooser.getSelectedFile().getPath();
4117       Cache.setProperty("LAST_DIRECTORY", filePath);
4118       NewickFile fin = null;
4119       try
4120       {
4121         fin = new NewickFile(filePath, DataSourceType.FILE);
4122         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4123       } catch (Exception ex)
4124       {
4125         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4126                 MessageManager.getString("label.problem_reading_tree_file"),
4127                 JvOptionPane.WARNING_MESSAGE);
4128         ex.printStackTrace();
4129       }
4130       if (fin != null && fin.hasWarningMessage())
4131       {
4132         JvOptionPane.showMessageDialog(Desktop.desktop,
4133                 fin.getWarningMessage(),
4134                 MessageManager
4135                         .getString("label.possible_problem_with_tree_file"),
4136                 JvOptionPane.WARNING_MESSAGE);
4137       }
4138     }
4139   }
4140
4141   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4142   {
4143     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4144   }
4145
4146   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4147           int h, int x, int y)
4148   {
4149     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4150   }
4151
4152   /**
4153    * Add a treeviewer for the tree extracted from a Newick file object to the
4154    * current alignment view
4155    *
4156    * @param nf
4157    *          the tree
4158    * @param title
4159    *          tree viewer title
4160    * @param input
4161    *          Associated alignment input data (or null)
4162    * @param w
4163    *          width
4164    * @param h
4165    *          height
4166    * @param x
4167    *          position
4168    * @param y
4169    *          position
4170    * @return TreePanel handle
4171    */
4172   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4173           AlignmentView input, int w, int h, int x, int y)
4174   {
4175     TreePanel tp = null;
4176
4177     try
4178     {
4179       nf.parse();
4180
4181       if (nf.getTree() != null)
4182       {
4183         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4184
4185         tp.setSize(w, h);
4186
4187         if (x > 0 && y > 0)
4188         {
4189           tp.setLocation(x, y);
4190         }
4191
4192         Desktop.addInternalFrame(tp, treeTitle, w, h);
4193       }
4194     } catch (Exception ex)
4195     {
4196       ex.printStackTrace();
4197     }
4198
4199     return tp;
4200   }
4201
4202   private boolean buildingMenu = false;
4203
4204   /**
4205    * Generates menu items and listener event actions for web service clients
4206    *
4207    */
4208   public void BuildWebServiceMenu()
4209   {
4210     while (buildingMenu)
4211     {
4212       try
4213       {
4214         System.err.println("Waiting for building menu to finish.");
4215         Thread.sleep(10);
4216       } catch (Exception e)
4217       {
4218       }
4219     }
4220     final AlignFrame me = this;
4221     buildingMenu = true;
4222     new Thread(new Runnable()
4223     {
4224       @Override
4225       public void run()
4226       {
4227         final List<JMenuItem> legacyItems = new ArrayList<>();
4228         try
4229         {
4230           // System.err.println("Building ws menu again "
4231           // + Thread.currentThread());
4232           // TODO: add support for context dependent disabling of services based
4233           // on
4234           // alignment and current selection
4235           // TODO: add additional serviceHandle parameter to specify abstract
4236           // handler
4237           // class independently of AbstractName
4238           // TODO: add in rediscovery GUI function to restart discoverer
4239           // TODO: group services by location as well as function and/or
4240           // introduce
4241           // object broker mechanism.
4242           final Vector<JMenu> wsmenu = new Vector<>();
4243           final IProgressIndicator af = me;
4244
4245           /*
4246            * do not i18n these strings - they are hard-coded in class
4247            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4248            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4249            */
4250           final JMenu msawsmenu = new JMenu("Alignment");
4251           final JMenu secstrmenu = new JMenu(
4252                   "Secondary Structure Prediction");
4253           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4254           final JMenu analymenu = new JMenu("Analysis");
4255           final JMenu dismenu = new JMenu("Protein Disorder");
4256           // JAL-940 - only show secondary structure prediction services from
4257           // the legacy server
4258           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4259               // &&
4260           Discoverer.services != null && (Discoverer.services.size() > 0))
4261           {
4262             // TODO: refactor to allow list of AbstractName/Handler bindings to
4263             // be
4264             // stored or retrieved from elsewhere
4265             // No MSAWS used any more:
4266             // Vector msaws = null; // (Vector)
4267             // Discoverer.services.get("MsaWS");
4268             Vector secstrpr = (Vector) Discoverer.services
4269                     .get("SecStrPred");
4270             if (secstrpr != null)
4271             {
4272               // Add any secondary structure prediction services
4273               for (int i = 0, j = secstrpr.size(); i < j; i++)
4274               {
4275                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4276                         .get(i);
4277                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4278                         .getServiceClient(sh);
4279                 int p = secstrmenu.getItemCount();
4280                 impl.attachWSMenuEntry(secstrmenu, me);
4281                 int q = secstrmenu.getItemCount();
4282                 for (int litm = p; litm < q; litm++)
4283                 {
4284                   legacyItems.add(secstrmenu.getItem(litm));
4285                 }
4286               }
4287             }
4288           }
4289
4290           // Add all submenus in the order they should appear on the web
4291           // services menu
4292           wsmenu.add(msawsmenu);
4293           wsmenu.add(secstrmenu);
4294           wsmenu.add(dismenu);
4295           wsmenu.add(analymenu);
4296           // No search services yet
4297           // wsmenu.add(seqsrchmenu);
4298
4299           javax.swing.SwingUtilities.invokeLater(new Runnable()
4300           {
4301             @Override
4302             public void run()
4303             {
4304               try
4305               {
4306                 webService.removeAll();
4307                 // first, add discovered services onto the webservices menu
4308                 if (wsmenu.size() > 0)
4309                 {
4310                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4311                   {
4312                     webService.add(wsmenu.get(i));
4313                   }
4314                 }
4315                 else
4316                 {
4317                   webService.add(me.webServiceNoServices);
4318                 }
4319                 // TODO: move into separate menu builder class.
