src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.GeneticCodeI;
  28 import jalview.analysis.ParseProperties;
  29 import jalview.analysis.SequenceIdMatcher;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.FeatureSettingsModelI;
  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
 150 /**
 151  * DOCUMENT ME!
 152  *
 153  * @author $author$
 154  * @version $Revision$
 155  */
 156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 157         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 158 {
 159
 160   public static final int DEFAULT_WIDTH = 700;
 161
 162   public static final int DEFAULT_HEIGHT = 500;
 163
 164   /*
 165    * The currently displayed panel (selected tabbed view if more than one)
 166    */
 167   public AlignmentPanel alignPanel;
 168
 169   AlignViewport viewport;
 170
 171   public AlignViewControllerI avc;
 172
 173   List<AlignmentPanel> alignPanels = new ArrayList<>();
 174
 175   /**
 176    * Last format used to load or save alignments in this window
 177    */
 178   FileFormatI currentFileFormat = null;
 179
 180   /**
 181    * Current filename for this alignment
 182    */
 183   String fileName = null;
 184
 185   /**
 186    * Creates a new AlignFrame object with specific width and height.
 187    *
 188    * @param al
 189    * @param width
 190    * @param height
 191    */
 192   public AlignFrame(AlignmentI al, int width, int height)
 193   {
 194     this(al, null, width, height);
 195   }
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width, height and
 199    * sequenceSetId
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    * @param sequenceSetId
 205    */
 206   public AlignFrame(AlignmentI al, int width, int height,
 207           String sequenceSetId)
 208   {
 209     this(al, null, width, height, sequenceSetId);
 210   }
 211
 212   /**
 213    * Creates a new AlignFrame object with specific width, height and
 214    * sequenceSetId
 215    *
 216    * @param al
 217    * @param width
 218    * @param height
 219    * @param sequenceSetId
 220    * @param viewId
 221    */
 222   public AlignFrame(AlignmentI al, int width, int height,
 223           String sequenceSetId, String viewId)
 224   {
 225     this(al, null, width, height, sequenceSetId, viewId);
 226   }
 227
 228   /**
 229    * new alignment window with hidden columns
 230    *
 231    * @param al
 232    *          AlignmentI
 233    * @param hiddenColumns
 234    *          ColumnSelection or null
 235    * @param width
 236    *          Width of alignment frame
 237    * @param height
 238    *          height of frame.
 239    */
 240   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 241           int height)
 242   {
 243     this(al, hiddenColumns, width, height, null);
 244   }
 245
 246   /**
 247    * Create alignment frame for al with hiddenColumns, a specific width and
 248    * height, and specific sequenceId
 249    *
 250    * @param al
 251    * @param hiddenColumns
 252    * @param width
 253    * @param height
 254    * @param sequenceSetId
 255    *          (may be null)
 256    */
 257   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 258           int height, String sequenceSetId)
 259   {
 260     this(al, hiddenColumns, width, height, sequenceSetId, null);
 261   }
 262
 263   /**
 264    * Create alignment frame for al with hiddenColumns, a specific width and
 265    * height, and specific sequenceId
 266    *
 267    * @param al
 268    * @param hiddenColumns
 269    * @param width
 270    * @param height
 271    * @param sequenceSetId
 272    *          (may be null)
 273    * @param viewId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 277           int height, String sequenceSetId, String viewId)
 278   {
 279     setSize(width, height);
 280
 281     if (al.getDataset() == null)
 282     {
 283       al.setDataset(null);
 284     }
 285
 286     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 287
 288     alignPanel = new AlignmentPanel(this, viewport);
 289
 290     addAlignmentPanel(alignPanel, true);
 291     init();
 292   }
 293
 294   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 295           HiddenColumns hiddenColumns, int width, int height)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns);
 305
 306     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 307     {
 308       viewport.hideSequence(hiddenSeqs);
 309     }
 310     alignPanel = new AlignmentPanel(this, viewport);
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   /**
 316    * Make a new AlignFrame from existing alignmentPanels
 317    *
 318    * @param ap
 319    *          AlignmentPanel
 320    * @param av
 321    *          AlignViewport
 322    */
 323   public AlignFrame(AlignmentPanel ap)
 324   {
 325     viewport = ap.av;
 326     alignPanel = ap;
 327     addAlignmentPanel(ap, false);
 328     init();
 329   }
 330
 331   /**
 332    * initalise the alignframe from the underlying viewport data and the
 333    * configurations
 334    */
 335   void init()
 336   {
 337     if (!Jalview.isHeadlessMode())
 338     {
 339       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 340     }
 341
 342     avc = new jalview.controller.AlignViewController(this, viewport,
 343             alignPanel);
 344     if (viewport.getAlignmentConservationAnnotation() == null)
 345     {
 346       // BLOSUM62Colour.setEnabled(false);
 347       conservationMenuItem.setEnabled(false);
 348       modifyConservation.setEnabled(false);
 349       // PIDColour.setEnabled(false);
 350       // abovePIDThreshold.setEnabled(false);
 351       // modifyPID.setEnabled(false);
 352     }
 353
 354     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 355             "No sort");
 356
 357     if (sortby.equals("Id"))
 358     {
 359       sortIDMenuItem_actionPerformed(null);
 360     }
 361     else if (sortby.equals("Pairwise Identity"))
 362     {
 363       sortPairwiseMenuItem_actionPerformed(null);
 364     }
 365
 366     this.alignPanel.av
 367             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 368
 369     setMenusFromViewport(viewport);
 370     buildSortByAnnotationScoresMenu();
 371     calculateTree.addActionListener(new ActionListener()
 372     {
 373
 374       @Override
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         openTreePcaDialog();
 378       }
 379     });
 380     buildColourMenu();
 381
 382     if (Desktop.desktop != null)
 383     {
 384       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 385       addServiceListeners();
 386       setGUINucleotide();
 387     }
 388
 389     if (viewport.getWrapAlignment())
 390     {
 391       wrapMenuItem_actionPerformed(null);
 392     }
 393
 394     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 395     {
 396       this.overviewMenuItem_actionPerformed(null);
 397     }
 398
 399     addKeyListener();
 400
 401     final List<AlignmentPanel> selviews = new ArrayList<>();
 402     final List<AlignmentPanel> origview = new ArrayList<>();
 403     final String menuLabel = MessageManager
 404             .getString("label.copy_format_from");
 405     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 406             new ViewSetProvider()
 407             {
 408
 409               @Override
 410               public AlignmentPanel[] getAllAlignmentPanels()
 411               {
 412                 origview.clear();
 413                 origview.add(alignPanel);
 414                 // make an array of all alignment panels except for this one
 415                 List<AlignmentPanel> aps = new ArrayList<>(
 416                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 417                 aps.remove(AlignFrame.this.alignPanel);
 418                 return aps.toArray(new AlignmentPanel[aps.size()]);
 419               }
 420             }, selviews, new ItemListener()
 421             {
 422
 423               @Override
 424               public void itemStateChanged(ItemEvent e)
 425               {
 426                 if (origview.size() > 0)
 427                 {
 428                   final AlignmentPanel ap = origview.get(0);
 429
 430                   /*
 431                    * Copy the ViewStyle of the selected panel to 'this one'.
 432                    * Don't change value of 'scaleProteinAsCdna' unless copying
 433                    * from a SplitFrame.
 434                    */
 435                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 436                           .getViewStyle();
 437                   boolean fromSplitFrame = selviews.get(0)
 438                           .getAlignViewport().getCodingComplement() != null;
 439                   if (!fromSplitFrame)
 440                   {
 441                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 442                             .getViewStyle().isScaleProteinAsCdna());
 443                   }
 444                   ap.getAlignViewport().setViewStyle(vs);
 445
 446                   /*
 447                    * Also rescale ViewStyle of SplitFrame complement if there is
 448                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 449                    * the whole ViewStyle (allow cDNA protein to have different
 450                    * fonts)
 451                    */
 452                   AlignViewportI complement = ap.getAlignViewport()
 453                           .getCodingComplement();
 454                   if (complement != null && vs.isScaleProteinAsCdna())
 455                   {
 456                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 457                     ((SplitFrame) af.getSplitViewContainer())
 458                             .adjustLayout();
 459                     af.setMenusForViewport();
 460                   }
 461
 462                   ap.updateLayout();
 463                   ap.setSelected(true);
 464                   ap.alignFrame.setMenusForViewport();
 465
 466                 }
 467               }
 468             });
 469     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 470             .indexOf("devel") > -1
 471             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 472                     .indexOf("test") > -1)
 473     {
 474       formatMenu.add(vsel);
 475     }
 476     addFocusListener(new FocusAdapter()
 477     {
 478       @Override
 479       public void focusGained(FocusEvent e)
 480       {
 481         Jalview.setCurrentAlignFrame(AlignFrame.this);
 482       }
 483     });
 484
 485   }
 486
 487   /**
 488    * Change the filename and format for the alignment, and enable the 'reload'
 489    * button functionality.
 490    *
 491    * @param file
 492    *          valid filename
 493    * @param format
 494    *          format of file
 495    */
 496   public void setFileName(String file, FileFormatI format)
 497   {
 498     fileName = file;
 499     setFileFormat(format);
 500     reload.setEnabled(true);
 501   }
 502
 503   /**
 504    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 505    * events
 506    */
 507   void addKeyListener()
 508   {
 509     addKeyListener(new KeyAdapter()
 510     {
 511       @Override
 512       public void keyPressed(KeyEvent evt)
 513       {
 514         if (viewport.cursorMode
 515                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 516                         && evt.getKeyCode() <= KeyEvent.VK_9)
 517                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 518                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 519                 && Character.isDigit(evt.getKeyChar()))
 520         {
 521           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 522         }
 523
 524         switch (evt.getKeyCode())
 525         {
 526
 527         case 27: // escape key
 528           deselectAllSequenceMenuItem_actionPerformed(null);
 529
 530           break;
 531
 532         case KeyEvent.VK_DOWN:
 533           if (evt.isAltDown() || !viewport.cursorMode)
 534           {
 535             moveSelectedSequences(false);
 536           }
 537           if (viewport.cursorMode)
 538           {
 539             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 540           }
 541           break;
 542
 543         case KeyEvent.VK_UP:
 544           if (evt.isAltDown() || !viewport.cursorMode)
 545           {
 546             moveSelectedSequences(true);
 547           }
 548           if (viewport.cursorMode)
 549           {
 550             alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
 551           }
 552
 553           break;
 554
 555         case KeyEvent.VK_LEFT:
 556           if (evt.isAltDown() || !viewport.cursorMode)
 557           {
 558             slideSequences(false,
 559                     alignPanel.getSeqPanel().getKeyboardNo1());
 560           }
 561           else
 562           {
 563             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 564           }
 565
 566           break;
 567
 568         case KeyEvent.VK_RIGHT:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 572           }
 573           else
 574           {
 575             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 576           }
 577           break;
 578
 579         case KeyEvent.VK_SPACE:
 580           if (viewport.cursorMode)
 581           {
 582             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 583                     || evt.isShiftDown() || evt.isAltDown());
 584           }
 585           break;
 586
 587         // case KeyEvent.VK_A:
 588         // if (viewport.cursorMode)
 589         // {
 590         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 591         // //System.out.println("A");
 592         // }
 593         // break;
 594         /*
 595          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 596          * System.out.println("closing bracket"); } break;
 597          */
 598         case KeyEvent.VK_DELETE:
 599         case KeyEvent.VK_BACK_SPACE:
 600           if (!viewport.cursorMode)
 601           {
 602             cut_actionPerformed(null);
 603           }
 604           else
 605           {
 606             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 607                     || evt.isShiftDown() || evt.isAltDown());
 608           }
 609
 610           break;
 611
 612         case KeyEvent.VK_S:
 613           if (viewport.cursorMode)
 614           {
 615             alignPanel.getSeqPanel().setCursorRow();
 616           }
 617           break;
 618         case KeyEvent.VK_C:
 619           if (viewport.cursorMode && !evt.isControlDown())
 620           {
 621             alignPanel.getSeqPanel().setCursorColumn();
 622           }
 623           break;
 624         case KeyEvent.VK_P:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setCursorPosition();
 628           }
 629           break;
 630
 631         case KeyEvent.VK_ENTER:
 632         case KeyEvent.VK_COMMA:
 633           if (viewport.cursorMode)
 634           {
 635             alignPanel.getSeqPanel().setCursorRowAndColumn();
 636           }
 637           break;
 638
 639         case KeyEvent.VK_Q:
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 643           }
 644           break;
 645         case KeyEvent.VK_M:
 646           if (viewport.cursorMode)
 647           {
 648             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 649           }
 650           break;
 651
 652         case KeyEvent.VK_F2:
 653           viewport.cursorMode = !viewport.cursorMode;
 654           statusBar.setText(MessageManager
 655                   .formatMessage("label.keyboard_editing_mode", new String[]
 656                   { (viewport.cursorMode ? "on" : "off") }));
 657           if (viewport.cursorMode)
 658           {
 659             ViewportRanges ranges = viewport.getRanges();
 660             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 661                     .getStartRes();
 662             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 663                     .getStartSeq();
 664           }
 665           alignPanel.getSeqPanel().seqCanvas.repaint();
 666           break;
 667
 668         case KeyEvent.VK_F1:
 669           try
 670           {
 671             Help.showHelpWindow();
 672           } catch (Exception ex)
 673           {
 674             ex.printStackTrace();
 675           }
 676           break;
 677         case KeyEvent.VK_H:
 678         {
 679           boolean toggleSeqs = !evt.isControlDown();
 680           boolean toggleCols = !evt.isShiftDown();
 681           toggleHiddenRegions(toggleSeqs, toggleCols);
 682           break;
 683         }
 684         case KeyEvent.VK_B:
 685         {
 686           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 687           boolean modifyExisting = true; // always modify, don't clear
 688                                          // evt.isShiftDown();
 689           boolean invertHighlighted = evt.isAltDown();
 690           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 691                   toggleSel);
 692           break;
 693         }
 694         case KeyEvent.VK_PAGE_UP:
 695           viewport.getRanges().pageUp();
 696           break;
 697         case KeyEvent.VK_PAGE_DOWN:
 698           viewport.getRanges().pageDown();
 699           break;
 700         }
 701       }
 702
 703       @Override
 704       public void keyReleased(KeyEvent evt)
 705       {
 706         switch (evt.getKeyCode())
 707         {
 708         case KeyEvent.VK_LEFT:
 709           if (evt.isAltDown() || !viewport.cursorMode)
 710           {
 711             viewport.firePropertyChange("alignment", null,
 712                     viewport.getAlignment().getSequences());
 713           }
 714           break;
 715
 716         case KeyEvent.VK_RIGHT:
 717           if (evt.isAltDown() || !viewport.cursorMode)
 718           {
 719             viewport.firePropertyChange("alignment", null,
 720                     viewport.getAlignment().getSequences());
 721           }
 722           break;
 723         }
 724       }
 725     });
 726   }
 727
 728   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 729   {
 730     ap.alignFrame = this;
 731     avc = new jalview.controller.AlignViewController(this, viewport,
 732             alignPanel);
 733
 734     alignPanels.add(ap);
 735
 736     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 737
 738     int aSize = alignPanels.size();
 739
 740     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 741
 742     if (aSize == 1 && ap.av.getViewName() == null)
 743     {
 744       this.getContentPane().add(ap, BorderLayout.CENTER);
 745     }
 746     else
 747     {
 748       if (aSize == 2)
 749       {
 750         setInitialTabVisible();
 751       }
 752
 753       expandViews.setEnabled(true);
 754       gatherViews.setEnabled(true);
 755       tabbedPane.addTab(ap.av.getViewName(), ap);
 756
 757       ap.setVisible(false);
 758     }
 759
 760     if (newPanel)
 761     {
 762       if (ap.av.isPadGaps())
 763       {
 764         ap.av.getAlignment().padGaps();
 765       }
 766       ap.av.updateConservation(ap);
 767       ap.av.updateConsensus(ap);
 768       ap.av.updateStrucConsensus(ap);
 769     }
 770   }
 771
 772   public void setInitialTabVisible()
 773   {
 774     expandViews.setEnabled(true);
 775     gatherViews.setEnabled(true);
 776     tabbedPane.setVisible(true);
 777     AlignmentPanel first = alignPanels.get(0);
 778     tabbedPane.addTab(first.av.getViewName(), first);
 779     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 780   }
 781
 782   public AlignViewport getViewport()
 783   {
 784     return viewport;
 785   }
 786
 787   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 788   private void addServiceListeners()
 789   {
 790     final java.beans.PropertyChangeListener thisListener;
 791     Desktop.instance.addJalviewPropertyChangeListener("services",
 792             thisListener = new java.beans.PropertyChangeListener()
 793             {
 794               @Override
 795               public void propertyChange(PropertyChangeEvent evt)
 796               {
 797                 // // System.out.println("Discoverer property change.");
 798                 // if (evt.getPropertyName().equals("services"))
 799                 {
 800                   SwingUtilities.invokeLater(new Runnable()
 801                   {
 802
 803                     @Override
 804                     public void run()
 805                     {
 806                       System.err.println(
 807                               "Rebuild WS Menu for service change");
 808                       BuildWebServiceMenu();
 809                     }
 810
 811                   });
 812                 }
 813               }
 814             });
 815     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 816     {
 817       @Override
 818       public void internalFrameClosed(
 819               javax.swing.event.InternalFrameEvent evt)
 820       {
 821         // System.out.println("deregistering discoverer listener");
 822         Desktop.instance.removeJalviewPropertyChangeListener("services",
 823                 thisListener);
 824         closeMenuItem_actionPerformed(true);
 825       };
 826     });
 827     // Finally, build the menu once to get current service state
 828     new Thread(new Runnable()
 829     {
 830       @Override
 831       public void run()
 832       {
 833         BuildWebServiceMenu();
 834       }
 835     }).start();
 836   }
 837
 838   /**
 839    * Configure menu items that vary according to whether the alignment is
 840    * nucleotide or protein
 841    */
 842   public void setGUINucleotide()
 843   {
 844     AlignmentI al = getViewport().getAlignment();
 845     boolean nucleotide = al.isNucleotide();
 846
 847     loadVcf.setVisible(nucleotide);
 848     showTranslation.setVisible(nucleotide);
 849     showReverse.setVisible(nucleotide);
 850     showReverseComplement.setVisible(nucleotide);
 851     conservationMenuItem.setEnabled(!nucleotide);
 852     modifyConservation
 853             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 854     showGroupConservation.setEnabled(!nucleotide);
 855
 856     showComplementMenuItem
 857             .setText(nucleotide ? MessageManager.getString("label.protein")
 858                     : MessageManager.getString("label.nucleotide"));
 859   }
 860
 861   /**
 862    * set up menus for the current viewport. This may be called after any
 863    * operation that affects the data in the current view (selection changed,
 864    * etc) to update the menus to reflect the new state.
