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.AlignExportSettingBeanI;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenColumns;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.io.vcf.VCFLoader;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.MessageManager;
  91 import jalview.util.dialogrunner.RunResponse;
  92 import jalview.viewmodel.AlignmentViewport;
  93 import jalview.viewmodel.ViewportRanges;
  94 import jalview.ws.DBRefFetcher;
  95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  96 import jalview.ws.jws1.Discoverer;
  97 import jalview.ws.jws2.Jws2Discoverer;
  98 import jalview.ws.jws2.jabaws2.Jws2Instance;
  99 import jalview.ws.seqfetcher.DbSourceProxy;
 100
 101 import java.awt.BorderLayout;
 102 import java.awt.Component;
 103 import java.awt.Rectangle;
 104 import java.awt.Toolkit;
 105 import java.awt.datatransfer.Clipboard;
 106 import java.awt.datatransfer.DataFlavor;
 107 import java.awt.datatransfer.StringSelection;
 108 import java.awt.datatransfer.Transferable;
 109 import java.awt.dnd.DnDConstants;
 110 import java.awt.dnd.DropTargetDragEvent;
 111 import java.awt.dnd.DropTargetDropEvent;
 112 import java.awt.dnd.DropTargetEvent;
 113 import java.awt.dnd.DropTargetListener;
 114 import java.awt.event.ActionEvent;
 115 import java.awt.event.ActionListener;
 116 import java.awt.event.FocusAdapter;
 117 import java.awt.event.FocusEvent;
 118 import java.awt.event.ItemEvent;
 119 import java.awt.event.ItemListener;
 120 import java.awt.event.KeyAdapter;
 121 import java.awt.event.KeyEvent;
 122 import java.awt.event.MouseEvent;
 123 import java.awt.print.PageFormat;
 124 import java.awt.print.PrinterJob;
 125 import java.beans.PropertyChangeEvent;
 126 import java.beans.PropertyChangeListener;
 127 import java.io.File;
 128 import java.io.FileWriter;
 129 import java.io.PrintWriter;
 130 import java.net.URL;
 131 import java.util.ArrayList;
 132 import java.util.Arrays;
 133 import java.util.Deque;
 134 import java.util.Enumeration;
 135 import java.util.Hashtable;
 136 import java.util.List;
 137 import java.util.Vector;
 138
 139 import javax.swing.JCheckBoxMenuItem;
 140 import javax.swing.JEditorPane;
 141 import javax.swing.JFileChooser;
 142 import javax.swing.JInternalFrame;
 143 import javax.swing.JLayeredPane;
 144 import javax.swing.JMenu;
 145 import javax.swing.JMenuItem;
 146 import javax.swing.JScrollPane;
 147 import javax.swing.SwingUtilities;
 148
 149 /**
 150  * DOCUMENT ME!
 151  *
 152  * @author $author$
 153  * @version $Revision$
 154  */
 155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 156         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
 157         PropertyChangeListener
 158 {
 159
 160   public static final int DEFAULT_WIDTH = 700;
 161
 162   public static final int DEFAULT_HEIGHT = 500;
 163
 164   /*
 165    * The currently displayed panel (selected tabbed view if more than one)
 166    */
 167   public AlignmentPanel alignPanel;
 168
 169   AlignViewport viewport;
 170
 171   public AlignViewControllerI avc;
 172
 173   List<AlignmentPanel> alignPanels = new ArrayList<>();
 174
 175   /**
 176    * Last format used to load or save alignments in this window
 177    */
 178   FileFormatI currentFileFormat = null;
 179
 180   /**
 181    * Current filename for this alignment
 182    */
 183   String fileName = null;
 184
 185   File fileObject;
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width and height.
 189    *
 190    * @param al
 191    * @param width
 192    * @param height
 193    */
 194   public AlignFrame(AlignmentI al, int width, int height)
 195   {
 196     this(al, null, width, height);
 197   }
 198
 199   /**
 200    * Creates a new AlignFrame object with specific width, height and
 201    * sequenceSetId
 202    *
 203    * @param al
 204    * @param width
 205    * @param height
 206    * @param sequenceSetId
 207    */
 208   public AlignFrame(AlignmentI al, int width, int height,
 209           String sequenceSetId)
 210   {
 211     this(al, null, width, height, sequenceSetId);
 212   }
 213
 214   /**
 215    * Creates a new AlignFrame object with specific width, height and
 216    * sequenceSetId
 217    *
 218    * @param al
 219    * @param width
 220    * @param height
 221    * @param sequenceSetId
 222    * @param viewId
 223    */
 224   public AlignFrame(AlignmentI al, int width, int height,
 225           String sequenceSetId, String viewId)
 226   {
 227     this(al, null, width, height, sequenceSetId, viewId);
 228   }
 229
 230   /**
 231    * new alignment window with hidden columns
 232    *
 233    * @param al
 234    *          AlignmentI
 235    * @param hiddenColumns
 236    *          ColumnSelection or null
 237    * @param width
 238    *          Width of alignment frame
 239    * @param height
 240    *          height of frame.
 241    */
 242   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 243           int height)
 244   {
 245     this(al, hiddenColumns, width, height, null);
 246   }
 247
 248   /**
 249    * Create alignment frame for al with hiddenColumns, a specific width and
 250    * height, and specific sequenceId
 251    *
 252    * @param al
 253    * @param hiddenColumns
 254    * @param width
 255    * @param height
 256    * @param sequenceSetId
 257    *          (may be null)
 258    */
 259   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 260           int height, String sequenceSetId)
 261   {
 262     this(al, hiddenColumns, width, height, sequenceSetId, null);
 263   }
 264
 265   /**
 266    * Create alignment frame for al with hiddenColumns, a specific width and
 267    * height, and specific sequenceId
 268    *
 269    * @param al
 270    * @param hiddenColumns
 271    * @param width
 272    * @param height
 273    * @param sequenceSetId
 274    *          (may be null)
 275    * @param viewId
 276    *          (may be null)
 277    */
 278   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 279           int height, String sequenceSetId, String viewId)
 280   {
 281     setSize(width, height);
 282
 283     if (al.getDataset() == null)
 284     {
 285       al.setDataset(null);
 286     }
 287
 288     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 289
 290     alignPanel = new AlignmentPanel(this, viewport);
 291
 292     addAlignmentPanel(alignPanel, true);
 293     init();
 294   }
 295
 296   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 297           HiddenColumns hiddenColumns, int width, int height)
 298   {
 299     setSize(width, height);
 300
 301     if (al.getDataset() == null)
 302     {
 303       al.setDataset(null);
 304     }
 305
 306     viewport = new AlignViewport(al, hiddenColumns);
 307
 308     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 309     {
 310       viewport.hideSequence(hiddenSeqs);
 311     }
 312     alignPanel = new AlignmentPanel(this, viewport);
 313     addAlignmentPanel(alignPanel, true);
 314     init();
 315   }
 316
 317   /**
 318    * Make a new AlignFrame from existing alignmentPanels
 319    *
 320    * @param ap
 321    *          AlignmentPanel
 322    * @param av
 323    *          AlignViewport
 324    */
 325   public AlignFrame(AlignmentPanel ap)
 326   {
 327     viewport = ap.av;
 328     alignPanel = ap;
 329     addAlignmentPanel(ap, false);
 330     init();
 331   }
 332
 333   @Override
 334   public void propertyChange(PropertyChangeEvent evt)
 335   {
 336     Desktop.getDesktop().propertyChange(evt);
 337   }
 338
 339   /**
 340    * BH 2018
 341    *
 342    * @return true if we have any features
 343    */
 344   @Override
 345   protected boolean haveAlignmentFeatures()
 346   {
 347     AlignmentI alignment = getViewport().getAlignment();
 348
 349     for (int i = 0; i < alignment.getHeight(); i++)
 350     {
 351       SequenceI seq = alignment.getSequenceAt(i);
 352       for (String group : seq.getFeatures().getFeatureGroups(true))
 353       {
 354         if (group != null)
 355           return true;
 356       }
 357     }
 358     return false;
 359   }
 360
 361   /**
 362    * initalise the alignframe from the underlying viewport data and the
 363    * configurations
 364    */
 365   void init()
 366   {
 367     if (!Jalview.isHeadlessMode())
 368     {
 369       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 370     }
 371
 372     avc = new jalview.controller.AlignViewController(this, viewport,
 373             alignPanel);
 374     if (viewport.getAlignmentConservationAnnotation() == null)
 375     {
 376       // BLOSUM62Colour.setEnabled(false);
 377       conservationMenuItem.setEnabled(false);
 378       modifyConservation.setEnabled(false);
 379       // PIDColour.setEnabled(false);
 380       // abovePIDThreshold.setEnabled(false);
 381       // modifyPID.setEnabled(false);
 382     }
 383
 384     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 385             "No sort");
 386
 387     if (sortby.equals("Id"))
 388     {
 389       sortIDMenuItem_actionPerformed(null);
 390     }
 391     else if (sortby.equals("Pairwise Identity"))
 392     {
 393       sortPairwiseMenuItem_actionPerformed(null);
 394     }
 395
 396     this.alignPanel.av
 397             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 398
 399     setMenusFromViewport(viewport);
 400     buildSortByAnnotationScoresMenu();
 401     calculateTree.addActionListener(new ActionListener()
 402     {
 403
 404       @Override
 405       public void actionPerformed(ActionEvent e)
 406       {
 407         openTreePcaDialog();
 408       }
 409     });
 410     buildColourMenu();
 411
 412     if (Desktop.desktop != null)
 413     {
 414       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 415       /**
 416        * BH 2018 ignore service listeners
 417        *
 418        * @j2sNative
 419        *
 420        */
 421       {
 422         addServiceListeners();
 423       }
 424       setGUINucleotide();
 425     }
 426
 427     if (viewport.getWrapAlignment())
 428     {
 429       wrapMenuItem_actionPerformed(null);
 430     }
 431
 432     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 433     {
 434       this.overviewMenuItem_actionPerformed(null);
 435     }
 436
 437     addKeyListener();
 438
 439     final List<AlignmentPanel> selviews = new ArrayList<>();
 440     final List<AlignmentPanel> origview = new ArrayList<>();
 441     final String menuLabel = MessageManager
 442             .getString("label.copy_format_from");
 443     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 444             new ViewSetProvider()
 445             {
 446
 447               @Override
 448               public AlignmentPanel[] getAllAlignmentPanels()
 449               {
 450                 origview.clear();
 451                 origview.add(alignPanel);
 452                 // make an array of all alignment panels except for this one
 453                 List<AlignmentPanel> aps = new ArrayList<>(
 454                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 455                 aps.remove(AlignFrame.this.alignPanel);
 456                 return aps.toArray(new AlignmentPanel[aps.size()]);
 457               }
 458             }, selviews, new ItemListener()
 459             {
 460
 461               @Override
 462               public void itemStateChanged(ItemEvent e)
 463               {
 464                 if (origview.size() > 0)
 465                 {
 466                   final AlignmentPanel ap = origview.get(0);
 467
 468                   /*
 469                    * Copy the ViewStyle of the selected panel to 'this one'.
 470                    * Don't change value of 'scaleProteinAsCdna' unless copying
 471                    * from a SplitFrame.
 472                    */
 473                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 474                           .getViewStyle();
 475                   boolean fromSplitFrame = selviews.get(0)
 476                           .getAlignViewport().getCodingComplement() != null;
 477                   if (!fromSplitFrame)
 478                   {
 479                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 480                             .getViewStyle().isScaleProteinAsCdna());
 481                   }
 482                   ap.getAlignViewport().setViewStyle(vs);
 483
 484                   /*
 485                    * Also rescale ViewStyle of SplitFrame complement if there is
 486                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 487                    * the whole ViewStyle (allow cDNA protein to have different
 488                    * fonts)
 489                    */
 490                   AlignViewportI complement = ap.getAlignViewport()
 491                           .getCodingComplement();
 492                   if (complement != null && vs.isScaleProteinAsCdna())
 493                   {
 494                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 495                     ((SplitFrame) af.getSplitViewContainer())
 496                             .adjustLayout();
 497                     af.setMenusForViewport();
 498                   }
 499
 500                   ap.updateLayout();
 501                   ap.setSelected(true);
 502                   ap.alignFrame.setMenusForViewport();
 503
 504                 }
 505               }
 506             });
 507     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 508             .indexOf("devel") > -1
 509             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 510                     .indexOf("test") > -1)
 511     {
 512       formatMenu.add(vsel);
 513     }
 514     addFocusListener(new FocusAdapter()
 515     {
 516       @Override
 517       public void focusGained(FocusEvent e)
 518       {
 519         Jalview.setCurrentAlignFrame(AlignFrame.this);
 520       }
 521     });
 522
 523   }
 524
 525   /**
 526    * Change the filename and format for the alignment, and enable the 'reload'
 527    * button functionality.
 528    *
 529    * @param file
 530    *          valid filename
 531    * @param format
 532    *          format of file
 533    */
 534   public void setFileName(String file, FileFormatI format)
 535   {
 536     fileName = file;
 537     setFileFormat(format);
 538     reload.setEnabled(true);
 539   }
 540
 541   /**
 542    * JavaScript will have this, maybe others. More dependable than a file name
 543    * and maintains a reference to the actual bytes loaded.
 544    *
 545    * @param file
 546    */
 547   public void setFileObject(File file)
 548   {
 549     this.fileObject = file;
 550   }
 551
 552   /**
 553    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 554    * events
 555    */
 556   void addKeyListener()
 557   {
 558     addKeyListener(new KeyAdapter()
 559     {
 560       @Override
 561       public void keyPressed(KeyEvent evt)
 562       {
 563         if (viewport.cursorMode
 564                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 565                         && evt.getKeyCode() <= KeyEvent.VK_9)
 566                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 567                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 568                 && Character.isDigit(evt.getKeyChar()))
 569         {
 570           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 571         }
 572
 573         switch (evt.getKeyCode())
 574         {
 575
 576         case 27: // escape key
 577           deselectAllSequenceMenuItem_actionPerformed(null);
 578
 579           break;
 580
 581         case KeyEvent.VK_DOWN:
 582           if (evt.isAltDown() || !viewport.cursorMode)
 583           {
 584             moveSelectedSequences(false);
 585           }
 586           if (viewport.cursorMode)
 587           {
 588             alignPanel.getSeqPanel().moveCursor(0, 1);
 589           }
 590           break;
 591
 592         case KeyEvent.VK_UP:
 593           if (evt.isAltDown() || !viewport.cursorMode)
 594           {
 595             moveSelectedSequences(true);
 596           }
 597           if (viewport.cursorMode)
 598           {
 599             alignPanel.getSeqPanel().moveCursor(0, -1);
 600           }
 601
 602           break;
 603
 604         case KeyEvent.VK_LEFT:
 605           if (evt.isAltDown() || !viewport.cursorMode)
 606           {
 607             slideSequences(false,
 608                     alignPanel.getSeqPanel().getKeyboardNo1());
 609           }
 610           else
 611           {
 612             alignPanel.getSeqPanel().moveCursor(-1, 0);
 613           }
 614
 615           break;
 616
 617         case KeyEvent.VK_RIGHT:
 618           if (evt.isAltDown() || !viewport.cursorMode)
 619           {
 620             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 621           }
 622           else
 623           {
 624             alignPanel.getSeqPanel().moveCursor(1, 0);
 625           }
 626           break;
 627
 628         case KeyEvent.VK_SPACE:
 629           if (viewport.cursorMode)
 630           {
 631             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 632                     || evt.isShiftDown() || evt.isAltDown());
 633           }
 634           break;
 635
 636         // case KeyEvent.VK_A:
 637         // if (viewport.cursorMode)
 638         // {
 639         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 640         // //System.out.println("A");
 641         // }
 642         // break;
 643         /*
 644          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 645          * System.out.println("closing bracket"); } break;
 646          */
 647         case KeyEvent.VK_DELETE:
 648         case KeyEvent.VK_BACK_SPACE:
 649           if (!viewport.cursorMode)
 650           {
 651             cut_actionPerformed(null);
 652           }
 653           else
 654           {
 655             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 656                     || evt.isShiftDown() || evt.isAltDown());
 657           }
 658
 659           break;
 660
 661         case KeyEvent.VK_S:
 662           if (viewport.cursorMode)
 663           {
 664             alignPanel.getSeqPanel().setCursorRow();
 665           }
 666           break;
 667         case KeyEvent.VK_C:
 668           if (viewport.cursorMode && !evt.isControlDown())
 669           {
 670             alignPanel.getSeqPanel().setCursorColumn();
 671           }
 672           break;
 673         case KeyEvent.VK_P:
 674           if (viewport.cursorMode)
 675           {
 676             alignPanel.getSeqPanel().setCursorPosition();
 677           }
 678           break;
 679
 680         case KeyEvent.VK_ENTER:
 681         case KeyEvent.VK_COMMA:
 682           if (viewport.cursorMode)
 683           {
 684             alignPanel.getSeqPanel().setCursorRowAndColumn();
 685           }
 686           break;
 687
 688         case KeyEvent.VK_Q:
 689           if (viewport.cursorMode)
 690           {
 691             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 692           }
 693           break;
 694         case KeyEvent.VK_M:
 695           if (viewport.cursorMode)
 696           {
 697             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 698           }
 699           break;
 700
 701         case KeyEvent.VK_F2:
 702           viewport.cursorMode = !viewport.cursorMode;
 703           statusBar.setText(MessageManager
 704                   .formatMessage("label.keyboard_editing_mode", new String[]
 705                   { (viewport.cursorMode ? "on" : "off") }));
 706           if (viewport.cursorMode)
 707           {
 708             ViewportRanges ranges = viewport.getRanges();
 709             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 710                     .getStartRes();
 711             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 712                     .getStartSeq();
 713           }
 714           alignPanel.getSeqPanel().seqCanvas.repaint();
 715           break;
 716
 717         case KeyEvent.VK_F1:
 718           try
 719           {
 720             Help.showHelpWindow();
 721           } catch (Exception ex)
 722           {
 723             ex.printStackTrace();
 724           }
 725           break;
 726         case KeyEvent.VK_H:
 727         {
 728           boolean toggleSeqs = !evt.isControlDown();
 729           boolean toggleCols = !evt.isShiftDown();
 730           toggleHiddenRegions(toggleSeqs, toggleCols);
 731           break;
 732         }
 733         case KeyEvent.VK_B:
 734         {
 735           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 736           boolean modifyExisting = true; // always modify, don't clear
 737                                          // evt.isShiftDown();
 738           boolean invertHighlighted = evt.isAltDown();
 739           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 740                   toggleSel);
 741           break;
 742         }
 743         case KeyEvent.VK_PAGE_UP:
 744           viewport.getRanges().pageUp();
 745           break;
 746         case KeyEvent.VK_PAGE_DOWN:
 747           viewport.getRanges().pageDown();
 748           break;
 749         }
 750       }
 751
 752       @Override
 753       public void keyReleased(KeyEvent evt)
 754       {
 755         switch (evt.getKeyCode())
 756         {
 757         case KeyEvent.VK_LEFT:
 758           if (evt.isAltDown() || !viewport.cursorMode)
 759           {
 760             viewport.firePropertyChange("alignment", null,
 761                     viewport.getAlignment().getSequences());
 762           }
 763           break;
 764
 765         case KeyEvent.VK_RIGHT:
 766           if (evt.isAltDown() || !viewport.cursorMode)
 767           {
 768             viewport.firePropertyChange("alignment", null,
 769                     viewport.getAlignment().getSequences());
 770           }
 771           break;
 772         }
 773       }
 774     });
 775   }
 776
 777   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 778   {
 779     ap.alignFrame = this;
 780     avc = new jalview.controller.AlignViewController(this, viewport,
 781             alignPanel);
 782
 783     alignPanels.add(ap);
 784
 785     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 786
 787     int aSize = alignPanels.size();
 788
 789     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 790
 791     if (aSize == 1 && ap.av.viewName == null)
 792     {
 793       this.getContentPane().add(ap, BorderLayout.CENTER);
 794     }
 795     else
 796     {
 797       if (aSize == 2)
 798       {
 799         setInitialTabVisible();
 800       }
 801
 802       expandViews.setEnabled(true);
 803       gatherViews.setEnabled(true);
 804       tabbedPane.addTab(ap.av.viewName, ap);
 805
 806       ap.setVisible(false);
 807     }
 808
 809     if (newPanel)
 810     {
 811       if (ap.av.isPadGaps())
 812       {
 813         ap.av.getAlignment().padGaps();
 814       }
 815       ap.av.updateConservation(ap);
 816       ap.av.updateConsensus(ap);
 817       ap.av.updateStrucConsensus(ap);
 818     }
 819   }
 820
 821   public void setInitialTabVisible()
 822   {
 823     expandViews.setEnabled(true);
 824     gatherViews.setEnabled(true);
 825     tabbedPane.setVisible(true);
 826     AlignmentPanel first = alignPanels.get(0);
 827     tabbedPane.addTab(first.av.viewName, first);
 828     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 829   }
 830
 831   public AlignViewport getViewport()
 832   {
 833     return viewport;
 834   }
 835
 836   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 837   private void addServiceListeners()
 838   {
 839     final java.beans.PropertyChangeListener thisListener;
 840     Desktop.instance.addJalviewPropertyChangeListener("services",
 841             thisListener = new java.beans.PropertyChangeListener()
 842             {
 843               @Override
 844               public void propertyChange(PropertyChangeEvent evt)
 845               {
 846                 // // System.out.println("Discoverer property change.");
 847                 // if (evt.getPropertyName().equals("services"))
 848                 {
 849                   SwingUtilities.invokeLater(new Runnable()
 850                   {
 851
 852                     @Override
 853                     public void run()
 854                     {
 855                       System.err.println(
 856                               "Rebuild WS Menu for service change");
 857                       BuildWebServiceMenu();
 858                     }
 859
 860                   });
 861                 }
 862               }
 863             });
 864     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 865     {
 866       @Override
 867       public void internalFrameClosed(
 868               javax.swing.event.InternalFrameEvent evt)
 869       {
 870         // System.out.println("deregistering discoverer listener");
 871         Desktop.instance.removeJalviewPropertyChangeListener("services",
 872                 thisListener);
 873         closeMenuItem_actionPerformed(true);
 874       };
 875     });
 876     // Finally, build the menu once to get current service state
 877     new Thread(new Runnable()
 878     {
 879       @Override
 880       public void run()
 881       {
 882         BuildWebServiceMenu();
 883       }
 884     }).start();
 885   }
 886
 887   /**
 888    * Configure menu items that vary according to whether the alignment is
 889    * nucleotide or protein
 890    */
 891   public void setGUINucleotide()
 892   {
 893     AlignmentI al = getViewport().getAlignment();
 894     boolean nucleotide = al.isNucleotide();
 895
 896     loadVcf.setVisible(nucleotide);
 897     showTranslation.setVisible(nucleotide);
 898     showReverse.setVisible(nucleotide);
 899     showReverseComplement.setVisible(nucleotide);
 900     conservationMenuItem.setEnabled(!nucleotide);
 901     modifyConservation
 902             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 903     showGroupConservation.setEnabled(!nucleotide);
 904
 905     showComplementMenuItem
 906             .setText(nucleotide ? MessageManager.getString("label.protein")
 907                     : MessageManager.getString("label.nucleotide"));
 908   }
 909
 910   /**
 911    * set up menus for the current viewport. This may be called after any
 912    * operation that affects the data in the current view (selection changed,
 913    * etc) to update the menus to reflect the new state.