4320                 boolean new_sspred = false;
4321                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4322                 {
4323                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4324                   if (jws2servs != null)
4325                   {
4326                     if (jws2servs.hasServices())
4327                     {
4328                       jws2servs.attachWSMenuEntry(webService, me);
4329                       for (Jws2Instance sv : jws2servs.getServices())
4330                       {
4331                         if (sv.description.toLowerCase().contains("jpred"))
4332                         {
4333                           for (JMenuItem jmi : legacyItems)
4334                           {
4335                             jmi.setVisible(false);
4336                           }
4337                         }
4338                       }
4339
4340                     }
4341                     if (jws2servs.isRunning())
4342                     {
4343                       JMenuItem tm = new JMenuItem(
4344                               "Still discovering JABA Services");
4345                       tm.setEnabled(false);
4346                       webService.add(tm);
4347                     }
4348                   }
4349                 }
4350                 build_urlServiceMenu(me.webService);
4351                 build_fetchdbmenu(webService);
4352                 for (JMenu item : wsmenu)
4353                 {
4354                   if (item.getItemCount() == 0)
4355                   {
4356                     item.setEnabled(false);
4357                   }
4358                   else
4359                   {
4360                     item.setEnabled(true);
4361                   }
4362                 }
4363               } catch (Exception e)
4364               {
4365                 Cache.log.debug(
4366                         "Exception during web service menu building process.",
4367                         e);
4368               }
4369             }
4370           });
4371         } catch (Exception e)
4372         {
4373         }
4374         buildingMenu = false;
4375       }
4376     }).start();
4377
4378   }
4379
4380   /**
4381    * construct any groupURL type service menu entries.
4382    *
4383    * @param webService
4384    */
4385   private void build_urlServiceMenu(JMenu webService)
4386   {
4387     // TODO: remove this code when 2.7 is released
4388     // DEBUG - alignmentView
4389     /*
4390      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4391      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4392      *
4393      * @Override public void actionPerformed(ActionEvent e) {
4394      * jalview.datamodel.AlignmentView
4395      * .testSelectionViews(af.viewport.getAlignment(),
4396      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4397      *
4398      * }); webService.add(testAlView);
4399      */
4400     // TODO: refactor to RestClient discoverer and merge menu entries for
4401     // rest-style services with other types of analysis/calculation service
4402     // SHmmr test client - still being implemented.
4403     // DEBUG - alignmentView
4404
4405     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4406             .getRestClients())
4407     {
4408       client.attachWSMenuEntry(
4409               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4410               this);
4411     }
4412   }
4413
4414   /**
4415    * Searches the alignment sequences for xRefs and builds the Show
4416    * Cross-References menu (formerly called Show Products), with database
4417    * sources for which cross-references are found (protein sources for a
4418    * nucleotide alignment and vice versa)
4419    *
4420    * @return true if Show Cross-references menu should be enabled
4421    */
4422   public boolean canShowProducts()
4423   {
4424     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4425     AlignmentI dataset = viewport.getAlignment().getDataset();
4426
4427     showProducts.removeAll();
4428     final boolean dna = viewport.getAlignment().isNucleotide();
4429
4430     if (seqs == null || seqs.length == 0)
4431     {
4432       // nothing to see here.
4433       return false;
4434     }
4435
4436     boolean showp = false;
4437     try
4438     {
4439       List<String> ptypes = new CrossRef(seqs, dataset)
4440               .findXrefSourcesForSequences(dna);
4441
4442       for (final String source : ptypes)
4443       {
4444         showp = true;
4445         final AlignFrame af = this;
4446         JMenuItem xtype = new JMenuItem(source);
4447         xtype.addActionListener(new ActionListener()
4448         {
4449           @Override
4450           public void actionPerformed(ActionEvent e)
4451           {
4452             showProductsFor(af.viewport.getSequenceSelection(), dna,
4453                     source);
4454           }
4455         });
4456         showProducts.add(xtype);
4457       }
4458       showProducts.setVisible(showp);
4459       showProducts.setEnabled(showp);
4460     } catch (Exception e)
4461     {
4462       Cache.log.warn(
4463               "canShowProducts threw an exception - please report to help@jalview.org",
4464               e);
4465       return false;
4466     }
4467     return showp;
4468   }
4469
4470   /**
4471    * Finds and displays cross-references for the selected sequences (protein
4472    * products for nucleotide sequences, dna coding sequences for peptides).
4473    *
4474    * @param sel
4475    *          the sequences to show cross-references for
4476    * @param dna
4477    *          true if from a nucleotide alignment (so showing proteins)
4478    * @param source
4479    *          the database to show cross-references for
4480    */
4481   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4482           final String source)
4483   {
4484     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4485             .start();
4486   }
4487
4488   /**
4489    * Construct and display a new frame containing the translation of this
4490    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4491    */
4492   @Override
4493   public void showTranslation_actionPerformed(ActionEvent e)
4494   {
4495     AlignmentI al = null;
4496     try
4497     {
4498       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4499
4500       al = dna.translateCdna();
4501     } catch (Exception ex)
4502     {
4503       jalview.bin.Cache.log.error(
4504               "Exception during translation. Please report this !", ex);
4505       final String msg = MessageManager.getString(
4506               "label.error_when_translating_sequences_submit_bug_report");
4507       final String errorTitle = MessageManager
4508               .getString("label.implementation_error")
4509               + MessageManager.getString("label.translation_failed");
4510       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4511               JvOptionPane.ERROR_MESSAGE);
4512       return;
4513     }
4514     if (al == null || al.getHeight() == 0)
4515     {
4516       final String msg = MessageManager.getString(
4517               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4518       final String errorTitle = MessageManager
4519               .getString("label.translation_failed");
4520       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4521               JvOptionPane.WARNING_MESSAGE);
4522     }
4523     else
4524     {
4525       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4526       af.setFileFormat(this.currentFileFormat);
4527       final String newTitle = MessageManager
4528               .formatMessage("label.translation_of_params", new Object[]
4529               { this.getTitle() });
4530       af.setTitle(newTitle);
4531       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4532       {
4533         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4534         viewport.openSplitFrame(af, new Alignment(seqs));
4535       }
4536       else
4537       {
4538         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4539                 DEFAULT_HEIGHT);
4540       }
4541     }
4542   }
4543
4544   /**
4545    * Set the file format
4546    *
4547    * @param format
4548    */
4549   public void setFileFormat(FileFormatI format)
4550   {
4551     this.currentFileFormat = format;
4552   }
4553
4554   /**
4555    * Try to load a features file onto the alignment.
4556    *
4557    * @param file
4558    *          contents or path to retrieve file
4559    * @param sourceType
4560    *          access mode of file (see jalview.io.AlignFile)
4561    * @return true if features file was parsed correctly.