 865    */
 866   @Override
 867   public void setMenusForViewport()
 868   {
 869     setMenusFromViewport(viewport);
 870   }
 871
 872   /**
 873    * Need to call this method when tabs are selected for multiple views, or when
 874    * loading from Jalview2XML.java
 875    *
 876    * @param av
 877    *          AlignViewport
 878    */
 879   public void setMenusFromViewport(AlignViewport av)
 880   {
 881     padGapsMenuitem.setSelected(av.isPadGaps());
 882     colourTextMenuItem.setSelected(av.isShowColourText());
 883     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 884     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 885     conservationMenuItem.setSelected(av.getConservationSelected());
 886     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 887     seqLimits.setSelected(av.getShowJVSuffix());
 888     idRightAlign.setSelected(av.isRightAlignIds());
 889     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 890     renderGapsMenuItem.setSelected(av.isRenderGaps());
 891     wrapMenuItem.setSelected(av.getWrapAlignment());
 892     scaleAbove.setVisible(av.getWrapAlignment());
 893     scaleLeft.setVisible(av.getWrapAlignment());
 894     scaleRight.setVisible(av.getWrapAlignment());
 895     annotationPanelMenuItem.setState(av.isShowAnnotation());
 896     /*
 897      * Show/hide annotations only enabled if annotation panel is shown
 898      */
 899     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 902     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 904     viewTextMenuItem.setSelected(av.getShowText());
 905     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 906     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 907     showGroupConservation.setSelected(av.isShowGroupConservation());
 908     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 909     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 910     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 911
 912     ColourMenuHelper.setColourSelected(colourMenu,
 913             av.getGlobalColourScheme());
 914
 915     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 916     hiddenMarkers.setState(av.getShowHiddenMarkers());
 917     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 918     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 919     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 920     autoCalculate.setSelected(av.autoCalculateConsensus);
 921     sortByTree.setSelected(av.sortByTree);
 922     listenToViewSelections.setSelected(av.followSelection);
 923
 924     showProducts.setEnabled(canShowProducts());
 925     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 926
 927     updateEditMenuBar();
 928   }
 929
 930   /**
 931    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 932    *
 933    * @param b
 934    */
 935   public void setGroovyEnabled(boolean b)
 936   {
 937     runGroovy.setEnabled(b);
 938   }
 939
 940   private IProgressIndicator progressBar;
 941
 942   /*
 943    * (non-Javadoc)
 944    *
 945    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 946    */
 947   @Override
 948   public void setProgressBar(String message, long id)
 949   {
 950     progressBar.setProgressBar(message, id);
 951   }
 952
 953   @Override
 954   public void registerHandler(final long id,
 955           final IProgressIndicatorHandler handler)
 956   {
 957     progressBar.registerHandler(id, handler);
 958   }
 959
 960   /**
 961    *
 962    * @return true if any progress bars are still active
 963    */
 964   @Override
 965   public boolean operationInProgress()
 966   {
 967     return progressBar.operationInProgress();
 968   }
 969
 970   /**
 971    * Sets the text of the status bar. Note that setting a null or empty value
 972    * will cause the status bar to be hidden, with possibly undesirable flicker
 973    * of the screen layout.
 974    */
 975   @Override
 976   public void setStatus(String text)
 977   {
 978     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 979   }
 980
 981   /*
 982    * Added so Castor Mapping file can obtain Jalview Version
 983    */
 984   public String getVersion()
 985   {
 986     return jalview.bin.Cache.getProperty("VERSION");
 987   }
 988
 989   public FeatureRenderer getFeatureRenderer()
 990   {
 991     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 992   }
 993
 994   @Override
 995   public void fetchSequence_actionPerformed(ActionEvent e)
 996   {
 997     new jalview.gui.SequenceFetcher(this);
 998   }
 999
1000   @Override
1001   public void addFromFile_actionPerformed(ActionEvent e)
1002   {
1003     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1004   }
1005
1006   @Override
1007   public void reload_actionPerformed(ActionEvent e)
1008   {
1009     if (fileName != null)
1010     {
1011       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1012       // originating file's format
1013       // TODO: work out how to recover feature settings for correct view(s) when
1014       // file is reloaded.
1015       if (FileFormat.Jalview.equals(currentFileFormat))
1016       {
1017         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1018         for (int i = 0; i < frames.length; i++)
1019         {
1020           if (frames[i] instanceof AlignFrame && frames[i] != this
1021                   && ((AlignFrame) frames[i]).fileName != null
1022                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1023           {
1024             try
1025             {
1026               frames[i].setSelected(true);
1027               Desktop.instance.closeAssociatedWindows();
1028             } catch (java.beans.PropertyVetoException ex)
1029             {
1030             }
1031           }
1032
1033         }
1034         Desktop.instance.closeAssociatedWindows();
1035
1036         FileLoader loader = new FileLoader();
1037         DataSourceType protocol = fileName.startsWith("http:")
1038                 ? DataSourceType.URL
1039                 : DataSourceType.FILE;
1040         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1041       }
1042       else
1043       {
1044         Rectangle bounds = this.getBounds();
1045
1046         FileLoader loader = new FileLoader();
1047         DataSourceType protocol = fileName.startsWith("http:")
1048                 ? DataSourceType.URL
1049                 : DataSourceType.FILE;
1050         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1051                 protocol, currentFileFormat);
1052
1053         newframe.setBounds(bounds);
1054         if (featureSettings != null && featureSettings.isShowing())
1055         {
1056           final Rectangle fspos = featureSettings.frame.getBounds();
1057           // TODO: need a 'show feature settings' function that takes bounds -
1058           // need to refactor Desktop.addFrame
1059           newframe.featureSettings_actionPerformed(null);
1060           final FeatureSettings nfs = newframe.featureSettings;
1061           SwingUtilities.invokeLater(new Runnable()
1062           {
1063             @Override
1064             public void run()
1065             {
1066               nfs.frame.setBounds(fspos);
1067             }
1068           });
1069           this.featureSettings.close();
1070           this.featureSettings = null;
1071         }
1072         this.closeMenuItem_actionPerformed(true);
1073       }
1074     }
1075   }
1076
1077   @Override
1078   public void addFromText_actionPerformed(ActionEvent e)
1079   {
1080     Desktop.instance
1081             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1082   }
1083
1084   @Override
1085   public void addFromURL_actionPerformed(ActionEvent e)
1086   {
1087     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1088   }
1089
1090   @Override
1091   public void save_actionPerformed(ActionEvent e)
1092   {
1093     if (fileName == null || (currentFileFormat == null)
1094             || fileName.startsWith("http"))
1095     {
1096       saveAs_actionPerformed(null);
1097     }
1098     else
1099     {
1100       saveAlignment(fileName, currentFileFormat);
1101     }
1102   }
1103
1104   /**
1105    * DOCUMENT ME!
1106    *
1107    * @param e
1108    *          DOCUMENT ME!
1109    */
1110   @Override
1111   public void saveAs_actionPerformed(ActionEvent e)
1112   {
1113     String format = currentFileFormat == null ? null
1114             : currentFileFormat.getName();
1115     JalviewFileChooser chooser = JalviewFileChooser
1116             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1117
1118     chooser.setFileView(new JalviewFileView());
1119     chooser.setDialogTitle(
1120             MessageManager.getString("label.save_alignment_to_file"));
1121     chooser.setToolTipText(MessageManager.getString("action.save"));
1122
1123     int value = chooser.showSaveDialog(this);
1124
1125     if (value == JalviewFileChooser.APPROVE_OPTION)
1126     {
1127       currentFileFormat = chooser.getSelectedFormat();
1128       while (currentFileFormat == null)
1129       {
1130         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1131                 MessageManager.getString(
1132                         "label.select_file_format_before_saving"),
1133                 MessageManager.getString("label.file_format_not_specified"),
1134                 JvOptionPane.WARNING_MESSAGE);
1135         currentFileFormat = chooser.getSelectedFormat();
1136         value = chooser.showSaveDialog(this);
1137         if (value != JalviewFileChooser.APPROVE_OPTION)
1138         {
1139           return;
1140         }
1141       }
1142
1143       fileName = chooser.getSelectedFile().getPath();
1144
1145       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1146
1147       Cache.setProperty("LAST_DIRECTORY", fileName);
1148       saveAlignment(fileName, currentFileFormat);
1149     }
1150   }
1151
1152   public boolean saveAlignment(String file, FileFormatI format)
1153   {
1154     boolean success = true;
1155
1156     if (FileFormat.Jalview.equals(format))
1157     {
1158       String shortName = title;
1159
1160       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161       {
1162         shortName = shortName.substring(
1163                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1164       }
1165
1166       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1167               shortName);
1168
1169       statusBar.setText(MessageManager.formatMessage(
1170               "label.successfully_saved_to_file_in_format", new Object[]
1171               { fileName, format }));
1172
1173     }
1174     else
1175     {
1176       AlignmentExportData exportData = getAlignmentForExport(format,
1177               viewport, null);
1178       if (exportData.getSettings().isCancelled())
1179       {
1180         return false;
1181       }
1182       FormatAdapter f = new FormatAdapter(alignPanel,
1183               exportData.getSettings());
1184       String output = f.formatSequences(format, exportData.getAlignment(), // class
1185                                                                            // cast
1186                                                                            // exceptions
1187                                                                            // will
1188               // occur in the distant future
1189               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1190               f.getCacheSuffixDefault(format),
1191               viewport.getAlignment().getHiddenColumns());
1192
1193       if (output == null)
1194       {
1195         success = false;
1196       }
1197       else
1198       {
1199         // create backupfiles object and get new temp filename destination
1200         BackupFiles backupfiles = new BackupFiles(file);
1201
1202         try
1203         {
1204           PrintWriter out = new PrintWriter(
1205                   new FileWriter(backupfiles.getTempFilePath()));
1206
1207           out.print(output);
1208           out.close();
1209           this.setTitle(file);
1210           statusBar.setText(MessageManager.formatMessage(
1211                   "label.successfully_saved_to_file_in_format", new Object[]
1212                   { fileName, format.getName() }));
1213         } catch (Exception ex)
1214         {
1215           success = false;
1216           ex.printStackTrace();
1217         }
1218
1219         backupfiles.setWriteSuccess(success);
1220         // do the backup file roll and rename the temp file to actual file
1221         success = backupfiles.rollBackupsAndRenameTempFile();
1222
1223       }
1224     }
1225
1226     if (!success)
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, MessageManager
1229               .formatMessage("label.couldnt_save_file", new Object[]
1230               { fileName }),
1231               MessageManager.getString("label.error_saving_file"),
1232               JvOptionPane.WARNING_MESSAGE);
1233     }
1234
1235     return success;
1236   }
1237
1238   private void warningMessage(String warning, String title)
1239   {
1240     if (new jalview.util.Platform().isHeadless())
1241     {
1242       System.err.println("Warning: " + title + "\nWarning: " + warning);
1243
1244     }
1245     else
1246     {
1247       JvOptionPane.showInternalMessageDialog(this, warning, title,
1248               JvOptionPane.WARNING_MESSAGE);
1249     }
1250     return;
1251   }
1252
1253   /**
1254    * DOCUMENT ME!
1255    *
1256    * @param e
1257    *          DOCUMENT ME!
1258    */
1259   @Override
1260   protected void outputText_actionPerformed(ActionEvent e)
1261   {
1262     FileFormatI fileFormat = FileFormats.getInstance()
1263             .forName(e.getActionCommand());
1264     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1265             viewport, null);
1266     if (exportData.getSettings().isCancelled())
1267     {
1268       return;
1269     }
1270     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1271     cap.setForInput(null);
1272     try
1273     {
1274       FileFormatI format = fileFormat;
1275       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1276               .formatSequences(format, exportData.getAlignment(),
1277                       exportData.getOmitHidden(),
1278                       exportData.getStartEndPostions(),
1279                       viewport.getAlignment().getHiddenColumns()));
1280       Desktop.addInternalFrame(cap, MessageManager
1281               .formatMessage("label.alignment_output_command", new Object[]
1282               { e.getActionCommand() }), 600, 500);
1283     } catch (OutOfMemoryError oom)
1284     {
1285       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1286               oom);
1287       cap.dispose();
1288     }
1289
1290   }
1291
1292   public static AlignmentExportData getAlignmentForExport(
1293           FileFormatI format, AlignViewportI viewport,
1294           AlignExportSettingI exportSettings)
1295   {
1296     AlignmentI alignmentToExport = null;
1297     AlignExportSettingI settings = exportSettings;
1298     String[] omitHidden = null;
1299
1300     HiddenSequences hiddenSeqs = viewport.getAlignment()
1301             .getHiddenSequences();
1302
1303     alignmentToExport = viewport.getAlignment();
1304
1305     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1306     if (settings == null)
1307     {
1308       settings = new AlignExportSettings(hasHiddenSeqs,
1309               viewport.hasHiddenColumns(), format);
1310     }
1311     // settings.isExportAnnotations();
1312
1313     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1314     {
1315       omitHidden = viewport.getViewAsString(false,
1316               settings.isExportHiddenSequences());
1317     }
1318
1319     int[] alignmentStartEnd = new int[2];
1320     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1321     {
1322       alignmentToExport = hiddenSeqs.getFullAlignment();
1323     }
1324     else
1325     {
1326       alignmentToExport = viewport.getAlignment();
1327     }
1328     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1329             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1330     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1331             omitHidden, alignmentStartEnd, settings);
1332     return ed;
1333   }
1334
1335   /**
1336    * DOCUMENT ME!
1337    *
1338    * @param e
1339    *          DOCUMENT ME!
1340    */
1341   @Override
1342   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343   {
1344     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1345     htmlSVG.exportHTML(null);
1346   }
1347
1348   @Override
1349   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350   {
1351     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1352     bjs.exportHTML(null);
1353   }
1354
1355   public void createImageMap(File file, String image)
1356   {
1357     alignPanel.makePNGImageMap(file, image);
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   @Override
1367   public void createPNG(File f)
1368   {
1369     alignPanel.makePNG(f);
1370   }
1371
1372   /**
1373    * DOCUMENT ME!
1374    *
1375    * @param e
1376    *          DOCUMENT ME!
1377    */
1378   @Override
1379   public void createEPS(File f)
1380   {
1381     alignPanel.makeEPS(f);
1382   }
1383
1384   @Override
1385   public void createSVG(File f)
1386   {
1387     alignPanel.makeSVG(f);
1388   }
1389
1390   @Override
1391   public void pageSetup_actionPerformed(ActionEvent e)
1392   {
1393     PrinterJob printJob = PrinterJob.getPrinterJob();
1394     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1395   }
1396
1397   /**
1398    * DOCUMENT ME!
1399    *
1400    * @param e
1401    *          DOCUMENT ME!
1402    */
1403   @Override
1404   public void printMenuItem_actionPerformed(ActionEvent e)
1405   {
1406     // Putting in a thread avoids Swing painting problems
1407     PrintThread thread = new PrintThread(alignPanel);
1408     thread.start();
1409   }
1410
1411   @Override
1412   public void exportFeatures_actionPerformed(ActionEvent e)
1413   {
1414     new AnnotationExporter(alignPanel).exportFeatures();
1415   }
1416
1417   @Override
1418   public void exportAnnotations_actionPerformed(ActionEvent e)
1419   {
1420     new AnnotationExporter(alignPanel).exportAnnotations();
1421   }
1422
1423   @Override
1424   public void associatedData_actionPerformed(ActionEvent e)
1425   {
1426     // Pick the tree file
1427     JalviewFileChooser chooser = new JalviewFileChooser(
1428             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429     chooser.setFileView(new JalviewFileView());
1430     chooser.setDialogTitle(
1431             MessageManager.getString("label.load_jalview_annotations"));
1432     chooser.setToolTipText(
1433             MessageManager.getString("label.load_jalview_annotations"));
1434
1435     int value = chooser.showOpenDialog(null);
1436
1437     if (value == JalviewFileChooser.APPROVE_OPTION)
1438     {
1439       String choice = chooser.getSelectedFile().getPath();
1440       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441       loadJalviewDataFile(choice, null, null, null);
1442     }
1443
1444   }
1445
1446   /**
1447    * Close the current view or all views in the alignment frame. If the frame
1448    * only contains one view then the alignment will be removed from memory.
1449    *
1450    * @param closeAllTabs
1451    */
1452   @Override
1453   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454   {
1455     if (alignPanels != null && alignPanels.size() < 2)
1456     {
1457       closeAllTabs = true;
1458     }
1459
1460     try
1461     {
1462       if (alignPanels != null)
1463       {
1464         if (closeAllTabs)
1465         {
1466           if (this.isClosed())
1467           {
1468             // really close all the windows - otherwise wait till
1469             // setClosed(true) is called
1470             for (int i = 0; i < alignPanels.size(); i++)
1471             {
1472               AlignmentPanel ap = alignPanels.get(i);
1473               ap.closePanel();
1474             }
1475           }
1476         }
1477         else
1478         {
1479           closeView(alignPanel);
1480         }
1481       }
1482       if (closeAllTabs)
1483       {
1484         if (featureSettings != null && featureSettings.isOpen())
1485         {
1486           featureSettings.close();
1487           featureSettings = null;
1488         }
1489         /*
1490          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1491          * be called recursively, with the frame now in 'closed' state
1492          */
1493         this.setClosed(true);
1494       }
1495     } catch (Exception ex)
1496     {
1497       ex.printStackTrace();
1498     }
1499   }
1500
1501   /**
1502    * Close the specified panel and close up tabs appropriately.
1503    *
1504    * @param panelToClose
1505    */
1506   public void closeView(AlignmentPanel panelToClose)
1507   {
1508     int index = tabbedPane.getSelectedIndex();
1509     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1510     alignPanels.remove(panelToClose);
1511     panelToClose.closePanel();
1512     panelToClose = null;
1513
1514     tabbedPane.removeTabAt(closedindex);
1515     tabbedPane.validate();
1516
1517     if (index > closedindex || index == tabbedPane.getTabCount())
1518     {
1519       // modify currently selected tab index if necessary.
1520       index--;
1521     }
1522
1523     this.tabSelectionChanged(index);
1524   }
1525
1526   /**
1527    * DOCUMENT ME!
1528    */
1529   void updateEditMenuBar()
1530   {
1531
1532     if (viewport.getHistoryList().size() > 0)
1533     {
1534       undoMenuItem.setEnabled(true);
1535       CommandI command = viewport.getHistoryList().peek();
1536       undoMenuItem.setText(MessageManager
1537               .formatMessage("label.undo_command", new Object[]
1538               { command.getDescription() }));
1539     }
1540     else
1541     {
1542       undoMenuItem.setEnabled(false);
1543       undoMenuItem.setText(MessageManager.getString("action.undo"));
1544     }
1545
1546     if (viewport.getRedoList().size() > 0)
1547     {
1548       redoMenuItem.setEnabled(true);
1549
1550       CommandI command = viewport.getRedoList().peek();
1551       redoMenuItem.setText(MessageManager
1552               .formatMessage("label.redo_command", new Object[]
1553               { command.getDescription() }));
1554     }
1555     else
1556     {
1557       redoMenuItem.setEnabled(false);
1558       redoMenuItem.setText(MessageManager.getString("action.redo"));
1559     }
1560   }
1561
1562   @Override
1563   public void addHistoryItem(CommandI command)
1564   {
1565     if (command.getSize() > 0)
1566     {
1567       viewport.addToHistoryList(command);
1568       viewport.clearRedoList();
1569       updateEditMenuBar();
1570       viewport.updateHiddenColumns();
1571       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1572       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1573       // viewport.getColumnSelection()
1574       // .getHiddenColumns().size() > 0);
1575     }
1576   }
1577
1578   /**
1579    *
1580    * @return alignment objects for all views
1581    */
1582   AlignmentI[] getViewAlignments()
1583   {
1584     if (alignPanels != null)
1585     {
1586       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1587       int i = 0;
1588       for (AlignmentPanel ap : alignPanels)
1589       {
1590         als[i++] = ap.av.getAlignment();
1591       }
1592       return als;
1593     }
1594     if (viewport != null)
1595     {
1596       return new AlignmentI[] { viewport.getAlignment() };
1597     }
1598     return null;
1599   }
1600
1601   /**
1602    * DOCUMENT ME!