 914    */
 915   @Override
 916   public void setMenusForViewport()
 917   {
 918     setMenusFromViewport(viewport);
 919   }
 920
 921   /**
 922    * Need to call this method when tabs are selected for multiple views, or when
 923    * loading from Jalview2XML.java
 924    *
 925    * @param av
 926    *          AlignViewport
 927    */
 928   void setMenusFromViewport(AlignViewport av)
 929   {
 930     padGapsMenuitem.setSelected(av.isPadGaps());
 931     colourTextMenuItem.setSelected(av.isShowColourText());
 932     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 933     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 934     conservationMenuItem.setSelected(av.getConservationSelected());
 935     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 936     seqLimits.setSelected(av.getShowJVSuffix());
 937     idRightAlign.setSelected(av.isRightAlignIds());
 938     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 939     renderGapsMenuItem.setSelected(av.isRenderGaps());
 940     wrapMenuItem.setSelected(av.getWrapAlignment());
 941     scaleAbove.setVisible(av.getWrapAlignment());
 942     scaleLeft.setVisible(av.getWrapAlignment());
 943     scaleRight.setVisible(av.getWrapAlignment());
 944     annotationPanelMenuItem.setState(av.isShowAnnotation());
 945     /*
 946      * Show/hide annotations only enabled if annotation panel is shown
 947      */
 948     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 949     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 950     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 951     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 952     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 953     viewTextMenuItem.setSelected(av.getShowText());
 954     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 955     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 956     showGroupConservation.setSelected(av.isShowGroupConservation());
 957     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 958     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 959     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 960
 961     ColourMenuHelper.setColourSelected(colourMenu,
 962             av.getGlobalColourScheme());
 963
 964     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 965     hiddenMarkers.setState(av.getShowHiddenMarkers());
 966     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 967     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 968     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 969     autoCalculate.setSelected(av.autoCalculateConsensus);
 970     sortByTree.setSelected(av.sortByTree);
 971     listenToViewSelections.setSelected(av.followSelection);
 972
 973     showProducts.setEnabled(canShowProducts());
 974     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 975
 976     updateEditMenuBar();
 977   }
 978
 979   /**
 980    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 981    *
 982    * @param b
 983    */
 984   public void setGroovyEnabled(boolean b)
 985   {
 986     runGroovy.setEnabled(b);
 987   }
 988
 989   private IProgressIndicator progressBar;
 990
 991   /*
 992    * (non-Javadoc)
 993    *
 994    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 995    */
 996   @Override
 997   public void setProgressBar(String message, long id)
 998   {
 999     progressBar.setProgressBar(message, id);
1000   }
1001
1002   @Override
1003   public void registerHandler(final long id,
1004           final IProgressIndicatorHandler handler)
1005   {
1006     progressBar.registerHandler(id, handler);
1007   }
1008
1009   /**
1010    *
1011    * @return true if any progress bars are still active
1012    */
1013   @Override
1014   public boolean operationInProgress()
1015   {
1016     return progressBar.operationInProgress();
1017   }
1018
1019   @Override
1020   public void setStatus(String text)
1021   {
1022     statusBar.setText(text);
1023   }
1024
1025   /*
1026    * Added so Castor Mapping file can obtain Jalview Version
1027    */
1028   public String getVersion()
1029   {
1030     return jalview.bin.Cache.getProperty("VERSION");
1031   }
1032
1033   public FeatureRenderer getFeatureRenderer()
1034   {
1035     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1036   }
1037
1038   @Override
1039   public void fetchSequence_actionPerformed(ActionEvent e)
1040   {
1041     new jalview.gui.SequenceFetcher(this);
1042   }
1043
1044   @Override
1045   public void addFromFile_actionPerformed(ActionEvent e)
1046   {
1047     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1048   }
1049
1050   @Override
1051   public void reload_actionPerformed(ActionEvent e)
1052   {
1053     if (fileName != null)
1054     {
1055       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1056       // originating file's format
1057       // TODO: work out how to recover feature settings for correct view(s) when
1058       // file is reloaded.
1059       if (FileFormat.Jalview.equals(currentFileFormat))
1060       {
1061         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1062         for (int i = 0; i < frames.length; i++)
1063         {
1064           if (frames[i] instanceof AlignFrame && frames[i] != this
1065                   && ((AlignFrame) frames[i]).fileName != null
1066                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1067           {
1068             try
1069             {
1070               frames[i].setSelected(true);
1071               Desktop.instance.closeAssociatedWindows();
1072             } catch (java.beans.PropertyVetoException ex)
1073             {
1074             }
1075           }
1076
1077         }
1078         Desktop.instance.closeAssociatedWindows();
1079
1080         FileLoader loader = new FileLoader();
1081         DataSourceType protocol = fileName.startsWith("http:")
1082                 ? DataSourceType.URL
1083                 : DataSourceType.FILE;
1084         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1085       }
1086       else
1087       {
1088         Rectangle bounds = this.getBounds();
1089
1090         FileLoader loader = new FileLoader();
1091
1092         AlignFrame newframe = null;
1093
1094         if (fileObject == null)
1095         {
1096
1097           DataSourceType protocol = (fileName.startsWith("http:")
1098                   ? DataSourceType.URL
1099                   : DataSourceType.FILE);
1100           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1101                   currentFileFormat);
1102         }
1103         else
1104         {
1105           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1106                   DataSourceType.FILE, currentFileFormat);
1107         }
1108
1109         newframe.setBounds(bounds);
1110         if (featureSettings != null && featureSettings.isShowing())
1111         {
1112           final Rectangle fspos = featureSettings.frame.getBounds();
1113           // TODO: need a 'show feature settings' function that takes bounds -
1114           // need to refactor Desktop.addFrame
1115           newframe.featureSettings_actionPerformed(null);
1116           final FeatureSettings nfs = newframe.featureSettings;
1117           SwingUtilities.invokeLater(new Runnable()
1118           {
1119             @Override
1120             public void run()
1121             {
1122               nfs.frame.setBounds(fspos);
1123             }
1124           });
1125           this.featureSettings.close();
1126           this.featureSettings = null;
1127         }
1128         this.closeMenuItem_actionPerformed(true);
1129       }
1130     }
1131   }
1132
1133   @Override
1134   public void addFromText_actionPerformed(ActionEvent e)
1135   {
1136     Desktop.instance
1137             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1138   }
1139
1140   @Override
1141   public void addFromURL_actionPerformed(ActionEvent e)
1142   {
1143     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1144   }
1145
1146   @Override
1147   public void save_actionPerformed(ActionEvent e)
1148   {
1149     if (fileName == null || (currentFileFormat == null)
1150             || fileName.startsWith("http"))
1151     {
1152       saveAs_actionPerformed(null);
1153     }
1154     else
1155     {
1156       saveAlignment(fileName, currentFileFormat);
1157     }
1158   }
1159
1160   /**
1161    * DOCUMENT ME!
1162    *
1163    * @param e
1164    *          DOCUMENT ME!
1165    */
1166   @Override
1167   public void saveAs_actionPerformed(ActionEvent e)
1168   {
1169     String format = currentFileFormat == null ? null
1170             : currentFileFormat.getName();
1171     final JalviewFileChooser chooser = JalviewFileChooser
1172             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1173     final AlignFrame us = this;
1174     chooser.setFileView(new JalviewFileView());
1175     chooser.setDialogTitle(
1176             MessageManager.getString("label.save_alignment_to_file"));
1177     chooser.setToolTipText(MessageManager.getString("action.save"));
1178
1179     chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1180     {
1181       @Override
1182       public void run()
1183       {
1184         currentFileFormat = chooser.getSelectedFormat();
1185         while (currentFileFormat == null)
1186         {
1187           JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1188                   MessageManager.getString(
1189                           "label.select_file_format_before_saving"),
1190                   MessageManager
1191                           .getString("label.file_format_not_specified"),
1192                   JvOptionPane.WARNING_MESSAGE);
1193           currentFileFormat = chooser.getSelectedFormat();
1194           chooser.showSaveDialog(us);
1195         }
1196
1197         fileName = chooser.getSelectedFile().getPath();
1198
1199         Cache.setProperty("DEFAULT_FILE_FORMAT",
1200                 currentFileFormat.getName());
1201
1202         Cache.setProperty("LAST_DIRECTORY", fileName);
1203         saveAlignment(fileName, currentFileFormat);
1204       }
1205     }).showSaveDialog(this);
1206   }
1207
1208   private boolean lastSaveSuccessful = false;
1209
1210   private FileFormatI lastFormatSaved;
1211
1212   private String lastFilenameSaved;
1213
1214   /**
1215    * Raise a dialog or status message for the last call to saveAlignment.
1216    *
1217    * @return true if last call to saveAlignment(file, format) was successful.
1218    */
1219   public boolean isSaveAlignmentSuccessful()
1220   {
1221
1222     if (!lastSaveSuccessful)
1223     {
1224       JvOptionPane.showInternalMessageDialog(this, MessageManager
1225               .formatMessage("label.couldnt_save_file", new Object[]
1226               { lastFilenameSaved }),
1227               MessageManager.getString("label.error_saving_file"),
1228               JvOptionPane.WARNING_MESSAGE);
1229     }
1230     else
1231     {
1232
1233       statusBar.setText(MessageManager.formatMessage(
1234               "label.successfully_saved_to_file_in_format", new Object[]
1235               { lastFilenameSaved, lastFormatSaved }));
1236
1237     }
1238     return lastSaveSuccessful;
1239   }
1240
1241   public void saveAlignment(String file, FileFormatI format)
1242   {
1243     lastSaveSuccessful = false;
1244     lastFilenameSaved = file;
1245     lastFormatSaved = format;
1246     AlignFrame us = this;
1247     if (FileFormat.Jalview.equals(format))
1248     {
1249       String shortName = title;
1250
1251       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1252       {
1253         shortName = shortName.substring(
1254                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1255       }
1256
1257       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1258               shortName);
1259     }
1260     else
1261     {
1262       AlignExportSettingI settings = getAlignmentForExport(format,
1263               alignPanel, null);
1264       settings.addActionListener(new ActionListener()
1265       {
1266         @Override
1267         public void actionPerformed(ActionEvent e)
1268         {
1269
1270           if (settings.isCancelled())
1271           {
1272             lastSaveSuccessful = false;
1273             return;
1274           }
1275           AlignmentExportData exportData = settings.getAlignExportData();
1276           FormatAdapter f = new FormatAdapter(alignPanel,
1277                   exportData.getSettings());
1278           String output = f.formatSequences(format,
1279                   exportData.getAlignment(), // class
1280                                              // cast
1281                                              // exceptions
1282                                              // will
1283                   // occur in the distant future
1284                   exportData.getOmitHidden(),
1285                   exportData.getStartEndPostions(),
1286                   f.getCacheSuffixDefault(format),
1287                   viewport.getAlignment().getHiddenColumns());
1288
1289           if (output == null)
1290           {
1291             lastSaveSuccessful = false;
1292           }
1293           else
1294           {
1295             try
1296             {
1297               PrintWriter out = new PrintWriter(new FileWriter(file));
1298
1299               out.print(output);
1300               out.close();
1301               us.setTitle(file);
1302               statusBar.setText(MessageManager.formatMessage(
1303                       "label.successfully_saved_to_file_in_format",
1304                       new Object[]
1305                       { fileName, format.getName() }));
1306             } catch (Exception ex)
1307             {
1308               lastSaveSuccessful = false;
1309               ex.printStackTrace();
1310             }
1311           }
1312         }
1313       });
1314
1315       settings.doShowSettings();
1316     }
1317   }
1318
1319   /**
1320    * DOCUMENT ME!
1321    *
1322    * @param e
1323    *          DOCUMENT ME!
1324    */
1325   @Override
1326   protected void outputText_actionPerformed(ActionEvent e)
1327   {
1328     FileFormatI fileFormat = FileFormats.getInstance()
1329             .forName(e.getActionCommand());
1330     AlignExportSettingI settings = getAlignmentForExport(fileFormat,
1331             alignPanel, null);
1332     settings.addActionListener(new ActionListener()
1333     {
1334       @Override
1335       public void actionPerformed(ActionEvent e)
1336       {
1337         if (settings.isCancelled())
1338         {
1339           return;
1340         }
1341         AlignmentExportData exportData = settings.getAlignExportData();
1342         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1343         cap.setForInput(null);
1344         try
1345         {
1346           FileFormatI format = fileFormat;
1347           cap.setText(new FormatAdapter(alignPanel, settings)
1348                   .formatSequences(format, exportData.getAlignment(),
1349                           exportData.getOmitHidden(),
1350                           exportData.getStartEndPostions(),
1351                           viewport.getAlignment().getHiddenColumns()));
1352           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1353                   "label.alignment_output_command", new Object[]
1354                   { fileFormat.getName() }), 600, 500);
1355         } catch (OutOfMemoryError oom)
1356         {
1357           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1358                   oom);
1359           cap.dispose();
1360         }
1361         // TODO Auto-generated method stub
1362
1363       }
1364     });
1365     settings.doShowSettings();
1366   }
1367
1368   public static AlignExportSettingI getAlignmentForExport(
1369           FileFormatI format, AlignmentPanel alignPanel,
1370           AlignExportSettingBeanI exportSettings)
1371   {
1372
1373     return new AlignExportSettings(alignPanel, format, exportSettings);
1374   }
1375
1376   /**
1377    * DOCUMENT ME!
1378    *
1379    * @param e
1380    *          DOCUMENT ME!
1381    */
1382   @Override
1383   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1384   {
1385     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1386     htmlSVG.exportHTML(null);
1387   }
1388
1389   @Override
1390   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1391   {
1392     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1393     bjs.exportHTML(null);
1394   }
1395
1396   public void createImageMap(File file, String image)
1397   {
1398     alignPanel.makePNGImageMap(file, image);
1399   }
1400
1401   /**
1402    * DOCUMENT ME!
1403    *
1404    * @param e
1405    *          DOCUMENT ME!
1406    */
1407   @Override
1408   public void createPNG(File f)
1409   {
1410     alignPanel.makePNG(f);
1411   }
1412
1413   /**
1414    * DOCUMENT ME!
1415    *
1416    * @param e
1417    *          DOCUMENT ME!
1418    */
1419   @Override
1420   public void createEPS(File f)
1421   {
1422     alignPanel.makeEPS(f);
1423   }
1424
1425   @Override
1426   public void createSVG(File f)
1427   {
1428     alignPanel.makeSVG(f);
1429   }
1430
1431   @Override
1432   public void pageSetup_actionPerformed(ActionEvent e)
1433   {
1434     PrinterJob printJob = PrinterJob.getPrinterJob();
1435     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1436   }
1437
1438   /**
1439    * DOCUMENT ME!
1440    *
1441    * @param e
1442    *          DOCUMENT ME!
1443    */
1444   @Override
1445   public void printMenuItem_actionPerformed(ActionEvent e)
1446   {
1447     // Putting in a thread avoids Swing painting problems
1448     PrintThread thread = new PrintThread(alignPanel);
1449     thread.start();
1450   }
1451
1452   @Override
1453   public void exportFeatures_actionPerformed(ActionEvent e)
1454   {
1455     new AnnotationExporter(alignPanel).exportFeatures();
1456   }
1457
1458   @Override
1459   public void exportAnnotations_actionPerformed(ActionEvent e)
1460   {
1461     new AnnotationExporter(alignPanel).exportAnnotations();
1462   }
1463
1464   @Override
1465   public void associatedData_actionPerformed(ActionEvent e)
1466   {
1467     final JalviewFileChooser chooser = new JalviewFileChooser(
1468             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1469     chooser.setFileView(new JalviewFileView());
1470     chooser.setDialogTitle(
1471             MessageManager.getString("label.load_jalview_annotations"));
1472     chooser.setToolTipText(
1473             MessageManager.getString("label.load_jalview_annotations"));
1474     chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1475     {
1476
1477       @Override
1478       public void run()
1479       {
1480         String choice = chooser.getSelectedFile().getPath();
1481         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1482         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1483       }
1484
1485     });
1486
1487     chooser.openDialog(this);
1488   }
1489
1490   /**
1491    * Close the current view or all views in the alignment frame. If the frame
1492    * only contains one view then the alignment will be removed from memory.