4562    */
4563   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4564   {
4565     return avc.parseFeaturesFile(file, sourceType,
4566             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4567
4568   }
4569
4570   @Override
4571   public void refreshFeatureUI(boolean enableIfNecessary)
4572   {
4573     // note - currently this is only still here rather than in the controller
4574     // because of the featureSettings hard reference that is yet to be
4575     // abstracted
4576     if (enableIfNecessary)
4577     {
4578       viewport.setShowSequenceFeatures(true);
4579       showSeqFeatures.setSelected(true);
4580     }
4581
4582   }
4583
4584   @Override
4585   public void dragEnter(DropTargetDragEvent evt)
4586   {
4587   }
4588
4589   @Override
4590   public void dragExit(DropTargetEvent evt)
4591   {
4592   }
4593
4594   @Override
4595   public void dragOver(DropTargetDragEvent evt)
4596   {
4597   }
4598
4599   @Override
4600   public void dropActionChanged(DropTargetDragEvent evt)
4601   {
4602   }
4603
4604   @Override
4605   public void drop(DropTargetDropEvent evt)
4606   {
4607     // JAL-1552 - acceptDrop required before getTransferable call for
4608     // Java's Transferable for native dnd
4609     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4610     Transferable t = evt.getTransferable();
4611     final AlignFrame thisaf = this;
4612     final List<String> files = new ArrayList<>();
4613     List<DataSourceType> protocols = new ArrayList<>();
4614
4615     try
4616     {
4617       Desktop.transferFromDropTarget(files, protocols, evt, t);
4618     } catch (Exception e)
4619     {
4620       e.printStackTrace();
4621     }
4622     if (files != null)
4623     {
4624       new Thread(new Runnable()
4625       {
4626         @Override
4627         public void run()
4628         {
4629           try
4630           {
4631             // check to see if any of these files have names matching sequences
4632             // in
4633             // the alignment
4634             SequenceIdMatcher idm = new SequenceIdMatcher(
4635                     viewport.getAlignment().getSequencesArray());
4636             /**
4637              * Object[] { String,SequenceI}
4638              */
4639             ArrayList<Object[]> filesmatched = new ArrayList<>();
4640             ArrayList<String> filesnotmatched = new ArrayList<>();
4641             for (int i = 0; i < files.size(); i++)
4642             {
4643               String file = files.get(i).toString();
4644               String pdbfn = "";
4645               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4646               if (protocol == DataSourceType.FILE)
4647               {
4648                 File fl = new File(file);
4649                 pdbfn = fl.getName();
4650               }
4651               else if (protocol == DataSourceType.URL)
4652               {
4653                 URL url = new URL(file);
4654                 pdbfn = url.getFile();
4655               }
4656               if (pdbfn.length() > 0)
4657               {
4658                 // attempt to find a match in the alignment
4659                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4660                 int l = 0, c = pdbfn.indexOf(".");
4661                 while (mtch == null && c != -1)
4662                 {
4663                   do
4664                   {
4665                     l = c;
4666                   } while ((c = pdbfn.indexOf(".", l)) > l);
4667                   if (l > -1)
4668                   {
4669                     pdbfn = pdbfn.substring(0, l);
4670                   }
4671                   mtch = idm.findAllIdMatches(pdbfn);
4672                 }
4673                 if (mtch != null)
4674                 {
4675                   FileFormatI type = null;
4676                   try
4677                   {
4678                     type = new IdentifyFile().identify(file, protocol);
4679                   } catch (Exception ex)
4680                   {
4681                     type = null;
4682                   }
4683                   if (type != null && type.isStructureFile())
4684                   {
4685                     filesmatched.add(new Object[] { file, protocol, mtch });
4686                     continue;
4687                   }
4688                 }
4689                 // File wasn't named like one of the sequences or wasn't a PDB
4690                 // file.
4691                 filesnotmatched.add(file);
4692               }
4693             }
4694             int assocfiles = 0;
4695             if (filesmatched.size() > 0)
4696             {
4697               if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4698                       || JvOptionPane.showConfirmDialog(thisaf,
4699                               MessageManager.formatMessage(
4700                                       "label.automatically_associate_structure_files_with_sequences_same_name",
4701                                       new Object[]
4702                                       { Integer.valueOf(filesmatched.size())
4703                                               .toString() }),
4704                               MessageManager.getString(
4705                                       "label.automatically_associate_structure_files_by_name"),
4706                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4707
4708               {
4709                 for (Object[] fm : filesmatched)
4710                 {
4711                   // try and associate
4712                   // TODO: may want to set a standard ID naming formalism for
4713                   // associating PDB files which have no IDs.
4714                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4715                   {
4716                     PDBEntry pe = new AssociatePdbFileWithSeq()
4717                             .associatePdbWithSeq((String) fm[0],
4718                                     (DataSourceType) fm[1], toassoc, false,
4719                                     Desktop.instance);
4720                     if (pe != null)
4721                     {
4722                       System.err.println("Associated file : "
4723                               + ((String) fm[0]) + " with "
4724                               + toassoc.getDisplayId(true));
4725                       assocfiles++;
4726                     }
4727                   }
4728                   // TODO: do we need to update overview ? only if features are
4729                   // shown I guess
4730                   alignPanel.paintAlignment(true, false);
4731                 }
4732               }
4733             }
4734             if (filesnotmatched.size() > 0)
4735             {
4736               if (assocfiles > 0 && (Cache.getDefault(
4737                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4738                       || JvOptionPane.showConfirmDialog(thisaf,
4739                               "<html>" + MessageManager.formatMessage(
4740                                       "label.ignore_unmatched_dropped_files_info",
4741                                       new Object[]
4742                                       { Integer.valueOf(
4743                                               filesnotmatched.size())
4744                                               .toString() })
4745                                       + "</html>",
4746                               MessageManager.getString(
4747                                       "label.ignore_unmatched_dropped_files"),
4748                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4749               {
4750                 return;
4751               }
4752               for (String fn : filesnotmatched)
4753               {
4754                 loadJalviewDataFile(fn, null, null, null);
4755               }
4756
4757             }
4758           } catch (Exception ex)
4759           {
4760             ex.printStackTrace();
4761           }
4762         }
4763       }).start();
4764     }
4765   }
4766
4767   /**
4768    * Attempt to load a "dropped" file or URL string, by testing in turn for
4769    * <ul>
4770    * <li>an Annotation file</li>
4771    * <li>a JNet file</li>
4772    * <li>a features file</li>
4773    * <li>else try to interpret as an alignment file</li>
4774    * </ul>
4775    *
4776    * @param file
4777    *          either a filename or a URL string.
4778    * @throws InterruptedException
4779    * @throws IOException
4780    */
4781   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4782           FileFormatI format, SequenceI assocSeq)
4783   {
4784     try
4785     {
4786       if (sourceType == null)
4787       {
4788         sourceType = FormatAdapter.checkProtocol(file);
4789       }
4790       // if the file isn't identified, or not positively identified as some
4791       // other filetype (PFAM is default unidentified alignment file type) then
4792       // try to parse as annotation.
