src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  26 import jalview.analysis.CrossRef;
  27 import jalview.analysis.Dna;
  28 import jalview.analysis.GeneticCodeI;
  29 import jalview.analysis.ParseProperties;
  30 import jalview.analysis.SequenceIdMatcher;
  31 import jalview.api.AlignExportSettingI;
  32 import jalview.api.AlignViewControllerGuiI;
  33 import jalview.api.AlignViewControllerI;
  34 import jalview.api.AlignViewportI;
  35 import jalview.api.AlignmentViewPanel;
  36 import jalview.api.FeatureSettingsControllerI;
  37 import jalview.api.SplitContainerI;
  38 import jalview.api.ViewStyleI;
  39 import jalview.api.analysis.SimilarityParamsI;
  40 import jalview.bin.Cache;
  41 import jalview.bin.Jalview;
  42 import jalview.commands.CommandI;
  43 import jalview.commands.EditCommand;
  44 import jalview.commands.EditCommand.Action;
  45 import jalview.commands.OrderCommand;
  46 import jalview.commands.RemoveGapColCommand;
  47 import jalview.commands.RemoveGapsCommand;
  48 import jalview.commands.SlideSequencesCommand;
  49 import jalview.commands.TrimRegionCommand;
  50 import jalview.datamodel.AlignedCodonFrame;
  51 import jalview.datamodel.Alignment;
  52 import jalview.datamodel.AlignmentAnnotation;
  53 import jalview.datamodel.AlignmentExportData;
  54 import jalview.datamodel.AlignmentI;
  55 import jalview.datamodel.AlignmentOrder;
  56 import jalview.datamodel.AlignmentView;
  57 import jalview.datamodel.ColumnSelection;
  58 import jalview.datamodel.HiddenColumns;
  59 import jalview.datamodel.HiddenSequences;
  60 import jalview.datamodel.PDBEntry;
  61 import jalview.datamodel.SeqCigar;
  62 import jalview.datamodel.Sequence;
  63 import jalview.datamodel.SequenceGroup;
  64 import jalview.datamodel.SequenceI;
  65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  67 import jalview.io.AlignmentProperties;
  68 import jalview.io.AnnotationFile;
  69 import jalview.io.BackupFiles;
  70 import jalview.io.BioJsHTMLOutput;
  71 import jalview.io.DataSourceType;
  72 import jalview.io.FileFormat;
  73 import jalview.io.FileFormatI;
  74 import jalview.io.FileFormats;
  75 import jalview.io.FileLoader;
  76 import jalview.io.FileParse;
  77 import jalview.io.FormatAdapter;
  78 import jalview.io.HtmlSvgOutput;
  79 import jalview.io.IdentifyFile;
  80 import jalview.io.JPredFile;
  81 import jalview.io.JalviewFileChooser;
  82 import jalview.io.JalviewFileView;
  83 import jalview.io.JnetAnnotationMaker;
  84 import jalview.io.NewickFile;
  85 import jalview.io.ScoreMatrixFile;
  86 import jalview.io.TCoffeeScoreFile;
  87 import jalview.io.vcf.VCFLoader;
  88 import jalview.jbgui.GAlignFrame;
  89 import jalview.schemes.ColourSchemeI;
  90 import jalview.schemes.ColourSchemes;
  91 import jalview.schemes.ResidueColourScheme;
  92 import jalview.schemes.TCoffeeColourScheme;
  93 import jalview.util.MessageManager;
  94 import jalview.viewmodel.AlignmentViewport;
  95 import jalview.viewmodel.ViewportRanges;
  96 import jalview.ws.DBRefFetcher;
  97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  98 import jalview.ws.jws1.Discoverer;
  99 import jalview.ws.jws2.Jws2Discoverer;
 100 import jalview.ws.jws2.jabaws2.Jws2Instance;
 101 import jalview.ws.seqfetcher.DbSourceProxy;
 102
 103 import java.awt.BorderLayout;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseEvent;
 125 import java.awt.print.PageFormat;
 126 import java.awt.print.PrinterJob;
 127 import java.beans.PropertyChangeEvent;
 128 import java.io.File;
 129 import java.io.FileWriter;
 130 import java.io.PrintWriter;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.ButtonGroup;
 141 import javax.swing.JCheckBoxMenuItem;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLayeredPane;
 145 import javax.swing.JMenu;
 146 import javax.swing.JMenuItem;
 147 import javax.swing.JScrollPane;
 148 import javax.swing.SwingUtilities;
 149
 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     setMenusFromViewport(viewport);
 367     buildSortByAnnotationScoresMenu();
 368     calculateTree.addActionListener(new ActionListener()
 369     {
 370
 371       @Override
 372       public void actionPerformed(ActionEvent e)
 373       {
 374         openTreePcaDialog();
 375       }
 376     });
 377     buildColourMenu();
 378
 379     if (Desktop.desktop != null)
 380     {
 381       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 382       addServiceListeners();
 383       setGUINucleotide();
 384     }
 385
 386     if (viewport.getWrapAlignment())
 387     {
 388       wrapMenuItem_actionPerformed(null);
 389     }
 390
 391     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 392     {
 393       this.overviewMenuItem_actionPerformed(null);
 394     }
 395
 396     addKeyListener();
 397
 398     final List<AlignmentPanel> selviews = new ArrayList<>();
 399     final List<AlignmentPanel> origview = new ArrayList<>();
 400     final String menuLabel = MessageManager
 401             .getString("label.copy_format_from");
 402     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 403             new ViewSetProvider()
 404             {
 405
 406               @Override
 407               public AlignmentPanel[] getAllAlignmentPanels()
 408               {
 409                 origview.clear();
 410                 origview.add(alignPanel);
 411                 // make an array of all alignment panels except for this one
 412                 List<AlignmentPanel> aps = new ArrayList<>(
 413                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 414                 aps.remove(AlignFrame.this.alignPanel);
 415                 return aps.toArray(new AlignmentPanel[aps.size()]);
 416               }
 417             }, selviews, new ItemListener()
 418             {
 419
 420               @Override
 421               public void itemStateChanged(ItemEvent e)
 422               {
 423                 if (origview.size() > 0)
 424                 {
 425                   final AlignmentPanel ap = origview.get(0);
 426
 427                   /*
 428                    * Copy the ViewStyle of the selected panel to 'this one'.
 429                    * Don't change value of 'scaleProteinAsCdna' unless copying
 430                    * from a SplitFrame.
 431                    */
 432                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 433                           .getViewStyle();
 434                   boolean fromSplitFrame = selviews.get(0)
 435                           .getAlignViewport().getCodingComplement() != null;
 436                   if (!fromSplitFrame)
 437                   {
 438                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 439                             .getViewStyle().isScaleProteinAsCdna());
 440                   }
 441                   ap.getAlignViewport().setViewStyle(vs);
 442
 443                   /*
 444                    * Also rescale ViewStyle of SplitFrame complement if there is
 445                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 446                    * the whole ViewStyle (allow cDNA protein to have different
 447                    * fonts)
 448                    */
 449                   AlignViewportI complement = ap.getAlignViewport()
 450                           .getCodingComplement();
 451                   if (complement != null && vs.isScaleProteinAsCdna())
 452                   {
 453                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 454                     ((SplitFrame) af.getSplitViewContainer())
 455                             .adjustLayout();
 456                     af.setMenusForViewport();
 457                   }
 458
 459                   ap.updateLayout();
 460                   ap.setSelected(true);
 461                   ap.alignFrame.setMenusForViewport();
 462
 463                 }
 464               }
 465             });
 466     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 467             .indexOf("devel") > -1
 468             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 469                     .indexOf("test") > -1)
 470     {
 471       formatMenu.add(vsel);
 472     }
 473     addFocusListener(new FocusAdapter()
 474     {
 475       @Override
 476       public void focusGained(FocusEvent e)
 477       {
 478         Jalview.setCurrentAlignFrame(AlignFrame.this);
 479       }
 480     });
 481
 482     alignPanel.sortAnnotations(false);
 483   }
 484
 485   /**
 486    * Change the filename and format for the alignment, and enable the 'reload'
 487    * button functionality.
 488    *
 489    * @param file
 490    *          valid filename
 491    * @param format
 492    *          format of file
 493    */
 494   public void setFileName(String file, FileFormatI format)
 495   {
 496     fileName = file;
 497     setFileFormat(format);
 498     reload.setEnabled(true);
 499   }
 500
 501   /**
 502    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 503    * events
 504    */
 505   void addKeyListener()
 506   {
 507     addKeyListener(new KeyAdapter()
 508     {
 509       @Override
 510       public void keyPressed(KeyEvent evt)
 511       {
 512         if (viewport.cursorMode
 513                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 514                         && evt.getKeyCode() <= KeyEvent.VK_9)
 515                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 516                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 517                 && Character.isDigit(evt.getKeyChar()))
 518         {
 519           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 520         }
 521
 522         switch (evt.getKeyCode())
 523         {
 524
 525         case 27: // escape key
 526           deselectAllSequenceMenuItem_actionPerformed(null);
 527
 528           break;
 529
 530         case KeyEvent.VK_DOWN:
 531           if (evt.isAltDown() || !viewport.cursorMode)
 532           {
 533             moveSelectedSequences(false);
 534           }
 535           if (viewport.cursorMode)
 536           {
 537             alignPanel.getSeqPanel().moveCursor(0, 1);
 538           }
 539           break;
 540
 541         case KeyEvent.VK_UP:
 542           if (evt.isAltDown() || !viewport.cursorMode)
 543           {
 544             moveSelectedSequences(true);
 545           }
 546           if (viewport.cursorMode)
 547           {
 548             alignPanel.getSeqPanel().moveCursor(0, -1);
 549           }
 550
 551           break;
 552
 553         case KeyEvent.VK_LEFT:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555           {
 556             slideSequences(false,
 557                     alignPanel.getSeqPanel().getKeyboardNo1());
 558           }
 559           else
 560           {
 561             alignPanel.getSeqPanel().moveCursor(-1, 0);
 562           }
 563
 564           break;
 565
 566         case KeyEvent.VK_RIGHT:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 570           }
 571           else
 572           {
 573             alignPanel.getSeqPanel().moveCursor(1, 0);
 574           }
 575           break;
 576
 577         case KeyEvent.VK_SPACE:
 578           if (viewport.cursorMode)
 579           {
 580             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 581                     || evt.isShiftDown() || evt.isAltDown());
 582           }
 583           break;
 584
 585         // case KeyEvent.VK_A:
 586         // if (viewport.cursorMode)
 587         // {
 588         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 589         // //System.out.println("A");
 590         // }
 591         // break;
 592         /*
 593          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 594          * System.out.println("closing bracket"); } break;
 595          */
 596         case KeyEvent.VK_DELETE:
 597         case KeyEvent.VK_BACK_SPACE:
 598           if (!viewport.cursorMode)
 599           {
 600             cut_actionPerformed(null);
 601           }
 602           else
 603           {
 604             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 605                     || evt.isShiftDown() || evt.isAltDown());
 606           }
 607
 608           break;
 609
 610         case KeyEvent.VK_S:
 611           if (viewport.cursorMode)
 612           {
 613             alignPanel.getSeqPanel().setCursorRow();
 614           }
 615           break;
 616         case KeyEvent.VK_C:
 617           if (viewport.cursorMode && !evt.isControlDown())
 618           {
 619             alignPanel.getSeqPanel().setCursorColumn();
 620           }
 621           break;
 622         case KeyEvent.VK_P:
 623           if (viewport.cursorMode)
 624           {
 625             alignPanel.getSeqPanel().setCursorPosition();
 626           }
 627           break;
 628
 629         case KeyEvent.VK_ENTER:
 630         case KeyEvent.VK_COMMA:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setCursorRowAndColumn();
 634           }
 635           break;
 636
 637         case KeyEvent.VK_Q:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 641           }
 642           break;
 643         case KeyEvent.VK_M:
 644           if (viewport.cursorMode)
 645           {
 646             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 647           }
 648           break;
 649
 650         case KeyEvent.VK_F2:
 651           viewport.cursorMode = !viewport.cursorMode;
 652           statusBar.setText(MessageManager
 653                   .formatMessage("label.keyboard_editing_mode", new String[]
 654                   { (viewport.cursorMode ? "on" : "off") }));
 655           if (viewport.cursorMode)
 656           {
 657             ViewportRanges ranges = viewport.getRanges();
 658             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 659                     .getStartRes();
 660             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 661                     .getStartSeq();
 662           }
 663           alignPanel.getSeqPanel().seqCanvas.repaint();
 664           break;
 665
 666         case KeyEvent.VK_F1:
 667           try
 668           {
 669             Help.showHelpWindow();
 670           } catch (Exception ex)
 671           {
 672             ex.printStackTrace();
 673           }
 674           break;
 675         case KeyEvent.VK_H:
 676         {