1603    *
1604    * @param e
1605    *          DOCUMENT ME!
1606    */
1607   @Override
1608   protected void undoMenuItem_actionPerformed(ActionEvent e)
1609   {
1610     if (viewport.getHistoryList().isEmpty())
1611     {
1612       return;
1613     }
1614     CommandI command = viewport.getHistoryList().pop();
1615     viewport.addToRedoList(command);
1616     command.undoCommand(getViewAlignments());
1617
1618     AlignmentViewport originalSource = getOriginatingSource(command);
1619     updateEditMenuBar();
1620
1621     if (originalSource != null)
1622     {
1623       if (originalSource != viewport)
1624       {
1625         Cache.log.warn(
1626                 "Implementation worry: mismatch of viewport origin for undo");
1627       }
1628       originalSource.updateHiddenColumns();
1629       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1630       // null
1631       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1632       // viewport.getColumnSelection()
1633       // .getHiddenColumns().size() > 0);
1634       originalSource.firePropertyChange("alignment", null,
1635               originalSource.getAlignment().getSequences());
1636     }
1637   }
1638
1639   /**
1640    * DOCUMENT ME!
1641    *
1642    * @param e
1643    *          DOCUMENT ME!
1644    */
1645   @Override
1646   protected void redoMenuItem_actionPerformed(ActionEvent e)
1647   {
1648     if (viewport.getRedoList().size() < 1)
1649     {
1650       return;
1651     }
1652
1653     CommandI command = viewport.getRedoList().pop();
1654     viewport.addToHistoryList(command);
1655     command.doCommand(getViewAlignments());
1656
1657     AlignmentViewport originalSource = getOriginatingSource(command);
1658     updateEditMenuBar();
1659
1660     if (originalSource != null)
1661     {
1662
1663       if (originalSource != viewport)
1664       {
1665         Cache.log.warn(
1666                 "Implementation worry: mismatch of viewport origin for redo");
1667       }
1668       originalSource.updateHiddenColumns();
1669       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1670       // null
1671       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1672       // viewport.getColumnSelection()
1673       // .getHiddenColumns().size() > 0);
1674       originalSource.firePropertyChange("alignment", null,
1675               originalSource.getAlignment().getSequences());
1676     }
1677   }
1678
1679   AlignmentViewport getOriginatingSource(CommandI command)
1680   {
1681     AlignmentViewport originalSource = null;
1682     // For sequence removal and addition, we need to fire
1683     // the property change event FROM the viewport where the
1684     // original alignment was altered
1685     AlignmentI al = null;
1686     if (command instanceof EditCommand)
1687     {
1688       EditCommand editCommand = (EditCommand) command;
1689       al = editCommand.getAlignment();
1690       List<Component> comps = PaintRefresher.components
1691               .get(viewport.getSequenceSetId());
1692
1693       for (Component comp : comps)
1694       {
1695         if (comp instanceof AlignmentPanel)
1696         {
1697           if (al == ((AlignmentPanel) comp).av.getAlignment())
1698           {
1699             originalSource = ((AlignmentPanel) comp).av;
1700             break;
1701           }
1702         }
1703       }
1704     }
1705
1706     if (originalSource == null)
1707     {
1708       // The original view is closed, we must validate
1709       // the current view against the closed view first
1710       if (al != null)
1711       {
1712         PaintRefresher.validateSequences(al, viewport.getAlignment());
1713       }
1714
1715       originalSource = viewport;
1716     }
1717
1718     return originalSource;
1719   }
1720
1721   /**
1722    * DOCUMENT ME!
1723    *
1724    * @param up
1725    *          DOCUMENT ME!
1726    */
1727   public void moveSelectedSequences(boolean up)
1728   {
1729     SequenceGroup sg = viewport.getSelectionGroup();
1730
1731     if (sg == null)
1732     {
1733       return;
1734     }
1735     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1736             viewport.getHiddenRepSequences(), up);
1737     alignPanel.paintAlignment(true, false);
1738   }
1739
1740   synchronized void slideSequences(boolean right, int size)
1741   {
1742     List<SequenceI> sg = new ArrayList<>();
1743     if (viewport.cursorMode)
1744     {
1745       sg.add(viewport.getAlignment()
1746               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1747     }
1748     else if (viewport.getSelectionGroup() != null
1749             && viewport.getSelectionGroup().getSize() != viewport
1750                     .getAlignment().getHeight())
1751     {
1752       sg = viewport.getSelectionGroup()
1753               .getSequences(viewport.getHiddenRepSequences());
1754     }
1755
1756     if (sg.size() < 1)
1757     {
1758       return;
1759     }
1760
1761     List<SequenceI> invertGroup = new ArrayList<>();
1762
1763     for (SequenceI seq : viewport.getAlignment().getSequences())
1764     {
1765       if (!sg.contains(seq))
1766       {
1767         invertGroup.add(seq);
1768       }
1769     }
1770
1771     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1772
1773     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1774     for (int i = 0; i < invertGroup.size(); i++)
1775     {
1776       seqs2[i] = invertGroup.get(i);
1777     }
1778
1779     SlideSequencesCommand ssc;
1780     if (right)
1781     {
1782       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1783               viewport.getGapCharacter());
1784     }
1785     else
1786     {
1787       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1788               viewport.getGapCharacter());
1789     }
1790
1791     int groupAdjustment = 0;
1792     if (ssc.getGapsInsertedBegin() && right)
1793     {
1794       if (viewport.cursorMode)
1795       {
1796         alignPanel.getSeqPanel().moveCursor(size, 0);
1797       }
1798       else
1799       {
1800         groupAdjustment = size;
1801       }
1802     }
1803     else if (!ssc.getGapsInsertedBegin() && !right)
1804     {
1805       if (viewport.cursorMode)
1806       {
1807         alignPanel.getSeqPanel().moveCursor(-size, 0);
1808       }
1809       else
1810       {
1811         groupAdjustment = -size;
1812       }
1813     }
1814
1815     if (groupAdjustment != 0)
1816     {
1817       viewport.getSelectionGroup().setStartRes(
1818               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1819       viewport.getSelectionGroup().setEndRes(
1820               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1821     }
1822
1823     /*
1824      * just extend the last slide command if compatible; but not if in
1825      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1826      */
1827     boolean appendHistoryItem = false;
1828     Deque<CommandI> historyList = viewport.getHistoryList();
1829     boolean inSplitFrame = getSplitViewContainer() != null;
1830     if (!inSplitFrame && historyList != null && historyList.size() > 0
1831             && historyList.peek() instanceof SlideSequencesCommand)
1832     {
1833       appendHistoryItem = ssc.appendSlideCommand(
1834               (SlideSequencesCommand) historyList.peek());
1835     }
1836
1837     if (!appendHistoryItem)
1838     {
1839       addHistoryItem(ssc);
1840     }
1841
1842     repaint();
1843   }
1844
1845   /**
1846    * DOCUMENT ME!
1847    *
1848    * @param e
1849    *          DOCUMENT ME!
1850    */
1851   @Override
1852   protected void copy_actionPerformed(ActionEvent e)
1853   {
1854     if (viewport.getSelectionGroup() == null)
1855     {
1856       return;
1857     }
1858     // TODO: preserve the ordering of displayed alignment annotation in any
1859     // internal paste (particularly sequence associated annotation)
1860     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1861     String[] omitHidden = null;
1862
1863     if (viewport.hasHiddenColumns())
1864     {
1865       omitHidden = viewport.getViewAsString(true);
1866     }
1867
1868     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1869             seqs, omitHidden, null);
1870
1871     StringSelection ss = new StringSelection(output);
1872
1873     try
1874     {
1875       jalview.gui.Desktop.internalCopy = true;
1876       // Its really worth setting the clipboard contents
1877       // to empty before setting the large StringSelection!!
1878       Toolkit.getDefaultToolkit().getSystemClipboard()
1879               .setContents(new StringSelection(""), null);
1880
1881       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1882               Desktop.instance);
1883     } catch (OutOfMemoryError er)
1884     {
1885       new OOMWarning("copying region", er);
1886       return;
1887     }
1888
1889     HiddenColumns hiddenColumns = null;
1890     if (viewport.hasHiddenColumns())
1891     {
1892       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1893       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1894
1895       // create new HiddenColumns object with copy of hidden regions
1896       // between startRes and endRes, offset by startRes
1897       hiddenColumns = new HiddenColumns(
1898               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1899               hiddenCutoff, hiddenOffset);
1900     }
1901
1902     Desktop.jalviewClipboard = new Object[] { seqs,
1903         viewport.getAlignment().getDataset(), hiddenColumns };
1904     statusBar.setText(MessageManager.formatMessage(
1905             "label.copied_sequences_to_clipboard", new Object[]
1906             { Integer.valueOf(seqs.length).toString() }));
1907   }
1908
1909   /**
1910    * DOCUMENT ME!
1911    *
1912    * @param e
1913    *          DOCUMENT ME!
1914    */
1915   @Override
1916   protected void pasteNew_actionPerformed(ActionEvent e)
1917   {
1918     paste(true);
1919   }
1920
1921   /**
1922    * DOCUMENT ME!
1923    *
1924    * @param e
1925    *          DOCUMENT ME!
1926    */
1927   @Override
1928   protected void pasteThis_actionPerformed(ActionEvent e)
1929   {
1930     paste(false);
1931   }
1932
1933   /**
1934    * Paste contents of Jalview clipboard
1935    *
1936    * @param newAlignment
1937    *          true to paste to a new alignment, otherwise add to this.
1938    */
1939   void paste(boolean newAlignment)
1940   {
1941     boolean externalPaste = true;
1942     try
1943     {
1944       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1945       Transferable contents = c.getContents(this);
1946
1947       if (contents == null)
1948       {
1949         return;
1950       }
1951
1952       String str;
1953       FileFormatI format;
1954       try
1955       {
1956         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957         if (str.length() < 1)
1958         {
1959           return;
1960         }
1961
1962         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1963
1964       } catch (OutOfMemoryError er)
1965       {
1966         new OOMWarning("Out of memory pasting sequences!!", er);
1967         return;
1968       }
1969
1970       SequenceI[] sequences;
1971       boolean annotationAdded = false;
1972       AlignmentI alignment = null;
1973
1974       if (Desktop.jalviewClipboard != null)
1975       {
1976         // The clipboard was filled from within Jalview, we must use the
1977         // sequences
1978         // And dataset from the copied alignment
1979         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980         // be doubly sure that we create *new* sequence objects.
1981         sequences = new SequenceI[newseq.length];
1982         for (int i = 0; i < newseq.length; i++)
1983         {
1984           sequences[i] = new Sequence(newseq[i]);
1985         }
1986         alignment = new Alignment(sequences);
1987         externalPaste = false;
1988       }
1989       else
1990       {
1991         // parse the clipboard as an alignment.
1992         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1993                 format);
1994         sequences = alignment.getSequencesArray();
1995       }
1996
1997       int alwidth = 0;
1998       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1999       int fgroup = -1;
2000
2001       if (newAlignment)
2002       {
2003
2004         if (Desktop.jalviewClipboard != null)
2005         {
2006           // dataset is inherited
2007           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2008         }
2009         else
2010         {
2011           // new dataset is constructed
2012           alignment.setDataset(null);
2013         }
2014         alwidth = alignment.getWidth() + 1;
2015       }
2016       else
2017       {
2018         AlignmentI pastedal = alignment; // preserve pasted alignment object
2019         // Add pasted sequences and dataset into existing alignment.
2020         alignment = viewport.getAlignment();
2021         alwidth = alignment.getWidth() + 1;
2022         // decide if we need to import sequences from an existing dataset
2023         boolean importDs = Desktop.jalviewClipboard != null
2024                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2025         // importDs==true instructs us to copy over new dataset sequences from
2026         // an existing alignment
2027         Vector newDs = (importDs) ? new Vector() : null; // used to create
2028         // minimum dataset set
2029
2030         for (int i = 0; i < sequences.length; i++)
2031         {
2032           if (importDs)
2033           {
2034             newDs.addElement(null);
2035           }
2036           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2037           // paste
2038           if (importDs && ds != null)
2039           {
2040             if (!newDs.contains(ds))
2041             {
2042               newDs.setElementAt(ds, i);
2043               ds = new Sequence(ds);
2044               // update with new dataset sequence
2045               sequences[i].setDatasetSequence(ds);
2046             }
2047             else
2048             {
2049               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2050             }
2051           }
2052           else
2053           {
2054             // copy and derive new dataset sequence
2055             sequences[i] = sequences[i].deriveSequence();
2056             alignment.getDataset()
2057                     .addSequence(sequences[i].getDatasetSequence());
2058             // TODO: avoid creation of duplicate dataset sequences with a
2059             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2060           }
2061           alignment.addSequence(sequences[i]); // merges dataset
2062         }
2063         if (newDs != null)
2064         {
2065           newDs.clear(); // tidy up
2066         }
2067         if (alignment.getAlignmentAnnotation() != null)
2068         {
2069           for (AlignmentAnnotation alan : alignment
2070                   .getAlignmentAnnotation())
2071           {
2072             if (alan.graphGroup > fgroup)
2073             {
2074               fgroup = alan.graphGroup;
2075             }
2076           }
2077         }
2078         if (pastedal.getAlignmentAnnotation() != null)
2079         {
2080           // Add any annotation attached to alignment.
2081           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2082           for (int i = 0; i < alann.length; i++)
2083           {
2084             annotationAdded = true;
2085             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2086             {
2087               AlignmentAnnotation newann = new AlignmentAnnotation(
2088                       alann[i]);
2089               if (newann.graphGroup > -1)
2090               {
2091                 if (newGraphGroups.size() <= newann.graphGroup
2092                         || newGraphGroups.get(newann.graphGroup) == null)
2093                 {
2094                   for (int q = newGraphGroups
2095                           .size(); q <= newann.graphGroup; q++)
2096                   {
2097                     newGraphGroups.add(q, null);
2098                   }
2099                   newGraphGroups.set(newann.graphGroup,
2100                           Integer.valueOf(++fgroup));
2101                 }
2102                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2103                         .intValue();
2104               }
2105
2106               newann.padAnnotation(alwidth);
2107               alignment.addAnnotation(newann);
2108             }
2109           }
2110         }
2111       }
2112       if (!newAlignment)
2113       {
2114         // /////
2115         // ADD HISTORY ITEM
2116         //
2117         addHistoryItem(new EditCommand(
2118                 MessageManager.getString("label.add_sequences"),
2119                 Action.PASTE, sequences, 0, alignment.getWidth(),
2120                 alignment));
2121       }
2122       // Add any annotations attached to sequences
2123       for (int i = 0; i < sequences.length; i++)
2124       {
2125         if (sequences[i].getAnnotation() != null)
2126         {
2127           AlignmentAnnotation newann;
2128           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2129           {
2130             annotationAdded = true;
2131             newann = sequences[i].getAnnotation()[a];
2132             newann.adjustForAlignment();
2133             newann.padAnnotation(alwidth);
2134             if (newann.graphGroup > -1)
2135             {
2136               if (newann.graphGroup > -1)
2137               {
2138                 if (newGraphGroups.size() <= newann.graphGroup
2139                         || newGraphGroups.get(newann.graphGroup) == null)
2140                 {
2141                   for (int q = newGraphGroups
2142                           .size(); q <= newann.graphGroup; q++)
2143                   {
2144                     newGraphGroups.add(q, null);
2145                   }
2146                   newGraphGroups.set(newann.graphGroup,
2147                           Integer.valueOf(++fgroup));
2148                 }
2149                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2150                         .intValue();
2151               }
2152             }
2153             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2154             // was
2155             // duplicated
2156             // earlier
2157             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2158                     a);
2159           }
2160         }
2161       }
2162       if (!newAlignment)
2163       {
2164
2165         // propagate alignment changed.
2166         viewport.getRanges().setEndSeq(alignment.getHeight());
2167         if (annotationAdded)
2168         {
2169           // Duplicate sequence annotation in all views.
2170           AlignmentI[] alview = this.getViewAlignments();
2171           for (int i = 0; i < sequences.length; i++)
2172           {
2173             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2174             if (sann == null)
2175             {
2176               continue;
2177             }
2178             for (int avnum = 0; avnum < alview.length; avnum++)
2179             {
2180               if (alview[avnum] != alignment)
2181               {
2182                 // duplicate in a view other than the one with input focus
2183                 int avwidth = alview[avnum].getWidth() + 1;
2184                 // this relies on sann being preserved after we
2185                 // modify the sequence's annotation array for each duplication
2186                 for (int a = 0; a < sann.length; a++)
2187                 {
2188                   AlignmentAnnotation newann = new AlignmentAnnotation(
2189                           sann[a]);
2190                   sequences[i].addAlignmentAnnotation(newann);
2191                   newann.padAnnotation(avwidth);
2192                   alview[avnum].addAnnotation(newann); // annotation was
2193                   // duplicated earlier
2194                   // TODO JAL-1145 graphGroups are not updated for sequence
2195                   // annotation added to several views. This may cause
2196                   // strangeness
2197                   alview[avnum].setAnnotationIndex(newann, a);
2198                 }
2199               }
2200             }
2201           }
2202           buildSortByAnnotationScoresMenu();
2203         }
2204         viewport.firePropertyChange("alignment", null,
2205                 alignment.getSequences());
2206         if (alignPanels != null)
2207         {
2208           for (AlignmentPanel ap : alignPanels)
2209           {
2210             ap.validateAnnotationDimensions(false);
2211           }
2212         }
2213         else
2214         {
2215           alignPanel.validateAnnotationDimensions(false);
2216         }
2217
2218       }
2219       else
2220       {
2221         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2222                 DEFAULT_HEIGHT);
2223         String newtitle = new String("Copied sequences");
2224
2225         if (Desktop.jalviewClipboard != null
2226                 && Desktop.jalviewClipboard[2] != null)
2227         {
2228           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2229           af.viewport.setHiddenColumns(hc);
2230         }
2231
2232         // >>>This is a fix for the moment, until a better solution is
2233         // found!!<<<
2234         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2235                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2236                         .getFeatureRenderer());
2237
2238         // TODO: maintain provenance of an alignment, rather than just make the
2239         // title a concatenation of operations.
2240         if (!externalPaste)
2241         {
2242           if (title.startsWith("Copied sequences"))
2243           {
2244             newtitle = title;
2245           }
2246           else
2247           {
2248             newtitle = newtitle.concat("- from " + title);
2249           }
2250         }
2251         else
2252         {
2253           newtitle = new String("Pasted sequences");
2254         }
2255
2256         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2257                 DEFAULT_HEIGHT);
2258
2259       }
2260
2261     } catch (Exception ex)
2262     {
2263       ex.printStackTrace();
2264       System.out.println("Exception whilst pasting: " + ex);
2265       // could be anything being pasted in here
2266     }
2267
2268   }
2269
2270   @Override
2271   protected void expand_newalign(ActionEvent e)
2272   {
2273     try
2274     {
2275       AlignmentI alignment = AlignmentUtils
2276               .expandContext(getViewport().getAlignment(), -1);
2277       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2278               DEFAULT_HEIGHT);
2279       String newtitle = new String("Flanking alignment");
2280
2281       if (Desktop.jalviewClipboard != null
2282               && Desktop.jalviewClipboard[2] != null)
2283       {
2284         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2285         af.viewport.setHiddenColumns(hc);
2286       }
2287
2288       // >>>This is a fix for the moment, until a better solution is
2289       // found!!<<<
2290       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2292                       .getFeatureRenderer());
2293
2294       // TODO: maintain provenance of an alignment, rather than just make the
2295       // title a concatenation of operations.