4793       boolean isAnnotation = (format == null
4794               || FileFormat.Pfam.equals(format))
4795                       ? new AnnotationFile().annotateAlignmentView(viewport,
4796                               file, sourceType)
4797                       : false;
4798
4799       if (!isAnnotation)
4800       {
4801         // first see if its a T-COFFEE score file
4802         TCoffeeScoreFile tcf = null;
4803         try
4804         {
4805           tcf = new TCoffeeScoreFile(file, sourceType);
4806           if (tcf.isValid())
4807           {
4808             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4809             {
4810               buildColourMenu();
4811               changeColour(
4812                       new TCoffeeColourScheme(viewport.getAlignment()));
4813               isAnnotation = true;
4814               statusBar.setText(MessageManager.getString(
4815                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4816             }
4817             else
4818             {
4819               // some problem - if no warning its probable that the ID matching
4820               // process didn't work
4821               JvOptionPane.showMessageDialog(Desktop.desktop,
4822                       tcf.getWarningMessage() == null
4823                               ? MessageManager.getString(
4824                                       "label.check_file_matches_sequence_ids_alignment")
4825                               : tcf.getWarningMessage(),
4826                       MessageManager.getString(
4827                               "label.problem_reading_tcoffee_score_file"),
4828                       JvOptionPane.WARNING_MESSAGE);
4829             }
4830           }
4831           else
4832           {
4833             tcf = null;
4834           }
4835         } catch (Exception x)
4836         {
4837           Cache.log.debug(
4838                   "Exception when processing data source as T-COFFEE score file",
4839                   x);
4840           tcf = null;
4841         }
4842         if (tcf == null)
4843         {
4844           // try to see if its a JNet 'concise' style annotation file *before*
4845           // we
4846           // try to parse it as a features file
4847           if (format == null)
4848           {
4849             format = new IdentifyFile().identify(file, sourceType);
4850           }
4851           if (FileFormat.ScoreMatrix == format)
4852           {
4853             ScoreMatrixFile sm = new ScoreMatrixFile(
4854                     new FileParse(file, sourceType));
4855             sm.parse();
4856             // todo: i18n this message
4857             statusBar.setText(MessageManager.formatMessage(
4858                     "label.successfully_loaded_matrix",
4859                     sm.getMatrixName()));
4860           }
4861           else if (FileFormat.Jnet.equals(format))
4862           {
4863             JPredFile predictions = new JPredFile(file, sourceType);
4864             new JnetAnnotationMaker();
4865             JnetAnnotationMaker.add_annotation(predictions,
4866                     viewport.getAlignment(), 0, false);
4867             viewport.getAlignment().setupJPredAlignment();
4868             isAnnotation = true;
4869           }
4870           // else if (IdentifyFile.FeaturesFile.equals(format))
4871           else if (FileFormat.Features.equals(format))
4872           {
4873             if (parseFeaturesFile(file, sourceType))
4874             {
4875               alignPanel.paintAlignment(true, true);
4876             }
4877           }
4878           else
4879           {
4880             new FileLoader().LoadFile(viewport, file, sourceType, format);
4881           }
4882         }
4883       }
4884       if (isAnnotation)
4885       {
4886         alignPanel.adjustAnnotationHeight();
4887         viewport.updateSequenceIdColours();
4888         buildSortByAnnotationScoresMenu();
4889         alignPanel.paintAlignment(true, true);
4890       }
4891     } catch (Exception ex)
4892     {
4893       ex.printStackTrace();
4894     } catch (OutOfMemoryError oom)
4895     {
4896       try
4897       {
4898         System.gc();
4899       } catch (Exception x)
4900       {
4901       }
4902       new OOMWarning(
4903               "loading data "
4904                       + (sourceType != null
4905                               ? (sourceType == DataSourceType.PASTE
4906                                       ? "from clipboard."
4907                                       : "using " + sourceType + " from "
4908                                               + file)
4909                               : ".")
4910                       + (format != null
4911                               ? "(parsing as '" + format + "' file)"
4912                               : ""),
4913               oom, Desktop.desktop);
4914     }
4915   }
4916
4917   /**
4918    * Method invoked by the ChangeListener on the tabbed pane, in other words
4919    * when a different tabbed pane is selected by the user or programmatically.
4920    */
4921   @Override
4922   public void tabSelectionChanged(int index)
4923   {
4924     if (index > -1)
4925     {
4926       alignPanel = alignPanels.get(index);
4927       viewport = alignPanel.av;
4928       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4929       setMenusFromViewport(viewport);
4930     }
4931
4932     /*
4933      * 'focus' any colour slider that is open to the selected viewport
4934      */
4935     if (viewport.getConservationSelected())
4936     {
4937       SliderPanel.setConservationSlider(alignPanel,
4938               viewport.getResidueShading(), alignPanel.getViewName());
4939     }
4940     else
4941     {
4942       SliderPanel.hideConservationSlider();
4943     }
4944     if (viewport.getAbovePIDThreshold())
4945     {
4946       SliderPanel.setPIDSliderSource(alignPanel,
4947               viewport.getResidueShading(), alignPanel.getViewName());
4948     }
4949     else
4950     {
4951       SliderPanel.hidePIDSlider();
4952     }
4953
4954     /*
4955      * If there is a frame linked to this one in a SplitPane, switch it to the
4956      * same view tab index. No infinite recursion of calls should happen, since
4957      * tabSelectionChanged() should not get invoked on setting the selected
4958      * index to an unchanged value. Guard against setting an invalid index
4959      * before the new view peer tab has been created.
4960      */
4961     final AlignViewportI peer = viewport.getCodingComplement();
4962     if (peer != null)
4963     {
4964       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4965               .getAlignPanel().alignFrame;
4966       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4967       {
4968         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4969       }
4970     }
4971   }
4972
4973   /**
4974    * On right mouse click on view tab, prompt for and set new view name.
4975    */
4976   @Override
4977   public void tabbedPane_mousePressed(MouseEvent e)
4978   {
4979     if (e.isPopupTrigger())
4980     {
4981       String msg = MessageManager.getString("label.enter_view_name");
4982       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4983               JvOptionPane.QUESTION_MESSAGE);
4984
4985       if (reply != null)
4986       {
4987         viewport.viewName = reply;
4988         // TODO warn if reply is in getExistingViewNames()?
4989         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4990       }
4991     }
4992   }
4993
4994   public AlignViewport getCurrentView()
4995   {
4996     return viewport;
4997   }
4998
4999   /**
5000    * Open the dialog for regex description parsing.