 677           boolean toggleSeqs = !evt.isControlDown();
 678           boolean toggleCols = !evt.isShiftDown();
 679           toggleHiddenRegions(toggleSeqs, toggleCols);
 680           break;
 681         }
 682         case KeyEvent.VK_B:
 683         {
 684           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 685           boolean modifyExisting = true; // always modify, don't clear
 686                                          // evt.isShiftDown();
 687           boolean invertHighlighted = evt.isAltDown();
 688           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 689                   toggleSel);
 690           break;
 691         }
 692         case KeyEvent.VK_PAGE_UP:
 693           viewport.getRanges().pageUp();
 694           break;
 695         case KeyEvent.VK_PAGE_DOWN:
 696           viewport.getRanges().pageDown();
 697           break;
 698         }
 699       }
 700
 701       @Override
 702       public void keyReleased(KeyEvent evt)
 703       {
 704         switch (evt.getKeyCode())
 705         {
 706         case KeyEvent.VK_LEFT:
 707           if (evt.isAltDown() || !viewport.cursorMode)
 708           {
 709             viewport.firePropertyChange("alignment", null,
 710                     viewport.getAlignment().getSequences());
 711           }
 712           break;
 713
 714         case KeyEvent.VK_RIGHT:
 715           if (evt.isAltDown() || !viewport.cursorMode)
 716           {
 717             viewport.firePropertyChange("alignment", null,
 718                     viewport.getAlignment().getSequences());
 719           }
 720           break;
 721         }
 722       }
 723     });
 724   }
 725
 726   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 727   {
 728     ap.alignFrame = this;
 729     avc = new jalview.controller.AlignViewController(this, viewport,
 730             alignPanel);
 731
 732     alignPanels.add(ap);
 733
 734     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 735
 736     int aSize = alignPanels.size();
 737
 738     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 739
 740     if (aSize == 1 && ap.av.getViewName() == null)
 741     {
 742       this.getContentPane().add(ap, BorderLayout.CENTER);
 743     }
 744     else
 745     {
 746       if (aSize == 2)
 747       {
 748         setInitialTabVisible();
 749       }
 750
 751       expandViews.setEnabled(true);
 752       gatherViews.setEnabled(true);
 753       tabbedPane.addTab(ap.av.getViewName(), ap);
 754
 755       ap.setVisible(false);
 756     }
 757
 758     if (newPanel)
 759     {
 760       if (ap.av.isPadGaps())
 761       {
 762         ap.av.getAlignment().padGaps();
 763       }
 764       ap.av.updateConservation(ap);
 765       ap.av.updateConsensus(ap);
 766       ap.av.updateStrucConsensus(ap);
 767     }
 768   }
 769
 770   public void setInitialTabVisible()
 771   {
 772     expandViews.setEnabled(true);
 773     gatherViews.setEnabled(true);
 774     tabbedPane.setVisible(true);
 775     AlignmentPanel first = alignPanels.get(0);
 776     tabbedPane.addTab(first.av.getViewName(), first);
 777     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 778   }
 779
 780   public AlignViewport getViewport()
 781   {
 782     return viewport;
 783   }
 784
 785   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 786   private void addServiceListeners()
 787   {
 788     final java.beans.PropertyChangeListener thisListener;
 789     Desktop.instance.addJalviewPropertyChangeListener("services",
 790             thisListener = new java.beans.PropertyChangeListener()
 791             {
 792               @Override
 793               public void propertyChange(PropertyChangeEvent evt)
 794               {
 795                 // // System.out.println("Discoverer property change.");
 796                 // if (evt.getPropertyName().equals("services"))
 797                 {
 798                   SwingUtilities.invokeLater(new Runnable()
 799                   {
 800
 801                     @Override
 802                     public void run()
 803                     {
 804                       System.err.println(
 805                               "Rebuild WS Menu for service change");
 806                       BuildWebServiceMenu();
 807                     }
 808
 809                   });
 810                 }
 811               }
 812             });
 813     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 814     {
 815       @Override
 816       public void internalFrameClosed(
 817               javax.swing.event.InternalFrameEvent evt)
 818       {
 819         // System.out.println("deregistering discoverer listener");
 820         Desktop.instance.removeJalviewPropertyChangeListener("services",
 821                 thisListener);
 822         closeMenuItem_actionPerformed(true);
 823       };
 824     });
 825     // Finally, build the menu once to get current service state
 826     new Thread(new Runnable()
 827     {
 828       @Override
 829       public void run()
 830       {
 831         BuildWebServiceMenu();
 832       }
 833     }).start();
 834   }
 835
 836   /**
 837    * Configure menu items that vary according to whether the alignment is
 838    * nucleotide or protein
 839    */
 840   public void setGUINucleotide()
 841   {
 842     AlignmentI al = getViewport().getAlignment();
 843     boolean nucleotide = al.isNucleotide();
 844
 845     loadVcf.setVisible(nucleotide);
 846     showTranslation.setVisible(nucleotide);
 847     showReverse.setVisible(nucleotide);
 848     showReverseComplement.setVisible(nucleotide);
 849     conservationMenuItem.setEnabled(!nucleotide);
 850     modifyConservation
 851             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 852     showGroupConservation.setEnabled(!nucleotide);
 853
 854     showComplementMenuItem
 855             .setText(nucleotide ? MessageManager.getString("label.protein")
 856                     : MessageManager.getString("label.nucleotide"));
 857   }
 858
 859   /**
 860    * set up menus for the current viewport. This may be called after any
 861    * operation that affects the data in the current view (selection changed,
 862    * etc) to update the menus to reflect the new state.
 863    */
 864   @Override
 865   public void setMenusForViewport()
 866   {
 867     setMenusFromViewport(viewport);
 868   }
 869
 870   /**
 871    * Need to call this method when tabs are selected for multiple views, or when
 872    * loading from Jalview2XML.java
 873    *
 874    * @param av
 875    *          AlignViewport
 876    */
 877   public void setMenusFromViewport(AlignViewport av)
 878   {
 879     padGapsMenuitem.setSelected(av.isPadGaps());
 880     colourTextMenuItem.setSelected(av.isShowColourText());
 881     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 882     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 883     conservationMenuItem.setSelected(av.getConservationSelected());
 884     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 885     seqLimits.setSelected(av.getShowJVSuffix());
 886     idRightAlign.setSelected(av.isRightAlignIds());
 887     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 888     renderGapsMenuItem.setSelected(av.isRenderGaps());
 889     wrapMenuItem.setSelected(av.getWrapAlignment());
 890     scaleAbove.setVisible(av.getWrapAlignment());
 891     scaleLeft.setVisible(av.getWrapAlignment());
 892     scaleRight.setVisible(av.getWrapAlignment());
 893     annotationPanelMenuItem.setState(av.isShowAnnotation());
 894     /*
 895      * Show/hide annotations only enabled if annotation panel is shown
 896      */
 897     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 902     viewTextMenuItem.setSelected(av.getShowText());
 903     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 904     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 905     showGroupConservation.setSelected(av.isShowGroupConservation());
 906     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 907     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 908     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 909
 910     ColourMenuHelper.setColourSelected(colourMenu,
 911             av.getGlobalColourScheme());
 912
 913     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 914     hiddenMarkers.setState(av.getShowHiddenMarkers());
 915     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 916     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 917     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 918     autoCalculate.setSelected(av.autoCalculateConsensus);
 919     sortByTree.setSelected(av.sortByTree);
 920     listenToViewSelections.setSelected(av.followSelection);
 921
 922     showProducts.setEnabled(canShowProducts());
 923     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 924
 925     updateEditMenuBar();
 926   }
 927
 928   /**
 929    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 930    *
 931    * @param b
 932    */
 933   public void setGroovyEnabled(boolean b)
 934   {
 935     runGroovy.setEnabled(b);
 936   }
 937
 938   private IProgressIndicator progressBar;
 939
 940   /*
 941    * (non-Javadoc)
 942    *
 943    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 944    */
 945   @Override
 946   public void setProgressBar(String message, long id)
 947   {
 948     progressBar.setProgressBar(message, id);
 949   }
 950
 951   @Override
 952   public void registerHandler(final long id,
 953           final IProgressIndicatorHandler handler)
 954   {
 955     progressBar.registerHandler(id, handler);
 956   }
 957
 958   /**
 959    *
 960    * @return true if any progress bars are still active
 961    */
 962   @Override
 963   public boolean operationInProgress()
 964   {
 965     return progressBar.operationInProgress();
 966   }
 967
 968   /**
 969    * Sets the text of the status bar. Note that setting a null or empty value
 970    * will cause the status bar to be hidden, with possibly undesirable flicker
 971    * of the screen layout.
 972    */
 973   @Override
 974   public void setStatus(String text)
 975   {
 976     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 977   }
 978
 979   /*
 980    * Added so Castor Mapping file can obtain Jalview Version
 981    */
 982   public String getVersion()
 983   {
 984     return jalview.bin.Cache.getProperty("VERSION");
 985   }
 986
 987   public FeatureRenderer getFeatureRenderer()
 988   {
 989     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 990   }
 991
 992   @Override
 993   public void fetchSequence_actionPerformed(ActionEvent e)
 994   {
 995     new jalview.gui.SequenceFetcher(this);
 996   }
 997
 998   @Override
 999   public void addFromFile_actionPerformed(ActionEvent e)
1000   {
1001     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1002   }
1003
1004   @Override
1005   public void reload_actionPerformed(ActionEvent e)
1006   {
1007     if (fileName != null)
1008     {
1009       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010       // originating file's format
1011       // TODO: work out how to recover feature settings for correct view(s) when
1012       // file is reloaded.
1013       if (FileFormat.Jalview.equals(currentFileFormat))
1014       {
1015         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016         for (int i = 0; i < frames.length; i++)
1017         {
1018           if (frames[i] instanceof AlignFrame && frames[i] != this
1019                   && ((AlignFrame) frames[i]).fileName != null
1020                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1021           {
1022             try
1023             {
1024               frames[i].setSelected(true);
1025               Desktop.instance.closeAssociatedWindows();
1026             } catch (java.beans.PropertyVetoException ex)
1027             {
1028             }
1029           }
1030
1031         }
1032         Desktop.instance.closeAssociatedWindows();
1033
1034         FileLoader loader = new FileLoader();
1035         DataSourceType protocol = fileName.startsWith("http:")
1036                 ? DataSourceType.URL
1037                 : DataSourceType.FILE;
1038         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1039       }
1040       else
1041       {
1042         Rectangle bounds = this.getBounds();
1043
1044         FileLoader loader = new FileLoader();
1045         DataSourceType protocol = fileName.startsWith("http:")
1046                 ? DataSourceType.URL
1047                 : DataSourceType.FILE;
1048         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1049                 protocol, currentFileFormat);
1050
1051         newframe.setBounds(bounds);
1052         if (featureSettings != null && featureSettings.isShowing())
1053         {
1054           final Rectangle fspos = featureSettings.frame.getBounds();
1055           // TODO: need a 'show feature settings' function that takes bounds -
1056           // need to refactor Desktop.addFrame
1057           newframe.featureSettings_actionPerformed(null);
1058           final FeatureSettings nfs = newframe.featureSettings;
1059           SwingUtilities.invokeLater(new Runnable()
1060           {
1061             @Override
1062             public void run()
1063             {
1064               nfs.frame.setBounds(fspos);
1065             }
1066           });
1067           this.featureSettings.close();
1068           this.featureSettings = null;
1069         }
1070         this.closeMenuItem_actionPerformed(true);
1071       }
1072     }
1073   }
1074
1075   @Override
1076   public void addFromText_actionPerformed(ActionEvent e)
1077   {
1078     Desktop.instance
1079             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1080   }
1081
1082   @Override
1083   public void addFromURL_actionPerformed(ActionEvent e)
1084   {
1085     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1086   }
1087
1088   @Override
1089   public void save_actionPerformed(ActionEvent e)
1090   {
1091     if (fileName == null || (currentFileFormat == null)
1092             || fileName.startsWith("http"))
1093     {
1094       saveAs_actionPerformed(null);
1095     }
1096     else
1097     {
1098       saveAlignment(fileName, currentFileFormat);
1099     }
1100   }
1101
1102   /**
1103    * DOCUMENT ME!
1104    *
1105    * @param e
1106    *          DOCUMENT ME!