2296       {
2297         if (title.startsWith("Copied sequences"))
2298         {
2299           newtitle = title;
2300         }
2301         else
2302         {
2303           newtitle = newtitle.concat("- from " + title);
2304         }
2305       }
2306
2307       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2308
2309     } catch (Exception ex)
2310     {
2311       ex.printStackTrace();
2312       System.out.println("Exception whilst pasting: " + ex);
2313       // could be anything being pasted in here
2314     } catch (OutOfMemoryError oom)
2315     {
2316       new OOMWarning("Viewing flanking region of alignment", oom);
2317     }
2318   }
2319
2320   /**
2321    * DOCUMENT ME!
2322    *
2323    * @param e
2324    *          DOCUMENT ME!
2325    */
2326   @Override
2327   protected void cut_actionPerformed(ActionEvent e)
2328   {
2329     copy_actionPerformed(null);
2330     delete_actionPerformed(null);
2331   }
2332
2333   /**
2334    * DOCUMENT ME!
2335    *
2336    * @param e
2337    *          DOCUMENT ME!
2338    */
2339   @Override
2340   protected void delete_actionPerformed(ActionEvent evt)
2341   {
2342
2343     SequenceGroup sg = viewport.getSelectionGroup();
2344     if (sg == null)
2345     {
2346       return;
2347     }
2348
2349     /*
2350      * If the cut affects all sequences, warn, remove highlighted columns
2351      */
2352     if (sg.getSize() == viewport.getAlignment().getHeight())
2353     {
2354       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2355               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2356       if (isEntireAlignWidth)
2357       {
2358         int confirm = JvOptionPane.showConfirmDialog(this,
2359                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2360                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2361                 JvOptionPane.OK_CANCEL_OPTION);
2362
2363         if (confirm == JvOptionPane.CANCEL_OPTION
2364                 || confirm == JvOptionPane.CLOSED_OPTION)
2365         {
2366           return;
2367         }
2368       }
2369       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2370               sg.getEndRes() + 1);
2371     }
2372     SequenceI[] cut = sg.getSequences()
2373             .toArray(new SequenceI[sg.getSize()]);
2374
2375     addHistoryItem(new EditCommand(
2376             MessageManager.getString("label.cut_sequences"), Action.CUT,
2377             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2378             viewport.getAlignment()));
2379
2380     viewport.setSelectionGroup(null);
2381     viewport.sendSelection();
2382     viewport.getAlignment().deleteGroup(sg);
2383
2384     viewport.firePropertyChange("alignment", null,
2385             viewport.getAlignment().getSequences());
2386     if (viewport.getAlignment().getHeight() < 1)
2387     {
2388       try
2389       {
2390         this.setClosed(true);
2391       } catch (Exception ex)
2392       {
2393       }
2394     }
2395   }
2396
2397   /**
2398    * DOCUMENT ME!
2399    *
2400    * @param e
2401    *          DOCUMENT ME!
2402    */
2403   @Override
2404   protected void deleteGroups_actionPerformed(ActionEvent e)
2405   {
2406     if (avc.deleteGroups())
2407     {
2408       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2409       alignPanel.updateAnnotation();
2410       alignPanel.paintAlignment(true, true);
2411     }
2412   }
2413
2414   /**
2415    * DOCUMENT ME!
2416    *
2417    * @param e
2418    *          DOCUMENT ME!
2419    */
2420   @Override
2421   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2422   {
2423     SequenceGroup sg = new SequenceGroup(
2424             viewport.getAlignment().getSequences());
2425
2426     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2427     viewport.setSelectionGroup(sg);
2428     viewport.isSelectionGroupChanged(true);
2429     viewport.sendSelection();
2430     // JAL-2034 - should delegate to
2431     // alignPanel to decide if overview needs
2432     // updating.
2433     alignPanel.paintAlignment(false, false);
2434     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2435   }
2436
2437   /**
2438    * DOCUMENT ME!
2439    *
2440    * @param e
2441    *          DOCUMENT ME!
2442    */
2443   @Override
2444   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2445   {
2446     if (viewport.cursorMode)
2447     {
2448       alignPanel.getSeqPanel().keyboardNo1 = null;
2449       alignPanel.getSeqPanel().keyboardNo2 = null;
2450     }
2451     viewport.setSelectionGroup(null);
2452     viewport.getColumnSelection().clear();
2453     viewport.setSearchResults(null);
2454     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2455     // JAL-2034 - should delegate to
2456     // alignPanel to decide if overview needs
2457     // updating.
2458     alignPanel.paintAlignment(false, false);
2459     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2460     viewport.sendSelection();
2461   }
2462
2463   /**
2464    * DOCUMENT ME!
2465    *
2466    * @param e
2467    *          DOCUMENT ME!
2468    */
2469   @Override
2470   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2471   {
2472     SequenceGroup sg = viewport.getSelectionGroup();
2473
2474     if (sg == null)
2475     {
2476       selectAllSequenceMenuItem_actionPerformed(null);
2477
2478       return;
2479     }
2480
2481     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2482     {
2483       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2484     }
2485     // JAL-2034 - should delegate to
2486     // alignPanel to decide if overview needs
2487     // updating.
2488
2489     alignPanel.paintAlignment(true, false);
2490     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2491     viewport.sendSelection();
2492   }
2493
2494   @Override
2495   public void invertColSel_actionPerformed(ActionEvent e)
2496   {
2497     viewport.invertColumnSelection();
2498     alignPanel.paintAlignment(true, false);
2499     viewport.sendSelection();
2500   }
2501
2502   /**
2503    * DOCUMENT ME!
2504    *
2505    * @param e
2506    *          DOCUMENT ME!
2507    */
2508   @Override
2509   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2510   {
2511     trimAlignment(true);
2512   }
2513
2514   /**
2515    * DOCUMENT ME!
2516    *
2517    * @param e
2518    *          DOCUMENT ME!
2519    */
2520   @Override
2521   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2522   {
2523     trimAlignment(false);
2524   }
2525
2526   void trimAlignment(boolean trimLeft)
2527   {
2528     ColumnSelection colSel = viewport.getColumnSelection();
2529     int column;
2530
2531     if (!colSel.isEmpty())
2532     {
2533       if (trimLeft)
2534       {
2535         column = colSel.getMin();
2536       }
2537       else
2538       {
2539         column = colSel.getMax();
2540       }
2541
2542       SequenceI[] seqs;
2543       if (viewport.getSelectionGroup() != null)
2544       {
2545         seqs = viewport.getSelectionGroup()
2546                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2547       }
2548       else
2549       {
2550         seqs = viewport.getAlignment().getSequencesArray();
2551       }
2552
2553       TrimRegionCommand trimRegion;
2554       if (trimLeft)
2555       {
2556         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2557                 column, viewport.getAlignment());
2558         viewport.getRanges().setStartRes(0);
2559       }
2560       else
2561       {
2562         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2563                 column, viewport.getAlignment());
2564       }
2565
2566       statusBar.setText(MessageManager
2567               .formatMessage("label.removed_columns", new String[]
2568               { Integer.valueOf(trimRegion.getSize()).toString() }));
2569
2570       addHistoryItem(trimRegion);
2571
2572       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2573       {
2574         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2575                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2576         {
2577           viewport.getAlignment().deleteGroup(sg);
2578         }
2579       }
2580
2581       viewport.firePropertyChange("alignment", null,
2582               viewport.getAlignment().getSequences());
2583     }
2584   }
2585
2586   /**
2587    * DOCUMENT ME!
2588    *
2589    * @param e
2590    *          DOCUMENT ME!
2591    */
2592   @Override
2593   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2594   {
2595     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2596
2597     SequenceI[] seqs;
2598     if (viewport.getSelectionGroup() != null)
2599     {
2600       seqs = viewport.getSelectionGroup()
2601               .getSequencesAsArray(viewport.getHiddenRepSequences());
2602       start = viewport.getSelectionGroup().getStartRes();
2603       end = viewport.getSelectionGroup().getEndRes();
2604     }
2605     else
2606     {
2607       seqs = viewport.getAlignment().getSequencesArray();
2608     }
2609
2610     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2611             "Remove Gapped Columns", seqs, start, end,
2612             viewport.getAlignment());
2613
2614     addHistoryItem(removeGapCols);
2615
2616     statusBar.setText(MessageManager
2617             .formatMessage("label.removed_empty_columns", new Object[]
2618             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2619
2620     // This is to maintain viewport position on first residue
2621     // of first sequence
2622     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2623     ViewportRanges ranges = viewport.getRanges();
2624     int startRes = seq.findPosition(ranges.getStartRes());
2625     // ShiftList shifts;
2626     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2627     // edit.alColumnChanges=shifts.getInverse();
2628     // if (viewport.hasHiddenColumns)
2629     // viewport.getColumnSelection().compensateForEdits(shifts);
2630     ranges.setStartRes(seq.findIndex(startRes) - 1);
2631     viewport.firePropertyChange("alignment", null,
2632             viewport.getAlignment().getSequences());
2633
2634   }
2635
2636   /**
2637    * DOCUMENT ME!
2638    *
2639    * @param e
2640    *          DOCUMENT ME!
2641    */
2642   @Override
2643   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2644   {
2645     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2646
2647     SequenceI[] seqs;
2648     if (viewport.getSelectionGroup() != null)
2649     {
2650       seqs = viewport.getSelectionGroup()
2651               .getSequencesAsArray(viewport.getHiddenRepSequences());
2652       start = viewport.getSelectionGroup().getStartRes();
2653       end = viewport.getSelectionGroup().getEndRes();
2654     }
2655     else
2656     {
2657       seqs = viewport.getAlignment().getSequencesArray();
2658     }
2659
2660     // This is to maintain viewport position on first residue
2661     // of first sequence
2662     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2663     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2664
2665     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2666             viewport.getAlignment()));
2667
2668     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2669
2670     viewport.firePropertyChange("alignment", null,
2671             viewport.getAlignment().getSequences());
2672
2673   }
2674
2675   /**
2676    * DOCUMENT ME!
2677    *
2678    * @param e
2679    *          DOCUMENT ME!
2680    */
2681   @Override
2682   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2683   {
2684     viewport.setPadGaps(padGapsMenuitem.isSelected());
2685     viewport.firePropertyChange("alignment", null,
2686             viewport.getAlignment().getSequences());
2687   }
2688
2689   /**
2690    * DOCUMENT ME!
2691    *
2692    * @param e
2693    *          DOCUMENT ME!
2694    */
2695   @Override
2696   public void findMenuItem_actionPerformed(ActionEvent e)
2697   {
2698     new Finder();
2699   }
2700
2701   /**
2702    * Create a new view of the current alignment.
2703    */
2704   @Override
2705   public void newView_actionPerformed(ActionEvent e)
2706   {
2707     newView(null, true);
2708   }
2709
2710   /**
2711    * Creates and shows a new view of the current alignment.
2712    *
2713    * @param viewTitle
2714    *          title of newly created view; if null, one will be generated
2715    * @param copyAnnotation
2716    *          if true then duplicate all annnotation, groups and settings
2717    * @return new alignment panel, already displayed.
2718    */
2719   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2720   {
2721     /*
2722      * Create a new AlignmentPanel (with its own, new Viewport)
2723      */
2724     AlignmentPanel newap = new jalview.project.Jalview2XML()
2725             .copyAlignPanel(alignPanel);
2726     if (!copyAnnotation)
2727     {
2728       /*
2729        * remove all groups and annotation except for the automatic stuff
2730        */
2731       newap.av.getAlignment().deleteAllGroups();
2732       newap.av.getAlignment().deleteAllAnnotations(false);
2733     }
2734
2735     newap.av.setGatherViewsHere(false);
2736
2737     if (viewport.getViewName() == null)
2738     {
2739       viewport.setViewName(MessageManager
2740               .getString("label.view_name_original"));
2741     }
2742
2743     /*
2744      * Views share the same edits undo and redo stacks
2745      */
2746     newap.av.setHistoryList(viewport.getHistoryList());
2747     newap.av.setRedoList(viewport.getRedoList());
2748
2749     /*
2750      * copy any visualisation settings that are not saved in the project
2751      */
2752     newap.av.setColourAppliesToAllGroups(
2753             viewport.getColourAppliesToAllGroups());
2754
2755     /*
2756      * Views share the same mappings; need to deregister any new mappings
2757      * created by copyAlignPanel, and register the new reference to the shared
2758      * mappings
2759      */
2760     newap.av.replaceMappings(viewport.getAlignment());
2761
2762     /*
2763      * start up cDNA consensus (if applicable) now mappings are in place
2764      */
2765     if (newap.av.initComplementConsensus())
2766     {
2767       newap.refresh(true); // adjust layout of annotations
2768     }
2769
2770     newap.av.setViewName(getNewViewName(viewTitle));
2771
2772     addAlignmentPanel(newap, true);
2773     newap.alignmentChanged();
2774
2775     if (alignPanels.size() == 2)
2776     {
2777       viewport.setGatherViewsHere(true);
2778     }
2779     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2780     return newap;
2781   }
2782
2783   /**
2784    * Make a new name for the view, ensuring it is unique within the current
2785    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2786    * these now use viewId. Unique view names are still desirable for usability.)
2787    *
2788    * @param viewTitle
2789    * @return
2790    */
2791   protected String getNewViewName(String viewTitle)
2792   {
2793     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2794     boolean addFirstIndex = false;
2795     if (viewTitle == null || viewTitle.trim().length() == 0)
2796     {
2797       viewTitle = MessageManager.getString("action.view");
2798       addFirstIndex = true;
2799     }
2800     else
2801     {
2802       index = 1;// we count from 1 if given a specific name
2803     }
2804     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2805
2806     List<Component> comps = PaintRefresher.components
2807             .get(viewport.getSequenceSetId());
2808
2809     List<String> existingNames = getExistingViewNames(comps);
2810
2811     while (existingNames.contains(newViewName))
2812     {
2813       newViewName = viewTitle + " " + (++index);
2814     }
2815     return newViewName;
2816   }
2817
2818   /**
2819    * Returns a list of distinct view names found in the given list of
2820    * components. View names are held on the viewport of an AlignmentPanel.
2821    *
2822    * @param comps
2823    * @return
2824    */
2825   protected List<String> getExistingViewNames(List<Component> comps)
2826   {
2827     List<String> existingNames = new ArrayList<>();
2828     for (Component comp : comps)
2829     {
2830       if (comp instanceof AlignmentPanel)
2831       {
2832         AlignmentPanel ap = (AlignmentPanel) comp;
2833         if (!existingNames.contains(ap.av.getViewName()))
2834         {
2835           existingNames.add(ap.av.getViewName());
2836         }
2837       }
2838     }
2839     return existingNames;
2840   }
2841
2842   /**
2843    * Explode tabbed views into separate windows.
2844    */
2845   @Override
2846   public void expandViews_actionPerformed(ActionEvent e)
2847   {
2848     Desktop.explodeViews(this);
2849   }
2850
2851   /**
2852    * Gather views in separate windows back into a tabbed presentation.
2853    */
2854   @Override
2855   public void gatherViews_actionPerformed(ActionEvent e)
2856   {
2857     Desktop.instance.gatherViews(this);
2858   }
2859
2860   /**
2861    * DOCUMENT ME!
2862    *
2863    * @param e
2864    *          DOCUMENT ME!
2865    */
2866   @Override
2867   public void font_actionPerformed(ActionEvent e)
2868   {
2869     new FontChooser(alignPanel);
2870   }
2871
2872   /**
2873    * DOCUMENT ME!
2874    *
2875    * @param e
2876    *          DOCUMENT ME!
2877    */
2878   @Override
2879   protected void seqLimit_actionPerformed(ActionEvent e)
2880   {
2881     viewport.setShowJVSuffix(seqLimits.isSelected());
2882
2883     alignPanel.getIdPanel().getIdCanvas()
2884             .setPreferredSize(alignPanel.calculateIdWidth());
2885     alignPanel.paintAlignment(true, false);
2886   }
2887
2888   @Override
2889   public void idRightAlign_actionPerformed(ActionEvent e)
2890   {
2891     viewport.setRightAlignIds(idRightAlign.isSelected());
2892     alignPanel.paintAlignment(false, false);
2893   }
2894
2895   @Override
2896   public void centreColumnLabels_actionPerformed(ActionEvent e)
2897   {
2898     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2899     alignPanel.paintAlignment(false, false);
2900   }
2901
2902   /*
2903    * (non-Javadoc)
2904    *
2905    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2906    */
2907   @Override
2908   protected void followHighlight_actionPerformed()
2909   {
2910     /*
2911      * Set the 'follow' flag on the Viewport (and scroll to position if now
2912      * true).
2913      */
2914     final boolean state = this.followHighlightMenuItem.getState();
2915     viewport.setFollowHighlight(state);
2916     if (state)
2917     {
2918       alignPanel.scrollToPosition(viewport.getSearchResults());
2919     }
2920   }
2921
2922   /**
2923    * DOCUMENT ME!
2924    *
2925    * @param e
2926    *          DOCUMENT ME!
2927    */
2928   @Override
2929   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2930   {
2931     viewport.setColourText(colourTextMenuItem.isSelected());
2932     alignPanel.paintAlignment(false, false);
2933   }
2934
2935   /**
2936    * DOCUMENT ME!
2937    *
2938    * @param e
2939    *          DOCUMENT ME!
2940    */
2941   @Override
2942   public void wrapMenuItem_actionPerformed(ActionEvent e)
2943   {
2944     scaleAbove.setVisible(wrapMenuItem.isSelected());
2945     scaleLeft.setVisible(wrapMenuItem.isSelected());
2946     scaleRight.setVisible(wrapMenuItem.isSelected());
2947     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2948     alignPanel.updateLayout();
2949   }
2950
2951   @Override
2952   public void showAllSeqs_actionPerformed(ActionEvent e)
2953   {
2954     viewport.showAllHiddenSeqs();
2955   }
2956
2957   @Override
2958   public void showAllColumns_actionPerformed(ActionEvent e)
2959   {
2960     viewport.showAllHiddenColumns();
2961     alignPanel.paintAlignment(true, true);
2962     viewport.sendSelection();
2963   }
2964
2965   @Override
2966   public void hideSelSequences_actionPerformed(ActionEvent e)
2967   {
2968     viewport.hideAllSelectedSeqs();
2969   }
2970
2971   /**
2972    * called by key handler and the hide all/show all menu items
2973    *
2974    * @param toggleSeqs
2975    * @param toggleCols
2976    */
2977   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2978   {
2979
2980     boolean hide = false;
2981     SequenceGroup sg = viewport.getSelectionGroup();
2982     if (!toggleSeqs && !toggleCols)
2983     {
2984       // Hide everything by the current selection - this is a hack - we do the
2985       // invert and then hide
2986       // first check that there will be visible columns after the invert.
2987       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2988               && sg.getStartRes() <= sg.getEndRes()))
2989       {
2990         // now invert the sequence set, if required - empty selection implies
2991         // that no hiding is required.