5001    */
5002   @Override
5003   protected void extractScores_actionPerformed(ActionEvent e)
5004   {
5005     ParseProperties pp = new jalview.analysis.ParseProperties(
5006             viewport.getAlignment());
5007     // TODO: verify regex and introduce GUI dialog for version 2.5
5008     // if (pp.getScoresFromDescription("col", "score column ",
5009     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5010     // true)>0)
5011     if (pp.getScoresFromDescription("description column",
5012             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5013     {
5014       buildSortByAnnotationScoresMenu();
5015     }
5016   }
5017
5018   /*
5019    * (non-Javadoc)
5020    *
5021    * @see
5022    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5023    * )
5024    */
5025   @Override
5026   protected void showDbRefs_actionPerformed(ActionEvent e)
5027   {
5028     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5029   }
5030
5031   /*
5032    * (non-Javadoc)
5033    *
5034    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5035    * ActionEvent)
5036    */
5037   @Override
5038   protected void showNpFeats_actionPerformed(ActionEvent e)
5039   {
5040     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5041   }
5042
5043   /**
5044    * find the viewport amongst the tabs in this alignment frame and close that
5045    * tab
5046    *
5047    * @param av
5048    */
5049   public boolean closeView(AlignViewportI av)
5050   {
5051     if (viewport == av)
5052     {
5053       this.closeMenuItem_actionPerformed(false);
5054       return true;
5055     }
5056     Component[] comp = tabbedPane.getComponents();
5057     for (int i = 0; comp != null && i < comp.length; i++)
5058     {
5059       if (comp[i] instanceof AlignmentPanel)
5060       {
5061         if (((AlignmentPanel) comp[i]).av == av)
5062         {
5063           // close the view.
5064           closeView((AlignmentPanel) comp[i]);
5065           return true;
5066         }
5067       }
5068     }
5069     return false;
5070   }
5071
5072   protected void build_fetchdbmenu(JMenu webService)
5073   {
5074     // Temporary hack - DBRef Fetcher always top level ws entry.
5075     // TODO We probably want to store a sequence database checklist in
5076     // preferences and have checkboxes.. rather than individual sources selected
5077     // here
5078     final JMenu rfetch = new JMenu(
5079             MessageManager.getString("action.fetch_db_references"));
5080     rfetch.setToolTipText(MessageManager.getString(
5081             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5082     webService.add(rfetch);
5083
5084     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5085             MessageManager.getString("option.trim_retrieved_seqs"));
5086     trimrs.setToolTipText(
5087             MessageManager.getString("label.trim_retrieved_sequences"));
5088     trimrs.setSelected(
5089             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5090     trimrs.addActionListener(new ActionListener()
5091     {
5092       @Override
5093       public void actionPerformed(ActionEvent e)
5094       {
5095         trimrs.setSelected(trimrs.isSelected());
5096         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5097                 Boolean.valueOf(trimrs.isSelected()).toString());
5098       };
5099     });
5100     rfetch.add(trimrs);
5101     JMenuItem fetchr = new JMenuItem(
5102             MessageManager.getString("label.standard_databases"));
5103     fetchr.setToolTipText(
5104             MessageManager.getString("label.fetch_embl_uniprot"));
5105     fetchr.addActionListener(new ActionListener()
5106     {
5107
5108       @Override
5109       public void actionPerformed(ActionEvent e)
5110       {
5111         new Thread(new Runnable()
5112         {
5113           @Override
5114           public void run()
5115           {
5116             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5117                     .getAlignment().isNucleotide();
5118             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5119                     alignPanel.av.getSequenceSelection(),
5120                     alignPanel.alignFrame, null,
5121                     alignPanel.alignFrame.featureSettings, isNucleotide);
5122             dbRefFetcher.addListener(new FetchFinishedListenerI()
5123             {
5124               @Override
5125               public void finished()
5126               {
5127                 AlignFrame.this.setMenusForViewport();
5128               }
5129             });
5130             dbRefFetcher.fetchDBRefs(false);
5131           }
5132         }).start();
5133
5134       }
5135
5136     });
5137     rfetch.add(fetchr);
5138     final AlignFrame me = this;
5139     new Thread(new Runnable()
5140     {
5141       @Override
5142       public void run()
5143       {
5144         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5145                 .getSequenceFetcherSingleton(me);
5146         javax.swing.SwingUtilities.invokeLater(new Runnable()
5147         {
5148           @Override
5149           public void run()
5150           {
5151             String[] dbclasses = sf.getOrderedSupportedSources();
5152             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5153             // jalview.util.QuickSort.sort(otherdb, otherdb);
5154             List<DbSourceProxy> otherdb;
5155             JMenu dfetch = new JMenu();
5156             JMenu ifetch = new JMenu();
5157             JMenuItem fetchr = null;
5158             int comp = 0, icomp = 0, mcomp = 15;
5159             String mname = null;
5160             int dbi = 0;
5161             for (String dbclass : dbclasses)
5162             {
5163               otherdb = sf.getSourceProxy(dbclass);
5164               // add a single entry for this class, or submenu allowing 'fetch
5165               // all' or pick one
5166               if (otherdb == null || otherdb.size() < 1)
5167               {
5168                 continue;
5169               }
5170               // List<DbSourceProxy> dbs=otherdb;
5171               // otherdb=new ArrayList<DbSourceProxy>();
5172               // for (DbSourceProxy db:dbs)
5173               // {
5174               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5175               // }
5176               if (mname == null)
5177               {
5178                 mname = "From " + dbclass;
5179               }
5180               if (otherdb.size() == 1)
5181               {
5182                 final DbSourceProxy[] dassource = otherdb
5183                         .toArray(new DbSourceProxy[0]);
5184                 DbSourceProxy src = otherdb.get(0);
5185                 fetchr = new JMenuItem(src.getDbSource());
5186                 fetchr.addActionListener(new ActionListener()
5187                 {
5188
5189                   @Override
5190                   public void actionPerformed(ActionEvent e)
5191                   {
5192                     new Thread(new Runnable()
5193                     {
5194
5195                       @Override
5196                       public void run()
5197                       {
5198                         boolean isNucleotide = alignPanel.alignFrame
5199                                 .getViewport().getAlignment()
5200                                 .isNucleotide();
5201                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5202                                 alignPanel.av.getSequenceSelection(),
5203                                 alignPanel.alignFrame, dassource,
5204                                 alignPanel.alignFrame.featureSettings,
5205                                 isNucleotide);
5206                         dbRefFetcher
5207                                 .addListener(new FetchFinishedListenerI()
5208                                 {
5209                                   @Override
5210                                   public void finished()