1107    */
1108   @Override
1109   public void saveAs_actionPerformed(ActionEvent e)
1110   {
1111     String format = currentFileFormat == null ? null
1112             : currentFileFormat.getName();
1113     JalviewFileChooser chooser = JalviewFileChooser
1114             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1115
1116     chooser.setFileView(new JalviewFileView());
1117     chooser.setDialogTitle(
1118             MessageManager.getString("label.save_alignment_to_file"));
1119     chooser.setToolTipText(MessageManager.getString("action.save"));
1120
1121     int value = chooser.showSaveDialog(this);
1122
1123     if (value == JalviewFileChooser.APPROVE_OPTION)
1124     {
1125       currentFileFormat = chooser.getSelectedFormat();
1126       while (currentFileFormat == null)
1127       {
1128         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1129                 MessageManager.getString(
1130                         "label.select_file_format_before_saving"),
1131                 MessageManager.getString("label.file_format_not_specified"),
1132                 JvOptionPane.WARNING_MESSAGE);
1133         currentFileFormat = chooser.getSelectedFormat();
1134         value = chooser.showSaveDialog(this);
1135         if (value != JalviewFileChooser.APPROVE_OPTION)
1136         {
1137           return;
1138         }
1139       }
1140
1141       fileName = chooser.getSelectedFile().getPath();
1142
1143       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1144
1145       Cache.setProperty("LAST_DIRECTORY", fileName);
1146       saveAlignment(fileName, currentFileFormat);
1147     }
1148   }
1149
1150   public boolean saveAlignment(String file, FileFormatI format)
1151   {
1152     boolean success = true;
1153
1154     if (FileFormat.Jalview.equals(format))
1155     {
1156       String shortName = title;
1157
1158       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1159       {
1160         shortName = shortName.substring(
1161                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1162       }
1163
1164       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1165               shortName);
1166
1167       statusBar.setText(MessageManager.formatMessage(
1168               "label.successfully_saved_to_file_in_format", new Object[]
1169               { fileName, format }));
1170
1171     }
1172     else
1173     {
1174       AlignmentExportData exportData = getAlignmentForExport(format,
1175               viewport, null);
1176       if (exportData.getSettings().isCancelled())
1177       {
1178         return false;
1179       }
1180       FormatAdapter f = new FormatAdapter(alignPanel,
1181               exportData.getSettings());
1182       String output = f.formatSequences(format, exportData.getAlignment(), // class
1183                                                                            // cast
1184                                                                            // exceptions
1185                                                                            // will
1186               // occur in the distant future
1187               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1188               f.getCacheSuffixDefault(format),
1189               viewport.getAlignment().getHiddenColumns());
1190
1191       if (output == null)
1192       {
1193         success = false;
1194       }
1195       else
1196       {
1197         // create backupfiles object and get new temp filename destination
1198         BackupFiles backupfiles = new BackupFiles(file);
1199
1200         try
1201         {
1202           PrintWriter out = new PrintWriter(
1203                   new FileWriter(backupfiles.getTempFilePath()));
1204
1205           out.print(output);
1206           out.close();
1207           this.setTitle(file);
1208           statusBar.setText(MessageManager.formatMessage(
1209                   "label.successfully_saved_to_file_in_format", new Object[]
1210                   { fileName, format.getName() }));
1211         } catch (Exception ex)
1212         {
1213           success = false;
1214           ex.printStackTrace();
1215         }
1216
1217         backupfiles.setWriteSuccess(success);
1218         // do the backup file roll and rename the temp file to actual file
1219         success = backupfiles.rollBackupsAndRenameTempFile();
1220
1221       }
1222     }
1223
1224     if (!success)
1225     {
1226       JvOptionPane.showInternalMessageDialog(this, MessageManager
1227               .formatMessage("label.couldnt_save_file", new Object[]
1228               { fileName }),
1229               MessageManager.getString("label.error_saving_file"),
1230               JvOptionPane.WARNING_MESSAGE);
1231     }
1232
1233     return success;
1234   }
1235
1236   private void warningMessage(String warning, String title)
1237   {
1238     if (new jalview.util.Platform().isHeadless())
1239     {
1240       System.err.println("Warning: " + title + "\nWarning: " + warning);
1241
1242     }
1243     else
1244     {
1245       JvOptionPane.showInternalMessageDialog(this, warning, title,
1246               JvOptionPane.WARNING_MESSAGE);
1247     }
1248     return;
1249   }
1250
1251   /**
1252    * DOCUMENT ME!
1253    *
1254    * @param e
1255    *          DOCUMENT ME!
1256    */
1257   @Override
1258   protected void outputText_actionPerformed(ActionEvent e)
1259   {
1260     FileFormatI fileFormat = FileFormats.getInstance()
1261             .forName(e.getActionCommand());
1262     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1263             viewport, null);
1264     if (exportData.getSettings().isCancelled())
1265     {
1266       return;
1267     }
1268     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1269     cap.setForInput(null);
1270     try
1271     {
1272       FileFormatI format = fileFormat;
1273       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1274               .formatSequences(format, exportData.getAlignment(),
1275                       exportData.getOmitHidden(),
1276                       exportData.getStartEndPostions(),
1277                       viewport.getAlignment().getHiddenColumns()));
1278       Desktop.addInternalFrame(cap, MessageManager
1279               .formatMessage("label.alignment_output_command", new Object[]
1280               { e.getActionCommand() }), 600, 500);
1281     } catch (OutOfMemoryError oom)
1282     {
1283       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1284               oom);
1285       cap.dispose();
1286     }
1287
1288   }
1289
1290   public static AlignmentExportData getAlignmentForExport(
1291           FileFormatI format, AlignViewportI viewport,
1292           AlignExportSettingI exportSettings)
1293   {
1294     AlignmentI alignmentToExport = null;
1295     AlignExportSettingI settings = exportSettings;
1296     String[] omitHidden = null;
1297
1298     HiddenSequences hiddenSeqs = viewport.getAlignment()
1299             .getHiddenSequences();
1300
1301     alignmentToExport = viewport.getAlignment();
1302
1303     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1304     if (settings == null)
1305     {
1306       settings = new AlignExportSettings(hasHiddenSeqs,
1307               viewport.hasHiddenColumns(), format);
1308     }
1309     // settings.isExportAnnotations();
1310
1311     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1312     {
1313       omitHidden = viewport.getViewAsString(false,
1314               settings.isExportHiddenSequences());
1315     }
1316
1317     int[] alignmentStartEnd = new int[2];
1318     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1319     {
1320       alignmentToExport = hiddenSeqs.getFullAlignment();
1321     }
1322     else
1323     {
1324       alignmentToExport = viewport.getAlignment();
1325     }
1326     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1327             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1328     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1329             omitHidden, alignmentStartEnd, settings);
1330     return ed;
1331   }
1332
1333   /**
1334    * DOCUMENT ME!
1335    *
1336    * @param e
1337    *          DOCUMENT ME!
1338    */
1339   @Override
1340   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1341   {
1342     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1343     htmlSVG.exportHTML(null);
1344   }
1345
1346   @Override
1347   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348   {
1349     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1350     bjs.exportHTML(null);
1351   }
1352
1353   public void createImageMap(File file, String image)
1354   {
1355     alignPanel.makePNGImageMap(file, image);
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *          DOCUMENT ME!
1363    */
1364   @Override
1365   public void createPNG(File f)
1366   {
1367     alignPanel.makePNG(f);
1368   }
1369
1370   /**
1371    * DOCUMENT ME!
1372    *
1373    * @param e
1374    *          DOCUMENT ME!
1375    */
1376   @Override
1377   public void createEPS(File f)
1378   {
1379     alignPanel.makeEPS(f);
1380   }
1381
1382   @Override
1383   public void createSVG(File f)
1384   {
1385     alignPanel.makeSVG(f);
1386   }
1387
1388   @Override
1389   public void pageSetup_actionPerformed(ActionEvent e)
1390   {
1391     PrinterJob printJob = PrinterJob.getPrinterJob();
1392     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1393   }
1394
1395   /**
1396    * DOCUMENT ME!
1397    *
1398    * @param e
1399    *          DOCUMENT ME!
1400    */
1401   @Override
1402   public void printMenuItem_actionPerformed(ActionEvent e)
1403   {
1404     // Putting in a thread avoids Swing painting problems
1405     PrintThread thread = new PrintThread(alignPanel);
1406     thread.start();
1407   }
1408
1409   @Override
1410   public void exportFeatures_actionPerformed(ActionEvent e)
1411   {
1412     new AnnotationExporter(alignPanel).exportFeatures();
1413   }
1414
1415   @Override
1416   public void exportAnnotations_actionPerformed(ActionEvent e)
1417   {
1418     new AnnotationExporter(alignPanel).exportAnnotations();
1419   }
1420
1421   @Override
1422   public void associatedData_actionPerformed(ActionEvent e)
1423   {
1424     // Pick the tree file
1425     JalviewFileChooser chooser = new JalviewFileChooser(
1426             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427     chooser.setFileView(new JalviewFileView());
1428     chooser.setDialogTitle(
1429             MessageManager.getString("label.load_jalview_annotations"));
1430     chooser.setToolTipText(
1431             MessageManager.getString("label.load_jalview_annotations"));
1432
1433     int value = chooser.showOpenDialog(null);
1434
1435     if (value == JalviewFileChooser.APPROVE_OPTION)
1436     {
1437       String choice = chooser.getSelectedFile().getPath();
1438       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439       loadJalviewDataFile(choice, null, null, null);
1440     }
1441
1442   }
1443
1444   /**
1445    * Close the current view or all views in the alignment frame. If the frame
1446    * only contains one view then the alignment will be removed from memory.
1447    *
1448    * @param closeAllTabs
1449    */
1450   @Override
1451   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452   {
1453     if (alignPanels != null && alignPanels.size() < 2)
1454     {
1455       closeAllTabs = true;
1456     }
1457
1458     try
1459     {
1460       if (alignPanels != null)
1461       {
1462         if (closeAllTabs)
1463         {
1464           if (this.isClosed())
1465           {
1466             // really close all the windows - otherwise wait till
1467             // setClosed(true) is called
1468             for (int i = 0; i < alignPanels.size(); i++)
1469             {
1470               AlignmentPanel ap = alignPanels.get(i);
1471               ap.closePanel();
1472             }
1473           }
1474         }
1475         else
1476         {
1477           closeView(alignPanel);
1478         }
1479       }
1480
1481       if (closeAllTabs)
1482       {
1483         /*
1484          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485          * be called recursively, with the frame now in 'closed' state
1486          */
1487         this.setClosed(true);
1488       }
1489     } catch (Exception ex)
1490     {
1491       ex.printStackTrace();
1492     }
1493   }
1494
1495   /**
1496    * Close the specified panel and close up tabs appropriately.
1497    *
1498    * @param panelToClose
1499    */
1500   public void closeView(AlignmentPanel panelToClose)
1501   {
1502     int index = tabbedPane.getSelectedIndex();
1503     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504     alignPanels.remove(panelToClose);
1505     panelToClose.closePanel();
1506     panelToClose = null;
1507
1508     tabbedPane.removeTabAt(closedindex);
1509     tabbedPane.validate();
1510
1511     if (index > closedindex || index == tabbedPane.getTabCount())
1512     {
1513       // modify currently selected tab index if necessary.
1514       index--;
1515     }
1516
1517     this.tabSelectionChanged(index);
1518   }
1519
1520   /**
1521    * DOCUMENT ME!
1522    */
1523   void updateEditMenuBar()
1524   {
1525
1526     if (viewport.getHistoryList().size() > 0)
1527     {
1528       undoMenuItem.setEnabled(true);
1529       CommandI command = viewport.getHistoryList().peek();
1530       undoMenuItem.setText(MessageManager
1531               .formatMessage("label.undo_command", new Object[]
1532               { command.getDescription() }));
1533     }
1534     else
1535     {
1536       undoMenuItem.setEnabled(false);
1537       undoMenuItem.setText(MessageManager.getString("action.undo"));
1538     }
1539
1540     if (viewport.getRedoList().size() > 0)
1541     {
1542       redoMenuItem.setEnabled(true);
1543
1544       CommandI command = viewport.getRedoList().peek();
1545       redoMenuItem.setText(MessageManager
1546               .formatMessage("label.redo_command", new Object[]
1547               { command.getDescription() }));
1548     }
1549     else
1550     {
1551       redoMenuItem.setEnabled(false);
1552       redoMenuItem.setText(MessageManager.getString("action.redo"));
1553     }
1554   }
1555
1556   @Override
1557   public void addHistoryItem(CommandI command)
1558   {
1559     if (command.getSize() > 0)
1560     {
1561       viewport.addToHistoryList(command);
1562       viewport.clearRedoList();
1563       updateEditMenuBar();
1564       viewport.updateHiddenColumns();
1565       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567       // viewport.getColumnSelection()
1568       // .getHiddenColumns().size() > 0);
1569     }
1570   }
1571
1572   /**
1573    *
1574    * @return alignment objects for all views
1575    */
1576   AlignmentI[] getViewAlignments()
1577   {
1578     if (alignPanels != null)
1579     {
1580       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581       int i = 0;
1582       for (AlignmentPanel ap : alignPanels)
1583       {
1584         als[i++] = ap.av.getAlignment();
1585       }
1586       return als;
1587     }
1588     if (viewport != null)
1589     {
1590       return new AlignmentI[] { viewport.getAlignment() };
1591     }
1592     return null;
1593   }
1594
1595   /**
1596    * DOCUMENT ME!
1597    *
1598    * @param e
1599    *          DOCUMENT ME!