2992         if (sg != null)
2993         {
2994           invertSequenceMenuItem_actionPerformed(null);
2995           sg = viewport.getSelectionGroup();
2996           toggleSeqs = true;
2997
2998         }
2999         viewport.expandColSelection(sg, true);
3000         // finally invert the column selection and get the new sequence
3001         // selection.
3002         invertColSel_actionPerformed(null);
3003         toggleCols = true;
3004       }
3005     }
3006
3007     if (toggleSeqs)
3008     {
3009       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3010       {
3011         hideSelSequences_actionPerformed(null);
3012         hide = true;
3013       }
3014       else if (!(toggleCols && viewport.hasSelectedColumns()))
3015       {
3016         showAllSeqs_actionPerformed(null);
3017       }
3018     }
3019
3020     if (toggleCols)
3021     {
3022       if (viewport.hasSelectedColumns())
3023       {
3024         hideSelColumns_actionPerformed(null);
3025         if (!toggleSeqs)
3026         {
3027           viewport.setSelectionGroup(sg);
3028         }
3029       }
3030       else if (!hide)
3031       {
3032         showAllColumns_actionPerformed(null);
3033       }
3034     }
3035   }
3036
3037   /*
3038    * (non-Javadoc)
3039    *
3040    * @see
3041    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3042    * event.ActionEvent)
3043    */
3044   @Override
3045   public void hideAllButSelection_actionPerformed(ActionEvent e)
3046   {
3047     toggleHiddenRegions(false, false);
3048     viewport.sendSelection();
3049   }
3050
3051   /*
3052    * (non-Javadoc)
3053    *
3054    * @see
3055    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3056    * .ActionEvent)
3057    */
3058   @Override
3059   public void hideAllSelection_actionPerformed(ActionEvent e)
3060   {
3061     SequenceGroup sg = viewport.getSelectionGroup();
3062     viewport.expandColSelection(sg, false);
3063     viewport.hideAllSelectedSeqs();
3064     viewport.hideSelectedColumns();
3065     alignPanel.updateLayout();
3066     alignPanel.paintAlignment(true, true);
3067     viewport.sendSelection();
3068   }
3069
3070   /*
3071    * (non-Javadoc)
3072    *
3073    * @see
3074    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3075    * ActionEvent)
3076    */
3077   @Override
3078   public void showAllhidden_actionPerformed(ActionEvent e)
3079   {
3080     viewport.showAllHiddenColumns();
3081     viewport.showAllHiddenSeqs();
3082     alignPanel.paintAlignment(true, true);
3083     viewport.sendSelection();
3084   }
3085
3086   @Override
3087   public void hideSelColumns_actionPerformed(ActionEvent e)
3088   {
3089     viewport.hideSelectedColumns();
3090     alignPanel.updateLayout();
3091     alignPanel.paintAlignment(true, true);
3092     viewport.sendSelection();
3093   }
3094
3095   @Override
3096   public void hiddenMarkers_actionPerformed(ActionEvent e)
3097   {
3098     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3099     repaint();
3100   }
3101
3102   /**
3103    * DOCUMENT ME!
3104    *
3105    * @param e
3106    *          DOCUMENT ME!
3107    */
3108   @Override
3109   protected void scaleAbove_actionPerformed(ActionEvent e)
3110   {
3111     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3112     alignPanel.updateLayout();
3113     alignPanel.paintAlignment(true, false);
3114   }
3115
3116   /**
3117    * DOCUMENT ME!
3118    *
3119    * @param e
3120    *          DOCUMENT ME!
3121    */
3122   @Override
3123   protected void scaleLeft_actionPerformed(ActionEvent e)
3124   {
3125     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3126     alignPanel.updateLayout();
3127     alignPanel.paintAlignment(true, false);
3128   }
3129
3130   /**
3131    * DOCUMENT ME!
3132    *
3133    * @param e
3134    *          DOCUMENT ME!
3135    */
3136   @Override
3137   protected void scaleRight_actionPerformed(ActionEvent e)
3138   {
3139     viewport.setScaleRightWrapped(scaleRight.isSelected());
3140     alignPanel.updateLayout();
3141     alignPanel.paintAlignment(true, false);
3142   }
3143
3144   /**
3145    * DOCUMENT ME!
3146    *
3147    * @param e
3148    *          DOCUMENT ME!
3149    */
3150   @Override
3151   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3152   {
3153     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3154     alignPanel.paintAlignment(false, false);
3155   }
3156
3157   /**
3158    * DOCUMENT ME!
3159    *
3160    * @param e
3161    *          DOCUMENT ME!
3162    */
3163   @Override
3164   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3165   {
3166     viewport.setShowText(viewTextMenuItem.isSelected());
3167     alignPanel.paintAlignment(false, false);
3168   }
3169
3170   /**
3171    * DOCUMENT ME!
3172    *
3173    * @param e
3174    *          DOCUMENT ME!
3175    */
3176   @Override
3177   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3178   {
3179     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3180     alignPanel.paintAlignment(false, false);
3181   }
3182
3183   public FeatureSettings featureSettings;
3184
3185   @Override
3186   public FeatureSettingsControllerI getFeatureSettingsUI()
3187   {
3188     return featureSettings;
3189   }
3190
3191   @Override
3192   public void featureSettings_actionPerformed(ActionEvent e)
3193   {
3194     showFeatureSettingsUI();
3195   }
3196
3197   @Override
3198   public FeatureSettingsControllerI showFeatureSettingsUI()
3199   {
3200     if (featureSettings != null)
3201     {
3202       featureSettings.closeOldSettings();
3203       featureSettings = null;
3204     }
3205     if (!showSeqFeatures.isSelected())
3206     {
3207       // make sure features are actually displayed
3208       showSeqFeatures.setSelected(true);
3209       showSeqFeatures_actionPerformed(null);
3210     }
3211     featureSettings = new FeatureSettings(this);
3212     return featureSettings;
3213   }
3214
3215   /**
3216    * Set or clear 'Show Sequence Features'
3217    *
3218    * @param evt
3219    *          DOCUMENT ME!
3220    */
3221   @Override
3222   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3223   {
3224     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3225     alignPanel.paintAlignment(true, true);
3226   }
3227
3228   /**
3229    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3230    * the annotations panel as a whole.
3231    *
3232    * The options to show/hide all annotations should be enabled when the panel
3233    * is shown, and disabled when the panel is hidden.
3234    *
3235    * @param e
3236    */
3237   @Override
3238   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3239   {
3240     final boolean setVisible = annotationPanelMenuItem.isSelected();
3241     viewport.setShowAnnotation(setVisible);
3242     this.showAllSeqAnnotations.setEnabled(setVisible);
3243     this.hideAllSeqAnnotations.setEnabled(setVisible);
3244     this.showAllAlAnnotations.setEnabled(setVisible);
3245     this.hideAllAlAnnotations.setEnabled(setVisible);
3246     alignPanel.updateLayout();
3247   }
3248
3249   @Override
3250   public void alignmentProperties()
3251   {
3252     JEditorPane editPane = new JEditorPane("text/html", "");
3253     editPane.setEditable(false);
3254     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3255             .formatAsHtml();
3256     editPane.setText(
3257             MessageManager.formatMessage("label.html_content", new Object[]
3258             { contents.toString() }));
3259     JInternalFrame frame = new JInternalFrame();
3260     frame.getContentPane().add(new JScrollPane(editPane));
3261
3262     Desktop.addInternalFrame(frame, MessageManager
3263             .formatMessage("label.alignment_properties", new Object[]
3264             { getTitle() }), 500, 400);
3265   }
3266
3267   /**
3268    * DOCUMENT ME!
3269    *
3270    * @param e
3271    *          DOCUMENT ME!
3272    */
3273   @Override
3274   public void overviewMenuItem_actionPerformed(ActionEvent e)
3275   {
3276     if (alignPanel.overviewPanel != null)
3277     {
3278       return;
3279     }
3280
3281     JInternalFrame frame = new JInternalFrame();
3282     final OverviewPanel overview = new OverviewPanel(alignPanel);
3283     frame.setContentPane(overview);
3284     Desktop.addInternalFrame(frame, MessageManager
3285             .formatMessage("label.overview_params", new Object[]
3286             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3287             true, true);
3288     frame.pack();
3289     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3290     frame.addInternalFrameListener(
3291             new javax.swing.event.InternalFrameAdapter()
3292             {
3293               @Override
3294               public void internalFrameClosed(
3295                       javax.swing.event.InternalFrameEvent evt)
3296               {
3297                 overview.dispose();
3298                 alignPanel.setOverviewPanel(null);
3299               };
3300             });
3301     if (getKeyListeners().length > 0)
3302     {
3303       frame.addKeyListener(getKeyListeners()[0]);
3304     }
3305
3306     alignPanel.setOverviewPanel(overview);
3307   }
3308
3309   @Override
3310   public void textColour_actionPerformed()
3311   {
3312     new TextColourChooser().chooseColour(alignPanel, null);
3313   }
3314
3315   /*
3316    * public void covariationColour_actionPerformed() {
3317    * changeColour(new
3318    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3319    * ()[0])); }
3320    */
3321   @Override
3322   public void annotationColour_actionPerformed()
3323   {
3324     new AnnotationColourChooser(viewport, alignPanel);
3325   }
3326
3327   @Override
3328   public void annotationColumn_actionPerformed(ActionEvent e)
3329   {
3330     new AnnotationColumnChooser(viewport, alignPanel);
3331   }
3332
3333   /**
3334    * Action on the user checking or unchecking the option to apply the selected
3335    * colour scheme to all groups. If unchecked, groups may have their own
3336    * independent colour schemes.
3337    *
3338    * @param selected
3339    */
3340   @Override
3341   public void applyToAllGroups_actionPerformed(boolean selected)
3342   {
3343     viewport.setColourAppliesToAllGroups(selected);
3344   }
3345
3346   /**
3347    * Action on user selecting a colour from the colour menu
3348    *
3349    * @param name
3350    *          the name (not the menu item label!) of the colour scheme
3351    */
3352   @Override
3353   public void changeColour_actionPerformed(String name)
3354   {
3355     /*
3356      * 'User Defined' opens a panel to configure or load a
3357      * user-defined colour scheme
3358      */
3359     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3360     {
3361       new UserDefinedColours(alignPanel);
3362       return;
3363     }
3364
3365     /*
3366      * otherwise set the chosen colour scheme (or null for 'None')
3367      */
3368     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3369             viewport,
3370             viewport.getAlignment(), viewport.getHiddenRepSequences());
3371     changeColour(cs);
3372   }
3373
3374   /**
3375    * Actions on setting or changing the alignment colour scheme
3376    *
3377    * @param cs
3378    */
3379   @Override
3380   public void changeColour(ColourSchemeI cs)
3381   {
3382     // TODO: pull up to controller method
3383     ColourMenuHelper.setColourSelected(colourMenu, cs);
3384
3385     viewport.setGlobalColourScheme(cs);
3386
3387     alignPanel.paintAlignment(true, true);
3388   }
3389
3390   /**
3391    * Show the PID threshold slider panel
3392    */
3393   @Override
3394   protected void modifyPID_actionPerformed()
3395   {
3396     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3397             alignPanel.getViewName());
3398     SliderPanel.showPIDSlider();
3399   }
3400
3401   /**
3402    * Show the Conservation slider panel
3403    */
3404   @Override
3405   protected void modifyConservation_actionPerformed()
3406   {
3407     SliderPanel.setConservationSlider(alignPanel,
3408             viewport.getResidueShading(), alignPanel.getViewName());
3409     SliderPanel.showConservationSlider();
3410   }
3411
3412   /**
3413    * Action on selecting or deselecting (Colour) By Conservation
3414    */
3415   @Override
3416   public void conservationMenuItem_actionPerformed(boolean selected)
3417   {
3418     modifyConservation.setEnabled(selected);
3419     viewport.setConservationSelected(selected);
3420     viewport.getResidueShading().setConservationApplied(selected);
3421
3422     changeColour(viewport.getGlobalColourScheme());
3423     if (selected)
3424     {
3425       modifyConservation_actionPerformed();
3426     }
3427     else
3428     {
3429       SliderPanel.hideConservationSlider();
3430     }
3431   }
3432
3433   /**
3434    * Action on selecting or deselecting (Colour) Above PID Threshold
3435    */
3436   @Override
3437   public void abovePIDThreshold_actionPerformed(boolean selected)
3438   {
3439     modifyPID.setEnabled(selected);
3440     viewport.setAbovePIDThreshold(selected);
3441     if (!selected)
3442     {
3443       viewport.getResidueShading().setThreshold(0,
3444               viewport.isIgnoreGapsConsensus());
3445     }
3446
3447     changeColour(viewport.getGlobalColourScheme());
3448     if (selected)
3449     {
3450       modifyPID_actionPerformed();
3451     }
3452     else
3453     {
3454       SliderPanel.hidePIDSlider();
3455     }
3456   }
3457
3458   /**
3459    * DOCUMENT ME!
3460    *
3461    * @param e
3462    *          DOCUMENT ME!
3463    */
3464   @Override
3465   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3466   {
3467     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3468     AlignmentSorter.sortByPID(viewport.getAlignment(),
3469             viewport.getAlignment().getSequenceAt(0));
3470     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3471             viewport.getAlignment()));
3472     alignPanel.paintAlignment(true, false);
3473   }
3474
3475   /**
3476    * DOCUMENT ME!
3477    *
3478    * @param e
3479    *          DOCUMENT ME!
3480    */
3481   @Override
3482   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3483   {
3484     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3485     AlignmentSorter.sortByID(viewport.getAlignment());
3486     addHistoryItem(
3487             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3488     alignPanel.paintAlignment(true, false);
3489   }
3490
3491   /**
3492    * DOCUMENT ME!
3493    *
3494    * @param e
3495    *          DOCUMENT ME!
3496    */
3497   @Override
3498   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3499   {
3500     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3501     AlignmentSorter.sortByLength(viewport.getAlignment());
3502     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3503             viewport.getAlignment()));
3504     alignPanel.paintAlignment(true, false);
3505   }
3506
3507   /**
3508    * DOCUMENT ME!
3509    *
3510    * @param e
3511    *          DOCUMENT ME!
3512    */
3513   @Override
3514   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3515   {
3516     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3517     AlignmentSorter.sortByGroup(viewport.getAlignment());
3518     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3519             viewport.getAlignment()));
3520
3521     alignPanel.paintAlignment(true, false);
3522   }
3523
3524   /**
3525    * DOCUMENT ME!
3526    *
3527    * @param e
3528    *          DOCUMENT ME!
3529    */
3530   @Override
3531   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3532   {
3533     new RedundancyPanel(alignPanel, this);
3534   }
3535
3536   /**
3537    * DOCUMENT ME!
3538    *
3539    * @param e
3540    *          DOCUMENT ME!
3541    */
3542   @Override
3543   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3544   {
3545     if ((viewport.getSelectionGroup() == null)
3546             || (viewport.getSelectionGroup().getSize() < 2))
3547     {
3548       JvOptionPane.showInternalMessageDialog(this,
3549               MessageManager.getString(
3550                       "label.you_must_select_least_two_sequences"),
3551               MessageManager.getString("label.invalid_selection"),
3552               JvOptionPane.WARNING_MESSAGE);
3553     }
3554     else
3555     {
3556       JInternalFrame frame = new JInternalFrame();
3557       frame.setContentPane(new PairwiseAlignPanel(viewport));
3558       Desktop.addInternalFrame(frame,
3559               MessageManager.getString("action.pairwise_alignment"), 600,
3560               500);
3561     }
3562   }
3563
3564   @Override
3565   public void autoCalculate_actionPerformed(ActionEvent e)
3566   {
3567     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3568     if (viewport.autoCalculateConsensus)
3569     {
3570       viewport.firePropertyChange("alignment", null,
3571               viewport.getAlignment().getSequences());
3572     }
3573   }
3574
3575   @Override
3576   public void sortByTreeOption_actionPerformed(ActionEvent e)
3577   {
3578     viewport.sortByTree = sortByTree.isSelected();
3579   }
3580
3581   @Override
3582   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3583   {
3584     viewport.followSelection = listenToViewSelections.isSelected();
3585   }
3586
3587   /**
3588    * Constructs a tree panel and adds it to the desktop
3589    *
3590    * @param type
3591    *          tree type (NJ or AV)
3592    * @param modelName
3593    *          name of score model used to compute the tree
3594    * @param options
3595    *          parameters for the distance or similarity calculation
3596    */
3597   void newTreePanel(String type, String modelName,
3598           SimilarityParamsI options)
3599   {
3600     String frameTitle = "";
3601     TreePanel tp;
3602
3603     boolean onSelection = false;
3604     if (viewport.getSelectionGroup() != null
3605             && viewport.getSelectionGroup().getSize() > 0)
3606     {
3607       SequenceGroup sg = viewport.getSelectionGroup();
3608
3609       /* Decide if the selection is a column region */
3610       for (SequenceI _s : sg.getSequences())
3611       {
3612         if (_s.getLength() < sg.getEndRes())
3613         {
3614           JvOptionPane.showMessageDialog(Desktop.desktop,
3615                   MessageManager.getString(
3616                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3617                   MessageManager.getString(
3618                           "label.sequences_selection_not_aligned"),
3619                   JvOptionPane.WARNING_MESSAGE);
3620
3621           return;
3622         }
3623       }
3624       onSelection = true;
3625     }
3626     else
3627     {
3628       if (viewport.getAlignment().getHeight() < 2)
3629       {
3630         return;
3631       }
3632     }
3633
3634     tp = new TreePanel(alignPanel, type, modelName, options);
3635     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3636
3637     frameTitle += " from ";
3638
3639     if (viewport.getViewName() != null)
3640     {
3641       frameTitle += viewport.getViewName() + " of ";
3642     }
3643
3644     frameTitle += this.title;
3645
3646     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3647   }
3648
3649   /**
3650    * DOCUMENT ME!
3651    *
3652    * @param title
3653    *          DOCUMENT ME!
3654    * @param order
3655    *          DOCUMENT ME!
3656    */
3657   public void addSortByOrderMenuItem(String title,
3658           final AlignmentOrder order)
3659   {
3660     final JMenuItem item = new JMenuItem(MessageManager
3661             .formatMessage("action.by_title_param", new Object[]
3662             { title }));
3663     sort.add(item);
3664     item.addActionListener(new java.awt.event.ActionListener()
3665     {
3666       @Override
3667       public void actionPerformed(ActionEvent e)
3668       {
3669         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3670
3671         // TODO: JBPNote - have to map order entries to curent SequenceI
3672         // pointers
3673         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3674
3675         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3676                 viewport.getAlignment()));
3677
3678         alignPanel.paintAlignment(true, false);
3679       }
3680     });
3681   }
3682
3683   /**
3684    * Add a new sort by annotation score menu item
3685    *
3686    * @param sort
3687    *          the menu to add the option to
3688    * @param scoreLabel
3689    *          the label used to retrieve scores for each sequence on the
3690    *          alignment
3691    */
3692   public void addSortByAnnotScoreMenuItem(JMenu sort,
3693           final String scoreLabel)
3694   {
3695     final JMenuItem item = new JMenuItem(scoreLabel);
3696     sort.add(item);
3697     item.addActionListener(new java.awt.event.ActionListener()
3698     {
3699       @Override
3700       public void actionPerformed(ActionEvent e)
3701       {
3702         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3703         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3704                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3705         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3706                 viewport.getAlignment()));
3707         alignPanel.paintAlignment(true, false);
3708       }
3709     });
3710   }
3711
3712   /**
3713    * last hash for alignment's annotation array - used to minimise cost of
3714    * rebuild.