1493    *
1494    * @param closeAllTabs
1495    */
1496   @Override
1497   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1498   {
1499     if (alignPanels != null && alignPanels.size() < 2)
1500     {
1501       closeAllTabs = true;
1502     }
1503
1504     try
1505     {
1506       if (alignPanels != null)
1507       {
1508         if (closeAllTabs)
1509         {
1510           if (this.isClosed())
1511           {
1512             // really close all the windows - otherwise wait till
1513             // setClosed(true) is called
1514             for (int i = 0; i < alignPanels.size(); i++)
1515             {
1516               AlignmentPanel ap = alignPanels.get(i);
1517               ap.closePanel();
1518             }
1519           }
1520         }
1521         else
1522         {
1523           closeView(alignPanel);
1524         }
1525       }
1526
1527       if (closeAllTabs)
1528       {
1529         /*
1530          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1531          * be called recursively, with the frame now in 'closed' state
1532          */
1533         this.setClosed(true);
1534       }
1535     } catch (Exception ex)
1536     {
1537       ex.printStackTrace();
1538     }
1539   }
1540
1541   /**
1542    * Close the specified panel and close up tabs appropriately.
1543    *
1544    * @param panelToClose
1545    */
1546   public void closeView(AlignmentPanel panelToClose)
1547   {
1548     int index = tabbedPane.getSelectedIndex();
1549     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1550     alignPanels.remove(panelToClose);
1551     panelToClose.closePanel();
1552     panelToClose = null;
1553
1554     tabbedPane.removeTabAt(closedindex);
1555     tabbedPane.validate();
1556
1557     if (index > closedindex || index == tabbedPane.getTabCount())
1558     {
1559       // modify currently selected tab index if necessary.
1560       index--;
1561     }
1562
1563     this.tabSelectionChanged(index);
1564   }
1565
1566   /**
1567    * DOCUMENT ME!
1568    */
1569   void updateEditMenuBar()
1570   {
1571
1572     if (viewport.getHistoryList().size() > 0)
1573     {
1574       undoMenuItem.setEnabled(true);
1575       CommandI command = viewport.getHistoryList().peek();
1576       undoMenuItem.setText(MessageManager
1577               .formatMessage("label.undo_command", new Object[]
1578               { command.getDescription() }));
1579     }
1580     else
1581     {
1582       undoMenuItem.setEnabled(false);
1583       undoMenuItem.setText(MessageManager.getString("action.undo"));
1584     }
1585
1586     if (viewport.getRedoList().size() > 0)
1587     {
1588       redoMenuItem.setEnabled(true);
1589
1590       CommandI command = viewport.getRedoList().peek();
1591       redoMenuItem.setText(MessageManager
1592               .formatMessage("label.redo_command", new Object[]
1593               { command.getDescription() }));
1594     }
1595     else
1596     {
1597       redoMenuItem.setEnabled(false);
1598       redoMenuItem.setText(MessageManager.getString("action.redo"));
1599     }
1600   }
1601
1602   @Override
1603   public void addHistoryItem(CommandI command)
1604   {
1605     if (command.getSize() > 0)
1606     {
1607       viewport.addToHistoryList(command);
1608       viewport.clearRedoList();
1609       updateEditMenuBar();
1610       viewport.updateHiddenColumns();
1611       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1612       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1613       // viewport.getColumnSelection()
1614       // .getHiddenColumns().size() > 0);
1615     }
1616   }
1617
1618   /**
1619    *
1620    * @return alignment objects for all views
1621    */
1622   AlignmentI[] getViewAlignments()
1623   {
1624     if (alignPanels != null)
1625     {
1626       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1627       int i = 0;
1628       for (AlignmentPanel ap : alignPanels)
1629       {
1630         als[i++] = ap.av.getAlignment();
1631       }
1632       return als;
1633     }
1634     if (viewport != null)
1635     {
1636       return new AlignmentI[] { viewport.getAlignment() };
1637     }
1638     return null;
1639   }
1640
1641   /**
1642    * DOCUMENT ME!
1643    *
1644    * @param e
1645    *          DOCUMENT ME!
1646    */
1647   @Override
1648   protected void undoMenuItem_actionPerformed(ActionEvent e)
1649   {
1650     if (viewport.getHistoryList().isEmpty())
1651     {
1652       return;
1653     }
1654     CommandI command = viewport.getHistoryList().pop();
1655     viewport.addToRedoList(command);
1656     command.undoCommand(getViewAlignments());
1657
1658     AlignmentViewport originalSource = getOriginatingSource(command);
1659     updateEditMenuBar();
1660
1661     if (originalSource != null)
1662     {
1663       if (originalSource != viewport)
1664       {
1665         Cache.log.warn(
1666                 "Implementation worry: mismatch of viewport origin for undo");
1667       }
1668       originalSource.updateHiddenColumns();
1669       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1670       // null
1671       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1672       // viewport.getColumnSelection()
1673       // .getHiddenColumns().size() > 0);
1674       originalSource.firePropertyChange("alignment", null,
1675               originalSource.getAlignment().getSequences());
1676     }
1677   }
1678
1679   /**
1680    * DOCUMENT ME!
1681    *
1682    * @param e
1683    *          DOCUMENT ME!
1684    */
1685   @Override
1686   protected void redoMenuItem_actionPerformed(ActionEvent e)
1687   {
1688     if (viewport.getRedoList().size() < 1)
1689     {
1690       return;
1691     }
1692
1693     CommandI command = viewport.getRedoList().pop();
1694     viewport.addToHistoryList(command);
1695     command.doCommand(getViewAlignments());
1696
1697     AlignmentViewport originalSource = getOriginatingSource(command);
1698     updateEditMenuBar();
1699
1700     if (originalSource != null)
1701     {
1702
1703       if (originalSource != viewport)
1704       {
1705         Cache.log.warn(
1706                 "Implementation worry: mismatch of viewport origin for redo");
1707       }
1708       originalSource.updateHiddenColumns();
1709       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1710       // null
1711       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1712       // viewport.getColumnSelection()
1713       // .getHiddenColumns().size() > 0);
1714       originalSource.firePropertyChange("alignment", null,
1715               originalSource.getAlignment().getSequences());
1716     }
1717   }
1718
1719   AlignmentViewport getOriginatingSource(CommandI command)
1720   {
1721     AlignmentViewport originalSource = null;
1722     // For sequence removal and addition, we need to fire
1723     // the property change event FROM the viewport where the
1724     // original alignment was altered
1725     AlignmentI al = null;
1726     if (command instanceof EditCommand)
1727     {
1728       EditCommand editCommand = (EditCommand) command;
1729       al = editCommand.getAlignment();
1730       List<Component> comps = PaintRefresher.components
1731               .get(viewport.getSequenceSetId());
1732
1733       for (Component comp : comps)
1734       {
1735         if (comp instanceof AlignmentPanel)
1736         {
1737           if (al == ((AlignmentPanel) comp).av.getAlignment())
1738           {
1739             originalSource = ((AlignmentPanel) comp).av;
1740             break;
1741           }
1742         }
1743       }
1744     }
1745
1746     if (originalSource == null)
1747     {
1748       // The original view is closed, we must validate
1749       // the current view against the closed view first
1750       if (al != null)
1751       {
1752         PaintRefresher.validateSequences(al, viewport.getAlignment());
1753       }
1754
1755       originalSource = viewport;
1756     }
1757
1758     return originalSource;
1759   }
1760
1761   /**
1762    * DOCUMENT ME!
1763    *
1764    * @param up
1765    *          DOCUMENT ME!
1766    */
1767   public void moveSelectedSequences(boolean up)
1768   {
1769     SequenceGroup sg = viewport.getSelectionGroup();
1770
1771     if (sg == null)
1772     {
1773       return;
1774     }
1775     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1776             viewport.getHiddenRepSequences(), up);
1777     alignPanel.paintAlignment(true, false);
1778   }
1779
1780   synchronized void slideSequences(boolean right, int size)
1781   {
1782     List<SequenceI> sg = new ArrayList<>();
1783     if (viewport.cursorMode)
1784     {
1785       sg.add(viewport.getAlignment()
1786               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1787     }
1788     else if (viewport.getSelectionGroup() != null
1789             && viewport.getSelectionGroup().getSize() != viewport
1790                     .getAlignment().getHeight())
1791     {
1792       sg = viewport.getSelectionGroup()
1793               .getSequences(viewport.getHiddenRepSequences());
1794     }
1795
1796     if (sg.size() < 1)
1797     {
1798       return;
1799     }
1800
1801     List<SequenceI> invertGroup = new ArrayList<>();
1802
1803     for (SequenceI seq : viewport.getAlignment().getSequences())
1804     {
1805       if (!sg.contains(seq))
1806       {
1807         invertGroup.add(seq);
1808       }
1809     }
1810
1811     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1812
1813     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1814     for (int i = 0; i < invertGroup.size(); i++)
1815     {
1816       seqs2[i] = invertGroup.get(i);
1817     }
1818
1819     SlideSequencesCommand ssc;
1820     if (right)
1821     {
1822       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1823               viewport.getGapCharacter());
1824     }
1825     else
1826     {
1827       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1828               viewport.getGapCharacter());
1829     }
1830
1831     int groupAdjustment = 0;
1832     if (ssc.getGapsInsertedBegin() && right)
1833     {
1834       if (viewport.cursorMode)
1835       {
1836         alignPanel.getSeqPanel().moveCursor(size, 0);
1837       }
1838       else
1839       {
1840         groupAdjustment = size;
1841       }
1842     }
1843     else if (!ssc.getGapsInsertedBegin() && !right)
1844     {
1845       if (viewport.cursorMode)
1846       {
1847         alignPanel.getSeqPanel().moveCursor(-size, 0);
1848       }
1849       else
1850       {
1851         groupAdjustment = -size;
1852       }
1853     }
1854
1855     if (groupAdjustment != 0)
1856     {
1857       viewport.getSelectionGroup().setStartRes(
1858               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1859       viewport.getSelectionGroup().setEndRes(
1860               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1861     }
1862
1863     /*
1864      * just extend the last slide command if compatible; but not if in
1865      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1866      */
1867     boolean appendHistoryItem = false;
1868     Deque<CommandI> historyList = viewport.getHistoryList();
1869     boolean inSplitFrame = getSplitViewContainer() != null;
1870     if (!inSplitFrame && historyList != null && historyList.size() > 0
1871             && historyList.peek() instanceof SlideSequencesCommand)
1872     {
1873       appendHistoryItem = ssc.appendSlideCommand(
1874               (SlideSequencesCommand) historyList.peek());
1875     }
1876
1877     if (!appendHistoryItem)
1878     {
1879       addHistoryItem(ssc);
1880     }
1881
1882     repaint();
1883   }
1884
1885   /**
1886    * DOCUMENT ME!
1887    *
1888    * @param e
1889    *          DOCUMENT ME!
1890    */
1891   @Override
1892   protected void copy_actionPerformed(ActionEvent e)
1893   {
1894     if (viewport.getSelectionGroup() == null)
1895     {
1896       return;
1897     }
1898     // TODO: preserve the ordering of displayed alignment annotation in any
1899     // internal paste (particularly sequence associated annotation)
1900     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1901     String[] omitHidden = null;
1902
1903     if (viewport.hasHiddenColumns())
1904     {
1905       omitHidden = viewport.getViewAsString(true);
1906     }
1907
1908     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1909             seqs, omitHidden, null);
1910
1911     StringSelection ss = new StringSelection(output);
1912
1913     try
1914     {
1915       jalview.gui.Desktop.internalCopy = true;
1916       // Its really worth setting the clipboard contents
1917       // to empty before setting the large StringSelection!!
1918       Toolkit.getDefaultToolkit().getSystemClipboard()
1919               .setContents(new StringSelection(""), null);
1920
1921       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1922               Desktop.instance);
1923     } catch (OutOfMemoryError er)
1924     {
1925       new OOMWarning("copying region", er);
1926       return;
1927     }
1928
1929     HiddenColumns hiddenColumns = null;
1930     if (viewport.hasHiddenColumns())
1931     {
1932       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1933       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1934
1935       // create new HiddenColumns object with copy of hidden regions
1936       // between startRes and endRes, offset by startRes
1937       hiddenColumns = new HiddenColumns(
1938               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1939               hiddenCutoff, hiddenOffset);
1940     }
1941
1942     Desktop.jalviewClipboard = new Object[] { seqs,
1943         viewport.getAlignment().getDataset(), hiddenColumns };
1944     statusBar.setText(MessageManager.formatMessage(
1945             "label.copied_sequences_to_clipboard", new Object[]
1946             { Integer.valueOf(seqs.length).toString() }));
1947   }
1948
1949   /**
1950    * DOCUMENT ME!
1951    *
1952    * @param e
1953    *          DOCUMENT ME!
1954    */
1955   @Override
1956   protected void pasteNew_actionPerformed(ActionEvent e)
1957   {
1958     paste(true);
1959   }
1960
1961   /**
1962    * DOCUMENT ME!
1963    *
1964    * @param e
1965    *          DOCUMENT ME!
1966    */
1967   @Override
1968   protected void pasteThis_actionPerformed(ActionEvent e)
1969   {
1970     paste(false);
1971   }
1972
1973   /**
1974    * Paste contents of Jalview clipboard
1975    *
1976    * @param newAlignment
1977    *          true to paste to a new alignment, otherwise add to this.
1978    */
1979   void paste(boolean newAlignment)
1980   {
1981     boolean externalPaste = true;
1982     try
1983     {
1984       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1985       Transferable contents = c.getContents(this);
1986
1987       if (contents == null)
1988       {
1989         return;
1990       }
1991
1992       String str;
1993       FileFormatI format;
1994       try
1995       {
1996         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1997         if (str.length() < 1)
1998         {
1999           return;
2000         }
2001
2002         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2003
2004       } catch (OutOfMemoryError er)
2005       {
2006         new OOMWarning("Out of memory pasting sequences!!", er);
2007         return;
2008       }
2009
2010       SequenceI[] sequences;
2011       boolean annotationAdded = false;
2012       AlignmentI alignment = null;
2013
2014       if (Desktop.jalviewClipboard != null)
2015       {
2016         // The clipboard was filled from within Jalview, we must use the
2017         // sequences
2018         // And dataset from the copied alignment
2019         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2020         // be doubly sure that we create *new* sequence objects.
2021         sequences = new SequenceI[newseq.length];
2022         for (int i = 0; i < newseq.length; i++)
2023         {
2024           sequences[i] = new Sequence(newseq[i]);
2025         }
2026         alignment = new Alignment(sequences);
2027         externalPaste = false;
2028       }
2029       else
2030       {
2031         // parse the clipboard as an alignment.
2032         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2033                 format);
2034         sequences = alignment.getSequencesArray();
2035       }
2036
2037       int alwidth = 0;
2038       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2039       int fgroup = -1;
2040
2041       if (newAlignment)
2042       {
2043
2044         if (Desktop.jalviewClipboard != null)
2045         {
2046           // dataset is inherited
2047           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2048         }
2049         else
2050         {
2051           // new dataset is constructed
2052           alignment.setDataset(null);
2053         }
2054         alwidth = alignment.getWidth() + 1;
2055       }
2056       else
2057       {
2058         AlignmentI pastedal = alignment; // preserve pasted alignment object
2059         // Add pasted sequences and dataset into existing alignment.
2060         alignment = viewport.getAlignment();
2061         alwidth = alignment.getWidth() + 1;
2062         // decide if we need to import sequences from an existing dataset
2063         boolean importDs = Desktop.jalviewClipboard != null
2064                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2065         // importDs==true instructs us to copy over new dataset sequences from
2066         // an existing alignment
2067         Vector newDs = (importDs) ? new Vector() : null; // used to create
2068         // minimum dataset set
2069
2070         for (int i = 0; i < sequences.length; i++)
2071         {
2072           if (importDs)
2073           {
2074             newDs.addElement(null);
2075           }
2076           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2077           // paste
2078           if (importDs && ds != null)
2079           {
2080             if (!newDs.contains(ds))
2081             {
2082               newDs.setElementAt(ds, i);
2083               ds = new Sequence(ds);
2084               // update with new dataset sequence
2085               sequences[i].setDatasetSequence(ds);
2086             }
2087             else
2088             {
2089               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2090             }
2091           }
2092           else
2093           {
2094             // copy and derive new dataset sequence
2095             sequences[i] = sequences[i].deriveSequence();
2096             alignment.getDataset()
2097                     .addSequence(sequences[i].getDatasetSequence());
2098             // TODO: avoid creation of duplicate dataset sequences with a
2099             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2100           }
2101           alignment.addSequence(sequences[i]); // merges dataset
2102         }
2103         if (newDs != null)
2104         {
2105           newDs.clear(); // tidy up
2106         }
2107         if (alignment.getAlignmentAnnotation() != null)
2108         {
2109           for (AlignmentAnnotation alan : alignment
2110                   .getAlignmentAnnotation())
2111           {
2112             if (alan.graphGroup > fgroup)
2113             {
2114               fgroup = alan.graphGroup;
2115             }
2116           }
2117         }
2118         if (pastedal.getAlignmentAnnotation() != null)
2119         {
2120           // Add any annotation attached to alignment.
2121           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2122           for (int i = 0; i < alann.length; i++)
2123           {
2124             annotationAdded = true;
2125             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2126             {
2127               AlignmentAnnotation newann = new AlignmentAnnotation(
2128                       alann[i]);
2129               if (newann.graphGroup > -1)
2130               {
2131                 if (newGraphGroups.size() <= newann.graphGroup
2132                         || newGraphGroups.get(newann.graphGroup) == null)
2133                 {
2134                   for (int q = newGraphGroups
2135                           .size(); q <= newann.graphGroup; q++)
2136                   {
2137                     newGraphGroups.add(q, null);
2138                   }
2139                   newGraphGroups.set(newann.graphGroup,
2140                           new Integer(++fgroup));
2141                 }
2142                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2143                         .intValue();
2144               }
2145
2146               newann.padAnnotation(alwidth);
2147               alignment.addAnnotation(newann);
2148             }
2149           }
2150         }
2151       }
2152       if (!newAlignment)
2153       {
2154         // /////
2155         // ADD HISTORY ITEM
2156         //
2157         addHistoryItem(new EditCommand(
2158                 MessageManager.getString("label.add_sequences"),
2159                 Action.PASTE, sequences, 0, alignment.getWidth(),
2160                 alignment));
2161       }
2162       // Add any annotations attached to sequences
2163       for (int i = 0; i < sequences.length; i++)
2164       {
2165         if (sequences[i].getAnnotation() != null)
2166         {
2167           AlignmentAnnotation newann;
2168           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2169           {
2170             annotationAdded = true;
2171             newann = sequences[i].getAnnotation()[a];
2172             newann.adjustForAlignment();
2173             newann.padAnnotation(alwidth);
2174             if (newann.graphGroup > -1)
2175             {
2176               if (newann.graphGroup > -1)
2177               {
2178                 if (newGraphGroups.size() <= newann.graphGroup
2179                         || newGraphGroups.get(newann.graphGroup) == null)
2180                 {
2181                   for (int q = newGraphGroups
2182                           .size(); q <= newann.graphGroup; q++)
2183                   {
2184                     newGraphGroups.add(q, null);
2185                   }
2186                   newGraphGroups.set(newann.graphGroup,
2187                           new Integer(++fgroup));
2188                 }
2189                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2190                         .intValue();
2191               }
2192             }
2193             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2194             // was
2195             // duplicated
2196             // earlier
2197             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2198                     a);
2199           }
2200         }
2201       }
2202       if (!newAlignment)
2203       {
2204
2205         // propagate alignment changed.