1600    */
1601   @Override
1602   protected void undoMenuItem_actionPerformed(ActionEvent e)
1603   {
1604     if (viewport.getHistoryList().isEmpty())
1605     {
1606       return;
1607     }
1608     CommandI command = viewport.getHistoryList().pop();
1609     viewport.addToRedoList(command);
1610     command.undoCommand(getViewAlignments());
1611
1612     AlignmentViewport originalSource = getOriginatingSource(command);
1613     updateEditMenuBar();
1614
1615     if (originalSource != null)
1616     {
1617       if (originalSource != viewport)
1618       {
1619         Cache.log.warn(
1620                 "Implementation worry: mismatch of viewport origin for undo");
1621       }
1622       originalSource.updateHiddenColumns();
1623       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624       // null
1625       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626       // viewport.getColumnSelection()
1627       // .getHiddenColumns().size() > 0);
1628       originalSource.firePropertyChange("alignment", null,
1629               originalSource.getAlignment().getSequences());
1630     }
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   @Override
1640   protected void redoMenuItem_actionPerformed(ActionEvent e)
1641   {
1642     if (viewport.getRedoList().size() < 1)
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getRedoList().pop();
1648     viewport.addToHistoryList(command);
1649     command.doCommand(getViewAlignments());
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     updateEditMenuBar();
1653
1654     if (originalSource != null)
1655     {
1656
1657       if (originalSource != viewport)
1658       {
1659         Cache.log.warn(
1660                 "Implementation worry: mismatch of viewport origin for redo");
1661       }
1662       originalSource.updateHiddenColumns();
1663       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664       // null
1665       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666       // viewport.getColumnSelection()
1667       // .getHiddenColumns().size() > 0);
1668       originalSource.firePropertyChange("alignment", null,
1669               originalSource.getAlignment().getSequences());
1670     }
1671   }
1672
1673   AlignmentViewport getOriginatingSource(CommandI command)
1674   {
1675     AlignmentViewport originalSource = null;
1676     // For sequence removal and addition, we need to fire
1677     // the property change event FROM the viewport where the
1678     // original alignment was altered
1679     AlignmentI al = null;
1680     if (command instanceof EditCommand)
1681     {
1682       EditCommand editCommand = (EditCommand) command;
1683       al = editCommand.getAlignment();
1684       List<Component> comps = PaintRefresher.components
1685               .get(viewport.getSequenceSetId());
1686
1687       for (Component comp : comps)
1688       {
1689         if (comp instanceof AlignmentPanel)
1690         {
1691           if (al == ((AlignmentPanel) comp).av.getAlignment())
1692           {
1693             originalSource = ((AlignmentPanel) comp).av;
1694             break;
1695           }
1696         }
1697       }
1698     }
1699
1700     if (originalSource == null)
1701     {
1702       // The original view is closed, we must validate
1703       // the current view against the closed view first
1704       if (al != null)
1705       {
1706         PaintRefresher.validateSequences(al, viewport.getAlignment());
1707       }
1708
1709       originalSource = viewport;
1710     }
1711
1712     return originalSource;
1713   }
1714
1715   /**
1716    * DOCUMENT ME!
1717    *
1718    * @param up
1719    *          DOCUMENT ME!
1720    */
1721   public void moveSelectedSequences(boolean up)
1722   {
1723     SequenceGroup sg = viewport.getSelectionGroup();
1724
1725     if (sg == null)
1726     {
1727       return;
1728     }
1729     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730             viewport.getHiddenRepSequences(), up);
1731     alignPanel.paintAlignment(true, false);
1732   }
1733
1734   synchronized void slideSequences(boolean right, int size)
1735   {
1736     List<SequenceI> sg = new ArrayList<>();
1737     if (viewport.cursorMode)
1738     {
1739       sg.add(viewport.getAlignment()
1740               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1741     }
1742     else if (viewport.getSelectionGroup() != null
1743             && viewport.getSelectionGroup().getSize() != viewport
1744                     .getAlignment().getHeight())
1745     {
1746       sg = viewport.getSelectionGroup()
1747               .getSequences(viewport.getHiddenRepSequences());
1748     }
1749
1750     if (sg.size() < 1)
1751     {
1752       return;
1753     }
1754
1755     List<SequenceI> invertGroup = new ArrayList<>();
1756
1757     for (SequenceI seq : viewport.getAlignment().getSequences())
1758     {
1759       if (!sg.contains(seq))
1760       {
1761         invertGroup.add(seq);
1762       }
1763     }
1764
1765     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766
1767     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768     for (int i = 0; i < invertGroup.size(); i++)
1769     {
1770       seqs2[i] = invertGroup.get(i);
1771     }
1772
1773     SlideSequencesCommand ssc;
1774     if (right)
1775     {
1776       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1777               viewport.getGapCharacter());
1778     }
1779     else
1780     {
1781       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1782               viewport.getGapCharacter());
1783     }
1784
1785     int groupAdjustment = 0;
1786     if (ssc.getGapsInsertedBegin() && right)
1787     {
1788       if (viewport.cursorMode)
1789       {
1790         alignPanel.getSeqPanel().moveCursor(size, 0);
1791       }
1792       else
1793       {
1794         groupAdjustment = size;
1795       }
1796     }
1797     else if (!ssc.getGapsInsertedBegin() && !right)
1798     {
1799       if (viewport.cursorMode)
1800       {
1801         alignPanel.getSeqPanel().moveCursor(-size, 0);
1802       }
1803       else
1804       {
1805         groupAdjustment = -size;
1806       }
1807     }
1808
1809     if (groupAdjustment != 0)
1810     {
1811       viewport.getSelectionGroup().setStartRes(
1812               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813       viewport.getSelectionGroup().setEndRes(
1814               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1815     }
1816
1817     /*
1818      * just extend the last slide command if compatible; but not if in
1819      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820      */
1821     boolean appendHistoryItem = false;
1822     Deque<CommandI> historyList = viewport.getHistoryList();
1823     boolean inSplitFrame = getSplitViewContainer() != null;
1824     if (!inSplitFrame && historyList != null && historyList.size() > 0
1825             && historyList.peek() instanceof SlideSequencesCommand)
1826     {
1827       appendHistoryItem = ssc.appendSlideCommand(
1828               (SlideSequencesCommand) historyList.peek());
1829     }
1830
1831     if (!appendHistoryItem)
1832     {
1833       addHistoryItem(ssc);
1834     }
1835
1836     repaint();
1837   }
1838
1839   /**
1840    * DOCUMENT ME!
1841    *
1842    * @param e
1843    *          DOCUMENT ME!
1844    */
1845   @Override
1846   protected void copy_actionPerformed(ActionEvent e)
1847   {
1848     if (viewport.getSelectionGroup() == null)
1849     {
1850       return;
1851     }
1852     // TODO: preserve the ordering of displayed alignment annotation in any
1853     // internal paste (particularly sequence associated annotation)
1854     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1855     String[] omitHidden = null;
1856
1857     if (viewport.hasHiddenColumns())
1858     {
1859       omitHidden = viewport.getViewAsString(true);
1860     }
1861
1862     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1863             seqs, omitHidden, null);
1864
1865     StringSelection ss = new StringSelection(output);
1866
1867     try
1868     {
1869       jalview.gui.Desktop.internalCopy = true;
1870       // Its really worth setting the clipboard contents
1871       // to empty before setting the large StringSelection!!
1872       Toolkit.getDefaultToolkit().getSystemClipboard()
1873               .setContents(new StringSelection(""), null);
1874
1875       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1876               Desktop.instance);
1877     } catch (OutOfMemoryError er)
1878     {
1879       new OOMWarning("copying region", er);
1880       return;
1881     }
1882
1883     HiddenColumns hiddenColumns = null;
1884     if (viewport.hasHiddenColumns())
1885     {
1886       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1887       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1888
1889       // create new HiddenColumns object with copy of hidden regions
1890       // between startRes and endRes, offset by startRes
1891       hiddenColumns = new HiddenColumns(
1892               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1893               hiddenCutoff, hiddenOffset);
1894     }
1895
1896     Desktop.jalviewClipboard = new Object[] { seqs,
1897         viewport.getAlignment().getDataset(), hiddenColumns };
1898     statusBar.setText(MessageManager.formatMessage(
1899             "label.copied_sequences_to_clipboard", new Object[]
1900             { Integer.valueOf(seqs.length).toString() }));
1901   }
1902
1903   /**
1904    * DOCUMENT ME!
1905    *
1906    * @param e
1907    *          DOCUMENT ME!
1908    */
1909   @Override
1910   protected void pasteNew_actionPerformed(ActionEvent e)
1911   {
1912     paste(true);
1913   }
1914
1915   /**
1916    * DOCUMENT ME!
1917    *
1918    * @param e
1919    *          DOCUMENT ME!
1920    */
1921   @Override
1922   protected void pasteThis_actionPerformed(ActionEvent e)
1923   {
1924     paste(false);
1925   }
1926
1927   /**
1928    * Paste contents of Jalview clipboard
1929    *
1930    * @param newAlignment
1931    *          true to paste to a new alignment, otherwise add to this.
1932    */
1933   void paste(boolean newAlignment)
1934   {
1935     boolean externalPaste = true;
1936     try
1937     {
1938       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1939       Transferable contents = c.getContents(this);
1940
1941       if (contents == null)
1942       {
1943         return;
1944       }
1945
1946       String str;
1947       FileFormatI format;
1948       try
1949       {
1950         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1951         if (str.length() < 1)
1952         {
1953           return;
1954         }
1955
1956         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1957
1958       } catch (OutOfMemoryError er)
1959       {
1960         new OOMWarning("Out of memory pasting sequences!!", er);
1961         return;
1962       }
1963
1964       SequenceI[] sequences;
1965       boolean annotationAdded = false;
1966       AlignmentI alignment = null;
1967
1968       if (Desktop.jalviewClipboard != null)
1969       {
1970         // The clipboard was filled from within Jalview, we must use the
1971         // sequences
1972         // And dataset from the copied alignment
1973         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1974         // be doubly sure that we create *new* sequence objects.
1975         sequences = new SequenceI[newseq.length];
1976         for (int i = 0; i < newseq.length; i++)
1977         {
1978           sequences[i] = new Sequence(newseq[i]);
1979         }
1980         alignment = new Alignment(sequences);
1981         externalPaste = false;
1982       }
1983       else
1984       {
1985         // parse the clipboard as an alignment.
1986         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1987                 format);
1988         sequences = alignment.getSequencesArray();
1989       }
1990
1991       int alwidth = 0;
1992       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1993       int fgroup = -1;
1994
1995       if (newAlignment)
1996       {
1997
1998         if (Desktop.jalviewClipboard != null)
1999         {
2000           // dataset is inherited
2001           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2002         }
2003         else
2004         {
2005           // new dataset is constructed
2006           alignment.setDataset(null);
2007         }
2008         alwidth = alignment.getWidth() + 1;
2009       }
2010       else
2011       {
2012         AlignmentI pastedal = alignment; // preserve pasted alignment object
2013         // Add pasted sequences and dataset into existing alignment.
2014         alignment = viewport.getAlignment();
2015         alwidth = alignment.getWidth() + 1;
2016         // decide if we need to import sequences from an existing dataset
2017         boolean importDs = Desktop.jalviewClipboard != null
2018                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2019         // importDs==true instructs us to copy over new dataset sequences from
2020         // an existing alignment
2021         Vector newDs = (importDs) ? new Vector() : null; // used to create
2022         // minimum dataset set
2023
2024         for (int i = 0; i < sequences.length; i++)
2025         {
2026           if (importDs)
2027           {
2028             newDs.addElement(null);
2029           }
2030           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2031           // paste
2032           if (importDs && ds != null)
2033           {
2034             if (!newDs.contains(ds))
2035             {
2036               newDs.setElementAt(ds, i);
2037               ds = new Sequence(ds);
2038               // update with new dataset sequence
2039               sequences[i].setDatasetSequence(ds);
2040             }
2041             else
2042             {
2043               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2044             }
2045           }
2046           else
2047           {
2048             // copy and derive new dataset sequence
2049             sequences[i] = sequences[i].deriveSequence();
2050             alignment.getDataset()
2051                     .addSequence(sequences[i].getDatasetSequence());
2052             // TODO: avoid creation of duplicate dataset sequences with a
2053             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2054           }
2055           alignment.addSequence(sequences[i]); // merges dataset
2056         }
2057         if (newDs != null)
2058         {
2059           newDs.clear(); // tidy up
2060         }
2061         if (alignment.getAlignmentAnnotation() != null)
2062         {
2063           for (AlignmentAnnotation alan : alignment
2064                   .getAlignmentAnnotation())
2065           {
2066             if (alan.graphGroup > fgroup)
2067             {
2068               fgroup = alan.graphGroup;
2069             }
2070           }
2071         }
2072         if (pastedal.getAlignmentAnnotation() != null)
2073         {
2074           // Add any annotation attached to alignment.
2075           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2076           for (int i = 0; i < alann.length; i++)
2077           {
2078             annotationAdded = true;
2079             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2080             {
2081               AlignmentAnnotation newann = new AlignmentAnnotation(
2082                       alann[i]);
2083               if (newann.graphGroup > -1)
2084               {
2085                 if (newGraphGroups.size() <= newann.graphGroup
2086                         || newGraphGroups.get(newann.graphGroup) == null)
2087                 {
2088                   for (int q = newGraphGroups
2089                           .size(); q <= newann.graphGroup; q++)
2090                   {
2091                     newGraphGroups.add(q, null);
2092                   }
2093                   newGraphGroups.set(newann.graphGroup,
2094                           new Integer(++fgroup));
2095                 }
2096                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2097                         .intValue();
2098               }
2099
2100               newann.padAnnotation(alwidth);
2101               alignment.addAnnotation(newann);
2102             }
2103           }
2104         }
2105       }
2106       if (!newAlignment)
2107       {
2108         // /////
2109         // ADD HISTORY ITEM
2110         //
2111         addHistoryItem(new EditCommand(
2112                 MessageManager.getString("label.add_sequences"),
2113                 Action.PASTE, sequences, 0, alignment.getWidth(),
2114                 alignment));
2115       }
2116       // Add any annotations attached to sequences
2117       for (int i = 0; i < sequences.length; i++)
2118       {
2119         if (sequences[i].getAnnotation() != null)
2120         {
2121           AlignmentAnnotation newann;
2122           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123           {
2124             annotationAdded = true;
2125             newann = sequences[i].getAnnotation()[a];
2126             newann.adjustForAlignment();
2127             newann.padAnnotation(alwidth);
2128             if (newann.graphGroup > -1)
2129             {
2130               if (newann.graphGroup > -1)
2131               {
2132                 if (newGraphGroups.size() <= newann.graphGroup
2133                         || newGraphGroups.get(newann.graphGroup) == null)
2134                 {
2135                   for (int q = newGraphGroups
2136                           .size(); q <= newann.graphGroup; q++)
2137                   {
2138                     newGraphGroups.add(q, null);
2139                   }
2140                   newGraphGroups.set(newann.graphGroup,
2141                           new Integer(++fgroup));
2142                 }
2143                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2144                         .intValue();
2145               }
2146             }
2147             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2148             // was
2149             // duplicated
2150             // earlier
2151             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2152                     a);
2153           }
2154         }
2155       }
2156       if (!newAlignment)
2157       {
2158
2159         // propagate alignment changed.