3715    */
3716   protected int _annotationScoreVectorHash;
3717
3718   /**
3719    * search the alignment and rebuild the sort by annotation score submenu the
3720    * last alignment annotation vector hash is stored to minimize cost of
3721    * rebuilding in subsequence calls.
3722    *
3723    */
3724   @Override
3725   public void buildSortByAnnotationScoresMenu()
3726   {
3727     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3728     {
3729       return;
3730     }
3731
3732     if (viewport.getAlignment().getAlignmentAnnotation()
3733             .hashCode() != _annotationScoreVectorHash)
3734     {
3735       sortByAnnotScore.removeAll();
3736       // almost certainly a quicker way to do this - but we keep it simple
3737       Hashtable scoreSorts = new Hashtable();
3738       AlignmentAnnotation aann[];
3739       for (SequenceI sqa : viewport.getAlignment().getSequences())
3740       {
3741         aann = sqa.getAnnotation();
3742         for (int i = 0; aann != null && i < aann.length; i++)
3743         {
3744           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3745           {
3746             scoreSorts.put(aann[i].label, aann[i].label);
3747           }
3748         }
3749       }
3750       Enumeration labels = scoreSorts.keys();
3751       while (labels.hasMoreElements())
3752       {
3753         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3754                 (String) labels.nextElement());
3755       }
3756       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3757       scoreSorts.clear();
3758
3759       _annotationScoreVectorHash = viewport.getAlignment()
3760               .getAlignmentAnnotation().hashCode();
3761     }
3762   }
3763
3764   /**
3765    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3766    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3767    * call. Listeners are added to remove the menu item when the treePanel is
3768    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3769    * modified.
3770    */
3771   @Override
3772   public void buildTreeSortMenu()
3773   {
3774     sortByTreeMenu.removeAll();
3775
3776     List<Component> comps = PaintRefresher.components
3777             .get(viewport.getSequenceSetId());
3778     List<TreePanel> treePanels = new ArrayList<>();
3779     for (Component comp : comps)
3780     {
3781       if (comp instanceof TreePanel)
3782       {
3783         treePanels.add((TreePanel) comp);
3784       }
3785     }
3786
3787     if (treePanels.size() < 1)
3788     {
3789       sortByTreeMenu.setVisible(false);
3790       return;
3791     }
3792
3793     sortByTreeMenu.setVisible(true);
3794
3795     for (final TreePanel tp : treePanels)
3796     {
3797       final JMenuItem item = new JMenuItem(tp.getTitle());
3798       item.addActionListener(new java.awt.event.ActionListener()
3799       {
3800         @Override
3801         public void actionPerformed(ActionEvent e)
3802         {
3803           tp.sortByTree_actionPerformed();
3804           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3805
3806         }
3807       });
3808
3809       sortByTreeMenu.add(item);
3810     }
3811   }
3812
3813   public boolean sortBy(AlignmentOrder alorder, String undoname)
3814   {
3815     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3816     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3817     if (undoname != null)
3818     {
3819       addHistoryItem(new OrderCommand(undoname, oldOrder,
3820               viewport.getAlignment()));
3821     }
3822     alignPanel.paintAlignment(true, false);
3823     return true;
3824   }
3825
3826   /**
3827    * Work out whether the whole set of sequences or just the selected set will
3828    * be submitted for multiple alignment.
3829    *
3830    */
3831   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3832   {
3833     // Now, check we have enough sequences
3834     AlignmentView msa = null;
3835
3836     if ((viewport.getSelectionGroup() != null)
3837             && (viewport.getSelectionGroup().getSize() > 1))
3838     {
3839       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3840       // some common interface!
3841       /*
3842        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3843        * SequenceI[sz = seqs.getSize(false)];
3844        *
3845        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3846        * seqs.getSequenceAt(i); }
3847        */
3848       msa = viewport.getAlignmentView(true);
3849     }
3850     else if (viewport.getSelectionGroup() != null
3851             && viewport.getSelectionGroup().getSize() == 1)
3852     {
3853       int option = JvOptionPane.showConfirmDialog(this,
3854               MessageManager.getString("warn.oneseq_msainput_selection"),
3855               MessageManager.getString("label.invalid_selection"),
3856               JvOptionPane.OK_CANCEL_OPTION);
3857       if (option == JvOptionPane.OK_OPTION)
3858       {
3859         msa = viewport.getAlignmentView(false);
3860       }
3861     }
3862     else
3863     {
3864       msa = viewport.getAlignmentView(false);
3865     }
3866     return msa;
3867   }
3868
3869   /**
3870    * Decides what is submitted to a secondary structure prediction service: the
3871    * first sequence in the alignment, or in the current selection, or, if the
3872    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3873    * region or the whole alignment. (where the first sequence in the set is the
3874    * one that the prediction will be for).
3875    */
3876   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3877   {
3878     AlignmentView seqs = null;
3879
3880     if ((viewport.getSelectionGroup() != null)
3881             && (viewport.getSelectionGroup().getSize() > 0))
3882     {
3883       seqs = viewport.getAlignmentView(true);
3884     }
3885     else
3886     {
3887       seqs = viewport.getAlignmentView(false);
3888     }
3889     // limit sequences - JBPNote in future - could spawn multiple prediction
3890     // jobs
3891     // TODO: viewport.getAlignment().isAligned is a global state - the local
3892     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3893     if (!viewport.getAlignment().isAligned(false))
3894     {
3895       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3896       // TODO: if seqs.getSequences().length>1 then should really have warned
3897       // user!
3898
3899     }
3900     return seqs;
3901   }
3902
3903   /**
3904    * DOCUMENT ME!
3905    *
3906    * @param e
3907    *          DOCUMENT ME!
3908    */
3909   @Override
3910   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3911   {
3912     // Pick the tree file
3913     JalviewFileChooser chooser = new JalviewFileChooser(
3914             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3915     chooser.setFileView(new JalviewFileView());
3916     chooser.setDialogTitle(
3917             MessageManager.getString("label.select_newick_like_tree_file"));
3918     chooser.setToolTipText(
3919             MessageManager.getString("label.load_tree_file"));
3920
3921     int value = chooser.showOpenDialog(null);
3922
3923     if (value == JalviewFileChooser.APPROVE_OPTION)
3924     {
3925       String filePath = chooser.getSelectedFile().getPath();
3926       Cache.setProperty("LAST_DIRECTORY", filePath);
3927       NewickFile fin = null;
3928       try
3929       {
3930         fin = new NewickFile(filePath, DataSourceType.FILE);
3931         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3932       } catch (Exception ex)
3933       {
3934         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3935                 MessageManager.getString("label.problem_reading_tree_file"),
3936                 JvOptionPane.WARNING_MESSAGE);
3937         ex.printStackTrace();
3938       }
3939       if (fin != null && fin.hasWarningMessage())
3940       {
3941         JvOptionPane.showMessageDialog(Desktop.desktop,
3942                 fin.getWarningMessage(),
3943                 MessageManager
3944                         .getString("label.possible_problem_with_tree_file"),
3945                 JvOptionPane.WARNING_MESSAGE);
3946       }
3947     }
3948   }
3949
3950   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3951   {
3952     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3953   }
3954
3955   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3956           int h, int x, int y)
3957   {
3958     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3959   }
3960
3961   /**
3962    * Add a treeviewer for the tree extracted from a Newick file object to the
3963    * current alignment view
3964    *
3965    * @param nf
3966    *          the tree
3967    * @param title
3968    *          tree viewer title
3969    * @param input
3970    *          Associated alignment input data (or null)
3971    * @param w
3972    *          width
3973    * @param h
3974    *          height
3975    * @param x
3976    *          position
3977    * @param y
3978    *          position
3979    * @return TreePanel handle
3980    */
3981   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3982           AlignmentView input, int w, int h, int x, int y)
3983   {
3984     TreePanel tp = null;
3985
3986     try
3987     {
3988       nf.parse();
3989
3990       if (nf.getTree() != null)
3991       {
3992         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3993
3994         tp.setSize(w, h);
3995
3996         if (x > 0 && y > 0)
3997         {
3998           tp.setLocation(x, y);
3999         }
4000
4001         Desktop.addInternalFrame(tp, treeTitle, w, h);
4002       }
4003     } catch (Exception ex)
4004     {
4005       ex.printStackTrace();
4006     }
4007
4008     return tp;
4009   }
4010
4011   private boolean buildingMenu = false;
4012
4013   /**
4014    * Generates menu items and listener event actions for web service clients
4015    *
4016    */
4017   public void BuildWebServiceMenu()
4018   {
4019     while (buildingMenu)
4020     {
4021       try
4022       {
4023         System.err.println("Waiting for building menu to finish.");
4024         Thread.sleep(10);
4025       } catch (Exception e)
4026       {
4027       }
4028     }
4029     final AlignFrame me = this;
4030     buildingMenu = true;
4031     new Thread(new Runnable()
4032     {
4033       @Override
4034       public void run()
4035       {
4036         final List<JMenuItem> legacyItems = new ArrayList<>();
4037         try
4038         {
4039           // System.err.println("Building ws menu again "
4040           // + Thread.currentThread());
4041           // TODO: add support for context dependent disabling of services based
4042           // on
4043           // alignment and current selection
4044           // TODO: add additional serviceHandle parameter to specify abstract
4045           // handler
4046           // class independently of AbstractName
4047           // TODO: add in rediscovery GUI function to restart discoverer
4048           // TODO: group services by location as well as function and/or
4049           // introduce
4050           // object broker mechanism.
4051           final Vector<JMenu> wsmenu = new Vector<>();
4052           final IProgressIndicator af = me;
4053
4054           /*
4055            * do not i18n these strings - they are hard-coded in class
4056            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4057            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4058            */
4059           final JMenu msawsmenu = new JMenu("Alignment");
4060           final JMenu secstrmenu = new JMenu(
4061                   "Secondary Structure Prediction");
4062           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4063           final JMenu analymenu = new JMenu("Analysis");
4064           final JMenu dismenu = new JMenu("Protein Disorder");
4065           // JAL-940 - only show secondary structure prediction services from
4066           // the legacy server
4067           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4068               // &&
4069           Discoverer.services != null && (Discoverer.services.size() > 0))
4070           {
4071             // TODO: refactor to allow list of AbstractName/Handler bindings to
4072             // be
4073             // stored or retrieved from elsewhere
4074             // No MSAWS used any more:
4075             // Vector msaws = null; // (Vector)
4076             // Discoverer.services.get("MsaWS");
4077             Vector secstrpr = (Vector) Discoverer.services
4078                     .get("SecStrPred");
4079             if (secstrpr != null)
4080             {
4081               // Add any secondary structure prediction services
4082               for (int i = 0, j = secstrpr.size(); i < j; i++)
4083               {
4084                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4085                         .get(i);
4086                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4087                         .getServiceClient(sh);
4088                 int p = secstrmenu.getItemCount();
4089                 impl.attachWSMenuEntry(secstrmenu, me);
4090                 int q = secstrmenu.getItemCount();
4091                 for (int litm = p; litm < q; litm++)
4092                 {
4093                   legacyItems.add(secstrmenu.getItem(litm));
4094                 }
4095               }
4096             }
4097           }
4098
4099           // Add all submenus in the order they should appear on the web
4100           // services menu
4101           wsmenu.add(msawsmenu);
4102           wsmenu.add(secstrmenu);
4103           wsmenu.add(dismenu);
4104           wsmenu.add(analymenu);
4105           // No search services yet
4106           // wsmenu.add(seqsrchmenu);
4107
4108           javax.swing.SwingUtilities.invokeLater(new Runnable()
4109           {
4110             @Override
4111             public void run()
4112             {
4113               try
4114               {
4115                 webService.removeAll();
4116                 // first, add discovered services onto the webservices menu
4117                 if (wsmenu.size() > 0)
4118                 {
4119                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4120                   {
4121                     webService.add(wsmenu.get(i));
4122                   }
4123                 }
4124                 else
4125                 {
4126                   webService.add(me.webServiceNoServices);
4127                 }
4128                 // TODO: move into separate menu builder class.
4129                 boolean new_sspred = false;
4130                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4131                 {
4132                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4133                   if (jws2servs != null)
4134                   {
4135                     if (jws2servs.hasServices())
4136                     {
4137                       jws2servs.attachWSMenuEntry(webService, me);
4138                       for (Jws2Instance sv : jws2servs.getServices())
4139                       {
4140                         if (sv.description.toLowerCase().contains("jpred"))
4141                         {
4142                           for (JMenuItem jmi : legacyItems)
4143                           {
4144                             jmi.setVisible(false);
4145                           }
4146                         }
4147                       }
4148
4149                     }
4150                     if (jws2servs.isRunning())
4151                     {
4152                       JMenuItem tm = new JMenuItem(
4153                               "Still discovering JABA Services");
4154                       tm.setEnabled(false);
4155                       webService.add(tm);
4156                     }
4157                   }
4158                 }
4159                 build_urlServiceMenu(me.webService);
4160                 build_fetchdbmenu(webService);
4161                 for (JMenu item : wsmenu)
4162                 {
4163                   if (item.getItemCount() == 0)
4164                   {
4165                     item.setEnabled(false);
4166                   }
4167                   else
4168                   {
4169                     item.setEnabled(true);
4170                   }
4171                 }
4172               } catch (Exception e)
4173               {
4174                 Cache.log.debug(
4175                         "Exception during web service menu building process.",
4176                         e);
4177               }
4178             }
4179           });
4180         } catch (Exception e)
4181         {
4182         }
4183         buildingMenu = false;
4184       }
4185     }).start();
4186
4187   }
4188
4189   /**
4190    * construct any groupURL type service menu entries.
4191    *
4192    * @param webService
4193    */
4194   private void build_urlServiceMenu(JMenu webService)
4195   {
4196     // TODO: remove this code when 2.7 is released
4197     // DEBUG - alignmentView
4198     /*
4199      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4200      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4201      *
4202      * @Override public void actionPerformed(ActionEvent e) {
4203      * jalview.datamodel.AlignmentView
4204      * .testSelectionViews(af.viewport.getAlignment(),
4205      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4206      *
4207      * }); webService.add(testAlView);
4208      */
4209     // TODO: refactor to RestClient discoverer and merge menu entries for
4210     // rest-style services with other types of analysis/calculation service
4211     // SHmmr test client - still being implemented.
4212     // DEBUG - alignmentView
4213
4214     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4215             .getRestClients())
4216     {
4217       client.attachWSMenuEntry(
4218               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4219               this);
4220     }
4221   }
4222
4223   /**
4224    * Searches the alignment sequences for xRefs and builds the Show
4225    * Cross-References menu (formerly called Show Products), with database
4226    * sources for which cross-references are found (protein sources for a
4227    * nucleotide alignment and vice versa)
4228    *
4229    * @return true if Show Cross-references menu should be enabled
4230    */
4231   public boolean canShowProducts()
4232   {
4233     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4234     AlignmentI dataset = viewport.getAlignment().getDataset();
4235
4236     showProducts.removeAll();
4237     final boolean dna = viewport.getAlignment().isNucleotide();
4238
4239     if (seqs == null || seqs.length == 0)
4240     {
4241       // nothing to see here.
4242       return false;
4243     }
4244
4245     boolean showp = false;
4246     try
4247     {
4248       List<String> ptypes = new CrossRef(seqs, dataset)
4249               .findXrefSourcesForSequences(dna);
4250
4251       for (final String source : ptypes)
4252       {
4253         showp = true;
4254         final AlignFrame af = this;
4255         JMenuItem xtype = new JMenuItem(source);
4256         xtype.addActionListener(new ActionListener()
4257         {
4258           @Override
4259           public void actionPerformed(ActionEvent e)
4260           {
4261             showProductsFor(af.viewport.getSequenceSelection(), dna,
4262                     source);
4263           }
4264         });
4265         showProducts.add(xtype);
4266       }
4267       showProducts.setVisible(showp);
4268       showProducts.setEnabled(showp);
4269     } catch (Exception e)
4270     {
4271       Cache.log.warn(
4272               "canShowProducts threw an exception - please report to help@jalview.org",
4273               e);
4274       return false;
4275     }
4276     return showp;
4277   }
4278
4279   /**
4280    * Finds and displays cross-references for the selected sequences (protein
4281    * products for nucleotide sequences, dna coding sequences for peptides).
4282    *
4283    * @param sel
4284    *          the sequences to show cross-references for
4285    * @param dna
4286    *          true if from a nucleotide alignment (so showing proteins)
4287    * @param source
4288    *          the database to show cross-references for
4289    */
4290   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4291           final String source)
4292   {
4293     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4294             .start();
4295   }
4296
4297   /**
4298    * Construct and display a new frame containing the translation of this
4299    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4300    */
4301   @Override
4302   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4303   {
4304     AlignmentI al = null;
4305     try
4306     {
4307       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4308
4309       al = dna.translateCdna(codeTable);
4310     } catch (Exception ex)
4311     {
4312       jalview.bin.Cache.log.error(
4313               "Exception during translation. Please report this !", ex);
4314       final String msg = MessageManager.getString(
4315               "label.error_when_translating_sequences_submit_bug_report");
4316       final String errorTitle = MessageManager
4317               .getString("label.implementation_error")
4318               + MessageManager.getString("label.translation_failed");
4319       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4320               JvOptionPane.ERROR_MESSAGE);
4321       return;
4322     }
4323     if (al == null || al.getHeight() == 0)
4324     {
4325       final String msg = MessageManager.getString(
4326               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4327       final String errorTitle = MessageManager
4328               .getString("label.translation_failed");
4329       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4330               JvOptionPane.WARNING_MESSAGE);
4331     }
4332     else
4333     {
4334       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4335       af.setFileFormat(this.currentFileFormat);
4336       final String newTitle = MessageManager
4337               .formatMessage("label.translation_of_params", new Object[]
4338               { this.getTitle(), codeTable.getId() });
4339       af.setTitle(newTitle);
4340       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4341       {
4342         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4343         viewport.openSplitFrame(af, new Alignment(seqs));
4344       }
4345       else
4346       {
4347         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4348                 DEFAULT_HEIGHT);
4349       }
4350     }
4351   }
4352
4353   /**
4354    * Set the file format
4355    *
4356    * @param format
4357    */
4358   public void setFileFormat(FileFormatI format)
4359   {
4360     this.currentFileFormat = format;
4361   }
4362
4363   /**
4364    * Try to load a features file onto the alignment.
4365    *
4366    * @param file
4367    *          contents or path to retrieve file
4368    * @param sourceType
4369    *          access mode of file (see jalview.io.AlignFile)
4370    * @return true if features file was parsed correctly.