2206         viewport.getRanges().setEndSeq(alignment.getHeight());
2207         if (annotationAdded)
2208         {
2209           // Duplicate sequence annotation in all views.
2210           AlignmentI[] alview = this.getViewAlignments();
2211           for (int i = 0; i < sequences.length; i++)
2212           {
2213             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2214             if (sann == null)
2215             {
2216               continue;
2217             }
2218             for (int avnum = 0; avnum < alview.length; avnum++)
2219             {
2220               if (alview[avnum] != alignment)
2221               {
2222                 // duplicate in a view other than the one with input focus
2223                 int avwidth = alview[avnum].getWidth() + 1;
2224                 // this relies on sann being preserved after we
2225                 // modify the sequence's annotation array for each duplication
2226                 for (int a = 0; a < sann.length; a++)
2227                 {
2228                   AlignmentAnnotation newann = new AlignmentAnnotation(
2229                           sann[a]);
2230                   sequences[i].addAlignmentAnnotation(newann);
2231                   newann.padAnnotation(avwidth);
2232                   alview[avnum].addAnnotation(newann); // annotation was
2233                   // duplicated earlier
2234                   // TODO JAL-1145 graphGroups are not updated for sequence
2235                   // annotation added to several views. This may cause
2236                   // strangeness
2237                   alview[avnum].setAnnotationIndex(newann, a);
2238                 }
2239               }
2240             }
2241           }
2242           buildSortByAnnotationScoresMenu();
2243         }
2244         viewport.firePropertyChange("alignment", null,
2245                 alignment.getSequences());
2246         if (alignPanels != null)
2247         {
2248           for (AlignmentPanel ap : alignPanels)
2249           {
2250             ap.validateAnnotationDimensions(false);
2251           }
2252         }
2253         else
2254         {
2255           alignPanel.validateAnnotationDimensions(false);
2256         }
2257
2258       }
2259       else
2260       {
2261         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2262                 DEFAULT_HEIGHT);
2263         String newtitle = new String("Copied sequences");
2264
2265         if (Desktop.jalviewClipboard != null
2266                 && Desktop.jalviewClipboard[2] != null)
2267         {
2268           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2269           af.viewport.setHiddenColumns(hc);
2270         }
2271
2272         // >>>This is a fix for the moment, until a better solution is
2273         // found!!<<<
2274         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2275                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2276                         .getFeatureRenderer());
2277
2278         // TODO: maintain provenance of an alignment, rather than just make the
2279         // title a concatenation of operations.
2280         if (!externalPaste)
2281         {
2282           if (title.startsWith("Copied sequences"))
2283           {
2284             newtitle = title;
2285           }
2286           else
2287           {
2288             newtitle = newtitle.concat("- from " + title);
2289           }
2290         }
2291         else
2292         {
2293           newtitle = new String("Pasted sequences");
2294         }
2295
2296         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2297                 DEFAULT_HEIGHT);
2298
2299       }
2300
2301     } catch (Exception ex)
2302     {
2303       ex.printStackTrace();
2304       System.out.println("Exception whilst pasting: " + ex);
2305       // could be anything being pasted in here
2306     }
2307
2308   }
2309
2310   @Override
2311   protected void expand_newalign(ActionEvent e)
2312   {
2313     try
2314     {
2315       AlignmentI alignment = AlignmentUtils
2316               .expandContext(getViewport().getAlignment(), -1);
2317       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2318               DEFAULT_HEIGHT);
2319       String newtitle = new String("Flanking alignment");
2320
2321       if (Desktop.jalviewClipboard != null
2322               && Desktop.jalviewClipboard[2] != null)
2323       {
2324         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2325         af.viewport.setHiddenColumns(hc);
2326       }
2327
2328       // >>>This is a fix for the moment, until a better solution is
2329       // found!!<<<
2330       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2331               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2332                       .getFeatureRenderer());
2333
2334       // TODO: maintain provenance of an alignment, rather than just make the
2335       // title a concatenation of operations.
2336       {
2337         if (title.startsWith("Copied sequences"))
2338         {
2339           newtitle = title;
2340         }
2341         else
2342         {
2343           newtitle = newtitle.concat("- from " + title);
2344         }
2345       }
2346
2347       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2348
2349     } catch (Exception ex)
2350     {
2351       ex.printStackTrace();
2352       System.out.println("Exception whilst pasting: " + ex);
2353       // could be anything being pasted in here
2354     } catch (OutOfMemoryError oom)
2355     {
2356       new OOMWarning("Viewing flanking region of alignment", oom);
2357     }
2358   }
2359
2360   /**
2361    * DOCUMENT ME!
2362    *
2363    * @param e
2364    *          DOCUMENT ME!
2365    */
2366   @Override
2367   protected void cut_actionPerformed(ActionEvent e)
2368   {
2369     copy_actionPerformed(null);
2370     delete_actionPerformed(null);
2371   }
2372
2373   /**
2374    * DOCUMENT ME!
2375    *
2376    * @param e
2377    *          DOCUMENT ME!
2378    */
2379   @Override
2380   protected void delete_actionPerformed(ActionEvent evt)
2381   {
2382
2383     SequenceGroup sg = viewport.getSelectionGroup();
2384     if (sg == null)
2385     {
2386       return;
2387     }
2388
2389     /*
2390      * If the cut affects all sequences, warn, remove highlighted columns
2391      */
2392     if (sg.getSize() == viewport.getAlignment().getHeight())
2393     {
2394       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2395               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2396       if (isEntireAlignWidth)
2397       {
2398         int confirm = JvOptionPane.showConfirmDialog(this,
2399                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2400                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2401                 JvOptionPane.OK_CANCEL_OPTION);
2402
2403         if (confirm == JvOptionPane.CANCEL_OPTION
2404                 || confirm == JvOptionPane.CLOSED_OPTION)
2405         {
2406           return;
2407         }
2408       }
2409       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2410               sg.getEndRes() + 1);
2411     }
2412     SequenceI[] cut = sg.getSequences()
2413             .toArray(new SequenceI[sg.getSize()]);
2414
2415     addHistoryItem(new EditCommand(
2416             MessageManager.getString("label.cut_sequences"), Action.CUT,
2417             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2418             viewport.getAlignment()));
2419
2420     viewport.setSelectionGroup(null);
2421     viewport.sendSelection();
2422     viewport.getAlignment().deleteGroup(sg);
2423
2424     viewport.firePropertyChange("alignment", null,
2425             viewport.getAlignment().getSequences());
2426     if (viewport.getAlignment().getHeight() < 1)
2427     {
2428       try
2429       {
2430         this.setClosed(true);
2431       } catch (Exception ex)
2432       {
2433       }
2434     }
2435   }
2436
2437   /**
2438    * DOCUMENT ME!
2439    *
2440    * @param e
2441    *          DOCUMENT ME!
2442    */
2443   @Override
2444   protected void deleteGroups_actionPerformed(ActionEvent e)
2445   {
2446     if (avc.deleteGroups())
2447     {
2448       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2449       alignPanel.updateAnnotation();
2450       alignPanel.paintAlignment(true, true);
2451     }
2452   }
2453
2454   /**
2455    * DOCUMENT ME!
2456    *
2457    * @param e
2458    *          DOCUMENT ME!
2459    */
2460   @Override
2461   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2462   {
2463     SequenceGroup sg = new SequenceGroup();
2464
2465     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2466     {
2467       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2468     }
2469
2470     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2471     viewport.setSelectionGroup(sg);
2472     viewport.sendSelection();
2473     // JAL-2034 - should delegate to
2474     // alignPanel to decide if overview needs
2475     // updating.
2476     alignPanel.paintAlignment(false, false);
2477     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2478   }
2479
2480   /**
2481    * DOCUMENT ME!
2482    *
2483    * @param e
2484    *          DOCUMENT ME!
2485    */
2486   @Override
2487   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2488   {
2489     if (viewport.cursorMode)
2490     {
2491       alignPanel.getSeqPanel().keyboardNo1 = null;
2492       alignPanel.getSeqPanel().keyboardNo2 = null;
2493     }
2494     viewport.setSelectionGroup(null);
2495     viewport.getColumnSelection().clear();
2496     viewport.setSelectionGroup(null);
2497     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2498     // JAL-2034 - should delegate to
2499     // alignPanel to decide if overview needs
2500     // updating.
2501     alignPanel.paintAlignment(false, false);
2502     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2503     viewport.sendSelection();
2504   }
2505
2506   /**
2507    * DOCUMENT ME!
2508    *
2509    * @param e
2510    *          DOCUMENT ME!
2511    */
2512   @Override
2513   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2514   {
2515     SequenceGroup sg = viewport.getSelectionGroup();
2516
2517     if (sg == null)
2518     {
2519       selectAllSequenceMenuItem_actionPerformed(null);
2520
2521       return;
2522     }
2523
2524     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2525     {
2526       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2527     }
2528     // JAL-2034 - should delegate to
2529     // alignPanel to decide if overview needs
2530     // updating.
2531
2532     alignPanel.paintAlignment(true, false);
2533     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2534     viewport.sendSelection();
2535   }
2536
2537   @Override
2538   public void invertColSel_actionPerformed(ActionEvent e)
2539   {
2540     viewport.invertColumnSelection();
2541     alignPanel.paintAlignment(true, false);
2542     viewport.sendSelection();
2543   }
2544
2545   /**
2546    * DOCUMENT ME!
2547    *
2548    * @param e
2549    *          DOCUMENT ME!
2550    */
2551   @Override
2552   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2553   {
2554     trimAlignment(true);
2555   }
2556
2557   /**
2558    * DOCUMENT ME!
2559    *
2560    * @param e
2561    *          DOCUMENT ME!
2562    */
2563   @Override
2564   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2565   {
2566     trimAlignment(false);
2567   }
2568
2569   void trimAlignment(boolean trimLeft)
2570   {
2571     ColumnSelection colSel = viewport.getColumnSelection();
2572     int column;
2573
2574     if (!colSel.isEmpty())
2575     {
2576       if (trimLeft)
2577       {
2578         column = colSel.getMin();
2579       }
2580       else
2581       {
2582         column = colSel.getMax();
2583       }
2584
2585       SequenceI[] seqs;
2586       if (viewport.getSelectionGroup() != null)
2587       {
2588         seqs = viewport.getSelectionGroup()
2589                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2590       }
2591       else
2592       {
2593         seqs = viewport.getAlignment().getSequencesArray();
2594       }
2595
2596       TrimRegionCommand trimRegion;
2597       if (trimLeft)
2598       {
2599         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2600                 column, viewport.getAlignment());
2601         viewport.getRanges().setStartRes(0);
2602       }
2603       else
2604       {
2605         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2606                 column, viewport.getAlignment());
2607       }
2608
2609       statusBar.setText(MessageManager
2610               .formatMessage("label.removed_columns", new String[]
2611               { Integer.valueOf(trimRegion.getSize()).toString() }));
2612
2613       addHistoryItem(trimRegion);
2614
2615       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2616       {
2617         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2618                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2619         {
2620           viewport.getAlignment().deleteGroup(sg);
2621         }
2622       }
2623
2624       viewport.firePropertyChange("alignment", null,
2625               viewport.getAlignment().getSequences());
2626     }
2627   }
2628
2629   /**
2630    * DOCUMENT ME!
2631    *
2632    * @param e
2633    *          DOCUMENT ME!
2634    */
2635   @Override
2636   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2637   {
2638     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639
2640     SequenceI[] seqs;
2641     if (viewport.getSelectionGroup() != null)
2642     {
2643       seqs = viewport.getSelectionGroup()
2644               .getSequencesAsArray(viewport.getHiddenRepSequences());
2645       start = viewport.getSelectionGroup().getStartRes();
2646       end = viewport.getSelectionGroup().getEndRes();
2647     }
2648     else
2649     {
2650       seqs = viewport.getAlignment().getSequencesArray();
2651     }
2652
2653     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2654             "Remove Gapped Columns", seqs, start, end,
2655             viewport.getAlignment());
2656
2657     addHistoryItem(removeGapCols);
2658
2659     statusBar.setText(MessageManager
2660             .formatMessage("label.removed_empty_columns", new Object[]
2661             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2662
2663     // This is to maintain viewport position on first residue
2664     // of first sequence
2665     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2666     ViewportRanges ranges = viewport.getRanges();
2667     int startRes = seq.findPosition(ranges.getStartRes());
2668     // ShiftList shifts;
2669     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2670     // edit.alColumnChanges=shifts.getInverse();
2671     // if (viewport.hasHiddenColumns)
2672     // viewport.getColumnSelection().compensateForEdits(shifts);
2673     ranges.setStartRes(seq.findIndex(startRes) - 1);
2674     viewport.firePropertyChange("alignment", null,
2675             viewport.getAlignment().getSequences());
2676
2677   }
2678
2679   /**
2680    * DOCUMENT ME!
2681    *
2682    * @param e
2683    *          DOCUMENT ME!
2684    */
2685   @Override
2686   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2687   {
2688     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2689
2690     SequenceI[] seqs;
2691     if (viewport.getSelectionGroup() != null)
2692     {
2693       seqs = viewport.getSelectionGroup()
2694               .getSequencesAsArray(viewport.getHiddenRepSequences());
2695       start = viewport.getSelectionGroup().getStartRes();
2696       end = viewport.getSelectionGroup().getEndRes();
2697     }
2698     else
2699     {
2700       seqs = viewport.getAlignment().getSequencesArray();
2701     }
2702
2703     // This is to maintain viewport position on first residue
2704     // of first sequence
2705     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2706     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2707
2708     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2709             viewport.getAlignment()));
2710
2711     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2712
2713     viewport.firePropertyChange("alignment", null,
2714             viewport.getAlignment().getSequences());
2715
2716   }
2717
2718   /**
2719    * DOCUMENT ME!
2720    *
2721    * @param e
2722    *          DOCUMENT ME!
2723    */
2724   @Override
2725   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2726   {
2727     viewport.setPadGaps(padGapsMenuitem.isSelected());
2728     viewport.firePropertyChange("alignment", null,
2729             viewport.getAlignment().getSequences());
2730   }
2731
2732   /**
2733    * DOCUMENT ME!
2734    *
2735    * @param e
2736    *          DOCUMENT ME!
2737    */
2738   @Override
2739   public void findMenuItem_actionPerformed(ActionEvent e)
2740   {
2741     new Finder();
2742   }
2743
2744   /**
2745    * Create a new view of the current alignment.
2746    */
2747   @Override
2748   public void newView_actionPerformed(ActionEvent e)
2749   {
2750     newView(null, true);
2751   }
2752
2753   /**
2754    * Creates and shows a new view of the current alignment.
2755    *
2756    * @param viewTitle
2757    *          title of newly created view; if null, one will be generated
2758    * @param copyAnnotation
2759    *          if true then duplicate all annnotation, groups and settings
2760    * @return new alignment panel, already displayed.
2761    */
2762   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2763   {
2764     /*
2765      * Create a new AlignmentPanel (with its own, new Viewport)
2766      */
2767     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2768     if (!copyAnnotation)
2769     {
2770       /*
2771        * remove all groups and annotation except for the automatic stuff
2772        */
2773       newap.av.getAlignment().deleteAllGroups();
2774       newap.av.getAlignment().deleteAllAnnotations(false);
2775     }
2776
2777     newap.av.setGatherViewsHere(false);
2778
2779     if (viewport.viewName == null)
2780     {
2781       viewport.viewName = MessageManager
2782               .getString("label.view_name_original");
2783     }
2784
2785     /*
2786      * Views share the same edits undo and redo stacks
2787      */
2788     newap.av.setHistoryList(viewport.getHistoryList());
2789     newap.av.setRedoList(viewport.getRedoList());
2790
2791     /*
2792      * Views share the same mappings; need to deregister any new mappings
2793      * created by copyAlignPanel, and register the new reference to the shared
2794      * mappings
2795      */
2796     newap.av.replaceMappings(viewport.getAlignment());
2797
2798     /*
2799      * start up cDNA consensus (if applicable) now mappings are in place
2800      */
2801     if (newap.av.initComplementConsensus())
2802     {
2803       newap.refresh(true); // adjust layout of annotations
2804     }
2805
2806     newap.av.viewName = getNewViewName(viewTitle);
2807
2808     addAlignmentPanel(newap, true);
2809     newap.alignmentChanged();
2810
2811     if (alignPanels.size() == 2)
2812     {
2813       viewport.setGatherViewsHere(true);
2814     }
2815     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2816     return newap;
2817   }
2818
2819   /**
2820    * Make a new name for the view, ensuring it is unique within the current
2821    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2822    * these now use viewId. Unique view names are still desirable for usability.)
2823    *
2824    * @param viewTitle
2825    * @return
2826    */
2827   protected String getNewViewName(String viewTitle)
2828   {
2829     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2830     boolean addFirstIndex = false;
2831     if (viewTitle == null || viewTitle.trim().length() == 0)
2832     {
2833       viewTitle = MessageManager.getString("action.view");
2834       addFirstIndex = true;
2835     }
2836     else
2837     {
2838       index = 1;// we count from 1 if given a specific name
2839     }
2840     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2841
2842     List<Component> comps = PaintRefresher.components
2843             .get(viewport.getSequenceSetId());
2844
2845     List<String> existingNames = getExistingViewNames(comps);
2846
2847     while (existingNames.contains(newViewName))
2848     {
2849       newViewName = viewTitle + " " + (++index);
2850     }
2851     return newViewName;
2852   }
2853
2854   /**
2855    * Returns a list of distinct view names found in the given list of
2856    * components. View names are held on the viewport of an AlignmentPanel.
2857    *
2858    * @param comps
2859    * @return
2860    */
2861   protected List<String> getExistingViewNames(List<Component> comps)
2862   {
2863     List<String> existingNames = new ArrayList<>();
2864     for (Component comp : comps)
2865     {
2866       if (comp instanceof AlignmentPanel)
2867       {
2868         AlignmentPanel ap = (AlignmentPanel) comp;
2869         if (!existingNames.contains(ap.av.viewName))
2870         {
2871           existingNames.add(ap.av.viewName);
2872         }
2873       }
2874     }
2875     return existingNames;
2876   }
2877
2878   /**
2879    * Explode tabbed views into separate windows.
2880    */
2881   @Override
2882   public void expandViews_actionPerformed(ActionEvent e)
2883   {
2884     Desktop.explodeViews(this);
2885   }
2886
2887   /**
2888    * Gather views in separate windows back into a tabbed presentation.
2889    */
2890   @Override
2891   public void gatherViews_actionPerformed(ActionEvent e)
2892   {
2893     Desktop.instance.gatherViews(this);
2894   }
2895
2896   /**
2897    * DOCUMENT ME!
2898    *
2899    * @param e
2900    *          DOCUMENT ME!
2901    */
2902   @Override
2903   public void font_actionPerformed(ActionEvent e)
2904   {
2905     new FontChooser(alignPanel);
2906   }
2907
2908   /**
2909    * DOCUMENT ME!
2910    *
2911    * @param e
2912    *          DOCUMENT ME!
2913    */
2914   @Override
2915   protected void seqLimit_actionPerformed(ActionEvent e)
2916   {
2917     viewport.setShowJVSuffix(seqLimits.isSelected());
2918
2919     alignPanel.getIdPanel().getIdCanvas()
2920             .setPreferredSize(alignPanel.calculateIdWidth());
2921     alignPanel.paintAlignment(true, false);
2922   }
2923
2924   @Override
2925   public void idRightAlign_actionPerformed(ActionEvent e)
2926   {
2927     viewport.setRightAlignIds(idRightAlign.isSelected());
2928     alignPanel.paintAlignment(false, false);
2929   }
2930
2931   @Override
2932   public void centreColumnLabels_actionPerformed(ActionEvent e)
2933   {
2934     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2935     alignPanel.paintAlignment(false, false);
2936   }
2937
2938   /*
2939    * (non-Javadoc)
2940    *
2941    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2942    */
2943   @Override
2944   protected void followHighlight_actionPerformed()
2945   {
2946     /*
2947      * Set the 'follow' flag on the Viewport (and scroll to position if now
2948      * true).