2160         viewport.getRanges().setEndSeq(alignment.getHeight());
2161         if (annotationAdded)
2162         {
2163           // Duplicate sequence annotation in all views.
2164           AlignmentI[] alview = this.getViewAlignments();
2165           for (int i = 0; i < sequences.length; i++)
2166           {
2167             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2168             if (sann == null)
2169             {
2170               continue;
2171             }
2172             for (int avnum = 0; avnum < alview.length; avnum++)
2173             {
2174               if (alview[avnum] != alignment)
2175               {
2176                 // duplicate in a view other than the one with input focus
2177                 int avwidth = alview[avnum].getWidth() + 1;
2178                 // this relies on sann being preserved after we
2179                 // modify the sequence's annotation array for each duplication
2180                 for (int a = 0; a < sann.length; a++)
2181                 {
2182                   AlignmentAnnotation newann = new AlignmentAnnotation(
2183                           sann[a]);
2184                   sequences[i].addAlignmentAnnotation(newann);
2185                   newann.padAnnotation(avwidth);
2186                   alview[avnum].addAnnotation(newann); // annotation was
2187                   // duplicated earlier
2188                   // TODO JAL-1145 graphGroups are not updated for sequence
2189                   // annotation added to several views. This may cause
2190                   // strangeness
2191                   alview[avnum].setAnnotationIndex(newann, a);
2192                 }
2193               }
2194             }
2195           }
2196           buildSortByAnnotationScoresMenu();
2197         }
2198         viewport.firePropertyChange("alignment", null,
2199                 alignment.getSequences());
2200         if (alignPanels != null)
2201         {
2202           for (AlignmentPanel ap : alignPanels)
2203           {
2204             ap.validateAnnotationDimensions(false);
2205           }
2206         }
2207         else
2208         {
2209           alignPanel.validateAnnotationDimensions(false);
2210         }
2211
2212       }
2213       else
2214       {
2215         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2216                 DEFAULT_HEIGHT);
2217         String newtitle = new String("Copied sequences");
2218
2219         if (Desktop.jalviewClipboard != null
2220                 && Desktop.jalviewClipboard[2] != null)
2221         {
2222           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2223           af.viewport.setHiddenColumns(hc);
2224         }
2225
2226         // >>>This is a fix for the moment, until a better solution is
2227         // found!!<<<
2228         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2229                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2230                         .getFeatureRenderer());
2231
2232         // TODO: maintain provenance of an alignment, rather than just make the
2233         // title a concatenation of operations.
2234         if (!externalPaste)
2235         {
2236           if (title.startsWith("Copied sequences"))
2237           {
2238             newtitle = title;
2239           }
2240           else
2241           {
2242             newtitle = newtitle.concat("- from " + title);
2243           }
2244         }
2245         else
2246         {
2247           newtitle = new String("Pasted sequences");
2248         }
2249
2250         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2251                 DEFAULT_HEIGHT);
2252
2253       }
2254
2255     } catch (Exception ex)
2256     {
2257       ex.printStackTrace();
2258       System.out.println("Exception whilst pasting: " + ex);
2259       // could be anything being pasted in here
2260     }
2261
2262   }
2263
2264   @Override
2265   protected void expand_newalign(ActionEvent e)
2266   {
2267     try
2268     {
2269       AlignmentI alignment = AlignmentUtils
2270               .expandContext(getViewport().getAlignment(), -1);
2271       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2272               DEFAULT_HEIGHT);
2273       String newtitle = new String("Flanking alignment");
2274
2275       if (Desktop.jalviewClipboard != null
2276               && Desktop.jalviewClipboard[2] != null)
2277       {
2278         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2279         af.viewport.setHiddenColumns(hc);
2280       }
2281
2282       // >>>This is a fix for the moment, until a better solution is
2283       // found!!<<<
2284       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2285               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2286                       .getFeatureRenderer());
2287
2288       // TODO: maintain provenance of an alignment, rather than just make the
2289       // title a concatenation of operations.
2290       {
2291         if (title.startsWith("Copied sequences"))
2292         {
2293           newtitle = title;
2294         }
2295         else
2296         {
2297           newtitle = newtitle.concat("- from " + title);
2298         }
2299       }
2300
2301       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2302
2303     } catch (Exception ex)
2304     {
2305       ex.printStackTrace();
2306       System.out.println("Exception whilst pasting: " + ex);
2307       // could be anything being pasted in here
2308     } catch (OutOfMemoryError oom)
2309     {
2310       new OOMWarning("Viewing flanking region of alignment", oom);
2311     }
2312   }
2313
2314   /**
2315    * DOCUMENT ME!
2316    *
2317    * @param e
2318    *          DOCUMENT ME!
2319    */
2320   @Override
2321   protected void cut_actionPerformed(ActionEvent e)
2322   {
2323     copy_actionPerformed(null);
2324     delete_actionPerformed(null);
2325   }
2326
2327   /**
2328    * DOCUMENT ME!
2329    *
2330    * @param e
2331    *          DOCUMENT ME!
2332    */
2333   @Override
2334   protected void delete_actionPerformed(ActionEvent evt)
2335   {
2336
2337     SequenceGroup sg = viewport.getSelectionGroup();
2338     if (sg == null)
2339     {
2340       return;
2341     }
2342
2343     /*
2344      * If the cut affects all sequences, warn, remove highlighted columns
2345      */
2346     if (sg.getSize() == viewport.getAlignment().getHeight())
2347     {
2348       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2349               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2350       if (isEntireAlignWidth)
2351       {
2352         int confirm = JvOptionPane.showConfirmDialog(this,
2353                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2354                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2355                 JvOptionPane.OK_CANCEL_OPTION);
2356
2357         if (confirm == JvOptionPane.CANCEL_OPTION
2358                 || confirm == JvOptionPane.CLOSED_OPTION)
2359         {
2360           return;
2361         }
2362       }
2363       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2364               sg.getEndRes() + 1);
2365     }
2366     SequenceI[] cut = sg.getSequences()
2367             .toArray(new SequenceI[sg.getSize()]);
2368
2369     addHistoryItem(new EditCommand(
2370             MessageManager.getString("label.cut_sequences"), Action.CUT,
2371             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2372             viewport.getAlignment()));
2373
2374     viewport.setSelectionGroup(null);
2375     viewport.sendSelection();
2376     viewport.getAlignment().deleteGroup(sg);
2377
2378     viewport.firePropertyChange("alignment", null,
2379             viewport.getAlignment().getSequences());
2380     if (viewport.getAlignment().getHeight() < 1)
2381     {
2382       try
2383       {
2384         this.setClosed(true);
2385       } catch (Exception ex)
2386       {
2387       }
2388     }
2389   }
2390
2391   /**
2392    * DOCUMENT ME!
2393    *
2394    * @param e
2395    *          DOCUMENT ME!
2396    */
2397   @Override
2398   protected void deleteGroups_actionPerformed(ActionEvent e)
2399   {
2400     if (avc.deleteGroups())
2401     {
2402       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2403       alignPanel.updateAnnotation();
2404       alignPanel.paintAlignment(true, true);
2405     }
2406   }
2407
2408   /**
2409    * DOCUMENT ME!
2410    *
2411    * @param e
2412    *          DOCUMENT ME!
2413    */
2414   @Override
2415   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2416   {
2417     SequenceGroup sg = new SequenceGroup(
2418             viewport.getAlignment().getSequences());
2419
2420     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2421     viewport.setSelectionGroup(sg);
2422     viewport.isSelectionGroupChanged(true);
2423     viewport.sendSelection();
2424     // JAL-2034 - should delegate to
2425     // alignPanel to decide if overview needs
2426     // updating.
2427     alignPanel.paintAlignment(false, false);
2428     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2429   }
2430
2431   /**
2432    * DOCUMENT ME!
2433    *
2434    * @param e
2435    *          DOCUMENT ME!
2436    */
2437   @Override
2438   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2439   {
2440     if (viewport.cursorMode)
2441     {
2442       alignPanel.getSeqPanel().keyboardNo1 = null;
2443       alignPanel.getSeqPanel().keyboardNo2 = null;
2444     }
2445     viewport.setSelectionGroup(null);
2446     viewport.getColumnSelection().clear();
2447     viewport.setSelectionGroup(null);
2448     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2449     // JAL-2034 - should delegate to
2450     // alignPanel to decide if overview needs
2451     // updating.
2452     alignPanel.paintAlignment(false, false);
2453     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2454     viewport.sendSelection();
2455   }
2456
2457   /**
2458    * DOCUMENT ME!
2459    *
2460    * @param e
2461    *          DOCUMENT ME!
2462    */
2463   @Override
2464   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2465   {
2466     SequenceGroup sg = viewport.getSelectionGroup();
2467
2468     if (sg == null)
2469     {
2470       selectAllSequenceMenuItem_actionPerformed(null);
2471
2472       return;
2473     }
2474
2475     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2476     {
2477       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2478     }
2479     // JAL-2034 - should delegate to
2480     // alignPanel to decide if overview needs
2481     // updating.
2482
2483     alignPanel.paintAlignment(true, false);
2484     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2485     viewport.sendSelection();
2486   }
2487
2488   @Override
2489   public void invertColSel_actionPerformed(ActionEvent e)
2490   {
2491     viewport.invertColumnSelection();
2492     alignPanel.paintAlignment(true, false);
2493     viewport.sendSelection();
2494   }
2495
2496   /**
2497    * DOCUMENT ME!
2498    *
2499    * @param e
2500    *          DOCUMENT ME!
2501    */
2502   @Override
2503   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2504   {
2505     trimAlignment(true);
2506   }
2507
2508   /**
2509    * DOCUMENT ME!
2510    *
2511    * @param e
2512    *          DOCUMENT ME!
2513    */
2514   @Override
2515   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2516   {
2517     trimAlignment(false);
2518   }
2519
2520   void trimAlignment(boolean trimLeft)
2521   {
2522     ColumnSelection colSel = viewport.getColumnSelection();
2523     int column;
2524
2525     if (!colSel.isEmpty())
2526     {
2527       if (trimLeft)
2528       {
2529         column = colSel.getMin();
2530       }
2531       else
2532       {
2533         column = colSel.getMax();
2534       }
2535
2536       SequenceI[] seqs;
2537       if (viewport.getSelectionGroup() != null)
2538       {
2539         seqs = viewport.getSelectionGroup()
2540                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2541       }
2542       else
2543       {
2544         seqs = viewport.getAlignment().getSequencesArray();
2545       }
2546
2547       TrimRegionCommand trimRegion;
2548       if (trimLeft)
2549       {
2550         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2551                 column, viewport.getAlignment());
2552         viewport.getRanges().setStartRes(0);
2553       }
2554       else
2555       {
2556         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2557                 column, viewport.getAlignment());
2558       }
2559
2560       statusBar.setText(MessageManager
2561               .formatMessage("label.removed_columns", new String[]
2562               { Integer.valueOf(trimRegion.getSize()).toString() }));
2563
2564       addHistoryItem(trimRegion);
2565
2566       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2567       {
2568         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2569                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2570         {
2571           viewport.getAlignment().deleteGroup(sg);
2572         }
2573       }
2574
2575       viewport.firePropertyChange("alignment", null,
2576               viewport.getAlignment().getSequences());
2577     }
2578   }
2579
2580   /**
2581    * DOCUMENT ME!
2582    *
2583    * @param e
2584    *          DOCUMENT ME!
2585    */
2586   @Override
2587   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2588   {
2589     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2590
2591     SequenceI[] seqs;
2592     if (viewport.getSelectionGroup() != null)
2593     {
2594       seqs = viewport.getSelectionGroup()
2595               .getSequencesAsArray(viewport.getHiddenRepSequences());
2596       start = viewport.getSelectionGroup().getStartRes();
2597       end = viewport.getSelectionGroup().getEndRes();
2598     }
2599     else
2600     {
2601       seqs = viewport.getAlignment().getSequencesArray();
2602     }
2603
2604     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2605             "Remove Gapped Columns", seqs, start, end,
2606             viewport.getAlignment());
2607
2608     addHistoryItem(removeGapCols);
2609
2610     statusBar.setText(MessageManager
2611             .formatMessage("label.removed_empty_columns", new Object[]
2612             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2613
2614     // This is to maintain viewport position on first residue
2615     // of first sequence
2616     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617     ViewportRanges ranges = viewport.getRanges();
2618     int startRes = seq.findPosition(ranges.getStartRes());
2619     // ShiftList shifts;
2620     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2621     // edit.alColumnChanges=shifts.getInverse();
2622     // if (viewport.hasHiddenColumns)
2623     // viewport.getColumnSelection().compensateForEdits(shifts);
2624     ranges.setStartRes(seq.findIndex(startRes) - 1);
2625     viewport.firePropertyChange("alignment", null,
2626             viewport.getAlignment().getSequences());
2627
2628   }
2629
2630   /**
2631    * DOCUMENT ME!