5211                                   {
5212                                     AlignFrame.this.setMenusForViewport();
5213                                   }
5214                                 });
5215                         dbRefFetcher.fetchDBRefs(false);
5216                       }
5217                     }).start();
5218                   }
5219
5220                 });
5221                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5222                         MessageManager.formatMessage(
5223                                 "label.fetch_retrieve_from", new Object[]
5224                                 { src.getDbName() })));
5225                 dfetch.add(fetchr);
5226                 comp++;
5227               }
5228               else
5229               {
5230                 final DbSourceProxy[] dassource = otherdb
5231                         .toArray(new DbSourceProxy[0]);
5232                 // fetch all entry
5233                 DbSourceProxy src = otherdb.get(0);
5234                 fetchr = new JMenuItem(MessageManager
5235                         .formatMessage("label.fetch_all_param", new Object[]
5236                         { src.getDbSource() }));
5237                 fetchr.addActionListener(new ActionListener()
5238                 {
5239                   @Override
5240                   public void actionPerformed(ActionEvent e)
5241                   {
5242                     new Thread(new Runnable()
5243                     {
5244
5245                       @Override
5246                       public void run()
5247                       {
5248                         boolean isNucleotide = alignPanel.alignFrame
5249                                 .getViewport().getAlignment()
5250                                 .isNucleotide();
5251                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5252                                 alignPanel.av.getSequenceSelection(),
5253                                 alignPanel.alignFrame, dassource,
5254                                 alignPanel.alignFrame.featureSettings,
5255                                 isNucleotide);
5256                         dbRefFetcher
5257                                 .addListener(new FetchFinishedListenerI()
5258                                 {
5259                                   @Override
5260                                   public void finished()
5261                                   {
5262                                     AlignFrame.this.setMenusForViewport();
5263                                   }
5264                                 });
5265                         dbRefFetcher.fetchDBRefs(false);
5266                       }
5267                     }).start();
5268                   }
5269                 });
5270
5271                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5272                         MessageManager.formatMessage(
5273                                 "label.fetch_retrieve_from_all_sources",
5274                                 new Object[]
5275                                 { Integer.valueOf(otherdb.size())
5276                                         .toString(),
5277                                     src.getDbSource(), src.getDbName() })));
5278                 dfetch.add(fetchr);
5279                 comp++;
5280                 // and then build the rest of the individual menus
5281                 ifetch = new JMenu(MessageManager.formatMessage(
5282                         "label.source_from_db_source", new Object[]
5283                         { src.getDbSource() }));
5284                 icomp = 0;
5285                 String imname = null;
5286                 int i = 0;
5287                 for (DbSourceProxy sproxy : otherdb)
5288                 {
5289                   String dbname = sproxy.getDbName();
5290                   String sname = dbname.length() > 5
5291                           ? dbname.substring(0, 5) + "..."
5292                           : dbname;
5293                   String msname = dbname.length() > 10
5294                           ? dbname.substring(0, 10) + "..."
5295                           : dbname;
5296                   if (imname == null)
5297                   {
5298                     imname = MessageManager
5299                             .formatMessage("label.from_msname", new Object[]
5300                             { sname });
5301                   }
5302                   fetchr = new JMenuItem(msname);
5303                   final DbSourceProxy[] dassrc = { sproxy };
5304                   fetchr.addActionListener(new ActionListener()
5305                   {
5306
5307                     @Override
5308                     public void actionPerformed(ActionEvent e)
5309                     {
5310                       new Thread(new Runnable()
5311                       {
5312
5313                         @Override
5314                         public void run()
5315                         {
5316                           boolean isNucleotide = alignPanel.alignFrame
5317                                   .getViewport().getAlignment()
5318                                   .isNucleotide();
5319                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5320                                   alignPanel.av.getSequenceSelection(),
5321                                   alignPanel.alignFrame, dassrc,
5322                                   alignPanel.alignFrame.featureSettings,
5323                                   isNucleotide);
5324                           dbRefFetcher
5325                                   .addListener(new FetchFinishedListenerI()
5326                                   {
5327                                     @Override
5328                                     public void finished()
5329                                     {
5330                                       AlignFrame.this.setMenusForViewport();
5331                                     }
5332                                   });
5333                           dbRefFetcher.fetchDBRefs(false);
5334                         }
5335                       }).start();
5336                     }
5337
5338                   });
5339                   fetchr.setToolTipText(
5340                           "<html>" + MessageManager.formatMessage(
5341                                   "label.fetch_retrieve_from", new Object[]
5342                                   { dbname }));
5343                   ifetch.add(fetchr);
5344                   ++i;
5345                   if (++icomp >= mcomp || i == (otherdb.size()))
5346                   {
5347                     ifetch.setText(MessageManager.formatMessage(
5348                             "label.source_to_target", imname, sname));
5349                     dfetch.add(ifetch);
5350                     ifetch = new JMenu();
5351                     imname = null;
5352                     icomp = 0;
5353                     comp++;
5354                   }
5355                 }
5356               }
5357               ++dbi;
5358               if (comp >= mcomp || dbi >= (dbclasses.length))
5359               {
5360                 dfetch.setText(MessageManager.formatMessage(
5361                         "label.source_to_target", mname, dbclass));
5362                 rfetch.add(dfetch);
5363                 dfetch = new JMenu();
5364                 mname = null;
5365                 comp = 0;
5366               }
5367             }
5368           }
5369         });
5370       }
5371     }).start();
5372
5373   }
5374
5375   /**
5376    * Left justify the whole alignment.
5377    */
5378   @Override
5379   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5380   {
5381     AlignmentI al = viewport.getAlignment();
5382     al.justify(false);
5383     viewport.firePropertyChange("alignment", null, al);
5384   }
5385
5386   /**
5387    * Right justify the whole alignment.