4371    */
4372   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4373   {
4374     return avc.parseFeaturesFile(file, sourceType,
4375             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4376
4377   }
4378
4379   @Override
4380   public void refreshFeatureUI(boolean enableIfNecessary)
4381   {
4382     // note - currently this is only still here rather than in the controller
4383     // because of the featureSettings hard reference that is yet to be
4384     // abstracted
4385     if (enableIfNecessary)
4386     {
4387       viewport.setShowSequenceFeatures(true);
4388       showSeqFeatures.setSelected(true);
4389     }
4390
4391   }
4392
4393   @Override
4394   public void dragEnter(DropTargetDragEvent evt)
4395   {
4396   }
4397
4398   @Override
4399   public void dragExit(DropTargetEvent evt)
4400   {
4401   }
4402
4403   @Override
4404   public void dragOver(DropTargetDragEvent evt)
4405   {
4406   }
4407
4408   @Override
4409   public void dropActionChanged(DropTargetDragEvent evt)
4410   {
4411   }
4412
4413   @Override
4414   public void drop(DropTargetDropEvent evt)
4415   {
4416     // JAL-1552 - acceptDrop required before getTransferable call for
4417     // Java's Transferable for native dnd
4418     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4419     Transferable t = evt.getTransferable();
4420     final AlignFrame thisaf = this;
4421     final List<String> files = new ArrayList<>();
4422     List<DataSourceType> protocols = new ArrayList<>();
4423
4424     try
4425     {
4426       Desktop.transferFromDropTarget(files, protocols, evt, t);
4427     } catch (Exception e)
4428     {
4429       e.printStackTrace();
4430     }
4431     if (files != null)
4432     {
4433       new Thread(new Runnable()
4434       {
4435         @Override
4436         public void run()
4437         {
4438           try
4439           {
4440             // check to see if any of these files have names matching sequences
4441             // in
4442             // the alignment
4443             SequenceIdMatcher idm = new SequenceIdMatcher(
4444                     viewport.getAlignment().getSequencesArray());
4445             /**
4446              * Object[] { String,SequenceI}
4447              */
4448             ArrayList<Object[]> filesmatched = new ArrayList<>();
4449             ArrayList<String> filesnotmatched = new ArrayList<>();
4450             for (int i = 0; i < files.size(); i++)
4451             {
4452               String file = files.get(i).toString();
4453               String pdbfn = "";
4454               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4455               if (protocol == DataSourceType.FILE)
4456               {
4457                 File fl = new File(file);
4458                 pdbfn = fl.getName();
4459               }
4460               else if (protocol == DataSourceType.URL)
4461               {
4462                 URL url = new URL(file);
4463                 pdbfn = url.getFile();
4464               }
4465               if (pdbfn.length() > 0)
4466               {
4467                 // attempt to find a match in the alignment
4468                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4469                 int l = 0, c = pdbfn.indexOf(".");
4470                 while (mtch == null && c != -1)
4471                 {
4472                   do
4473                   {
4474                     l = c;
4475                   } while ((c = pdbfn.indexOf(".", l)) > l);
4476                   if (l > -1)
4477                   {
4478                     pdbfn = pdbfn.substring(0, l);
4479                   }
4480                   mtch = idm.findAllIdMatches(pdbfn);
4481                 }
4482                 if (mtch != null)
4483                 {
4484                   FileFormatI type = null;
4485                   try
4486                   {
4487                     type = new IdentifyFile().identify(file, protocol);
4488                   } catch (Exception ex)
4489                   {
4490                     type = null;
4491                   }
4492                   if (type != null && type.isStructureFile())
4493                   {
4494                     filesmatched.add(new Object[] { file, protocol, mtch });
4495                     continue;
4496                   }
4497                 }
4498                 // File wasn't named like one of the sequences or wasn't a PDB
4499                 // file.
4500                 filesnotmatched.add(file);
4501               }
4502             }
4503             int assocfiles = 0;
4504             if (filesmatched.size() > 0)
4505             {
4506               boolean autoAssociate = Cache
4507                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4508               if (!autoAssociate)
4509               {
4510                 String msg = MessageManager.formatMessage(
4511                         "label.automatically_associate_structure_files_with_sequences_same_name",
4512                         new Object[]
4513                         { Integer.valueOf(filesmatched.size())
4514                                 .toString() });
4515                 String ttl = MessageManager.getString(
4516                         "label.automatically_associate_structure_files_by_name");
4517                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4518                         ttl, JvOptionPane.YES_NO_OPTION);
4519                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4520               }
4521               if (autoAssociate)
4522               {
4523                 for (Object[] fm : filesmatched)
4524                 {
4525                   // try and associate
4526                   // TODO: may want to set a standard ID naming formalism for
4527                   // associating PDB files which have no IDs.
4528                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4529                   {
4530                     PDBEntry pe = new AssociatePdbFileWithSeq()
4531                             .associatePdbWithSeq((String) fm[0],
4532                                     (DataSourceType) fm[1], toassoc, false,
4533                                     Desktop.instance);
4534                     if (pe != null)
4535                     {
4536                       System.err.println("Associated file : "
4537                               + ((String) fm[0]) + " with "
4538                               + toassoc.getDisplayId(true));
4539                       assocfiles++;
4540                     }
4541                   }
4542                   // TODO: do we need to update overview ? only if features are
4543                   // shown I guess
4544                   alignPanel.paintAlignment(true, false);
4545                 }
4546               }
4547               else
4548               {
4549                 /*
4550                  * add declined structures as sequences
4551                  */
4552                 for (Object[] o : filesmatched)
4553                 {
4554                   filesnotmatched.add((String) o[0]);
4555                 }
4556               }
4557             }
4558             if (filesnotmatched.size() > 0)
4559             {
4560               if (assocfiles > 0 && (Cache.getDefault(
4561                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4562                       || JvOptionPane.showConfirmDialog(thisaf,
4563                               "<html>" + MessageManager.formatMessage(
4564                                       "label.ignore_unmatched_dropped_files_info",
4565                                       new Object[]
4566                                       { Integer.valueOf(
4567                                               filesnotmatched.size())
4568                                               .toString() })
4569                                       + "</html>",
4570                               MessageManager.getString(
4571                                       "label.ignore_unmatched_dropped_files"),
4572                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4573               {
4574                 return;
4575               }
4576               for (String fn : filesnotmatched)
4577               {
4578                 loadJalviewDataFile(fn, null, null, null);
4579               }
4580
4581             }
4582           } catch (Exception ex)
4583           {
4584             ex.printStackTrace();
4585           }
4586         }
4587       }).start();
4588     }
4589   }
4590
4591   /**
4592    * Attempt to load a "dropped" file or URL string, by testing in turn for
4593    * <ul>
4594    * <li>an Annotation file</li>
4595    * <li>a JNet file</li>
4596    * <li>a features file</li>
4597    * <li>else try to interpret as an alignment file</li>
4598    * </ul>
4599    *
4600    * @param file
4601    *          either a filename or a URL string.
4602    */
4603   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4604           FileFormatI format, SequenceI assocSeq)
4605   {
4606     try
4607     {
4608       if (sourceType == null)
4609       {
4610         sourceType = FormatAdapter.checkProtocol(file);
4611       }
4612       // if the file isn't identified, or not positively identified as some
4613       // other filetype (PFAM is default unidentified alignment file type) then
4614       // try to parse as annotation.
4615       boolean isAnnotation = (format == null
4616               || FileFormat.Pfam.equals(format))
4617                       ? new AnnotationFile().annotateAlignmentView(viewport,
4618                               file, sourceType)
4619                       : false;
4620
4621       if (!isAnnotation)
4622       {
4623         // first see if its a T-COFFEE score file
4624         TCoffeeScoreFile tcf = null;
4625         try
4626         {
4627           tcf = new TCoffeeScoreFile(file, sourceType);
4628           if (tcf.isValid())
4629           {
4630             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4631             {
4632               buildColourMenu();
4633               changeColour(
4634                       new TCoffeeColourScheme(viewport.getAlignment()));
4635               isAnnotation = true;
4636               statusBar.setText(MessageManager.getString(
4637                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4638             }
4639             else
4640             {
4641               // some problem - if no warning its probable that the ID matching
4642               // process didn't work
4643               JvOptionPane.showMessageDialog(Desktop.desktop,
4644                       tcf.getWarningMessage() == null
4645                               ? MessageManager.getString(
4646                                       "label.check_file_matches_sequence_ids_alignment")
4647                               : tcf.getWarningMessage(),
4648                       MessageManager.getString(
4649                               "label.problem_reading_tcoffee_score_file"),
4650                       JvOptionPane.WARNING_MESSAGE);
4651             }
4652           }
4653           else
4654           {
4655             tcf = null;
4656           }
4657         } catch (Exception x)
4658         {
4659           Cache.log.debug(
4660                   "Exception when processing data source as T-COFFEE score file",
4661                   x);
4662           tcf = null;
4663         }
4664         if (tcf == null)
4665         {
4666           // try to see if its a JNet 'concise' style annotation file *before*
4667           // we
4668           // try to parse it as a features file
4669           if (format == null)
4670           {
4671             format = new IdentifyFile().identify(file, sourceType);
4672           }
4673           if (FileFormat.ScoreMatrix == format)
4674           {
4675             ScoreMatrixFile sm = new ScoreMatrixFile(
4676                     new FileParse(file, sourceType));
4677             sm.parse();
4678             // todo: i18n this message
4679             statusBar.setText(MessageManager.formatMessage(
4680                     "label.successfully_loaded_matrix",
4681                     sm.getMatrixName()));
4682           }
4683           else if (FileFormat.Jnet.equals(format))
4684           {
4685             JPredFile predictions = new JPredFile(file, sourceType);
4686             new JnetAnnotationMaker();
4687             JnetAnnotationMaker.add_annotation(predictions,
4688                     viewport.getAlignment(), 0, false);
4689             viewport.getAlignment().setupJPredAlignment();
4690             isAnnotation = true;
4691           }
4692           // else if (IdentifyFile.FeaturesFile.equals(format))
4693           else if (FileFormat.Features.equals(format))
4694           {
4695             if (parseFeaturesFile(file, sourceType))
4696             {
4697               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4698               if (splitFrame != null)
4699               {
4700                 splitFrame.repaint();
4701               }
4702               else
4703               {
4704                 alignPanel.paintAlignment(true, true);
4705               }
4706             }
4707           }
4708           else
4709           {
4710             new FileLoader().LoadFile(viewport, file, sourceType, format);
4711           }
4712         }
4713       }
4714       if (isAnnotation)
4715       {
4716
4717         alignPanel.adjustAnnotationHeight();
4718         viewport.updateSequenceIdColours();
4719         buildSortByAnnotationScoresMenu();
4720         alignPanel.paintAlignment(true, true);
4721       }
4722     } catch (Exception ex)
4723     {
4724       ex.printStackTrace();
4725     } catch (OutOfMemoryError oom)
4726     {
4727       try
4728       {
4729         System.gc();
4730       } catch (Exception x)
4731       {
4732       }
4733       new OOMWarning(
4734               "loading data "
4735                       + (sourceType != null
4736                               ? (sourceType == DataSourceType.PASTE
4737                                       ? "from clipboard."
4738                                       : "using " + sourceType + " from "
4739                                               + file)
4740                               : ".")
4741                       + (format != null
4742                               ? "(parsing as '" + format + "' file)"
4743                               : ""),
4744               oom, Desktop.desktop);
4745     }
4746   }
4747
4748   /**
4749    * Method invoked by the ChangeListener on the tabbed pane, in other words
4750    * when a different tabbed pane is selected by the user or programmatically.
4751    */
4752   @Override
4753   public void tabSelectionChanged(int index)
4754   {
4755     if (index > -1)
4756     {
4757       alignPanel = alignPanels.get(index);
4758       viewport = alignPanel.av;
4759       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4760       setMenusFromViewport(viewport);
4761       if (featureSettings != null && featureSettings.isOpen()
4762               && featureSettings.fr.getViewport() != viewport)
4763       {
4764         if (viewport.isShowSequenceFeatures())
4765         {
4766           // refresh the featureSettings to reflect UI change
4767           showFeatureSettingsUI();
4768         }
4769         else
4770         {
4771           // close feature settings for this view.
4772           featureSettings.close();
4773         }
4774       }
4775
4776     }
4777
4778     /*
4779      * 'focus' any colour slider that is open to the selected viewport
4780      */
4781     if (viewport.getConservationSelected())
4782     {
4783       SliderPanel.setConservationSlider(alignPanel,
4784               viewport.getResidueShading(), alignPanel.getViewName());
4785     }
4786     else
4787     {
4788       SliderPanel.hideConservationSlider();
4789     }
4790     if (viewport.getAbovePIDThreshold())
4791     {
4792       SliderPanel.setPIDSliderSource(alignPanel,
4793               viewport.getResidueShading(), alignPanel.getViewName());
4794     }
4795     else
4796     {
4797       SliderPanel.hidePIDSlider();
4798     }
4799
4800     /*
4801      * If there is a frame linked to this one in a SplitPane, switch it to the
4802      * same view tab index. No infinite recursion of calls should happen, since
4803      * tabSelectionChanged() should not get invoked on setting the selected
4804      * index to an unchanged value. Guard against setting an invalid index
4805      * before the new view peer tab has been created.
4806      */
4807     final AlignViewportI peer = viewport.getCodingComplement();
4808     if (peer != null)
4809     {
4810       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4811               .getAlignPanel().alignFrame;
4812       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4813       {
4814         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4815       }
4816     }
4817   }
4818
4819   /**
4820    * On right mouse click on view tab, prompt for and set new view name.
4821    */
4822   @Override
4823   public void tabbedPane_mousePressed(MouseEvent e)
4824   {
4825     if (e.isPopupTrigger())
4826     {
4827       String msg = MessageManager.getString("label.enter_view_name");
4828       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4829               JvOptionPane.QUESTION_MESSAGE);
4830
4831       if (reply != null)
4832       {
4833         viewport.setViewName(reply);
4834         // TODO warn if reply is in getExistingViewNames()?
4835         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4836       }
4837     }
4838   }
4839
4840   public AlignViewport getCurrentView()
4841   {
4842     return viewport;
4843   }
4844
4845   /**
4846    * Open the dialog for regex description parsing.
4847    */
4848   @Override
4849   protected void extractScores_actionPerformed(ActionEvent e)
4850   {
4851     ParseProperties pp = new jalview.analysis.ParseProperties(
4852             viewport.getAlignment());
4853     // TODO: verify regex and introduce GUI dialog for version 2.5
4854     // if (pp.getScoresFromDescription("col", "score column ",
4855     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4856     // true)>0)
4857     if (pp.getScoresFromDescription("description column",
4858             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4859     {
4860       buildSortByAnnotationScoresMenu();
4861     }
4862   }
4863
4864   /*
4865    * (non-Javadoc)
4866    *
4867    * @see
4868    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4869    * )
4870    */
4871   @Override
4872   protected void showDbRefs_actionPerformed(ActionEvent e)
4873   {
4874     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4875   }
4876
4877   /*
4878    * (non-Javadoc)
4879    *
4880    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4881    * ActionEvent)
4882    */
4883   @Override
4884   protected void showNpFeats_actionPerformed(ActionEvent e)
4885   {
4886     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4887   }
4888
4889   /**
4890    * find the viewport amongst the tabs in this alignment frame and close that
4891    * tab
4892    *
4893    * @param av
4894    */
4895   public boolean closeView(AlignViewportI av)
4896   {
4897     if (viewport == av)
4898     {
4899       this.closeMenuItem_actionPerformed(false);
4900       return true;
4901     }
4902     Component[] comp = tabbedPane.getComponents();
4903     for (int i = 0; comp != null && i < comp.length; i++)
4904     {
4905       if (comp[i] instanceof AlignmentPanel)
4906       {
4907         if (((AlignmentPanel) comp[i]).av == av)
4908         {
4909           // close the view.
4910           closeView((AlignmentPanel) comp[i]);
4911           return true;
4912         }
4913       }
4914     }
4915     return false;
4916   }
4917
4918   protected void build_fetchdbmenu(JMenu webService)
4919   {
4920     // Temporary hack - DBRef Fetcher always top level ws entry.
4921     // TODO We probably want to store a sequence database checklist in
4922     // preferences and have checkboxes.. rather than individual sources selected
4923     // here
4924     final JMenu rfetch = new JMenu(
4925             MessageManager.getString("action.fetch_db_references"));
4926     rfetch.setToolTipText(MessageManager.getString(
4927             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4928     webService.add(rfetch);
4929
4930     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4931             MessageManager.getString("option.trim_retrieved_seqs"));
4932     trimrs.setToolTipText(
4933             MessageManager.getString("label.trim_retrieved_sequences"));
4934     trimrs.setSelected(
4935             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4936     trimrs.addActionListener(new ActionListener()
4937     {
4938       @Override
4939       public void actionPerformed(ActionEvent e)
4940       {
4941         trimrs.setSelected(trimrs.isSelected());
4942         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4943                 Boolean.valueOf(trimrs.isSelected()).toString());
4944       };
4945     });
4946     rfetch.add(trimrs);
4947     JMenuItem fetchr = new JMenuItem(
4948             MessageManager.getString("label.standard_databases"));
4949     fetchr.setToolTipText(
4950             MessageManager.getString("label.fetch_embl_uniprot"));
4951     fetchr.addActionListener(new ActionListener()
4952     {
4953
4954       @Override
4955       public void actionPerformed(ActionEvent e)
4956       {
4957         new Thread(new Runnable()
4958         {
4959           @Override
4960           public void run()
4961           {
4962             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4963                     .getAlignment().isNucleotide();
4964             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4965                     alignPanel.av.getSequenceSelection(),
4966                     alignPanel.alignFrame, null,
4967                     alignPanel.alignFrame.featureSettings, isNucleotide);
4968             dbRefFetcher.addListener(new FetchFinishedListenerI()
4969             {
4970               @Override
4971               public void finished()
4972               {
4973
4974                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
4975                         .getFeatureSettingsModels())
4976                 {
4977
4978                   alignPanel.av.mergeFeaturesStyle(srcSettings);
4979                 }
4980                 AlignFrame.this.setMenusForViewport();
4981               }
4982             });
4983             dbRefFetcher.fetchDBRefs(false);
4984           }
4985         }).start();
4986
4987       }
4988
4989     });
4990     rfetch.add(fetchr);
4991     final AlignFrame me = this;
4992     new Thread(new Runnable()
4993     {
4994       @Override
4995       public void run()
4996       {
4997         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4998                 .getSequenceFetcherSingleton(me);
4999         javax.swing.SwingUtilities.invokeLater(new Runnable()
5000         {
5001           @Override
5002           public void run()
5003           {
5004             String[] dbclasses = sf.getOrderedSupportedSources();
5005             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5006             // jalview.util.QuickSort.sort(otherdb, otherdb);
5007             List<DbSourceProxy> otherdb;
5008             JMenu dfetch = new JMenu();
5009             JMenu ifetch = new JMenu();
5010             JMenuItem fetchr = null;
5011             int comp = 0, icomp = 0, mcomp = 15;
5012             String mname = null;
5013             int dbi = 0;
5014             for (String dbclass : dbclasses)
5015             {
5016               otherdb = sf.getSourceProxy(dbclass);
5017               // add a single entry for this class, or submenu allowing 'fetch
5018               // all' or pick one
5019               if (otherdb == null || otherdb.size() < 1)
5020               {
5021                 continue;
5022               }
5023               // List<DbSourceProxy> dbs=otherdb;
5024               // otherdb=new ArrayList<DbSourceProxy>();
5025               // for (DbSourceProxy db:dbs)
5026               // {
5027               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5028               // }
5029               if (mname == null)
5030               {
5031                 mname = "From " + dbclass;
5032               }
5033               if (otherdb.size() == 1)
5034               {
5035                 final DbSourceProxy[] dassource = otherdb
5036                         .toArray(new DbSourceProxy[0]);
5037                 DbSourceProxy src = otherdb.get(0);
5038                 fetchr = new JMenuItem(src.getDbSource());
5039                 fetchr.addActionListener(new ActionListener()
5040                 {
5041
5042                   @Override
5043                   public void actionPerformed(ActionEvent e)
5044                   {
5045                     new Thread(new Runnable()
5046                     {
5047
5048                       @Override
5049                       public void run()
5050                       {
5051                         boolean isNucleotide = alignPanel.alignFrame
5052                                 .getViewport().getAlignment()
5053                                 .isNucleotide();
5054                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5055                                 alignPanel.av.getSequenceSelection(),
5056                                 alignPanel.alignFrame, dassource,
5057                                 alignPanel.alignFrame.featureSettings,
5058                                 isNucleotide);
5059                         dbRefFetcher
5060                                 .addListener(new FetchFinishedListenerI()
5061                                 {
5062                                   @Override
5063                                   public void finished()
5064                                   {
5065                                     FeatureSettingsModelI srcSettings = dassource[0]
5066                                             .getFeatureColourScheme();
5067                                     alignPanel.av.mergeFeaturesStyle(
5068                                             srcSettings);
5069                                     AlignFrame.this.setMenusForViewport();
5070                                   }
5071                                 });
5072                         dbRefFetcher.fetchDBRefs(false);
5073                       }
5074                     }).start();
5075                   }
5076
5077                 });
5078                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5079                         MessageManager.formatMessage(
5080                                 "label.fetch_retrieve_from", new Object[]
5081                                 { src.getDbName() })));
5082                 dfetch.add(fetchr);
5083                 comp++;
5084               }
5085               else
5086               {
5087                 final DbSourceProxy[] dassource = otherdb
5088                         .toArray(new DbSourceProxy[0]);
5089                 // fetch all entry
5090                 DbSourceProxy src = otherdb.get(0);
5091                 fetchr = new JMenuItem(MessageManager
5092                         .formatMessage("label.fetch_all_param", new Object[]
5093                         { src.getDbSource() }));
5094                 fetchr.addActionListener(new ActionListener()
5095                 {
5096                   @Override
5097                   public void actionPerformed(ActionEvent e)
5098                   {
5099                     new Thread(new Runnable()
5100                     {
5101
5102                       @Override
5103                       public void run()
5104                       {
5105                         boolean isNucleotide = alignPanel.alignFrame
5106                                 .getViewport().getAlignment()
5107                                 .isNucleotide();
5108                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5109                                 alignPanel.av.getSequenceSelection(),
5110                                 alignPanel.alignFrame, dassource,
5111                                 alignPanel.alignFrame.featureSettings,
5112                                 isNucleotide);
5113                         dbRefFetcher
5114                                 .addListener(new FetchFinishedListenerI()
5115                                 {
5116                                   @Override
5117                                   public void finished()
5118                                   {
5119                                     AlignFrame.this.setMenusForViewport();
5120                                   }
5121                                 });
5122                         dbRefFetcher.fetchDBRefs(false);
5123                       }
5124                     }).start();
5125                   }
5126                 });
5127
5128                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5129                         MessageManager.formatMessage(
5130                                 "label.fetch_retrieve_from_all_sources",
5131                                 new Object[]
5132                                 { Integer.valueOf(otherdb.size())
5133                                         .toString(),
5134                                     src.getDbSource(), src.getDbName() })));
5135                 dfetch.add(fetchr);
5136                 comp++;
5137                 // and then build the rest of the individual menus
5138                 ifetch = new JMenu(MessageManager.formatMessage(
5139                         "label.source_from_db_source", new Object[]
5140                         { src.getDbSource() }));
5141                 icomp = 0;
5142                 String imname = null;
5143                 int i = 0;
5144                 for (DbSourceProxy sproxy : otherdb)
5145                 {
5146                   String dbname = sproxy.getDbName();
5147                   String sname = dbname.length() > 5
5148                           ? dbname.substring(0, 5) + "..."