2632    *
2633    * @param e
2634    *          DOCUMENT ME!
2635    */
2636   @Override
2637   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2638   {
2639     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2640
2641     SequenceI[] seqs;
2642     if (viewport.getSelectionGroup() != null)
2643     {
2644       seqs = viewport.getSelectionGroup()
2645               .getSequencesAsArray(viewport.getHiddenRepSequences());
2646       start = viewport.getSelectionGroup().getStartRes();
2647       end = viewport.getSelectionGroup().getEndRes();
2648     }
2649     else
2650     {
2651       seqs = viewport.getAlignment().getSequencesArray();
2652     }
2653
2654     // This is to maintain viewport position on first residue
2655     // of first sequence
2656     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2657     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2658
2659     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2660             viewport.getAlignment()));
2661
2662     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2663
2664     viewport.firePropertyChange("alignment", null,
2665             viewport.getAlignment().getSequences());
2666
2667   }
2668
2669   /**
2670    * DOCUMENT ME!
2671    *
2672    * @param e
2673    *          DOCUMENT ME!
2674    */
2675   @Override
2676   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2677   {
2678     viewport.setPadGaps(padGapsMenuitem.isSelected());
2679     viewport.firePropertyChange("alignment", null,
2680             viewport.getAlignment().getSequences());
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e
2687    *          DOCUMENT ME!
2688    */
2689   @Override
2690   public void findMenuItem_actionPerformed(ActionEvent e)
2691   {
2692     new Finder();
2693   }
2694
2695   /**
2696    * Create a new view of the current alignment.
2697    */
2698   @Override
2699   public void newView_actionPerformed(ActionEvent e)
2700   {
2701     newView(null, true);
2702   }
2703
2704   /**
2705    * Creates and shows a new view of the current alignment.
2706    *
2707    * @param viewTitle
2708    *          title of newly created view; if null, one will be generated
2709    * @param copyAnnotation
2710    *          if true then duplicate all annnotation, groups and settings
2711    * @return new alignment panel, already displayed.
2712    */
2713   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2714   {
2715     /*
2716      * Create a new AlignmentPanel (with its own, new Viewport)
2717      */
2718     AlignmentPanel newap = new jalview.project.Jalview2XML()
2719             .copyAlignPanel(alignPanel);
2720     if (!copyAnnotation)
2721     {
2722       /*
2723        * remove all groups and annotation except for the automatic stuff
2724        */
2725       newap.av.getAlignment().deleteAllGroups();
2726       newap.av.getAlignment().deleteAllAnnotations(false);
2727     }
2728
2729     newap.av.setGatherViewsHere(false);
2730
2731     if (viewport.getViewName() == null)
2732     {
2733       viewport.setViewName(MessageManager
2734               .getString("label.view_name_original"));
2735     }
2736
2737     /*
2738      * Views share the same edits undo and redo stacks
2739      */
2740     newap.av.setHistoryList(viewport.getHistoryList());
2741     newap.av.setRedoList(viewport.getRedoList());
2742
2743     /*
2744      * copy any visualisation settings that are not saved in the project
2745      */
2746     newap.av.setColourAppliesToAllGroups(
2747             viewport.getColourAppliesToAllGroups());
2748
2749     /*
2750      * Views share the same mappings; need to deregister any new mappings
2751      * created by copyAlignPanel, and register the new reference to the shared
2752      * mappings
2753      */
2754     newap.av.replaceMappings(viewport.getAlignment());
2755
2756     /*
2757      * start up cDNA consensus (if applicable) now mappings are in place
2758      */
2759     if (newap.av.initComplementConsensus())
2760     {
2761       newap.refresh(true); // adjust layout of annotations
2762     }
2763
2764     newap.av.setViewName(getNewViewName(viewTitle));
2765
2766     addAlignmentPanel(newap, true);
2767     newap.alignmentChanged();
2768
2769     if (alignPanels.size() == 2)
2770     {
2771       viewport.setGatherViewsHere(true);
2772     }
2773     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2774     return newap;
2775   }
2776
2777   /**
2778    * Make a new name for the view, ensuring it is unique within the current
2779    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2780    * these now use viewId. Unique view names are still desirable for usability.)
2781    *
2782    * @param viewTitle
2783    * @return
2784    */
2785   protected String getNewViewName(String viewTitle)
2786   {
2787     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2788     boolean addFirstIndex = false;
2789     if (viewTitle == null || viewTitle.trim().length() == 0)
2790     {
2791       viewTitle = MessageManager.getString("action.view");
2792       addFirstIndex = true;
2793     }
2794     else
2795     {
2796       index = 1;// we count from 1 if given a specific name
2797     }
2798     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2799
2800     List<Component> comps = PaintRefresher.components
2801             .get(viewport.getSequenceSetId());
2802
2803     List<String> existingNames = getExistingViewNames(comps);
2804
2805     while (existingNames.contains(newViewName))
2806     {
2807       newViewName = viewTitle + " " + (++index);
2808     }
2809     return newViewName;
2810   }
2811
2812   /**
2813    * Returns a list of distinct view names found in the given list of
2814    * components. View names are held on the viewport of an AlignmentPanel.
2815    *
2816    * @param comps
2817    * @return
2818    */
2819   protected List<String> getExistingViewNames(List<Component> comps)
2820   {
2821     List<String> existingNames = new ArrayList<>();
2822     for (Component comp : comps)
2823     {
2824       if (comp instanceof AlignmentPanel)
2825       {
2826         AlignmentPanel ap = (AlignmentPanel) comp;
2827         if (!existingNames.contains(ap.av.getViewName()))
2828         {
2829           existingNames.add(ap.av.getViewName());
2830         }
2831       }
2832     }
2833     return existingNames;
2834   }
2835
2836   /**
2837    * Explode tabbed views into separate windows.
2838    */
2839   @Override
2840   public void expandViews_actionPerformed(ActionEvent e)
2841   {
2842     Desktop.explodeViews(this);
2843   }
2844
2845   /**
2846    * Gather views in separate windows back into a tabbed presentation.
2847    */
2848   @Override
2849   public void gatherViews_actionPerformed(ActionEvent e)
2850   {
2851     Desktop.instance.gatherViews(this);
2852   }
2853
2854   /**
2855    * DOCUMENT ME!
2856    *
2857    * @param e
2858    *          DOCUMENT ME!
2859    */
2860   @Override
2861   public void font_actionPerformed(ActionEvent e)
2862   {
2863     new FontChooser(alignPanel);
2864   }
2865
2866   /**
2867    * DOCUMENT ME!
2868    *
2869    * @param e
2870    *          DOCUMENT ME!
2871    */
2872   @Override
2873   protected void seqLimit_actionPerformed(ActionEvent e)
2874   {
2875     viewport.setShowJVSuffix(seqLimits.isSelected());
2876
2877     alignPanel.getIdPanel().getIdCanvas()
2878             .setPreferredSize(alignPanel.calculateIdWidth());
2879     alignPanel.paintAlignment(true, false);
2880   }
2881
2882   @Override
2883   public void idRightAlign_actionPerformed(ActionEvent e)
2884   {
2885     viewport.setRightAlignIds(idRightAlign.isSelected());
2886     alignPanel.paintAlignment(false, false);
2887   }
2888
2889   @Override
2890   public void centreColumnLabels_actionPerformed(ActionEvent e)
2891   {
2892     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2893     alignPanel.paintAlignment(false, false);
2894   }
2895
2896   /*
2897    * (non-Javadoc)
2898    *
2899    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2900    */
2901   @Override
2902   protected void followHighlight_actionPerformed()
2903   {
2904     /*
2905      * Set the 'follow' flag on the Viewport (and scroll to position if now
2906      * true).
2907      */
2908     final boolean state = this.followHighlightMenuItem.getState();
2909     viewport.setFollowHighlight(state);
2910     if (state)
2911     {
2912       alignPanel.scrollToPosition(viewport.getSearchResults());
2913     }
2914   }
2915
2916   /**
2917    * DOCUMENT ME!
2918    *
2919    * @param e
2920    *          DOCUMENT ME!
2921    */
2922   @Override
2923   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2924   {
2925     viewport.setColourText(colourTextMenuItem.isSelected());
2926     alignPanel.paintAlignment(false, false);
2927   }
2928
2929   /**
2930    * DOCUMENT ME!
2931    *
2932    * @param e
2933    *          DOCUMENT ME!
2934    */
2935   @Override
2936   public void wrapMenuItem_actionPerformed(ActionEvent e)
2937   {
2938     scaleAbove.setVisible(wrapMenuItem.isSelected());
2939     scaleLeft.setVisible(wrapMenuItem.isSelected());
2940     scaleRight.setVisible(wrapMenuItem.isSelected());
2941     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2942     alignPanel.updateLayout();
2943   }
2944
2945   @Override
2946   public void showAllSeqs_actionPerformed(ActionEvent e)
2947   {
2948     viewport.showAllHiddenSeqs();
2949   }
2950
2951   @Override
2952   public void showAllColumns_actionPerformed(ActionEvent e)
2953   {
2954     viewport.showAllHiddenColumns();
2955     alignPanel.paintAlignment(true, true);
2956     viewport.sendSelection();
2957   }
2958
2959   @Override
2960   public void hideSelSequences_actionPerformed(ActionEvent e)
2961   {
2962     viewport.hideAllSelectedSeqs();
2963   }
2964
2965   /**
2966    * called by key handler and the hide all/show all menu items
2967    *
2968    * @param toggleSeqs
2969    * @param toggleCols
2970    */
2971   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2972   {
2973
2974     boolean hide = false;
2975     SequenceGroup sg = viewport.getSelectionGroup();
2976     if (!toggleSeqs && !toggleCols)
2977     {
2978       // Hide everything by the current selection - this is a hack - we do the
2979       // invert and then hide
2980       // first check that there will be visible columns after the invert.
2981       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2982               && sg.getStartRes() <= sg.getEndRes()))
2983       {
2984         // now invert the sequence set, if required - empty selection implies
2985         // that no hiding is required.
2986         if (sg != null)
2987         {
2988           invertSequenceMenuItem_actionPerformed(null);
2989           sg = viewport.getSelectionGroup();
2990           toggleSeqs = true;
2991
2992         }
2993         viewport.expandColSelection(sg, true);
2994         // finally invert the column selection and get the new sequence
2995         // selection.
2996         invertColSel_actionPerformed(null);
2997         toggleCols = true;
2998       }
2999     }
3000
3001     if (toggleSeqs)
3002     {
3003       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3004       {
3005         hideSelSequences_actionPerformed(null);
3006         hide = true;
3007       }
3008       else if (!(toggleCols && viewport.hasSelectedColumns()))
3009       {
3010         showAllSeqs_actionPerformed(null);
3011       }
3012     }
3013
3014     if (toggleCols)
3015     {
3016       if (viewport.hasSelectedColumns())
3017       {
3018         hideSelColumns_actionPerformed(null);
3019         if (!toggleSeqs)
3020         {
3021           viewport.setSelectionGroup(sg);
3022         }
3023       }
3024       else if (!hide)
3025       {
3026         showAllColumns_actionPerformed(null);
3027       }
3028     }
3029   }
3030
3031   /*
3032    * (non-Javadoc)
3033    *
3034    * @see
3035    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036    * event.ActionEvent)
3037    */
3038   @Override
3039   public void hideAllButSelection_actionPerformed(ActionEvent e)
3040   {
3041     toggleHiddenRegions(false, false);
3042     viewport.sendSelection();
3043   }
3044
3045   /*
3046    * (non-Javadoc)
3047    *
3048    * @see
3049    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3050    * .ActionEvent)
3051    */
3052   @Override
3053   public void hideAllSelection_actionPerformed(ActionEvent e)
3054   {
3055     SequenceGroup sg = viewport.getSelectionGroup();
3056     viewport.expandColSelection(sg, false);
3057     viewport.hideAllSelectedSeqs();
3058     viewport.hideSelectedColumns();
3059     alignPanel.updateLayout();
3060     alignPanel.paintAlignment(true, true);
3061     viewport.sendSelection();
3062   }
3063
3064   /*
3065    * (non-Javadoc)
3066    *
3067    * @see
3068    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3069    * ActionEvent)
3070    */
3071   @Override
3072   public void showAllhidden_actionPerformed(ActionEvent e)
3073   {
3074     viewport.showAllHiddenColumns();
3075     viewport.showAllHiddenSeqs();
3076     alignPanel.paintAlignment(true, true);
3077     viewport.sendSelection();
3078   }
3079
3080   @Override
3081   public void hideSelColumns_actionPerformed(ActionEvent e)
3082   {
3083     viewport.hideSelectedColumns();
3084     alignPanel.updateLayout();
3085     alignPanel.paintAlignment(true, true);
3086     viewport.sendSelection();
3087   }
3088
3089   @Override
3090   public void hiddenMarkers_actionPerformed(ActionEvent e)
3091   {
3092     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3093     repaint();
3094   }
3095
3096   /**
3097    * DOCUMENT ME!
3098    *
3099    * @param e
3100    *          DOCUMENT ME!