2949      */
2950     final boolean state = this.followHighlightMenuItem.getState();
2951     viewport.setFollowHighlight(state);
2952     if (state)
2953     {
2954       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2955     }
2956   }
2957
2958   /**
2959    * DOCUMENT ME!
2960    *
2961    * @param e
2962    *          DOCUMENT ME!
2963    */
2964   @Override
2965   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2966   {
2967     viewport.setColourText(colourTextMenuItem.isSelected());
2968     alignPanel.paintAlignment(false, false);
2969   }
2970
2971   /**
2972    * DOCUMENT ME!
2973    *
2974    * @param e
2975    *          DOCUMENT ME!
2976    */
2977   @Override
2978   public void wrapMenuItem_actionPerformed(ActionEvent e)
2979   {
2980     scaleAbove.setVisible(wrapMenuItem.isSelected());
2981     scaleLeft.setVisible(wrapMenuItem.isSelected());
2982     scaleRight.setVisible(wrapMenuItem.isSelected());
2983     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2984     alignPanel.updateLayout();
2985   }
2986
2987   @Override
2988   public void showAllSeqs_actionPerformed(ActionEvent e)
2989   {
2990     viewport.showAllHiddenSeqs();
2991   }
2992
2993   @Override
2994   public void showAllColumns_actionPerformed(ActionEvent e)
2995   {
2996     viewport.showAllHiddenColumns();
2997     alignPanel.paintAlignment(true, true);
2998     viewport.sendSelection();
2999   }
3000
3001   @Override
3002   public void hideSelSequences_actionPerformed(ActionEvent e)
3003   {
3004     viewport.hideAllSelectedSeqs();
3005   }
3006
3007   /**
3008    * called by key handler and the hide all/show all menu items
3009    *
3010    * @param toggleSeqs
3011    * @param toggleCols
3012    */
3013   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3014   {
3015
3016     boolean hide = false;
3017     SequenceGroup sg = viewport.getSelectionGroup();
3018     if (!toggleSeqs && !toggleCols)
3019     {
3020       // Hide everything by the current selection - this is a hack - we do the
3021       // invert and then hide
3022       // first check that there will be visible columns after the invert.
3023       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3024               && sg.getStartRes() <= sg.getEndRes()))
3025       {
3026         // now invert the sequence set, if required - empty selection implies
3027         // that no hiding is required.
3028         if (sg != null)
3029         {
3030           invertSequenceMenuItem_actionPerformed(null);
3031           sg = viewport.getSelectionGroup();
3032           toggleSeqs = true;
3033
3034         }
3035         viewport.expandColSelection(sg, true);
3036         // finally invert the column selection and get the new sequence
3037         // selection.
3038         invertColSel_actionPerformed(null);
3039         toggleCols = true;
3040       }
3041     }
3042
3043     if (toggleSeqs)
3044     {
3045       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3046       {
3047         hideSelSequences_actionPerformed(null);
3048         hide = true;
3049       }
3050       else if (!(toggleCols && viewport.hasSelectedColumns()))
3051       {
3052         showAllSeqs_actionPerformed(null);
3053       }
3054     }
3055
3056     if (toggleCols)
3057     {
3058       if (viewport.hasSelectedColumns())
3059       {
3060         hideSelColumns_actionPerformed(null);
3061         if (!toggleSeqs)
3062         {
3063           viewport.setSelectionGroup(sg);
3064         }
3065       }
3066       else if (!hide)
3067       {
3068         showAllColumns_actionPerformed(null);
3069       }
3070     }
3071   }
3072
3073   /*
3074    * (non-Javadoc)
3075    *
3076    * @see
3077    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3078    * event.ActionEvent)
3079    */
3080   @Override
3081   public void hideAllButSelection_actionPerformed(ActionEvent e)
3082   {
3083     toggleHiddenRegions(false, false);
3084     viewport.sendSelection();
3085   }
3086
3087   /*
3088    * (non-Javadoc)
3089    *
3090    * @see
3091    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3092    * .ActionEvent)
3093    */
3094   @Override
3095   public void hideAllSelection_actionPerformed(ActionEvent e)
3096   {
3097     SequenceGroup sg = viewport.getSelectionGroup();
3098     viewport.expandColSelection(sg, false);
3099     viewport.hideAllSelectedSeqs();
3100     viewport.hideSelectedColumns();
3101     alignPanel.paintAlignment(true, true);
3102     viewport.sendSelection();
3103   }
3104
3105   /*
3106    * (non-Javadoc)
3107    *
3108    * @see
3109    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3110    * ActionEvent)
3111    */
3112   @Override
3113   public void showAllhidden_actionPerformed(ActionEvent e)
3114   {
3115     viewport.showAllHiddenColumns();
3116     viewport.showAllHiddenSeqs();
3117     alignPanel.paintAlignment(true, true);
3118     viewport.sendSelection();
3119   }
3120
3121   @Override
3122   public void hideSelColumns_actionPerformed(ActionEvent e)
3123   {
3124     viewport.hideSelectedColumns();
3125     alignPanel.paintAlignment(true, true);
3126     viewport.sendSelection();
3127   }
3128
3129   @Override
3130   public void hiddenMarkers_actionPerformed(ActionEvent e)
3131   {
3132     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3133     repaint();
3134   }
3135
3136   /**
3137    * DOCUMENT ME!
3138    *
3139    * @param e
3140    *          DOCUMENT ME!
3141    */
3142   @Override
3143   protected void scaleAbove_actionPerformed(ActionEvent e)
3144   {
3145     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3146     // TODO: do we actually need to update overview for scale above change ?
3147     alignPanel.paintAlignment(true, false);
3148   }
3149
3150   /**
3151    * DOCUMENT ME!
3152    *
3153    * @param e
3154    *          DOCUMENT ME!
3155    */
3156   @Override
3157   protected void scaleLeft_actionPerformed(ActionEvent e)
3158   {
3159     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3160     alignPanel.paintAlignment(true, false);
3161   }
3162
3163   /**
3164    * DOCUMENT ME!
3165    *
3166    * @param e
3167    *          DOCUMENT ME!
3168    */
3169   @Override
3170   protected void scaleRight_actionPerformed(ActionEvent e)
3171   {
3172     viewport.setScaleRightWrapped(scaleRight.isSelected());
3173     alignPanel.paintAlignment(true, false);
3174   }
3175
3176   /**
3177    * DOCUMENT ME!
3178    *
3179    * @param e
3180    *          DOCUMENT ME!
3181    */
3182   @Override
3183   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3184   {
3185     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3186     alignPanel.paintAlignment(false, false);
3187   }
3188
3189   /**
3190    * DOCUMENT ME!
3191    *
3192    * @param e
3193    *          DOCUMENT ME!
3194    */
3195   @Override
3196   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3197   {
3198     viewport.setShowText(viewTextMenuItem.isSelected());
3199     alignPanel.paintAlignment(false, false);
3200   }
3201
3202   /**
3203    * DOCUMENT ME!
3204    *
3205    * @param e
3206    *          DOCUMENT ME!
3207    */
3208   @Override
3209   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3210   {
3211     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3212     alignPanel.paintAlignment(false, false);
3213   }
3214
3215   public FeatureSettings featureSettings;
3216
3217   @Override
3218   public FeatureSettingsControllerI getFeatureSettingsUI()
3219   {
3220     return featureSettings;
3221   }
3222
3223   @Override
3224   public void featureSettings_actionPerformed(ActionEvent e)
3225   {
3226     if (featureSettings != null)
3227     {
3228       featureSettings.close();
3229       featureSettings = null;
3230     }
3231     if (!showSeqFeatures.isSelected())
3232     {
3233       // make sure features are actually displayed
3234       showSeqFeatures.setSelected(true);
3235       showSeqFeatures_actionPerformed(null);
3236     }
3237     featureSettings = new FeatureSettings(this);
3238   }
3239
3240   /**
3241    * Set or clear 'Show Sequence Features'
3242    *
3243    * @param evt
3244    *          DOCUMENT ME!
3245    */
3246   @Override
3247   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3248   {
3249     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3250     alignPanel.paintAlignment(true, true);
3251   }
3252
3253   /**
3254    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3255    * the annotations panel as a whole.
3256    *
3257    * The options to show/hide all annotations should be enabled when the panel
3258    * is shown, and disabled when the panel is hidden.
3259    *
3260    * @param e
3261    */
3262   @Override
3263   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3264   {
3265     final boolean setVisible = annotationPanelMenuItem.isSelected();
3266     viewport.setShowAnnotation(setVisible);
3267     this.showAllSeqAnnotations.setEnabled(setVisible);
3268     this.hideAllSeqAnnotations.setEnabled(setVisible);
3269     this.showAllAlAnnotations.setEnabled(setVisible);
3270     this.hideAllAlAnnotations.setEnabled(setVisible);
3271     alignPanel.updateLayout();
3272   }
3273
3274   @Override
3275   public void alignmentProperties()
3276   {
3277     JEditorPane editPane = new JEditorPane("text/html", "");
3278     editPane.setEditable(false);
3279     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3280             .formatAsHtml();
3281     editPane.setText(
3282             MessageManager.formatMessage("label.html_content", new Object[]
3283             { contents.toString() }));
3284     JInternalFrame frame = new JInternalFrame();
3285     frame.getContentPane().add(new JScrollPane(editPane));
3286
3287     Desktop.addInternalFrame(frame, MessageManager
3288             .formatMessage("label.alignment_properties", new Object[]
3289             { getTitle() }), 500, 400);
3290   }
3291
3292   /**
3293    * DOCUMENT ME!
3294    *
3295    * @param e
3296    *          DOCUMENT ME!
3297    */
3298   @Override
3299   public void overviewMenuItem_actionPerformed(ActionEvent e)
3300   {
3301     if (alignPanel.overviewPanel != null)
3302     {
3303       return;
3304     }
3305
3306     JInternalFrame frame = new JInternalFrame();
3307     final OverviewPanel overview = new OverviewPanel(alignPanel);
3308     frame.setContentPane(overview);
3309     Desktop.addInternalFrame(frame, MessageManager
3310             .formatMessage("label.overview_params", new Object[]
3311             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3312             true, true);
3313     frame.pack();
3314     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3315     frame.addInternalFrameListener(
3316             new javax.swing.event.InternalFrameAdapter()
3317             {
3318               @Override
3319               public void internalFrameClosed(
3320                       javax.swing.event.InternalFrameEvent evt)
3321               {
3322                 overview.dispose();
3323                 alignPanel.setOverviewPanel(null);
3324               };
3325             });
3326     if (getKeyListeners().length > 0)
3327     {
3328       frame.addKeyListener(getKeyListeners()[0]);
3329     }
3330
3331     alignPanel.setOverviewPanel(overview);
3332   }
3333
3334   @Override
3335   public void textColour_actionPerformed()
3336   {
3337     new TextColourChooser().chooseColour(alignPanel, null);
3338   }
3339
3340   /*
3341    * public void covariationColour_actionPerformed() {
3342    * changeColour(new
3343    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3344    * ()[0])); }
3345    */
3346   @Override
3347   public void annotationColour_actionPerformed()
3348   {
3349     new AnnotationColourChooser(viewport, alignPanel);
3350   }
3351
3352   @Override
3353   public void annotationColumn_actionPerformed(ActionEvent e)
3354   {
3355     new AnnotationColumnChooser(viewport, alignPanel);
3356   }
3357
3358   /**
3359    * Action on the user checking or unchecking the option to apply the selected
3360    * colour scheme to all groups. If unchecked, groups may have their own
3361    * independent colour schemes.
3362    *
3363    * @param selected
3364    */
3365   @Override
3366   public void applyToAllGroups_actionPerformed(boolean selected)
3367   {
3368     viewport.setColourAppliesToAllGroups(selected);
3369   }
3370
3371   /**
3372    * Action on user selecting a colour from the colour menu
3373    *
3374    * @param name
3375    *          the name (not the menu item label!) of the colour scheme
3376    */
3377   @Override
3378   public void changeColour_actionPerformed(String name)
3379   {
3380     /*
3381      * 'User Defined' opens a panel to configure or load a
3382      * user-defined colour scheme
3383      */
3384     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3385     {
3386       new UserDefinedColours(alignPanel);
3387       return;
3388     }
3389
3390     /*
3391      * otherwise set the chosen colour scheme (or null for 'None')
3392      */
3393     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3394             viewport.getAlignment(), viewport.getHiddenRepSequences());
3395     changeColour(cs);
3396   }
3397
3398   /**
3399    * Actions on setting or changing the alignment colour scheme
3400    *
3401    * @param cs
3402    */
3403   @Override
3404   public void changeColour(ColourSchemeI cs)
3405   {
3406     // TODO: pull up to controller method
3407     ColourMenuHelper.setColourSelected(colourMenu, cs);
3408
3409     viewport.setGlobalColourScheme(cs);
3410
3411     alignPanel.paintAlignment(true, true);
3412   }
3413
3414   /**
3415    * Show the PID threshold slider panel
3416    */
3417   @Override
3418   protected void modifyPID_actionPerformed()
3419   {
3420     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3421             alignPanel.getViewName());
3422     SliderPanel.showPIDSlider();
3423   }
3424
3425   /**
3426    * Show the Conservation slider panel
3427    */
3428   @Override
3429   protected void modifyConservation_actionPerformed()
3430   {
3431     SliderPanel.setConservationSlider(alignPanel,
3432             viewport.getResidueShading(), alignPanel.getViewName());
3433     SliderPanel.showConservationSlider();
3434   }
3435
3436   /**
3437    * Action on selecting or deselecting (Colour) By Conservation
3438    */
3439   @Override
3440   public void conservationMenuItem_actionPerformed(boolean selected)
3441   {
3442     modifyConservation.setEnabled(selected);
3443     viewport.setConservationSelected(selected);
3444     viewport.getResidueShading().setConservationApplied(selected);
3445
3446     changeColour(viewport.getGlobalColourScheme());
3447     if (selected)
3448     {
3449       modifyConservation_actionPerformed();
3450     }
3451     else
3452     {
3453       SliderPanel.hideConservationSlider();
3454     }
3455   }
3456
3457   /**
3458    * Action on selecting or deselecting (Colour) Above PID Threshold
3459    */
3460   @Override
3461   public void abovePIDThreshold_actionPerformed(boolean selected)
3462   {
3463     modifyPID.setEnabled(selected);
3464     viewport.setAbovePIDThreshold(selected);
3465     if (!selected)
3466     {
3467       viewport.getResidueShading().setThreshold(0,
3468               viewport.isIgnoreGapsConsensus());
3469     }
3470
3471     changeColour(viewport.getGlobalColourScheme());
3472     if (selected)
3473     {
3474       modifyPID_actionPerformed();
3475     }
3476     else
3477     {
3478       SliderPanel.hidePIDSlider();
3479     }
3480   }
3481
3482   /**
3483    * DOCUMENT ME!
3484    *
3485    * @param e
3486    *          DOCUMENT ME!
3487    */
3488   @Override
3489   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3490   {
3491     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3492     AlignmentSorter.sortByPID(viewport.getAlignment(),
3493             viewport.getAlignment().getSequenceAt(0));
3494     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3495             viewport.getAlignment()));
3496     alignPanel.paintAlignment(true, false);
3497   }
3498
3499   /**
3500    * DOCUMENT ME!
3501    *
3502    * @param e
3503    *          DOCUMENT ME!
3504    */
3505   @Override
3506   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3507   {
3508     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3509     AlignmentSorter.sortByID(viewport.getAlignment());
3510     addHistoryItem(
3511             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3512     alignPanel.paintAlignment(true, false);
3513   }
3514
3515   /**
3516    * DOCUMENT ME!
3517    *
3518    * @param e
3519    *          DOCUMENT ME!
3520    */
3521   @Override
3522   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3523   {
3524     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3525     AlignmentSorter.sortByLength(viewport.getAlignment());
3526     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3527             viewport.getAlignment()));
3528     alignPanel.paintAlignment(true, false);
3529   }
3530
3531   /**
3532    * DOCUMENT ME!
3533    *
3534    * @param e
3535    *          DOCUMENT ME!
3536    */
3537   @Override
3538   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3539   {
3540     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3541     AlignmentSorter.sortByGroup(viewport.getAlignment());
3542     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3543             viewport.getAlignment()));
3544
3545     alignPanel.paintAlignment(true, false);
3546   }
3547
3548   /**
3549    * DOCUMENT ME!
3550    *
3551    * @param e
3552    *          DOCUMENT ME!
3553    */
3554   @Override
3555   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3556   {
3557     new RedundancyPanel(alignPanel, this);
3558   }
3559
3560   /**
3561    * DOCUMENT ME!
3562    *
3563    * @param e
3564    *          DOCUMENT ME!
3565    */
3566   @Override
3567   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3568   {
3569     if ((viewport.getSelectionGroup() == null)
3570             || (viewport.getSelectionGroup().getSize() < 2))
3571     {
3572       JvOptionPane.showInternalMessageDialog(this,
3573               MessageManager.getString(
3574                       "label.you_must_select_least_two_sequences"),
3575               MessageManager.getString("label.invalid_selection"),
3576               JvOptionPane.WARNING_MESSAGE);
3577     }
3578     else
3579     {
3580       JInternalFrame frame = new JInternalFrame();
3581       frame.setContentPane(new PairwiseAlignPanel(viewport));
3582       Desktop.addInternalFrame(frame,
3583               MessageManager.getString("action.pairwise_alignment"), 600,
3584               500);
3585     }
3586   }
3587
3588   @Override
3589   public void autoCalculate_actionPerformed(ActionEvent e)
3590   {
3591     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3592     if (viewport.autoCalculateConsensus)
3593     {
3594       viewport.firePropertyChange("alignment", null,
3595               viewport.getAlignment().getSequences());
3596     }
3597   }
3598
3599   @Override
3600   public void sortByTreeOption_actionPerformed(ActionEvent e)
3601   {
3602     viewport.sortByTree = sortByTree.isSelected();
3603   }
3604
3605   @Override
3606   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3607   {
3608     viewport.followSelection = listenToViewSelections.isSelected();
3609   }
3610
3611   /**
3612    * Constructs a tree panel and adds it to the desktop
3613    *
3614    * @param type
3615    *          tree type (NJ or AV)
3616    * @param modelName
3617    *          name of score model used to compute the tree
3618    * @param options
3619    *          parameters for the distance or similarity calculation
3620    */
3621   void newTreePanel(String type, String modelName,
3622           SimilarityParamsI options)
3623   {
3624     String frameTitle = "";
3625     TreePanel tp;
3626
3627     boolean onSelection = false;
3628     if (viewport.getSelectionGroup() != null
3629             && viewport.getSelectionGroup().getSize() > 0)
3630     {
3631       SequenceGroup sg = viewport.getSelectionGroup();
3632
3633       /* Decide if the selection is a column region */
3634       for (SequenceI _s : sg.getSequences())
3635       {
3636         if (_s.getLength() < sg.getEndRes())
3637         {
3638           JvOptionPane.showMessageDialog(Desktop.desktop,
3639                   MessageManager.getString(
3640                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3641                   MessageManager.getString(
3642                           "label.sequences_selection_not_aligned"),
3643                   JvOptionPane.WARNING_MESSAGE);
3644
3645           return;
3646         }
3647       }
3648       onSelection = true;
3649     }
3650     else
3651     {
3652       if (viewport.getAlignment().getHeight() < 2)
3653       {
3654         return;
3655       }
3656     }
3657
3658     tp = new TreePanel(alignPanel, type, modelName, options);
3659     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3660
3661     frameTitle += " from ";
3662
3663     if (viewport.viewName != null)
3664     {
3665       frameTitle += viewport.viewName + " of ";
3666     }
3667
3668     frameTitle += this.title;
3669
3670     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3671   }
3672
3673   /**
3674    * DOCUMENT ME!