5388    */
5389   @Override
5390   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5391   {
5392     AlignmentI al = viewport.getAlignment();
5393     al.justify(true);
5394     viewport.firePropertyChange("alignment", null, al);
5395   }
5396
5397   @Override
5398   public void setShowSeqFeatures(boolean b)
5399   {
5400     showSeqFeatures.setSelected(b);
5401     viewport.setShowSequenceFeatures(b);
5402   }
5403
5404   /*
5405    * (non-Javadoc)
5406    *
5407    * @see
5408    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5409    * awt.event.ActionEvent)
5410    */
5411   @Override
5412   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5413   {
5414     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5415     alignPanel.paintAlignment(false, false);
5416   }
5417
5418   /*
5419    * (non-Javadoc)
5420    *
5421    * @see
5422    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5423    * .ActionEvent)
5424    */
5425   @Override
5426   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5427   {
5428     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5429     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5430
5431   }
5432
5433   /*
5434    * (non-Javadoc)
5435    *
5436    * @see
5437    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5438    * .event.ActionEvent)
5439    */
5440   @Override
5441   protected void showGroupConservation_actionPerformed(ActionEvent e)
5442   {
5443     viewport.setShowGroupConservation(showGroupConservation.getState());
5444     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5445   }
5446
5447   /*
5448    * (non-Javadoc)
5449    *
5450    * @see
5451    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5452    * .event.ActionEvent)
5453    */
5454   @Override
5455   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5456   {
5457     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5458     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5459   }
5460
5461   /*
5462    * (non-Javadoc)
5463    *
5464    * @see
5465    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5466    * .event.ActionEvent)
5467    */
5468   @Override
5469   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5470   {
5471     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5472     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5473   }
5474
5475   @Override
5476   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5477   {
5478     showSequenceLogo.setState(true);
5479     viewport.setShowSequenceLogo(true);
5480     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5481     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5482   }
5483
5484   @Override
5485   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5486   {
5487     viewport.setShowInformationHistogram(
5488             showInformationHistogram.getState());
5489     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5490   }
5491
5492   @Override
5493   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5494   {
5495     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5496     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5497   }
5498
5499   @Override
5500   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5501   {
5502     showHMMSequenceLogo.setState(true);
5503     viewport.setShowHMMSequenceLogo(true);
5504     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5505     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5506   }
5507
5508   @Override
5509   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5510   {
5511     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5512   }
5513
5514   /*
5515    * (non-Javadoc)
5516    *
5517    * @see
5518    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5519    * .event.ActionEvent)
5520    */
5521   @Override
5522   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5523   {
5524     if (avc.makeGroupsFromSelection())
5525     {
5526       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5527       alignPanel.updateAnnotation();
5528       alignPanel.paintAlignment(true, true);
5529     }
5530   }
5531
5532   public void clearAlignmentSeqRep()
5533   {
5534     // TODO refactor alignmentseqrep to controller
5535     if (viewport.getAlignment().hasSeqrep())
5536     {
5537       viewport.getAlignment().setSeqrep(null);
5538       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5539       alignPanel.updateAnnotation();
5540       alignPanel.paintAlignment(true, true);
5541     }
5542   }
5543
5544   @Override
5545   protected void createGroup_actionPerformed(ActionEvent e)
5546   {
5547     if (avc.createGroup())
5548     {
5549       alignPanel.alignmentChanged();
5550     }
5551   }
5552
5553   @Override
5554   protected void unGroup_actionPerformed(ActionEvent e)
5555   {
5556     if (avc.unGroup())
5557     {
5558       alignPanel.alignmentChanged();
5559     }
5560   }
5561
5562   /**
5563    * make the given alignmentPanel the currently selected tab
5564    *
5565    * @param alignmentPanel
5566    */
5567   public void setDisplayedView(AlignmentPanel alignmentPanel)
5568   {
5569     if (!viewport.getSequenceSetId()
5570             .equals(alignmentPanel.av.getSequenceSetId()))
5571     {
5572       throw new Error(MessageManager.getString(
5573               "error.implementation_error_cannot_show_view_alignment_frame"));
5574     }
5575     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5576             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5577     {
5578       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5579     }
5580   }
5581
5582   /**
5583    * Action on selection of menu options to Show or Hide annotations.
5584    *
5585    * @param visible
5586    * @param forSequences
5587    *          update sequence-related annotations
5588    * @param forAlignment
5589    *          update non-sequence-related annotations
5590    */
5591   @Override
5592   protected void setAnnotationsVisibility(boolean visible,
5593           boolean forSequences, boolean forAlignment)
5594   {
5595     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5596             .getAlignmentAnnotation();
5597     if (anns == null)
5598     {
5599       return;
5600     }
5601     for (AlignmentAnnotation aa : anns)
5602     {
5603       /*
5604        * don't display non-positional annotations on an alignment
5605        */
5606       if (aa.annotations == null)
5607       {
5608         continue;
5609       }
5610       boolean apply = (aa.sequenceRef == null && forAlignment)
5611               || (aa.sequenceRef != null && forSequences);
5612       if (apply)
5613       {
5614         aa.visible = visible;
5615       }
5616     }
5617     alignPanel.validateAnnotationDimensions(true);
5618     alignPanel.alignmentChanged();
5619   }
5620
5621   /**
5622    * Store selected annotation sort order for the view and repaint.
5623    */
5624   @Override
5625   protected void sortAnnotations_actionPerformed()
5626   {
5627     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5628     this.alignPanel.av
5629             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5630     alignPanel.paintAlignment(false, false);
5631   }
5632
5633   /**
5634    *
5635    * @return alignment panels in this alignment frame
5636    */
5637   public List<? extends AlignmentViewPanel> getAlignPanels()
5638   {
5639     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5640   }
5641
5642   /**
5643    * Open a new alignment window, with the cDNA associated with this (protein)
5644    * alignment, aligned as is the protein.
5645    */
5646   protected void viewAsCdna_actionPerformed()
5647   {
5648     // TODO no longer a menu action - refactor as required
5649     final AlignmentI alignment = getViewport().getAlignment();
5650     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5651     if (mappings == null)
5652     {
5653       return;
5654     }
5655     List<SequenceI> cdnaSeqs = new ArrayList<>();
5656     for (SequenceI aaSeq : alignment.getSequences())
5657     {
5658       for (AlignedCodonFrame acf : mappings)
5659       {
5660         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5661         if (dnaSeq != null)
5662         {
5663           /*
5664            * There is a cDNA mapping for this protein sequence - add to new
5665            * alignment. It will share the same dataset sequence as other mapped
5666            * cDNA (no new mappings need to be created).
5667            */
5668           final Sequence newSeq = new Sequence(dnaSeq);
5669           newSeq.setDatasetSequence(dnaSeq);
5670           cdnaSeqs.add(newSeq);
5671         }
5672       }
5673     }
5674     if (cdnaSeqs.size() == 0)
5675     {
5676       // show a warning dialog no mapped cDNA
5677       return;
5678     }
5679     AlignmentI cdna = new Alignment(
5680             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5681     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5682             AlignFrame.DEFAULT_HEIGHT);
5683     cdna.alignAs(alignment);
5684     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5685             + this.title;
5686     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5687             AlignFrame.DEFAULT_HEIGHT);
5688   }
5689
5690   /**
5691    * Set visibility of dna/protein complement view (available when shown in a
5692    * split frame).