3101    */
3102   @Override
3103   protected void scaleAbove_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3106     alignPanel.updateLayout();
3107     alignPanel.paintAlignment(true, false);
3108   }
3109
3110   /**
3111    * DOCUMENT ME!
3112    *
3113    * @param e
3114    *          DOCUMENT ME!
3115    */
3116   @Override
3117   protected void scaleLeft_actionPerformed(ActionEvent e)
3118   {
3119     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3120     alignPanel.updateLayout();
3121     alignPanel.paintAlignment(true, false);
3122   }
3123
3124   /**
3125    * DOCUMENT ME!
3126    *
3127    * @param e
3128    *          DOCUMENT ME!
3129    */
3130   @Override
3131   protected void scaleRight_actionPerformed(ActionEvent e)
3132   {
3133     viewport.setScaleRightWrapped(scaleRight.isSelected());
3134     alignPanel.updateLayout();
3135     alignPanel.paintAlignment(true, false);
3136   }
3137
3138   /**
3139    * DOCUMENT ME!
3140    *
3141    * @param e
3142    *          DOCUMENT ME!
3143    */
3144   @Override
3145   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3146   {
3147     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3148     alignPanel.paintAlignment(false, false);
3149   }
3150
3151   /**
3152    * DOCUMENT ME!
3153    *
3154    * @param e
3155    *          DOCUMENT ME!
3156    */
3157   @Override
3158   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3159   {
3160     viewport.setShowText(viewTextMenuItem.isSelected());
3161     alignPanel.paintAlignment(false, false);
3162   }
3163
3164   /**
3165    * DOCUMENT ME!
3166    *
3167    * @param e
3168    *          DOCUMENT ME!
3169    */
3170   @Override
3171   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3172   {
3173     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3174     alignPanel.paintAlignment(false, false);
3175   }
3176
3177   public FeatureSettings featureSettings;
3178
3179   @Override
3180   public FeatureSettingsControllerI getFeatureSettingsUI()
3181   {
3182     return featureSettings;
3183   }
3184
3185   @Override
3186   public void featureSettings_actionPerformed(ActionEvent e)
3187   {
3188     if (featureSettings != null)
3189     {
3190       featureSettings.close();
3191       featureSettings = null;
3192     }
3193     if (!showSeqFeatures.isSelected())
3194     {
3195       // make sure features are actually displayed
3196       showSeqFeatures.setSelected(true);
3197       showSeqFeatures_actionPerformed(null);
3198     }
3199     featureSettings = new FeatureSettings(this);
3200   }
3201
3202   /**
3203    * Set or clear 'Show Sequence Features'
3204    *
3205    * @param evt
3206    *          DOCUMENT ME!
3207    */
3208   @Override
3209   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3210   {
3211     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3212     alignPanel.paintAlignment(true, true);
3213   }
3214
3215   /**
3216    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3217    * the annotations panel as a whole.
3218    *
3219    * The options to show/hide all annotations should be enabled when the panel
3220    * is shown, and disabled when the panel is hidden.
3221    *
3222    * @param e
3223    */
3224   @Override
3225   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3226   {
3227     final boolean setVisible = annotationPanelMenuItem.isSelected();
3228     viewport.setShowAnnotation(setVisible);
3229     this.showAllSeqAnnotations.setEnabled(setVisible);
3230     this.hideAllSeqAnnotations.setEnabled(setVisible);
3231     this.showAllAlAnnotations.setEnabled(setVisible);
3232     this.hideAllAlAnnotations.setEnabled(setVisible);
3233     alignPanel.updateLayout();
3234   }
3235
3236   @Override
3237   public void alignmentProperties()
3238   {
3239     JEditorPane editPane = new JEditorPane("text/html", "");
3240     editPane.setEditable(false);
3241     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3242             .formatAsHtml();
3243     editPane.setText(
3244             MessageManager.formatMessage("label.html_content", new Object[]
3245             { contents.toString() }));
3246     JInternalFrame frame = new JInternalFrame();
3247     frame.getContentPane().add(new JScrollPane(editPane));
3248
3249     Desktop.addInternalFrame(frame, MessageManager
3250             .formatMessage("label.alignment_properties", new Object[]
3251             { getTitle() }), 500, 400);
3252   }
3253
3254   /**
3255    * DOCUMENT ME!
3256    *
3257    * @param e
3258    *          DOCUMENT ME!
3259    */
3260   @Override
3261   public void overviewMenuItem_actionPerformed(ActionEvent e)
3262   {
3263     if (alignPanel.overviewPanel != null)
3264     {
3265       return;
3266     }
3267
3268     JInternalFrame frame = new JInternalFrame();
3269     final OverviewPanel overview = new OverviewPanel(alignPanel);
3270     frame.setContentPane(overview);
3271     Desktop.addInternalFrame(frame, MessageManager
3272             .formatMessage("label.overview_params", new Object[]
3273             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3274             true, true);
3275     frame.pack();
3276     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3277     frame.addInternalFrameListener(
3278             new javax.swing.event.InternalFrameAdapter()
3279             {
3280               @Override
3281               public void internalFrameClosed(
3282                       javax.swing.event.InternalFrameEvent evt)
3283               {
3284                 overview.dispose();
3285                 alignPanel.setOverviewPanel(null);
3286               };
3287             });
3288     if (getKeyListeners().length > 0)
3289     {
3290       frame.addKeyListener(getKeyListeners()[0]);
3291     }
3292
3293     alignPanel.setOverviewPanel(overview);
3294   }
3295
3296   @Override
3297   public void textColour_actionPerformed()
3298   {
3299     new TextColourChooser().chooseColour(alignPanel, null);
3300   }
3301
3302   /*
3303    * public void covariationColour_actionPerformed() {
3304    * changeColour(new
3305    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3306    * ()[0])); }
3307    */
3308   @Override
3309   public void annotationColour_actionPerformed()
3310   {
3311     new AnnotationColourChooser(viewport, alignPanel);
3312   }
3313
3314   @Override
3315   public void annotationColumn_actionPerformed(ActionEvent e)
3316   {
3317     new AnnotationColumnChooser(viewport, alignPanel);
3318   }
3319
3320   /**
3321    * Action on the user checking or unchecking the option to apply the selected
3322    * colour scheme to all groups. If unchecked, groups may have their own
3323    * independent colour schemes.
3324    *
3325    * @param selected
3326    */
3327   @Override
3328   public void applyToAllGroups_actionPerformed(boolean selected)
3329   {
3330     viewport.setColourAppliesToAllGroups(selected);
3331   }
3332
3333   /**
3334    * Action on user selecting a colour from the colour menu
3335    *
3336    * @param name
3337    *          the name (not the menu item label!) of the colour scheme
3338    */
3339   @Override
3340   public void changeColour_actionPerformed(String name)
3341   {
3342     /*
3343      * 'User Defined' opens a panel to configure or load a
3344      * user-defined colour scheme
3345      */
3346     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3347     {
3348       new UserDefinedColours(alignPanel);
3349       return;
3350     }
3351
3352     /*
3353      * otherwise set the chosen colour scheme (or null for 'None')
3354      */
3355     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3356             viewport,
3357             viewport.getAlignment(), viewport.getHiddenRepSequences());
3358     changeColour(cs);
3359   }
3360
3361   /**
3362    * Actions on setting or changing the alignment colour scheme
3363    *
3364    * @param cs
3365    */
3366   @Override
3367   public void changeColour(ColourSchemeI cs)
3368   {
3369     // TODO: pull up to controller method
3370     ColourMenuHelper.setColourSelected(colourMenu, cs);
3371
3372     viewport.setGlobalColourScheme(cs);
3373
3374     alignPanel.paintAlignment(true, true);
3375   }
3376
3377   /**
3378    * Show the PID threshold slider panel
3379    */
3380   @Override
3381   protected void modifyPID_actionPerformed()
3382   {
3383     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3384             alignPanel.getViewName());
3385     SliderPanel.showPIDSlider();
3386   }
3387
3388   /**
3389    * Show the Conservation slider panel
3390    */
3391   @Override
3392   protected void modifyConservation_actionPerformed()
3393   {
3394     SliderPanel.setConservationSlider(alignPanel,
3395             viewport.getResidueShading(), alignPanel.getViewName());
3396     SliderPanel.showConservationSlider();
3397   }
3398
3399   /**
3400    * Action on selecting or deselecting (Colour) By Conservation
3401    */
3402   @Override
3403   public void conservationMenuItem_actionPerformed(boolean selected)
3404   {
3405     modifyConservation.setEnabled(selected);
3406     viewport.setConservationSelected(selected);
3407     viewport.getResidueShading().setConservationApplied(selected);
3408
3409     changeColour(viewport.getGlobalColourScheme());
3410     if (selected)
3411     {
3412       modifyConservation_actionPerformed();
3413     }
3414     else
3415     {
3416       SliderPanel.hideConservationSlider();
3417     }
3418   }
3419
3420   /**
3421    * Action on selecting or deselecting (Colour) Above PID Threshold
3422    */
3423   @Override
3424   public void abovePIDThreshold_actionPerformed(boolean selected)
3425   {
3426     modifyPID.setEnabled(selected);
3427     viewport.setAbovePIDThreshold(selected);
3428     if (!selected)
3429     {
3430       viewport.getResidueShading().setThreshold(0,
3431               viewport.isIgnoreGapsConsensus());
3432     }
3433
3434     changeColour(viewport.getGlobalColourScheme());
3435     if (selected)
3436     {
3437       modifyPID_actionPerformed();
3438     }
3439     else
3440     {
3441       SliderPanel.hidePIDSlider();
3442     }
3443   }
3444
3445   /**
3446    * DOCUMENT ME!
3447    *
3448    * @param e
3449    *          DOCUMENT ME!
3450    */
3451   @Override
3452   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3453   {
3454     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3455     AlignmentSorter.sortByPID(viewport.getAlignment(),
3456             viewport.getAlignment().getSequenceAt(0));
3457     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3458             viewport.getAlignment()));
3459     alignPanel.paintAlignment(true, false);
3460   }
3461
3462   /**
3463    * DOCUMENT ME!
3464    *
3465    * @param e
3466    *          DOCUMENT ME!
3467    */
3468   @Override
3469   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3470   {
3471     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472     AlignmentSorter.sortByID(viewport.getAlignment());
3473     addHistoryItem(
3474             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3475     alignPanel.paintAlignment(true, false);
3476   }
3477
3478   /**
3479    * DOCUMENT ME!
3480    *
3481    * @param e
3482    *          DOCUMENT ME!
3483    */
3484   @Override
3485   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3486   {
3487     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488     AlignmentSorter.sortByLength(viewport.getAlignment());
3489     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3490             viewport.getAlignment()));
3491     alignPanel.paintAlignment(true, false);
3492   }
3493
3494   /**
3495    * DOCUMENT ME!
3496    *
3497    * @param e
3498    *          DOCUMENT ME!
3499    */
3500   @Override
3501   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3502   {
3503     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3504     AlignmentSorter.sortByGroup(viewport.getAlignment());
3505     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3506             viewport.getAlignment()));
3507
3508     alignPanel.paintAlignment(true, false);
3509   }
3510
3511   /**
3512    * DOCUMENT ME!
3513    *
3514    * @param e
3515    *          DOCUMENT ME!
3516    */
3517   @Override
3518   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3519   {
3520     new RedundancyPanel(alignPanel, this);
3521   }
3522
3523   /**
3524    * DOCUMENT ME!
3525    *
3526    * @param e
3527    *          DOCUMENT ME!
3528    */
3529   @Override
3530   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3531   {
3532     if ((viewport.getSelectionGroup() == null)
3533             || (viewport.getSelectionGroup().getSize() < 2))
3534     {
3535       JvOptionPane.showInternalMessageDialog(this,
3536               MessageManager.getString(
3537                       "label.you_must_select_least_two_sequences"),
3538               MessageManager.getString("label.invalid_selection"),
3539               JvOptionPane.WARNING_MESSAGE);
3540     }
3541     else
3542     {
3543       JInternalFrame frame = new JInternalFrame();
3544       frame.setContentPane(new PairwiseAlignPanel(viewport));
3545       Desktop.addInternalFrame(frame,
3546               MessageManager.getString("action.pairwise_alignment"), 600,
3547               500);
3548     }
3549   }
3550
3551   @Override
3552   public void autoCalculate_actionPerformed(ActionEvent e)
3553   {
3554     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3555     if (viewport.autoCalculateConsensus)
3556     {
3557       viewport.firePropertyChange("alignment", null,
3558               viewport.getAlignment().getSequences());
3559     }
3560   }
3561
3562   @Override
3563   public void sortByTreeOption_actionPerformed(ActionEvent e)
3564   {
3565     viewport.sortByTree = sortByTree.isSelected();
3566   }
3567
3568   @Override
3569   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3570   {
3571     viewport.followSelection = listenToViewSelections.isSelected();
3572   }
3573
3574   /**
3575    * Constructs a tree panel and adds it to the desktop
3576    *
3577    * @param type
3578    *          tree type (NJ or AV)
3579    * @param modelName
3580    *          name of score model used to compute the tree
3581    * @param options
3582    *          parameters for the distance or similarity calculation
3583    */
3584   void newTreePanel(String type, String modelName,
3585           SimilarityParamsI options)
3586   {
3587     String frameTitle = "";
3588     TreePanel tp;
3589
3590     boolean onSelection = false;
3591     if (viewport.getSelectionGroup() != null
3592             && viewport.getSelectionGroup().getSize() > 0)
3593     {
3594       SequenceGroup sg = viewport.getSelectionGroup();
3595
3596       /* Decide if the selection is a column region */
3597       for (SequenceI _s : sg.getSequences())
3598       {
3599         if (_s.getLength() < sg.getEndRes())
3600         {
3601           JvOptionPane.showMessageDialog(Desktop.desktop,
3602                   MessageManager.getString(
3603                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3604                   MessageManager.getString(
3605                           "label.sequences_selection_not_aligned"),
3606                   JvOptionPane.WARNING_MESSAGE);
3607
3608           return;
3609         }
3610       }
3611       onSelection = true;
3612     }
3613     else
3614     {
3615       if (viewport.getAlignment().getHeight() < 2)
3616       {
3617         return;
3618       }
3619     }
3620
3621     tp = new TreePanel(alignPanel, type, modelName, options);
3622     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3623
3624     frameTitle += " from ";
3625
3626     if (viewport.getViewName() != null)
3627     {
3628       frameTitle += viewport.getViewName() + " of ";
3629     }
3630
3631     frameTitle += this.title;
3632
3633     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3634   }
3635
3636   /**
3637    * DOCUMENT ME!