3675    *
3676    * @param title
3677    *          DOCUMENT ME!
3678    * @param order
3679    *          DOCUMENT ME!
3680    */
3681   public void addSortByOrderMenuItem(String title,
3682           final AlignmentOrder order)
3683   {
3684     final JMenuItem item = new JMenuItem(MessageManager
3685             .formatMessage("action.by_title_param", new Object[]
3686             { title }));
3687     sort.add(item);
3688     item.addActionListener(new java.awt.event.ActionListener()
3689     {
3690       @Override
3691       public void actionPerformed(ActionEvent e)
3692       {
3693         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3694
3695         // TODO: JBPNote - have to map order entries to curent SequenceI
3696         // pointers
3697         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3698
3699         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3700                 viewport.getAlignment()));
3701
3702         alignPanel.paintAlignment(true, false);
3703       }
3704     });
3705   }
3706
3707   /**
3708    * Add a new sort by annotation score menu item
3709    *
3710    * @param sort
3711    *          the menu to add the option to
3712    * @param scoreLabel
3713    *          the label used to retrieve scores for each sequence on the
3714    *          alignment
3715    */
3716   public void addSortByAnnotScoreMenuItem(JMenu sort,
3717           final String scoreLabel)
3718   {
3719     final JMenuItem item = new JMenuItem(scoreLabel);
3720     sort.add(item);
3721     item.addActionListener(new java.awt.event.ActionListener()
3722     {
3723       @Override
3724       public void actionPerformed(ActionEvent e)
3725       {
3726         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3727         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3728                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3729         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3730                 viewport.getAlignment()));
3731         alignPanel.paintAlignment(true, false);
3732       }
3733     });
3734   }
3735
3736   /**
3737    * last hash for alignment's annotation array - used to minimise cost of
3738    * rebuild.
3739    */
3740   protected int _annotationScoreVectorHash;
3741
3742   /**
3743    * search the alignment and rebuild the sort by annotation score submenu the
3744    * last alignment annotation vector hash is stored to minimize cost of
3745    * rebuilding in subsequence calls.
3746    *
3747    */
3748   @Override
3749   public void buildSortByAnnotationScoresMenu()
3750   {
3751     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3752     {
3753       return;
3754     }
3755
3756     if (viewport.getAlignment().getAlignmentAnnotation()
3757             .hashCode() != _annotationScoreVectorHash)
3758     {
3759       sortByAnnotScore.removeAll();
3760       // almost certainly a quicker way to do this - but we keep it simple
3761       Hashtable scoreSorts = new Hashtable();
3762       AlignmentAnnotation aann[];
3763       for (SequenceI sqa : viewport.getAlignment().getSequences())
3764       {
3765         aann = sqa.getAnnotation();
3766         for (int i = 0; aann != null && i < aann.length; i++)
3767         {
3768           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3769           {
3770             scoreSorts.put(aann[i].label, aann[i].label);
3771           }
3772         }
3773       }
3774       Enumeration labels = scoreSorts.keys();
3775       while (labels.hasMoreElements())
3776       {
3777         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3778                 (String) labels.nextElement());
3779       }
3780       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3781       scoreSorts.clear();
3782
3783       _annotationScoreVectorHash = viewport.getAlignment()
3784               .getAlignmentAnnotation().hashCode();
3785     }
3786   }
3787
3788   /**
3789    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3790    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3791    * call. Listeners are added to remove the menu item when the treePanel is
3792    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3793    * modified.
3794    */
3795   @Override
3796   public void buildTreeSortMenu()
3797   {
3798     sortByTreeMenu.removeAll();
3799
3800     List<Component> comps = PaintRefresher.components
3801             .get(viewport.getSequenceSetId());
3802     List<TreePanel> treePanels = new ArrayList<>();
3803     for (Component comp : comps)
3804     {
3805       if (comp instanceof TreePanel)
3806       {
3807         treePanels.add((TreePanel) comp);
3808       }
3809     }
3810
3811     if (treePanels.size() < 1)
3812     {
3813       sortByTreeMenu.setVisible(false);
3814       return;
3815     }
3816
3817     sortByTreeMenu.setVisible(true);
3818
3819     for (final TreePanel tp : treePanels)
3820     {
3821       final JMenuItem item = new JMenuItem(tp.getTitle());
3822       item.addActionListener(new java.awt.event.ActionListener()
3823       {
3824         @Override
3825         public void actionPerformed(ActionEvent e)
3826         {
3827           tp.sortByTree_actionPerformed();
3828           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3829
3830         }
3831       });
3832
3833       sortByTreeMenu.add(item);
3834     }
3835   }
3836
3837   public boolean sortBy(AlignmentOrder alorder, String undoname)
3838   {
3839     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3840     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3841     if (undoname != null)
3842     {
3843       addHistoryItem(new OrderCommand(undoname, oldOrder,
3844               viewport.getAlignment()));
3845     }
3846     alignPanel.paintAlignment(true, false);
3847     return true;
3848   }
3849
3850   /**
3851    * Work out whether the whole set of sequences or just the selected set will
3852    * be submitted for multiple alignment.
3853    *
3854    */
3855   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3856   {
3857     // Now, check we have enough sequences
3858     AlignmentView msa = null;
3859
3860     if ((viewport.getSelectionGroup() != null)
3861             && (viewport.getSelectionGroup().getSize() > 1))
3862     {
3863       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3864       // some common interface!
3865       /*
3866        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3867        * SequenceI[sz = seqs.getSize(false)];
3868        *
3869        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3870        * seqs.getSequenceAt(i); }
3871        */
3872       msa = viewport.getAlignmentView(true);
3873     }
3874     else if (viewport.getSelectionGroup() != null
3875             && viewport.getSelectionGroup().getSize() == 1)
3876     {
3877       int option = JvOptionPane.showConfirmDialog(this,
3878               MessageManager.getString("warn.oneseq_msainput_selection"),
3879               MessageManager.getString("label.invalid_selection"),
3880               JvOptionPane.OK_CANCEL_OPTION);
3881       if (option == JvOptionPane.OK_OPTION)
3882       {
3883         msa = viewport.getAlignmentView(false);
3884       }
3885     }
3886     else
3887     {
3888       msa = viewport.getAlignmentView(false);
3889     }
3890     return msa;
3891   }
3892
3893   /**
3894    * Decides what is submitted to a secondary structure prediction service: the
3895    * first sequence in the alignment, or in the current selection, or, if the
3896    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3897    * region or the whole alignment. (where the first sequence in the set is the
3898    * one that the prediction will be for).
3899    */
3900   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3901   {
3902     AlignmentView seqs = null;
3903
3904     if ((viewport.getSelectionGroup() != null)
3905             && (viewport.getSelectionGroup().getSize() > 0))
3906     {
3907       seqs = viewport.getAlignmentView(true);
3908     }
3909     else
3910     {
3911       seqs = viewport.getAlignmentView(false);
3912     }
3913     // limit sequences - JBPNote in future - could spawn multiple prediction
3914     // jobs
3915     // TODO: viewport.getAlignment().isAligned is a global state - the local
3916     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3917     if (!viewport.getAlignment().isAligned(false))
3918     {
3919       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3920       // TODO: if seqs.getSequences().length>1 then should really have warned
3921       // user!
3922
3923     }
3924     return seqs;
3925   }
3926
3927   /**
3928    * DOCUMENT ME!
3929    *
3930    * @param e
3931    *          DOCUMENT ME!
3932    */
3933   @Override
3934   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3935   {
3936     // Pick the tree file
3937     JalviewFileChooser chooser = new JalviewFileChooser(
3938             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3939     chooser.setFileView(new JalviewFileView());
3940     chooser.setDialogTitle(
3941             MessageManager.getString("label.select_newick_like_tree_file"));
3942     chooser.setToolTipText(
3943             MessageManager.getString("label.load_tree_file"));
3944
3945     chooser.response(new jalview.util.dialogrunner.RunResponse(
3946             JalviewFileChooser.APPROVE_OPTION)
3947     {
3948       @Override
3949       public void run()
3950       {
3951         String filePath = chooser.getSelectedFile().getPath();
3952         Cache.setProperty("LAST_DIRECTORY", filePath);
3953         NewickFile fin = null;
3954         try
3955         {
3956           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3957                   DataSourceType.FILE));
3958           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3959         } catch (Exception ex)
3960         {
3961           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3962                   MessageManager
3963                           .getString("label.problem_reading_tree_file"),
3964                   JvOptionPane.WARNING_MESSAGE);
3965           ex.printStackTrace();
3966         }
3967         if (fin != null && fin.hasWarningMessage())
3968         {
3969           JvOptionPane.showMessageDialog(Desktop.desktop,
3970                   fin.getWarningMessage(),
3971                   MessageManager.getString(
3972                           "label.possible_problem_with_tree_file"),
3973                   JvOptionPane.WARNING_MESSAGE);
3974         }
3975       }
3976     }).openDialog(this);
3977   }
3978
3979   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3980   {
3981     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3982   }
3983
3984   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3985           int h, int x, int y)
3986   {
3987     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3988   }
3989
3990   /**
3991    * Add a treeviewer for the tree extracted from a Newick file object to the
3992    * current alignment view
3993    *
3994    * @param nf
3995    *          the tree
3996    * @param title
3997    *          tree viewer title
3998    * @param input
3999    *          Associated alignment input data (or null)
4000    * @param w
4001    *          width
4002    * @param h
4003    *          height
4004    * @param x
4005    *          position
4006    * @param y
4007    *          position
4008    * @return TreePanel handle
4009    */
4010   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4011           AlignmentView input, int w, int h, int x, int y)
4012   {
4013     TreePanel tp = null;
4014
4015     try
4016     {
4017       nf.parse();
4018
4019       if (nf.getTree() != null)
4020       {
4021         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4022
4023         tp.setSize(w, h);
4024
4025         if (x > 0 && y > 0)
4026         {
4027           tp.setLocation(x, y);
4028         }
4029
4030         Desktop.addInternalFrame(tp, treeTitle, w, h);
4031       }
4032     } catch (Exception ex)
4033     {
4034       ex.printStackTrace();
4035     }
4036
4037     return tp;
4038   }
4039
4040   private boolean buildingMenu = false;
4041
4042   /**
4043    * Generates menu items and listener event actions for web service clients
4044    *
4045    */
4046   public void BuildWebServiceMenu()
4047   {
4048     while (buildingMenu)
4049     {
4050       try
4051       {
4052         System.err.println("Waiting for building menu to finish.");
4053         Thread.sleep(10);
4054       } catch (Exception e)
4055       {
4056       }
4057     }
4058     final AlignFrame me = this;
4059     buildingMenu = true;
4060     new Thread(new Runnable()
4061     {
4062       @Override
4063       public void run()
4064       {
4065         final List<JMenuItem> legacyItems = new ArrayList<>();
4066         try
4067         {
4068           // System.err.println("Building ws menu again "
4069           // + Thread.currentThread());
4070           // TODO: add support for context dependent disabling of services based
4071           // on
4072           // alignment and current selection
4073           // TODO: add additional serviceHandle parameter to specify abstract
4074           // handler
4075           // class independently of AbstractName
4076           // TODO: add in rediscovery GUI function to restart discoverer
4077           // TODO: group services by location as well as function and/or
4078           // introduce
4079           // object broker mechanism.
4080           final Vector<JMenu> wsmenu = new Vector<>();
4081           final IProgressIndicator af = me;
4082
4083           /*
4084            * do not i18n these strings - they are hard-coded in class
4085            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4086            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4087            */
4088           final JMenu msawsmenu = new JMenu("Alignment");
4089           final JMenu secstrmenu = new JMenu(
4090                   "Secondary Structure Prediction");
4091           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4092           final JMenu analymenu = new JMenu("Analysis");
4093           final JMenu dismenu = new JMenu("Protein Disorder");
4094           // JAL-940 - only show secondary structure prediction services from
4095           // the legacy server
4096           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4097               // &&
4098           Discoverer.services != null && (Discoverer.services.size() > 0))
4099           {
4100             // TODO: refactor to allow list of AbstractName/Handler bindings to
4101             // be
4102             // stored or retrieved from elsewhere
4103             // No MSAWS used any more:
4104             // Vector msaws = null; // (Vector)
4105             // Discoverer.services.get("MsaWS");
4106             Vector secstrpr = (Vector) Discoverer.services
4107                     .get("SecStrPred");
4108             if (secstrpr != null)
4109             {
4110               // Add any secondary structure prediction services
4111               for (int i = 0, j = secstrpr.size(); i < j; i++)
4112               {
4113                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4114                         .get(i);
4115                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4116                         .getServiceClient(sh);
4117                 int p = secstrmenu.getItemCount();
4118                 impl.attachWSMenuEntry(secstrmenu, me);
4119                 int q = secstrmenu.getItemCount();
4120                 for (int litm = p; litm < q; litm++)
4121                 {
4122                   legacyItems.add(secstrmenu.getItem(litm));
4123                 }
4124               }
4125             }
4126           }
4127
4128           // Add all submenus in the order they should appear on the web
4129           // services menu
4130           wsmenu.add(msawsmenu);
4131           wsmenu.add(secstrmenu);
4132           wsmenu.add(dismenu);
4133           wsmenu.add(analymenu);
4134           // No search services yet
4135           // wsmenu.add(seqsrchmenu);
4136
4137           javax.swing.SwingUtilities.invokeLater(new Runnable()
4138           {
4139             @Override
4140             public void run()
4141             {
4142               try
4143               {
4144                 webService.removeAll();
4145                 // first, add discovered services onto the webservices menu
4146                 if (wsmenu.size() > 0)
4147                 {
4148                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4149                   {
4150                     webService.add(wsmenu.get(i));
4151                   }
4152                 }
4153                 else
4154                 {
4155                   webService.add(me.webServiceNoServices);
4156                 }
4157                 // TODO: move into separate menu builder class.
4158                 boolean new_sspred = false;
4159                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4160                 {
4161                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4162                   if (jws2servs != null)
4163                   {
4164                     if (jws2servs.hasServices())
4165                     {
4166                       jws2servs.attachWSMenuEntry(webService, me);
4167                       for (Jws2Instance sv : jws2servs.getServices())
4168                       {
4169                         if (sv.description.toLowerCase().contains("jpred"))
4170                         {
4171                           for (JMenuItem jmi : legacyItems)
4172                           {
4173                             jmi.setVisible(false);
4174                           }
4175                         }
4176                       }
4177
4178                     }
4179                     if (jws2servs.isRunning())
4180                     {
4181                       JMenuItem tm = new JMenuItem(
4182                               "Still discovering JABA Services");
4183                       tm.setEnabled(false);
4184                       webService.add(tm);
4185                     }
4186                   }
4187                 }
4188                 build_urlServiceMenu(me.webService);
4189                 build_fetchdbmenu(webService);
4190                 for (JMenu item : wsmenu)
4191                 {
4192                   if (item.getItemCount() == 0)
4193                   {
4194                     item.setEnabled(false);
4195                   }
4196                   else
4197                   {
4198                     item.setEnabled(true);
4199                   }
4200                 }
4201               } catch (Exception e)
4202               {
4203                 Cache.log.debug(
4204                         "Exception during web service menu building process.",
4205                         e);
4206               }
4207             }
4208           });
4209         } catch (Exception e)
4210         {
4211         }
4212         buildingMenu = false;
4213       }
4214     }).start();
4215
4216   }
4217
4218   /**
4219    * construct any groupURL type service menu entries.
4220    *
4221    * @param webService
4222    */
4223   private void build_urlServiceMenu(JMenu webService)
4224   {
4225     // TODO: remove this code when 2.7 is released
4226     // DEBUG - alignmentView
4227     /*
4228      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4229      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4230      *
4231      * @Override public void actionPerformed(ActionEvent e) {
4232      * jalview.datamodel.AlignmentView
4233      * .testSelectionViews(af.viewport.getAlignment(),
4234      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4235      *
4236      * }); webService.add(testAlView);
4237      */
4238     // TODO: refactor to RestClient discoverer and merge menu entries for
4239     // rest-style services with other types of analysis/calculation service
4240     // SHmmr test client - still being implemented.
4241     // DEBUG - alignmentView
4242
4243     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4244             .getRestClients())
4245     {
4246       client.attachWSMenuEntry(
4247               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4248               this);
4249     }
4250   }
4251
4252   /**
4253    * Searches the alignment sequences for xRefs and builds the Show
4254    * Cross-References menu (formerly called Show Products), with database
4255    * sources for which cross-references are found (protein sources for a
4256    * nucleotide alignment and vice versa)
4257    *
4258    * @return true if Show Cross-references menu should be enabled
4259    */
4260   public boolean canShowProducts()
4261   {
4262     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4263     AlignmentI dataset = viewport.getAlignment().getDataset();
4264
4265     showProducts.removeAll();
4266     final boolean dna = viewport.getAlignment().isNucleotide();
4267
4268     if (seqs == null || seqs.length == 0)
4269     {
4270       // nothing to see here.
4271       return false;
4272     }
4273
4274     boolean showp = false;
4275     try
4276     {
4277       List<String> ptypes = new CrossRef(seqs, dataset)
4278               .findXrefSourcesForSequences(dna);
4279
4280       for (final String source : ptypes)
4281       {
4282         showp = true;
4283         final AlignFrame af = this;
4284         JMenuItem xtype = new JMenuItem(source);
4285         xtype.addActionListener(new ActionListener()
4286         {
4287           @Override
4288           public void actionPerformed(ActionEvent e)
4289           {
4290             showProductsFor(af.viewport.getSequenceSelection(), dna,
4291                     source);
4292           }
4293         });
4294         showProducts.add(xtype);
4295       }
4296       showProducts.setVisible(showp);
4297       showProducts.setEnabled(showp);
4298     } catch (Exception e)
4299     {
4300       Cache.log.warn(
4301               "canShowProducts threw an exception - please report to help@jalview.org",
4302               e);
4303       return false;
4304     }
4305     return showp;
4306   }
4307
4308   /**
4309    * Finds and displays cross-references for the selected sequences (protein
4310    * products for nucleotide sequences, dna coding sequences for peptides).
4311    *
4312    * @param sel
4313    *          the sequences to show cross-references for
4314    * @param dna
4315    *          true if from a nucleotide alignment (so showing proteins)
4316    * @param source
4317    *          the database to show cross-references for
4318    */
4319   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4320           final String source)
4321   {
4322     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4323             .start();
4324   }
4325
4326   /**
4327    * Construct and display a new frame containing the translation of this
4328    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4329    */
4330   @Override
4331   public void showTranslation_actionPerformed(ActionEvent e)
4332   {
4333     AlignmentI al = null;
4334     try
4335     {
4336       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4337
4338       al = dna.translateCdna();
4339     } catch (Exception ex)
4340     {
4341       jalview.bin.Cache.log.error(
4342               "Exception during translation. Please report this !", ex);
4343       final String msg = MessageManager.getString(
4344               "label.error_when_translating_sequences_submit_bug_report");
4345       final String errorTitle = MessageManager
4346               .getString("label.implementation_error")
4347               + MessageManager.getString("label.translation_failed");
4348       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4349               JvOptionPane.ERROR_MESSAGE);
4350       return;
4351     }
4352     if (al == null || al.getHeight() == 0)
4353     {
4354       final String msg = MessageManager.getString(
4355               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4356       final String errorTitle = MessageManager
4357               .getString("label.translation_failed");
4358       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4359               JvOptionPane.WARNING_MESSAGE);
4360     }
4361     else
4362     {
4363       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4364       af.setFileFormat(this.currentFileFormat);
4365       final String newTitle = MessageManager
4366               .formatMessage("label.translation_of_params", new Object[]
4367               { this.getTitle() });
4368       af.setTitle(newTitle);
4369       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4370       {
4371         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4372         viewport.openSplitFrame(af, new Alignment(seqs));
4373       }
4374       else
4375       {
4376         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4377                 DEFAULT_HEIGHT);
4378       }
4379     }
4380   }
4381
4382   /**
4383    * Set the file format
4384    *
4385    * @param format
4386    */
4387   public void setFileFormat(FileFormatI format)
4388   {
4389     this.currentFileFormat = format;
4390   }
4391
4392   /**
4393    * Try to load a features file onto the alignment.