5693    *
5694    * @param show
5695    */
5696   @Override
5697   protected void showComplement_actionPerformed(boolean show)
5698   {
5699     SplitContainerI sf = getSplitViewContainer();
5700     if (sf != null)
5701     {
5702       sf.setComplementVisible(this, show);
5703     }
5704   }
5705
5706   /**
5707    * Generate the reverse (optionally complemented) of the selected sequences,
5708    * and add them to the alignment
5709    */
5710   @Override
5711   protected void showReverse_actionPerformed(boolean complement)
5712   {
5713     AlignmentI al = null;
5714     try
5715     {
5716       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5717       al = dna.reverseCdna(complement);
5718       viewport.addAlignment(al, "");
5719       addHistoryItem(new EditCommand(
5720               MessageManager.getString("label.add_sequences"), Action.PASTE,
5721               al.getSequencesArray(), 0, al.getWidth(),
5722               viewport.getAlignment()));
5723     } catch (Exception ex)
5724     {
5725       System.err.println(ex.getMessage());
5726       return;
5727     }
5728   }
5729
5730   /**
5731    * Try to run a script in the Groovy console, having first ensured that this
5732    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5733    * be targeted at this alignment.
5734    */
5735   @Override
5736   protected void runGroovy_actionPerformed()
5737   {
5738     Jalview.setCurrentAlignFrame(this);
5739     groovy.ui.Console console = Desktop.getGroovyConsole();
5740     if (console != null)
5741     {
5742       try
5743       {
5744         console.runScript();
5745       } catch (Exception ex)
5746       {
5747         System.err.println((ex.toString()));
5748         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5749                 MessageManager.getString("label.couldnt_run_groovy_script"),
5750                 MessageManager.getString("label.groovy_support_failed"),
5751                 JvOptionPane.ERROR_MESSAGE);
5752       }
5753     }
5754     else
5755     {
5756       System.err.println("Can't run Groovy script as console not found");
5757     }
5758   }
5759
5760   /**
5761    * Hides columns containing (or not containing) a specified feature, provided
5762    * that would not leave all columns hidden
5763    *
5764    * @param featureType
5765    * @param columnsContaining
5766    * @return
5767    */
5768   public boolean hideFeatureColumns(String featureType,
5769           boolean columnsContaining)
5770   {
5771     boolean notForHiding = avc.markColumnsContainingFeatures(
5772             columnsContaining, false, false, featureType);
5773     if (notForHiding)
5774     {
5775       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5776               false, featureType))
5777       {
5778         getViewport().hideSelectedColumns();
5779         return true;
5780       }
5781     }
5782     return false;
5783   }
5784
5785   @Override
5786   protected void selectHighlightedColumns_actionPerformed(
5787           ActionEvent actionEvent)
5788   {
5789     // include key modifier check in case user selects from menu
5790     avc.markHighlightedColumns(
5791             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5792             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5793                     | ActionEvent.CTRL_MASK)) != 0);
5794   }
5795
5796   /**
5797    * Rebuilds the Colour menu, including any user-defined colours which have
5798    * been loaded either on startup or during the session
5799    */
5800   public void buildColourMenu()
5801   {
5802     colourMenu.removeAll();
5803
5804     colourMenu.add(applyToAllGroups);
5805     colourMenu.add(textColour);
5806     colourMenu.addSeparator();
5807
5808     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5809             false);
5810
5811     colourMenu.addSeparator();
5812     colourMenu.add(conservationMenuItem);
5813     colourMenu.add(modifyConservation);
5814     colourMenu.add(abovePIDThreshold);
5815     colourMenu.add(modifyPID);
5816     colourMenu.add(annotationColour);
5817
5818     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5819     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5820   }
5821
5822   /**
5823    * Open a dialog (if not already open) that allows the user to select and
5824    * calculate PCA or Tree analysis
5825    */
5826   protected void openTreePcaDialog()
5827   {
5828     if (alignPanel.getCalculationDialog() == null)
5829     {
5830       new CalculationChooser(AlignFrame.this);
5831     }
5832   }
5833
5834   /**
5835    * Sets the status of the HMMER menu
5836    */
5837   public void updateHMMERStatus()
5838   {
5839     hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5840   }
5841
5842   /**
5843    * Returns the selected hidden Markov model.
5844    *
5845    * @return
5846    */
5847   public HiddenMarkovModel getSelectedHMM()
5848   {
5849     if (selectedHMMSequence == null)
5850     {
5851       return null;
5852     }
5853     return selectedHMMSequence.getHMM();
5854   }
5855
5856   /**
5857    * Returns the selected hidden Markov model.
5858    *
5859    * @return
5860    */
5861   public SequenceI getSelectedHMMSequence()
5862   {
5863     return selectedHMMSequence;
5864   }
5865
5866   /**
5867    * Sets the selected hidden Markov model
5868    *
5869    * @param selectedHMM
5870    */
5871   public void setSelectedHMMSequence(SequenceI selectedHMM)
5872   {
5873     this.selectedHMMSequence = selectedHMM;
5874     hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5875             + selectedHMM.getHMM().getName());
5876     hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5877             + selectedHMM.getHMM().getName());
5878   }
5879
5880   @Override
5881   public void hmmerMenu_actionPerformed(ActionEvent e)
5882   {
5883     SequenceGroup grp = getViewport().getSelectionGroup();
5884     if (grp != null)
5885     {
5886       hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5887               + grp.getName());
5888     }
5889     else
5890     {
5891       hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5892               + " from Alignment");
5893     }
5894   }
5895
5896   @Override
5897   protected void loadVcf_actionPerformed()
5898   {
5899     JalviewFileChooser chooser = new JalviewFileChooser(
5900             Cache.getProperty("LAST_DIRECTORY"));
5901     chooser.setFileView(new JalviewFileView());
5902     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5903     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5904
5905     int value = chooser.showOpenDialog(null);
5906
5907     if (value == JalviewFileChooser.APPROVE_OPTION)
5908     {
5909       String choice = chooser.getSelectedFile().getPath();
5910       Cache.setProperty("LAST_DIRECTORY", choice);
5911       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5912       new VCFLoader(choice).loadVCF(seqs, this);
5913     }
5914
5915   }
5916 }
5917
5918 class PrintThread extends Thread
5919 {
5920   AlignmentPanel ap;
5921
5922   public PrintThread(AlignmentPanel ap)
5923   {
5924     this.ap = ap;
5925   }
5926
5927   static PageFormat pf;
5928
5929   @Override
5930   public void run()
5931   {
5932     PrinterJob printJob = PrinterJob.getPrinterJob();
5933
5934     if (pf != null)
5935     {
5936       printJob.setPrintable(ap, pf);
5937     }
5938     else
5939     {
5940       printJob.setPrintable(ap);
5941     }
5942
5943     if (printJob.printDialog())
5944     {
5945       try
5946       {
5947         printJob.print();
5948       } catch (Exception PrintException)
5949       {
5950         PrintException.printStackTrace();
5951       }
5952     }
5953   }
5954 }