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