4394    *
4395    * @param file
4396    *          contents or path to retrieve file or a File object
4397    * @param sourceType
4398    *          access mode of file (see jalview.io.AlignFile)
4399    * @return true if features file was parsed correctly.
4400    */
4401   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4402   {
4403     // BH 2018
4404     return avc.parseFeaturesFile(file, sourceType,
4405             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4406
4407   }
4408
4409   @Override
4410   public void refreshFeatureUI(boolean enableIfNecessary)
4411   {
4412     // note - currently this is only still here rather than in the controller
4413     // because of the featureSettings hard reference that is yet to be
4414     // abstracted
4415     if (enableIfNecessary)
4416     {
4417       viewport.setShowSequenceFeatures(true);
4418       showSeqFeatures.setSelected(true);
4419     }
4420
4421   }
4422
4423   @Override
4424   public void dragEnter(DropTargetDragEvent evt)
4425   {
4426   }
4427
4428   @Override
4429   public void dragExit(DropTargetEvent evt)
4430   {
4431   }
4432
4433   @Override
4434   public void dragOver(DropTargetDragEvent evt)
4435   {
4436   }
4437
4438   @Override
4439   public void dropActionChanged(DropTargetDragEvent evt)
4440   {
4441   }
4442
4443   @Override
4444   public void drop(DropTargetDropEvent evt)
4445   {
4446     // JAL-1552 - acceptDrop required before getTransferable call for
4447     // Java's Transferable for native dnd
4448     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4449     Transferable t = evt.getTransferable();
4450
4451     final AlignFrame thisaf = this;
4452     final List<Object> files = new ArrayList<>();
4453     List<DataSourceType> protocols = new ArrayList<>();
4454
4455     try
4456     {
4457       Desktop.transferFromDropTarget(files, protocols, evt, t);
4458     } catch (Exception e)
4459     {
4460       e.printStackTrace();
4461     }
4462     if (files != null)
4463     {
4464       new Thread(new Runnable()
4465       {
4466         @Override
4467         public void run()
4468         {
4469           try
4470           {
4471             // check to see if any of these files have names matching sequences
4472             // in
4473             // the alignment
4474             SequenceIdMatcher idm = new SequenceIdMatcher(
4475                     viewport.getAlignment().getSequencesArray());
4476             /**
4477              * Object[] { String,SequenceI}
4478              */
4479             ArrayList<Object[]> filesmatched = new ArrayList<>();
4480             ArrayList<Object> filesnotmatched = new ArrayList<>();
4481             for (int i = 0; i < files.size(); i++)
4482             {
4483               // BH 2018
4484               Object file = files.get(i);
4485               String fileName = file.toString();
4486               String pdbfn = "";
4487               DataSourceType protocol = (file instanceof File
4488                       ? DataSourceType.FILE
4489                       : FormatAdapter.checkProtocol(fileName));
4490               if (protocol == DataSourceType.FILE)
4491               {
4492                 File fl = (file instanceof File ? (File) file
4493                         : new File(fileName));
4494                 pdbfn = fl.getName();
4495               }
4496               else if (protocol == DataSourceType.URL)
4497               {
4498                 URL url = new URL(fileName);
4499                 pdbfn = url.getFile();
4500               }
4501               if (pdbfn.length() > 0)
4502               {
4503                 // attempt to find a match in the alignment
4504                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4505                 int l = 0, c = pdbfn.indexOf(".");
4506                 while (mtch == null && c != -1)
4507                 {
4508                   do
4509                   {
4510                     l = c;
4511                   } while ((c = pdbfn.indexOf(".", l)) > l);
4512                   if (l > -1)
4513                   {
4514                     pdbfn = pdbfn.substring(0, l);
4515                   }
4516                   mtch = idm.findAllIdMatches(pdbfn);
4517                 }
4518                 if (mtch != null)
4519                 {
4520                   FileFormatI type;
4521                   try
4522                   {
4523                     type = new IdentifyFile().identify(file, protocol);
4524                   } catch (Exception ex)
4525                   {
4526                     type = null;
4527                   }
4528                   if (type != null && type.isStructureFile())
4529                   {
4530                     filesmatched.add(new Object[] { file, protocol, mtch });
4531                     continue;
4532                   }
4533                 }
4534                 // File wasn't named like one of the sequences or wasn't a PDB
4535                 // file.
4536                 filesnotmatched.add(file);
4537               }
4538             }
4539             int assocfiles = 0;
4540             if (filesmatched.size() > 0)
4541             {
4542               boolean autoAssociate = Cache
4543                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4544               if (!autoAssociate)
4545               {
4546                 String msg = MessageManager.formatMessage(
4547                         "label.automatically_associate_structure_files_with_sequences_same_name",
4548                         new Object[]
4549                         { Integer.valueOf(filesmatched.size())
4550                                 .toString() });
4551                 String ttl = MessageManager.getString(
4552                         "label.automatically_associate_structure_files_by_name");
4553                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4554                         ttl, JvOptionPane.YES_NO_OPTION);
4555                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4556               }
4557               if (autoAssociate)
4558               {
4559                 for (Object[] fm : filesmatched)
4560                 {
4561                   // try and associate
4562                   // TODO: may want to set a standard ID naming formalism for
4563                   // associating PDB files which have no IDs.
4564                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4565                   {
4566                     PDBEntry pe = new AssociatePdbFileWithSeq()
4567                             .associatePdbWithSeq((String) fm[0],
4568                                     (DataSourceType) fm[1], toassoc, false,
4569                                     Desktop.instance);
4570                     if (pe != null)
4571                     {
4572                       System.err.println("Associated file : "
4573                               + ((String) fm[0]) + " with "
4574                               + toassoc.getDisplayId(true));
4575                       assocfiles++;
4576                     }
4577                   }
4578                   // TODO: do we need to update overview ? only if features are
4579                   // shown I guess
4580                   alignPanel.paintAlignment(true, false);
4581                 }
4582               }
4583               else
4584               {
4585                 /*
4586                  * add declined structures as sequences
4587                  */
4588                 for (Object[] o : filesmatched)
4589                 {
4590                   filesnotmatched.add(o[0]);
4591                 }
4592               }
4593             }
4594             if (filesnotmatched.size() > 0)
4595             {
4596               if (assocfiles > 0 && (Cache.getDefault(
4597                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4598                       || JvOptionPane.showConfirmDialog(thisaf,
4599                               "<html>" + MessageManager.formatMessage(
4600                                       "label.ignore_unmatched_dropped_files_info",
4601                                       new Object[]
4602                                       { Integer.valueOf(
4603                                               filesnotmatched.size())
4604                                               .toString() })
4605                                       + "</html>",
4606                               MessageManager.getString(
4607                                       "label.ignore_unmatched_dropped_files"),
4608                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4609               {
4610                 return;
4611               }
4612               for (Object fn : filesnotmatched)
4613               {
4614                 loadJalviewDataFile(fn, null, null, null);
4615               }
4616
4617             }
4618           } catch (Exception ex)
4619           {
4620             ex.printStackTrace();
4621           }
4622         }
4623       }).start();
4624     }
4625   }
4626
4627   /**
4628    * Attempt to load a "dropped" file or URL string, by testing in turn for
4629    * <ul>
4630    * <li>an Annotation file</li>
4631    * <li>a JNet file</li>
4632    * <li>a features file</li>
4633    * <li>else try to interpret as an alignment file</li>
4634    * </ul>
4635    *
4636    * @param file
4637    *          either a filename or a URL string.
4638    */
4639   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4640           FileFormatI format, SequenceI assocSeq)
4641   {
4642     // BH 2018 was String file
4643     try
4644     {
4645       if (sourceType == null)
4646       {
4647         sourceType = FormatAdapter.checkProtocol(file);
4648       }
4649       // if the file isn't identified, or not positively identified as some
4650       // other filetype (PFAM is default unidentified alignment file type) then
4651       // try to parse as annotation.
4652       boolean isAnnotation = (format == null
4653               || FileFormat.Pfam.equals(format))
4654                       ? new AnnotationFile().annotateAlignmentView(viewport,
4655                               file, sourceType)
4656                       : false;
4657
4658       if (!isAnnotation)
4659       {
4660         // first see if its a T-COFFEE score file
4661         TCoffeeScoreFile tcf = null;
4662         try
4663         {
4664           tcf = new TCoffeeScoreFile(file, sourceType);
4665           if (tcf.isValid())
4666           {
4667             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4668             {
4669               buildColourMenu();
4670               changeColour(
4671                       new TCoffeeColourScheme(viewport.getAlignment()));
4672               isAnnotation = true;
4673               statusBar.setText(MessageManager.getString(
4674                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4675             }
4676             else
4677             {
4678               // some problem - if no warning its probable that the ID matching
4679               // process didn't work
4680               JvOptionPane.showMessageDialog(Desktop.desktop,
4681                       tcf.getWarningMessage() == null
4682                               ? MessageManager.getString(
4683                                       "label.check_file_matches_sequence_ids_alignment")
4684                               : tcf.getWarningMessage(),
4685                       MessageManager.getString(
4686                               "label.problem_reading_tcoffee_score_file"),
4687                       JvOptionPane.WARNING_MESSAGE);
4688             }
4689           }
4690           else
4691           {
4692             tcf = null;
4693           }
4694         } catch (Exception x)
4695         {
4696           Cache.log.debug(
4697                   "Exception when processing data source as T-COFFEE score file",
4698                   x);
4699           tcf = null;
4700         }
4701         if (tcf == null)
4702         {
4703           // try to see if its a JNet 'concise' style annotation file *before*
4704           // we
4705           // try to parse it as a features file
4706           if (format == null)
4707           {
4708             format = new IdentifyFile().identify(file, sourceType);
4709           }
4710           if (FileFormat.ScoreMatrix == format)
4711           {
4712             ScoreMatrixFile sm = new ScoreMatrixFile(
4713                     new FileParse(file, sourceType));
4714             sm.parse();
4715             // todo: i18n this message
4716             statusBar.setText(MessageManager.formatMessage(
4717                     "label.successfully_loaded_matrix",
4718                     sm.getMatrixName()));
4719           }
4720           else if (FileFormat.Jnet.equals(format))
4721           {
4722             JPredFile predictions = new JPredFile(file, sourceType);
4723             new JnetAnnotationMaker();
4724             JnetAnnotationMaker.add_annotation(predictions,
4725                     viewport.getAlignment(), 0, false);
4726             viewport.getAlignment().setupJPredAlignment();
4727             isAnnotation = true;
4728           }
4729           // else if (IdentifyFile.FeaturesFile.equals(format))
4730           else if (FileFormat.Features.equals(format))
4731           {
4732             if (parseFeaturesFile(file, sourceType))
4733             {
4734               alignPanel.paintAlignment(true, true);
4735             }
4736           }
4737           else
4738           {
4739             new FileLoader().LoadFile(viewport, file, sourceType, format);
4740           }
4741         }
4742       }
4743       if (isAnnotation)
4744       {
4745
4746         alignPanel.adjustAnnotationHeight();
4747         viewport.updateSequenceIdColours();
4748         buildSortByAnnotationScoresMenu();
4749         alignPanel.paintAlignment(true, true);
4750       }
4751     } catch (Exception ex)
4752     {
4753       ex.printStackTrace();
4754     } catch (OutOfMemoryError oom)
4755     {
4756       try
4757       {
4758         System.gc();
4759       } catch (Exception x)
4760       {
4761       }
4762       new OOMWarning(
4763               "loading data "
4764                       + (sourceType != null
4765                               ? (sourceType == DataSourceType.PASTE
4766                                       ? "from clipboard."
4767                                       : "using " + sourceType + " from "
4768                                               + file)
4769                               : ".")
4770                       + (format != null
4771                               ? "(parsing as '" + format + "' file)"
4772                               : ""),
4773               oom, Desktop.desktop);
4774     }
4775   }
4776
4777   /**
4778    * Method invoked by the ChangeListener on the tabbed pane, in other words
4779    * when a different tabbed pane is selected by the user or programmatically.
4780    */
4781   @Override
4782   public void tabSelectionChanged(int index)
4783   {
4784     if (index > -1)
4785     {
4786       alignPanel = alignPanels.get(index);
4787       viewport = alignPanel.av;
4788       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4789       setMenusFromViewport(viewport);
4790     }
4791
4792     /*
4793      * 'focus' any colour slider that is open to the selected viewport
4794      */
4795     if (viewport.getConservationSelected())
4796     {
4797       SliderPanel.setConservationSlider(alignPanel,
4798               viewport.getResidueShading(), alignPanel.getViewName());
4799     }
4800     else
4801     {
4802       SliderPanel.hideConservationSlider();
4803     }
4804     if (viewport.getAbovePIDThreshold())
4805     {
4806       SliderPanel.setPIDSliderSource(alignPanel,
4807               viewport.getResidueShading(), alignPanel.getViewName());
4808     }
4809     else
4810     {
4811       SliderPanel.hidePIDSlider();
4812     }
4813
4814     /*
4815      * If there is a frame linked to this one in a SplitPane, switch it to the
4816      * same view tab index. No infinite recursion of calls should happen, since
4817      * tabSelectionChanged() should not get invoked on setting the selected
4818      * index to an unchanged value. Guard against setting an invalid index
4819      * before the new view peer tab has been created.
4820      */
4821     final AlignViewportI peer = viewport.getCodingComplement();
4822     if (peer != null)
4823     {
4824       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4825               .getAlignPanel().alignFrame;
4826       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4827       {
4828         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4829       }
4830     }
4831   }
4832
4833   /**
4834    * On right mouse click on view tab, prompt for and set new view name.
4835    */
4836   @Override
4837   public void tabbedPane_mousePressed(MouseEvent e)
4838   {
4839     if (e.isPopupTrigger())
4840     {
4841       String msg = MessageManager.getString("label.enter_view_name");
4842       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4843               JvOptionPane.QUESTION_MESSAGE);
4844
4845       if (reply != null)
4846       {
4847         viewport.viewName = reply;
4848         // TODO warn if reply is in getExistingViewNames()?
4849         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4850       }
4851     }
4852   }
4853
4854   public AlignViewport getCurrentView()
4855   {
4856     return viewport;
4857   }
4858
4859   /**
4860    * Open the dialog for regex description parsing.
4861    */
4862   @Override
4863   protected void extractScores_actionPerformed(ActionEvent e)
4864   {
4865     ParseProperties pp = new jalview.analysis.ParseProperties(
4866             viewport.getAlignment());
4867     // TODO: verify regex and introduce GUI dialog for version 2.5
4868     // if (pp.getScoresFromDescription("col", "score column ",
4869     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4870     // true)>0)
4871     if (pp.getScoresFromDescription("description column",
4872             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4873     {
4874       buildSortByAnnotationScoresMenu();
4875     }
4876   }
4877
4878   /*
4879    * (non-Javadoc)
4880    *
4881    * @see
4882    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4883    * )
4884    */
4885   @Override
4886   protected void showDbRefs_actionPerformed(ActionEvent e)
4887   {
4888     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4889   }
4890
4891   /*
4892    * (non-Javadoc)
4893    *
4894    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4895    * ActionEvent)
4896    */
4897   @Override
4898   protected void showNpFeats_actionPerformed(ActionEvent e)
4899   {
4900     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4901   }
4902
4903   /**
4904    * find the viewport amongst the tabs in this alignment frame and close that
4905    * tab
4906    *
4907    * @param av
4908    */
4909   public boolean closeView(AlignViewportI av)
4910   {
4911     if (viewport == av)
4912     {
4913       this.closeMenuItem_actionPerformed(false);
4914       return true;
4915     }
4916     Component[] comp = tabbedPane.getComponents();
4917     for (int i = 0; comp != null && i < comp.length; i++)
4918     {
4919       if (comp[i] instanceof AlignmentPanel)
4920       {
4921         if (((AlignmentPanel) comp[i]).av == av)
4922         {
4923           // close the view.
4924           closeView((AlignmentPanel) comp[i]);
4925           return true;
4926         }
4927       }
4928     }
4929     return false;
4930   }
4931
4932   protected void build_fetchdbmenu(JMenu webService)
4933   {
4934     // Temporary hack - DBRef Fetcher always top level ws entry.