5149                           : dbname;
5150                   String msname = dbname.length() > 10
5151                           ? dbname.substring(0, 10) + "..."
5152                           : dbname;
5153                   if (imname == null)
5154                   {
5155                     imname = MessageManager
5156                             .formatMessage("label.from_msname", new Object[]
5157                             { sname });
5158                   }
5159                   fetchr = new JMenuItem(msname);
5160                   final DbSourceProxy[] dassrc = { sproxy };
5161                   fetchr.addActionListener(new ActionListener()
5162                   {
5163
5164                     @Override
5165                     public void actionPerformed(ActionEvent e)
5166                     {
5167                       new Thread(new Runnable()
5168                       {
5169
5170                         @Override
5171                         public void run()
5172                         {
5173                           boolean isNucleotide = alignPanel.alignFrame
5174                                   .getViewport().getAlignment()
5175                                   .isNucleotide();
5176                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5177                                   alignPanel.av.getSequenceSelection(),
5178                                   alignPanel.alignFrame, dassrc,
5179                                   alignPanel.alignFrame.featureSettings,
5180                                   isNucleotide);
5181                           dbRefFetcher
5182                                   .addListener(new FetchFinishedListenerI()
5183                                   {
5184                                     @Override
5185                                     public void finished()
5186                                     {
5187                                       AlignFrame.this.setMenusForViewport();
5188                                     }
5189                                   });
5190                           dbRefFetcher.fetchDBRefs(false);
5191                         }
5192                       }).start();
5193                     }
5194
5195                   });
5196                   fetchr.setToolTipText(
5197                           "<html>" + MessageManager.formatMessage(
5198                                   "label.fetch_retrieve_from", new Object[]
5199                                   { dbname }));
5200                   ifetch.add(fetchr);
5201                   ++i;
5202                   if (++icomp >= mcomp || i == (otherdb.size()))
5203                   {
5204                     ifetch.setText(MessageManager.formatMessage(
5205                             "label.source_to_target", imname, sname));
5206                     dfetch.add(ifetch);
5207                     ifetch = new JMenu();
5208                     imname = null;
5209                     icomp = 0;
5210                     comp++;
5211                   }
5212                 }
5213               }
5214               ++dbi;
5215               if (comp >= mcomp || dbi >= (dbclasses.length))
5216               {
5217                 dfetch.setText(MessageManager.formatMessage(
5218                         "label.source_to_target", mname, dbclass));
5219                 rfetch.add(dfetch);
5220                 dfetch = new JMenu();
5221                 mname = null;
5222                 comp = 0;
5223               }
5224             }
5225           }
5226         });
5227       }
5228     }).start();
5229
5230   }
5231
5232   /**
5233    * Left justify the whole alignment.
5234    */
5235   @Override
5236   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5237   {
5238     AlignmentI al = viewport.getAlignment();
5239     al.justify(false);
5240     viewport.firePropertyChange("alignment", null, al);
5241   }
5242
5243   /**
5244    * Right justify the whole alignment.
5245    */
5246   @Override
5247   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5248   {
5249     AlignmentI al = viewport.getAlignment();
5250     al.justify(true);
5251     viewport.firePropertyChange("alignment", null, al);
5252   }
5253
5254   @Override
5255   public void setShowSeqFeatures(boolean b)
5256   {
5257     showSeqFeatures.setSelected(b);
5258     viewport.setShowSequenceFeatures(b);
5259   }
5260
5261   /*
5262    * (non-Javadoc)
5263    *
5264    * @see
5265    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5266    * awt.event.ActionEvent)
5267    */
5268   @Override
5269   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5270   {
5271     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5272     alignPanel.paintAlignment(false, false);
5273   }
5274
5275   /*
5276    * (non-Javadoc)
5277    *
5278    * @see
5279    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5280    * .ActionEvent)
5281    */
5282   @Override
5283   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5284   {
5285     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5286     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5287
5288   }
5289
5290   /*
5291    * (non-Javadoc)
5292    *
5293    * @see
5294    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5295    * .event.ActionEvent)
5296    */
5297   @Override
5298   protected void showGroupConservation_actionPerformed(ActionEvent e)
5299   {
5300     viewport.setShowGroupConservation(showGroupConservation.getState());
5301     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5302   }
5303
5304   /*
5305    * (non-Javadoc)
5306    *
5307    * @see
5308    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5309    * .event.ActionEvent)
5310    */
5311   @Override
5312   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5313   {
5314     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5315     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5316   }
5317
5318   /*
5319    * (non-Javadoc)
5320    *
5321    * @see
5322    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5323    * .event.ActionEvent)
5324    */
5325   @Override
5326   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5327   {
5328     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5329     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5330   }
5331
5332   @Override
5333   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5334   {
5335     showSequenceLogo.setState(true);
5336     viewport.setShowSequenceLogo(true);
5337     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5338     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5339   }
5340
5341   @Override
5342   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5343   {
5344     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5345   }
5346
5347   /*
5348    * (non-Javadoc)
5349    *
5350    * @see
5351    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5352    * .event.ActionEvent)
5353    */
5354   @Override
5355   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5356   {
5357     if (avc.makeGroupsFromSelection())
5358     {
5359       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5360       alignPanel.updateAnnotation();
5361       alignPanel.paintAlignment(true,
5362               viewport.needToUpdateStructureViews());
5363     }
5364   }
5365
5366   public void clearAlignmentSeqRep()
5367   {
5368     // TODO refactor alignmentseqrep to controller
5369     if (viewport.getAlignment().hasSeqrep())
5370     {
5371       viewport.getAlignment().setSeqrep(null);
5372       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5373       alignPanel.updateAnnotation();
5374       alignPanel.paintAlignment(true, true);
5375     }
5376   }
5377
5378   @Override
5379   protected void createGroup_actionPerformed(ActionEvent e)
5380   {
5381     if (avc.createGroup())
5382     {
5383       if (applyAutoAnnotationSettings.isSelected())
5384       {
5385         alignPanel.updateAnnotation(true, false);
5386       }
5387       alignPanel.alignmentChanged();
5388     }
5389   }
5390
5391   @Override
5392   protected void unGroup_actionPerformed(ActionEvent e)
5393   {
5394     if (avc.unGroup())
5395     {
5396       alignPanel.alignmentChanged();
5397     }
5398   }
5399
5400   /**
5401    * make the given alignmentPanel the currently selected tab
5402    *
5403    * @param alignmentPanel
5404    */
5405   public void setDisplayedView(AlignmentPanel alignmentPanel)
5406   {
5407     if (!viewport.getSequenceSetId()
5408             .equals(alignmentPanel.av.getSequenceSetId()))
5409     {
5410       throw new Error(MessageManager.getString(
5411               "error.implementation_error_cannot_show_view_alignment_frame"));
5412     }
5413     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5414             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5415     {
5416       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5417     }
5418   }
5419
5420   /**
5421    * Action on selection of menu options to Show or Hide annotations.
5422    *
5423    * @param visible
5424    * @param forSequences
5425    *          update sequence-related annotations
5426    * @param forAlignment
5427    *          update non-sequence-related annotations
5428    */
5429   @Override
5430   protected void setAnnotationsVisibility(boolean visible,
5431           boolean forSequences, boolean forAlignment)
5432   {
5433     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5434             .getAlignmentAnnotation();
5435     if (anns == null)
5436     {
5437       return;
5438     }
5439     for (AlignmentAnnotation aa : anns)
5440     {
5441       /*
5442        * don't display non-positional annotations on an alignment
5443        */
5444       if (aa.annotations == null)
5445       {
5446         continue;
5447       }
5448       boolean apply = (aa.sequenceRef == null && forAlignment)
5449               || (aa.sequenceRef != null && forSequences);
5450       if (apply)
5451       {
5452         aa.visible = visible;
5453       }
5454     }
5455     alignPanel.validateAnnotationDimensions(true);
5456     alignPanel.alignmentChanged();
5457   }
5458
5459   /**
5460    * Store selected annotation sort order for the view and repaint.
5461    */
5462   @Override
5463   protected void sortAnnotations_actionPerformed()
5464   {
5465     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5466     this.alignPanel.av
5467             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5468     alignPanel.paintAlignment(false, false);
5469   }
5470
5471   /**
5472    *
5473    * @return alignment panels in this alignment frame
5474    */
5475   public List<? extends AlignmentViewPanel> getAlignPanels()
5476   {
5477     // alignPanels is never null
5478     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5479     return alignPanels;
5480   }
5481
5482   /**
5483    * Open a new alignment window, with the cDNA associated with this (protein)
5484    * alignment, aligned as is the protein.
5485    */
5486   protected void viewAsCdna_actionPerformed()
5487   {
5488     // TODO no longer a menu action - refactor as required
5489     final AlignmentI alignment = getViewport().getAlignment();
5490     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5491     if (mappings == null)
5492     {
5493       return;
5494     }
5495     List<SequenceI> cdnaSeqs = new ArrayList<>();
5496     for (SequenceI aaSeq : alignment.getSequences())
5497     {
5498       for (AlignedCodonFrame acf : mappings)
5499       {
5500         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5501         if (dnaSeq != null)
5502         {
5503           /*
5504            * There is a cDNA mapping for this protein sequence - add to new
5505            * alignment. It will share the same dataset sequence as other mapped
5506            * cDNA (no new mappings need to be created).
5507            */
5508           final Sequence newSeq = new Sequence(dnaSeq);
5509           newSeq.setDatasetSequence(dnaSeq);
5510           cdnaSeqs.add(newSeq);
5511         }
5512       }
5513     }
5514     if (cdnaSeqs.size() == 0)
5515     {
5516       // show a warning dialog no mapped cDNA
5517       return;
5518     }
5519     AlignmentI cdna = new Alignment(
5520             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5521     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5522             AlignFrame.DEFAULT_HEIGHT);
5523     cdna.alignAs(alignment);
5524     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5525             + this.title;
5526     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5527             AlignFrame.DEFAULT_HEIGHT);
5528   }
5529
5530   /**
5531    * Set visibility of dna/protein complement view (available when shown in a
5532    * split frame).
5533    *
5534    * @param show
5535    */
5536   @Override
5537   protected void showComplement_actionPerformed(boolean show)
5538   {
5539     SplitContainerI sf = getSplitViewContainer();
5540     if (sf != null)
5541     {
5542       sf.setComplementVisible(this, show);
5543     }
5544   }
5545
5546   /**
5547    * Generate the reverse (optionally complemented) of the selected sequences,
5548    * and add them to the alignment
5549    */
5550   @Override
5551   protected void showReverse_actionPerformed(boolean complement)
5552   {
5553     AlignmentI al = null;
5554     try
5555     {
5556       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5557       al = dna.reverseCdna(complement);
5558       viewport.addAlignment(al, "");
5559       addHistoryItem(new EditCommand(
5560               MessageManager.getString("label.add_sequences"), Action.PASTE,
5561               al.getSequencesArray(), 0, al.getWidth(),
5562               viewport.getAlignment()));
5563     } catch (Exception ex)
5564     {
5565       System.err.println(ex.getMessage());
5566       return;
5567     }
5568   }
5569
5570   /**
5571    * Try to run a script in the Groovy console, having first ensured that this
5572    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5573    * be targeted at this alignment.
5574    */
5575   @Override
5576   protected void runGroovy_actionPerformed()
5577   {
5578     Jalview.setCurrentAlignFrame(this);
5579     groovy.ui.Console console = Desktop.getGroovyConsole();
5580     if (console != null)
5581     {
5582       try
5583       {
5584         console.runScript();
5585       } catch (Exception ex)
5586       {
5587         System.err.println((ex.toString()));
5588         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5589                 MessageManager.getString("label.couldnt_run_groovy_script"),
5590                 MessageManager.getString("label.groovy_support_failed"),
5591                 JvOptionPane.ERROR_MESSAGE);
5592       }
5593     }
5594     else
5595     {
5596       System.err.println("Can't run Groovy script as console not found");
5597     }
5598   }
5599
5600   /**
5601    * Hides columns containing (or not containing) a specified feature, provided
5602    * that would not leave all columns hidden
5603    *
5604    * @param featureType
5605    * @param columnsContaining
5606    * @return
5607    */
5608   public boolean hideFeatureColumns(String featureType,
5609           boolean columnsContaining)
5610   {
5611     boolean notForHiding = avc.markColumnsContainingFeatures(
5612             columnsContaining, false, false, featureType);
5613     if (notForHiding)
5614     {
5615       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5616               false, featureType))
5617       {
5618         getViewport().hideSelectedColumns();
5619         return true;
5620       }
5621     }
5622     return false;
5623   }
5624
5625   @Override
5626   protected void selectHighlightedColumns_actionPerformed(
5627           ActionEvent actionEvent)
5628   {
5629     // include key modifier check in case user selects from menu
5630     avc.markHighlightedColumns(
5631             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5632             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5633                     | ActionEvent.CTRL_MASK)) != 0);
5634   }
5635
5636   /**
5637    * Rebuilds the Colour menu, including any user-defined colours which have
5638    * been loaded either on startup or during the session
5639    */
5640   public void buildColourMenu()
5641   {
5642     colourMenu.removeAll();
5643
5644     colourMenu.add(applyToAllGroups);
5645     colourMenu.add(textColour);
5646     colourMenu.addSeparator();
5647
5648     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5649             viewport.getAlignment(), false);
5650
5651     colourMenu.add(annotationColour);
5652     bg.add(annotationColour);
5653     colourMenu.addSeparator();
5654     colourMenu.add(conservationMenuItem);
5655     colourMenu.add(modifyConservation);
5656     colourMenu.add(abovePIDThreshold);
5657     colourMenu.add(modifyPID);
5658
5659     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5660     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5661   }
5662
5663   /**
5664    * Open a dialog (if not already open) that allows the user to select and
5665    * calculate PCA or Tree analysis
5666    */
5667   protected void openTreePcaDialog()
5668   {
5669     if (alignPanel.getCalculationDialog() == null)
5670     {
5671       new CalculationChooser(AlignFrame.this);
5672     }
5673   }
5674
5675   @Override
5676   protected void loadVcf_actionPerformed()
5677   {
5678     JalviewFileChooser chooser = new JalviewFileChooser(
5679             Cache.getProperty("LAST_DIRECTORY"));
5680     chooser.setFileView(new JalviewFileView());
5681     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5682     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5683
5684     int value = chooser.showOpenDialog(null);
5685
5686     if (value == JalviewFileChooser.APPROVE_OPTION)
5687     {
5688       String choice = chooser.getSelectedFile().getPath();
5689       Cache.setProperty("LAST_DIRECTORY", choice);
5690       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5691       new VCFLoader(choice).loadVCF(seqs, this);
5692     }
5693
5694   }
5695
5696   private Rectangle lastFeatureSettingsBounds = null;
5697   @Override
5698   public void setFeatureSettingsGeometry(Rectangle bounds)
5699   {
5700     lastFeatureSettingsBounds = bounds;
5701   }
5702
5703   @Override
5704   public Rectangle getFeatureSettingsGeometry()
5705   {
5706     return lastFeatureSettingsBounds;
5707   }
5708 }
5709
5710 class PrintThread extends Thread
5711 {
5712   AlignmentPanel ap;
5713
5714   public PrintThread(AlignmentPanel ap)
5715   {
5716     this.ap = ap;
5717   }
5718
5719   static PageFormat pf;
5720
5721   @Override
5722   public void run()
5723   {
5724     PrinterJob printJob = PrinterJob.getPrinterJob();
5725
5726     if (pf != null)
5727     {
5728       printJob.setPrintable(ap, pf);
5729     }
5730     else
5731     {
5732       printJob.setPrintable(ap);
5733     }
5734
5735     if (printJob.printDialog())
5736     {
5737       try
5738       {
5739         printJob.print();
5740       } catch (Exception PrintException)
5741       {
5742         PrintException.printStackTrace();
5743       }
5744     }
5745   }
5746 }