4935     // TODO We probably want to store a sequence database checklist in
4936     // preferences and have checkboxes.. rather than individual sources selected
4937     // here
4938     final JMenu rfetch = new JMenu(
4939             MessageManager.getString("action.fetch_db_references"));
4940     rfetch.setToolTipText(MessageManager.getString(
4941             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4942     webService.add(rfetch);
4943
4944     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4945             MessageManager.getString("option.trim_retrieved_seqs"));
4946     trimrs.setToolTipText(
4947             MessageManager.getString("label.trim_retrieved_sequences"));
4948     trimrs.setSelected(
4949             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4950     trimrs.addActionListener(new ActionListener()
4951     {
4952       @Override
4953       public void actionPerformed(ActionEvent e)
4954       {
4955         trimrs.setSelected(trimrs.isSelected());
4956         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4957                 Boolean.valueOf(trimrs.isSelected()).toString());
4958       };
4959     });
4960     rfetch.add(trimrs);
4961     JMenuItem fetchr = new JMenuItem(
4962             MessageManager.getString("label.standard_databases"));
4963     fetchr.setToolTipText(
4964             MessageManager.getString("label.fetch_embl_uniprot"));
4965     fetchr.addActionListener(new ActionListener()
4966     {
4967
4968       @Override
4969       public void actionPerformed(ActionEvent e)
4970       {
4971         new Thread(new Runnable()
4972         {
4973           @Override
4974           public void run()
4975           {
4976             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4977                     .getAlignment().isNucleotide();
4978             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4979                     alignPanel.av.getSequenceSelection(),
4980                     alignPanel.alignFrame, null,
4981                     alignPanel.alignFrame.featureSettings, isNucleotide);
4982             dbRefFetcher.addListener(new FetchFinishedListenerI()
4983             {
4984               @Override
4985               public void finished()
4986               {
4987                 AlignFrame.this.setMenusForViewport();
4988               }
4989             });
4990             dbRefFetcher.fetchDBRefs(false);
4991           }
4992         }).start();
4993
4994       }
4995
4996     });
4997     rfetch.add(fetchr);
4998     final AlignFrame me = this;
4999     new Thread(new Runnable()
5000     {
5001       @Override
5002       public void run()
5003       {
5004         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5005                 .getSequenceFetcherSingleton(me);
5006         javax.swing.SwingUtilities.invokeLater(new Runnable()
5007         {
5008           @Override
5009           public void run()
5010           {
5011             String[] dbclasses = sf.getOrderedSupportedSources();
5012             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5013             // jalview.util.QuickSort.sort(otherdb, otherdb);
5014             List<DbSourceProxy> otherdb;
5015             JMenu dfetch = new JMenu();
5016             JMenu ifetch = new JMenu();
5017             JMenuItem fetchr = null;
5018             int comp = 0, icomp = 0, mcomp = 15;
5019             String mname = null;
5020             int dbi = 0;
5021             for (String dbclass : dbclasses)
5022             {
5023               otherdb = sf.getSourceProxy(dbclass);
5024               // add a single entry for this class, or submenu allowing 'fetch
5025               // all' or pick one
5026               if (otherdb == null || otherdb.size() < 1)
5027               {
5028                 continue;
5029               }
5030               // List<DbSourceProxy> dbs=otherdb;
5031               // otherdb=new ArrayList<DbSourceProxy>();
5032               // for (DbSourceProxy db:dbs)
5033               // {
5034               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5035               // }
5036               if (mname == null)
5037               {
5038                 mname = "From " + dbclass;
5039               }
5040               if (otherdb.size() == 1)
5041               {
5042                 final DbSourceProxy[] dassource = otherdb
5043                         .toArray(new DbSourceProxy[0]);
5044                 DbSourceProxy src = otherdb.get(0);
5045                 fetchr = new JMenuItem(src.getDbSource());
5046                 fetchr.addActionListener(new ActionListener()
5047                 {
5048
5049                   @Override
5050                   public void actionPerformed(ActionEvent e)
5051                   {
5052                     new Thread(new Runnable()
5053                     {
5054
5055                       @Override
5056                       public void run()
5057                       {
5058                         boolean isNucleotide = alignPanel.alignFrame
5059                                 .getViewport().getAlignment()
5060                                 .isNucleotide();
5061                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5062                                 alignPanel.av.getSequenceSelection(),
5063                                 alignPanel.alignFrame, dassource,
5064                                 alignPanel.alignFrame.featureSettings,
5065                                 isNucleotide);
5066                         dbRefFetcher
5067                                 .addListener(new FetchFinishedListenerI()
5068                                 {
5069                                   @Override
5070                                   public void finished()
5071                                   {
5072                                     AlignFrame.this.setMenusForViewport();
5073                                   }
5074                                 });
5075                         dbRefFetcher.fetchDBRefs(false);
5076                       }
5077                     }).start();
5078                   }
5079
5080                 });
5081                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5082                         MessageManager.formatMessage(
5083                                 "label.fetch_retrieve_from", new Object[]
5084                                 { src.getDbName() })));
5085                 dfetch.add(fetchr);
5086                 comp++;
5087               }
5088               else
5089               {
5090                 final DbSourceProxy[] dassource = otherdb
5091                         .toArray(new DbSourceProxy[0]);
5092                 // fetch all entry
5093                 DbSourceProxy src = otherdb.get(0);
5094                 fetchr = new JMenuItem(MessageManager
5095                         .formatMessage("label.fetch_all_param", new Object[]
5096                         { src.getDbSource() }));
5097                 fetchr.addActionListener(new ActionListener()
5098                 {
5099                   @Override
5100                   public void actionPerformed(ActionEvent e)
5101                   {
5102                     new Thread(new Runnable()
5103                     {
5104
5105                       @Override
5106                       public void run()
5107                       {
5108                         boolean isNucleotide = alignPanel.alignFrame
5109                                 .getViewport().getAlignment()
5110                                 .isNucleotide();
5111                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5112                                 alignPanel.av.getSequenceSelection(),
5113                                 alignPanel.alignFrame, dassource,
5114                                 alignPanel.alignFrame.featureSettings,
5115                                 isNucleotide);
5116                         dbRefFetcher
5117                                 .addListener(new FetchFinishedListenerI()
5118                                 {
5119                                   @Override
5120                                   public void finished()
5121                                   {
5122                                     AlignFrame.this.setMenusForViewport();
5123                                   }
5124                                 });
5125                         dbRefFetcher.fetchDBRefs(false);
5126                       }
5127                     }).start();
5128                   }
5129                 });
5130
5131                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5132                         MessageManager.formatMessage(
5133                                 "label.fetch_retrieve_from_all_sources",
5134                                 new Object[]
5135                                 { Integer.valueOf(otherdb.size())
5136                                         .toString(),
5137                                     src.getDbSource(), src.getDbName() })));
5138                 dfetch.add(fetchr);
5139                 comp++;
5140                 // and then build the rest of the individual menus
5141                 ifetch = new JMenu(MessageManager.formatMessage(
5142                         "label.source_from_db_source", new Object[]
5143                         { src.getDbSource() }));
5144                 icomp = 0;
5145                 String imname = null;
5146                 int i = 0;
5147                 for (DbSourceProxy sproxy : otherdb)
5148                 {
5149                   String dbname = sproxy.getDbName();
5150                   String sname = dbname.length() > 5
5151                           ? dbname.substring(0, 5) + "..."
5152                           : dbname;
5153                   String msname = dbname.length() > 10
5154                           ? dbname.substring(0, 10) + "..."
5155                           : dbname;
5156                   if (imname == null)
5157                   {
5158                     imname = MessageManager
5159                             .formatMessage("label.from_msname", new Object[]
5160                             { sname });
5161                   }
5162                   fetchr = new JMenuItem(msname);
5163                   final DbSourceProxy[] dassrc = { sproxy };
5164                   fetchr.addActionListener(new ActionListener()
5165                   {
5166
5167                     @Override
5168                     public void actionPerformed(ActionEvent e)
5169                     {
5170                       new Thread(new Runnable()
5171                       {
5172
5173                         @Override
5174                         public void run()
5175                         {
5176                           boolean isNucleotide = alignPanel.alignFrame
5177                                   .getViewport().getAlignment()
5178                                   .isNucleotide();
5179                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5180                                   alignPanel.av.getSequenceSelection(),
5181                                   alignPanel.alignFrame, dassrc,
5182                                   alignPanel.alignFrame.featureSettings,
5183                                   isNucleotide);
5184                           dbRefFetcher
5185                                   .addListener(new FetchFinishedListenerI()
5186                                   {
5187                                     @Override
5188                                     public void finished()
5189                                     {
5190                                       AlignFrame.this.setMenusForViewport();
5191                                     }
5192                                   });
5193                           dbRefFetcher.fetchDBRefs(false);
5194                         }
5195                       }).start();
5196                     }
5197
5198                   });
5199                   fetchr.setToolTipText(
5200                           "<html>" + MessageManager.formatMessage(
5201                                   "label.fetch_retrieve_from", new Object[]
5202                                   { dbname }));
5203                   ifetch.add(fetchr);
5204                   ++i;
5205                   if (++icomp >= mcomp || i == (otherdb.size()))
5206                   {
5207                     ifetch.setText(MessageManager.formatMessage(
5208                             "label.source_to_target", imname, sname));
5209                     dfetch.add(ifetch);
5210                     ifetch = new JMenu();
5211                     imname = null;
5212                     icomp = 0;
5213                     comp++;
5214                   }
5215                 }
5216               }
5217               ++dbi;
5218               if (comp >= mcomp || dbi >= (dbclasses.length))
5219               {
5220                 dfetch.setText(MessageManager.formatMessage(
5221                         "label.source_to_target", mname, dbclass));
5222                 rfetch.add(dfetch);
5223                 dfetch = new JMenu();
5224                 mname = null;
5225                 comp = 0;
5226               }
5227             }
5228           }
5229         });
5230       }
5231     }).start();
5232
5233   }
5234
5235   /**
5236    * Left justify the whole alignment.
5237    */
5238   @Override
5239   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5240   {
5241     AlignmentI al = viewport.getAlignment();
5242     al.justify(false);
5243     viewport.firePropertyChange("alignment", null, al);
5244   }
5245
5246   /**
5247    * Right justify the whole alignment.
5248    */
5249   @Override
5250   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5251   {
5252     AlignmentI al = viewport.getAlignment();
5253     al.justify(true);
5254     viewport.firePropertyChange("alignment", null, al);
5255   }
5256
5257   @Override
5258   public void setShowSeqFeatures(boolean b)
5259   {
5260     showSeqFeatures.setSelected(b);
5261     viewport.setShowSequenceFeatures(b);
5262   }
5263
5264   /*
5265    * (non-Javadoc)
5266    *
5267    * @see
5268    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5269    * awt.event.ActionEvent)
5270    */
5271   @Override
5272   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5273   {
5274     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5275     alignPanel.paintAlignment(false, false);
5276   }
5277
5278   /*
5279    * (non-Javadoc)
5280    *
5281    * @see
5282    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5283    * .ActionEvent)
5284    */
5285   @Override
5286   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5287   {
5288     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5289     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5290
5291   }
5292
5293   /*
5294    * (non-Javadoc)
5295    *
5296    * @see
5297    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5298    * .event.ActionEvent)
5299    */
5300   @Override
5301   protected void showGroupConservation_actionPerformed(ActionEvent e)
5302   {
5303     viewport.setShowGroupConservation(showGroupConservation.getState());
5304     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5305   }
5306
5307   /*
5308    * (non-Javadoc)
5309    *
5310    * @see
5311    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5312    * .event.ActionEvent)
5313    */
5314   @Override
5315   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5316   {
5317     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5318     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5319   }
5320
5321   /*
5322    * (non-Javadoc)
5323    *
5324    * @see
5325    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5326    * .event.ActionEvent)
5327    */
5328   @Override
5329   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5330   {
5331     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5332     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5333   }
5334
5335   @Override
5336   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5337   {
5338     showSequenceLogo.setState(true);
5339     viewport.setShowSequenceLogo(true);
5340     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5341     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5342   }
5343
5344   @Override
5345   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5346   {
5347     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5348   }
5349
5350   /*
5351    * (non-Javadoc)
5352    *
5353    * @see
5354    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5355    * .event.ActionEvent)
5356    */
5357   @Override
5358   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5359   {
5360     if (avc.makeGroupsFromSelection())
5361     {
5362       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5363       alignPanel.updateAnnotation();
5364       alignPanel.paintAlignment(true, true);
5365     }
5366   }
5367
5368   public void clearAlignmentSeqRep()
5369   {
5370     // TODO refactor alignmentseqrep to controller
5371     if (viewport.getAlignment().hasSeqrep())
5372     {
5373       viewport.getAlignment().setSeqrep(null);
5374       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5375       alignPanel.updateAnnotation();
5376       alignPanel.paintAlignment(true, true);
5377     }
5378   }
5379
5380   @Override
5381   protected void createGroup_actionPerformed(ActionEvent e)
5382   {
5383     if (avc.createGroup())
5384     {
5385       alignPanel.alignmentChanged();
5386     }
5387   }
5388
5389   @Override
5390   protected void unGroup_actionPerformed(ActionEvent e)
5391   {
5392     if (avc.unGroup())
5393     {
5394       alignPanel.alignmentChanged();
5395     }
5396   }
5397
5398   /**
5399    * make the given alignmentPanel the currently selected tab
5400    *
5401    * @param alignmentPanel
5402    */
5403   public void setDisplayedView(AlignmentPanel alignmentPanel)
5404   {
5405     if (!viewport.getSequenceSetId()
5406             .equals(alignmentPanel.av.getSequenceSetId()))
5407     {
5408       throw new Error(MessageManager.getString(
5409               "error.implementation_error_cannot_show_view_alignment_frame"));
5410     }
5411     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5412             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5413     {
5414       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5415     }
5416   }
5417
5418   /**
5419    * Action on selection of menu options to Show or Hide annotations.
5420    *
5421    * @param visible
5422    * @param forSequences
5423    *          update sequence-related annotations
5424    * @param forAlignment
5425    *          update non-sequence-related annotations
5426    */
5427   @Override
5428   protected void setAnnotationsVisibility(boolean visible,
5429           boolean forSequences, boolean forAlignment)
5430   {
5431     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5432             .getAlignmentAnnotation();
5433     if (anns == null)
5434     {
5435       return;
5436     }
5437     for (AlignmentAnnotation aa : anns)
5438     {
5439       /*
5440        * don't display non-positional annotations on an alignment
5441        */
5442       if (aa.annotations == null)
5443       {
5444         continue;
5445       }
5446       boolean apply = (aa.sequenceRef == null && forAlignment)
5447               || (aa.sequenceRef != null && forSequences);
5448       if (apply)
5449       {
5450         aa.visible = visible;
5451       }
5452     }
5453     alignPanel.validateAnnotationDimensions(true);
5454     alignPanel.alignmentChanged();
5455   }
5456
5457   /**
5458    * Store selected annotation sort order for the view and repaint.
5459    */
5460   @Override
5461   protected void sortAnnotations_actionPerformed()
5462   {
5463     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5464     this.alignPanel.av
5465             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5466     alignPanel.paintAlignment(false, false);
5467   }
5468
5469   /**
5470    *
5471    * @return alignment panels in this alignment frame
5472    */
5473   public List<? extends AlignmentViewPanel> getAlignPanels()
5474   {
5475     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5476   }
5477
5478   /**
5479    * Open a new alignment window, with the cDNA associated with this (protein)
5480    * alignment, aligned as is the protein.
5481    */
5482   protected void viewAsCdna_actionPerformed()
5483   {
5484     // TODO no longer a menu action - refactor as required
5485     final AlignmentI alignment = getViewport().getAlignment();
5486     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5487     if (mappings == null)
5488     {
5489       return;
5490     }
5491     List<SequenceI> cdnaSeqs = new ArrayList<>();
5492     for (SequenceI aaSeq : alignment.getSequences())
5493     {
5494       for (AlignedCodonFrame acf : mappings)
5495       {
5496         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5497         if (dnaSeq != null)
5498         {
5499           /*
5500            * There is a cDNA mapping for this protein sequence - add to new
5501            * alignment. It will share the same dataset sequence as other mapped
5502            * cDNA (no new mappings need to be created).
5503            */
5504           final Sequence newSeq = new Sequence(dnaSeq);
5505           newSeq.setDatasetSequence(dnaSeq);
5506           cdnaSeqs.add(newSeq);
5507         }
5508       }
5509     }
5510     if (cdnaSeqs.size() == 0)
5511     {
5512       // show a warning dialog no mapped cDNA
5513       return;
5514     }
5515     AlignmentI cdna = new Alignment(
5516             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5517     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5518             AlignFrame.DEFAULT_HEIGHT);
5519     cdna.alignAs(alignment);
5520     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5521             + this.title;
5522     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5523             AlignFrame.DEFAULT_HEIGHT);
5524   }
5525
5526   /**
5527    * Set visibility of dna/protein complement view (available when shown in a
5528    * split frame).
5529    *
5530    * @param show
5531    */
5532   @Override
5533   protected void showComplement_actionPerformed(boolean show)
5534   {
5535     SplitContainerI sf = getSplitViewContainer();
5536     if (sf != null)
5537     {
5538       sf.setComplementVisible(this, show);
5539     }
5540   }
5541
5542   /**
5543    * Generate the reverse (optionally complemented) of the selected sequences,
5544    * and add them to the alignment
5545    */
5546   @Override
5547   protected void showReverse_actionPerformed(boolean complement)
5548   {
5549     AlignmentI al = null;
5550     try
5551     {
5552       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5553       al = dna.reverseCdna(complement);
5554       viewport.addAlignment(al, "");
5555       addHistoryItem(new EditCommand(
5556               MessageManager.getString("label.add_sequences"), Action.PASTE,
5557               al.getSequencesArray(), 0, al.getWidth(),
5558               viewport.getAlignment()));
5559     } catch (Exception ex)
5560     {
5561       System.err.println(ex.getMessage());
5562       return;
5563     }
5564   }
5565
5566   /**
5567    * Try to run a script in the Groovy console, having first ensured that this
5568    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5569    * be targeted at this alignment.
5570    */
5571   @Override
5572   protected void runGroovy_actionPerformed()
5573   {
5574     Jalview.setCurrentAlignFrame(this);
5575     groovy.ui.Console console = Desktop.getGroovyConsole();
5576     if (console != null)
5577     {
5578       try
5579       {
5580         console.runScript();
5581       } catch (Exception ex)
5582       {
5583         System.err.println((ex.toString()));
5584         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5585                 MessageManager.getString("label.couldnt_run_groovy_script"),
5586                 MessageManager.getString("label.groovy_support_failed"),
5587                 JvOptionPane.ERROR_MESSAGE);
5588       }
5589     }
5590     else
5591     {
5592       System.err.println("Can't run Groovy script as console not found");
5593     }
5594   }
5595
5596   /**
5597    * Hides columns containing (or not containing) a specified feature, provided
5598    * that would not leave all columns hidden
5599    *
5600    * @param featureType
5601    * @param columnsContaining
5602    * @return
5603    */
5604   public boolean hideFeatureColumns(String featureType,
5605           boolean columnsContaining)
5606   {
5607     boolean notForHiding = avc.markColumnsContainingFeatures(
5608             columnsContaining, false, false, featureType);
5609     if (notForHiding)
5610     {
5611       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5612               false, featureType))
5613       {
5614         getViewport().hideSelectedColumns();
5615         return true;
5616       }
5617     }
5618     return false;
5619   }
5620
5621   @Override
5622   protected void selectHighlightedColumns_actionPerformed(
5623           ActionEvent actionEvent)
5624   {
5625     // include key modifier check in case user selects from menu
5626     avc.markHighlightedColumns(
5627             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5628             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5629                     | ActionEvent.CTRL_MASK)) != 0);
5630   }
5631
5632   /**
5633    * Rebuilds the Colour menu, including any user-defined colours which have
5634    * been loaded either on startup or during the session
5635    */
5636   public void buildColourMenu()
5637   {
5638     colourMenu.removeAll();
5639
5640     colourMenu.add(applyToAllGroups);
5641     colourMenu.add(textColour);
5642     colourMenu.addSeparator();
5643
5644     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5645             false);
5646
5647     colourMenu.addSeparator();
5648     colourMenu.add(conservationMenuItem);
5649     colourMenu.add(modifyConservation);
5650     colourMenu.add(abovePIDThreshold);
5651     colourMenu.add(modifyPID);
5652     colourMenu.add(annotationColour);
5653
5654     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5655     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5656   }
5657
5658   /**
5659    * Open a dialog (if not already open) that allows the user to select and
5660    * calculate PCA or Tree analysis
5661    */
5662   protected void openTreePcaDialog()
5663   {
5664     if (alignPanel.getCalculationDialog() == null)
5665     {
5666       new CalculationChooser(AlignFrame.this);
5667     }
5668   }
5669
5670   @Override
5671   protected void loadVcf_actionPerformed()
5672   {
5673     JalviewFileChooser chooser = new JalviewFileChooser(
5674             Cache.getProperty("LAST_DIRECTORY"));
5675     chooser.setFileView(new JalviewFileView());
5676     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5677     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5678     final AlignFrame us = this;
5679     chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5680     {
5681       @Override
5682       public void run()
5683       {
5684
5685         {
5686           String choice = chooser.getSelectedFile().getPath();
5687           Cache.setProperty("LAST_DIRECTORY", choice);
5688           SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5689           new VCFLoader(choice).loadVCF(seqs, us);
5690         }
5691
5692       };
5693     }).openDialog(null);
5694
5695   }
5696
5697 }
5698
5699 class PrintThread extends Thread
5700 {
5701   AlignmentPanel ap;
5702
5703   public PrintThread(AlignmentPanel ap)
5704   {
5705     this.ap = ap;
5706   }
5707
5708   static PageFormat pf;
5709
5710   @Override
5711   public void run()
5712   {
5713     PrinterJob printJob = PrinterJob.getPrinterJob();
5714
5715     if (pf != null)
5716     {
5717       printJob.setPrintable(ap, pf);
5718     }
5719     else
5720     {
5721       printJob.setPrintable(ap);
5722     }
5723
5724     if (printJob.printDialog())
5725     {
5726       try
5727       {
5728         printJob.print();
5729       } catch (Exception PrintException)
5730       {
5731         PrintException.printStackTrace();
5732       }
5733     }
5734   }
5735 }