3638    *
3639    * @param title
3640    *          DOCUMENT ME!
3641    * @param order
3642    *          DOCUMENT ME!
3643    */
3644   public void addSortByOrderMenuItem(String title,
3645           final AlignmentOrder order)
3646   {
3647     final JMenuItem item = new JMenuItem(MessageManager
3648             .formatMessage("action.by_title_param", new Object[]
3649             { title }));
3650     sort.add(item);
3651     item.addActionListener(new java.awt.event.ActionListener()
3652     {
3653       @Override
3654       public void actionPerformed(ActionEvent e)
3655       {
3656         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3657
3658         // TODO: JBPNote - have to map order entries to curent SequenceI
3659         // pointers
3660         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3661
3662         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3663                 viewport.getAlignment()));
3664
3665         alignPanel.paintAlignment(true, false);
3666       }
3667     });
3668   }
3669
3670   /**
3671    * Add a new sort by annotation score menu item
3672    *
3673    * @param sort
3674    *          the menu to add the option to
3675    * @param scoreLabel
3676    *          the label used to retrieve scores for each sequence on the
3677    *          alignment
3678    */
3679   public void addSortByAnnotScoreMenuItem(JMenu sort,
3680           final String scoreLabel)
3681   {
3682     final JMenuItem item = new JMenuItem(scoreLabel);
3683     sort.add(item);
3684     item.addActionListener(new java.awt.event.ActionListener()
3685     {
3686       @Override
3687       public void actionPerformed(ActionEvent e)
3688       {
3689         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3690         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3691                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3692         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3693                 viewport.getAlignment()));
3694         alignPanel.paintAlignment(true, false);
3695       }
3696     });
3697   }
3698
3699   /**
3700    * last hash for alignment's annotation array - used to minimise cost of
3701    * rebuild.
3702    */
3703   protected int _annotationScoreVectorHash;
3704
3705   /**
3706    * search the alignment and rebuild the sort by annotation score submenu the
3707    * last alignment annotation vector hash is stored to minimize cost of
3708    * rebuilding in subsequence calls.
3709    *
3710    */
3711   @Override
3712   public void buildSortByAnnotationScoresMenu()
3713   {
3714     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3715     {
3716       return;
3717     }
3718
3719     if (viewport.getAlignment().getAlignmentAnnotation()
3720             .hashCode() != _annotationScoreVectorHash)
3721     {
3722       sortByAnnotScore.removeAll();
3723       // almost certainly a quicker way to do this - but we keep it simple
3724       Hashtable scoreSorts = new Hashtable();
3725       AlignmentAnnotation aann[];
3726       for (SequenceI sqa : viewport.getAlignment().getSequences())
3727       {
3728         aann = sqa.getAnnotation();
3729         for (int i = 0; aann != null && i < aann.length; i++)
3730         {
3731           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3732           {
3733             scoreSorts.put(aann[i].label, aann[i].label);
3734           }
3735         }
3736       }
3737       Enumeration labels = scoreSorts.keys();
3738       while (labels.hasMoreElements())
3739       {
3740         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3741                 (String) labels.nextElement());
3742       }
3743       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3744       scoreSorts.clear();
3745
3746       _annotationScoreVectorHash = viewport.getAlignment()
3747               .getAlignmentAnnotation().hashCode();
3748     }
3749   }
3750
3751   /**
3752    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3753    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3754    * call. Listeners are added to remove the menu item when the treePanel is
3755    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3756    * modified.
3757    */
3758   @Override
3759   public void buildTreeSortMenu()
3760   {
3761     sortByTreeMenu.removeAll();
3762
3763     List<Component> comps = PaintRefresher.components
3764             .get(viewport.getSequenceSetId());
3765     List<TreePanel> treePanels = new ArrayList<>();
3766     for (Component comp : comps)
3767     {
3768       if (comp instanceof TreePanel)
3769       {
3770         treePanels.add((TreePanel) comp);
3771       }
3772     }
3773
3774     if (treePanels.size() < 1)
3775     {
3776       sortByTreeMenu.setVisible(false);
3777       return;
3778     }
3779
3780     sortByTreeMenu.setVisible(true);
3781
3782     for (final TreePanel tp : treePanels)
3783     {
3784       final JMenuItem item = new JMenuItem(tp.getTitle());
3785       item.addActionListener(new java.awt.event.ActionListener()
3786       {
3787         @Override
3788         public void actionPerformed(ActionEvent e)
3789         {
3790           tp.sortByTree_actionPerformed();
3791           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3792
3793         }
3794       });
3795
3796       sortByTreeMenu.add(item);
3797     }
3798   }
3799
3800   public boolean sortBy(AlignmentOrder alorder, String undoname)
3801   {
3802     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3803     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3804     if (undoname != null)
3805     {
3806       addHistoryItem(new OrderCommand(undoname, oldOrder,
3807               viewport.getAlignment()));
3808     }
3809     alignPanel.paintAlignment(true, false);
3810     return true;
3811   }
3812
3813   /**
3814    * Work out whether the whole set of sequences or just the selected set will
3815    * be submitted for multiple alignment.
3816    *
3817    */
3818   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3819   {
3820     // Now, check we have enough sequences
3821     AlignmentView msa = null;
3822
3823     if ((viewport.getSelectionGroup() != null)
3824             && (viewport.getSelectionGroup().getSize() > 1))
3825     {
3826       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3827       // some common interface!
3828       /*
3829        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3830        * SequenceI[sz = seqs.getSize(false)];
3831        *
3832        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3833        * seqs.getSequenceAt(i); }
3834        */
3835       msa = viewport.getAlignmentView(true);
3836     }
3837     else if (viewport.getSelectionGroup() != null
3838             && viewport.getSelectionGroup().getSize() == 1)
3839     {
3840       int option = JvOptionPane.showConfirmDialog(this,
3841               MessageManager.getString("warn.oneseq_msainput_selection"),
3842               MessageManager.getString("label.invalid_selection"),
3843               JvOptionPane.OK_CANCEL_OPTION);
3844       if (option == JvOptionPane.OK_OPTION)
3845       {
3846         msa = viewport.getAlignmentView(false);
3847       }
3848     }
3849     else
3850     {
3851       msa = viewport.getAlignmentView(false);
3852     }
3853     return msa;
3854   }
3855
3856   /**
3857    * Decides what is submitted to a secondary structure prediction service: the
3858    * first sequence in the alignment, or in the current selection, or, if the
3859    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3860    * region or the whole alignment. (where the first sequence in the set is the
3861    * one that the prediction will be for).
3862    */
3863   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3864   {
3865     AlignmentView seqs = null;
3866
3867     if ((viewport.getSelectionGroup() != null)
3868             && (viewport.getSelectionGroup().getSize() > 0))
3869     {
3870       seqs = viewport.getAlignmentView(true);
3871     }
3872     else
3873     {
3874       seqs = viewport.getAlignmentView(false);
3875     }
3876     // limit sequences - JBPNote in future - could spawn multiple prediction
3877     // jobs
3878     // TODO: viewport.getAlignment().isAligned is a global state - the local
3879     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3880     if (!viewport.getAlignment().isAligned(false))
3881     {
3882       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3883       // TODO: if seqs.getSequences().length>1 then should really have warned
3884       // user!
3885
3886     }
3887     return seqs;
3888   }
3889
3890   /**
3891    * DOCUMENT ME!
3892    *
3893    * @param e
3894    *          DOCUMENT ME!
3895    */
3896   @Override
3897   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3898   {
3899     // Pick the tree file
3900     JalviewFileChooser chooser = new JalviewFileChooser(
3901             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3902     chooser.setFileView(new JalviewFileView());
3903     chooser.setDialogTitle(
3904             MessageManager.getString("label.select_newick_like_tree_file"));
3905     chooser.setToolTipText(
3906             MessageManager.getString("label.load_tree_file"));
3907
3908     int value = chooser.showOpenDialog(null);
3909
3910     if (value == JalviewFileChooser.APPROVE_OPTION)
3911     {
3912       String filePath = chooser.getSelectedFile().getPath();
3913       Cache.setProperty("LAST_DIRECTORY", filePath);
3914       NewickFile fin = null;
3915       try
3916       {
3917         fin = new NewickFile(filePath, DataSourceType.FILE);
3918         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3919       } catch (Exception ex)
3920       {
3921         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3922                 MessageManager.getString("label.problem_reading_tree_file"),
3923                 JvOptionPane.WARNING_MESSAGE);
3924         ex.printStackTrace();
3925       }
3926       if (fin != null && fin.hasWarningMessage())
3927       {
3928         JvOptionPane.showMessageDialog(Desktop.desktop,
3929                 fin.getWarningMessage(),
3930                 MessageManager
3931                         .getString("label.possible_problem_with_tree_file"),
3932                 JvOptionPane.WARNING_MESSAGE);
3933       }
3934     }
3935   }
3936
3937   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3938   {
3939     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3940   }
3941
3942   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3943           int h, int x, int y)
3944   {
3945     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3946   }
3947
3948   /**
3949    * Add a treeviewer for the tree extracted from a Newick file object to the
3950    * current alignment view
3951    *
3952    * @param nf
3953    *          the tree
3954    * @param title
3955    *          tree viewer title
3956    * @param input
3957    *          Associated alignment input data (or null)
3958    * @param w
3959    *          width
3960    * @param h
3961    *          height
3962    * @param x
3963    *          position
3964    * @param y
3965    *          position
3966    * @return TreePanel handle
3967    */
3968   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3969           AlignmentView input, int w, int h, int x, int y)
3970   {
3971     TreePanel tp = null;
3972
3973     try
3974     {
3975       nf.parse();
3976
3977       if (nf.getTree() != null)
3978       {
3979         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3980
3981         tp.setSize(w, h);
3982
3983         if (x > 0 && y > 0)
3984         {
3985           tp.setLocation(x, y);
3986         }
3987
3988         Desktop.addInternalFrame(tp, treeTitle, w, h);
3989       }
3990     } catch (Exception ex)
3991     {
3992       ex.printStackTrace();
3993     }
3994
3995     return tp;
3996   }
3997
3998   private boolean buildingMenu = false;
3999
4000   /**
4001    * Generates menu items and listener event actions for web service clients
4002    *
4003    */
4004   public void BuildWebServiceMenu()
4005   {
4006     while (buildingMenu)
4007     {
4008       try
4009       {
4010         System.err.println("Waiting for building menu to finish.");
4011         Thread.sleep(10);
4012       } catch (Exception e)
4013       {
4014       }
4015     }
4016     final AlignFrame me = this;
4017     buildingMenu = true;
4018     new Thread(new Runnable()
4019     {
4020       @Override
4021       public void run()
4022       {
4023         final List<JMenuItem> legacyItems = new ArrayList<>();
4024         try
4025         {
4026           // System.err.println("Building ws menu again "
4027           // + Thread.currentThread());
4028           // TODO: add support for context dependent disabling of services based
4029           // on
4030           // alignment and current selection
4031           // TODO: add additional serviceHandle parameter to specify abstract
4032           // handler
4033           // class independently of AbstractName
4034           // TODO: add in rediscovery GUI function to restart discoverer
4035           // TODO: group services by location as well as function and/or
4036           // introduce
4037           // object broker mechanism.
4038           final Vector<JMenu> wsmenu = new Vector<>();
4039           final IProgressIndicator af = me;
4040
4041           /*
4042            * do not i18n these strings - they are hard-coded in class
4043            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4044            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4045            */
4046           final JMenu msawsmenu = new JMenu("Alignment");
4047           final JMenu secstrmenu = new JMenu(
4048                   "Secondary Structure Prediction");
4049           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4050           final JMenu analymenu = new JMenu("Analysis");
4051           final JMenu dismenu = new JMenu("Protein Disorder");
4052           // JAL-940 - only show secondary structure prediction services from
4053           // the legacy server
4054           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4055               // &&
4056           Discoverer.services != null && (Discoverer.services.size() > 0))
4057           {
4058             // TODO: refactor to allow list of AbstractName/Handler bindings to
4059             // be
4060             // stored or retrieved from elsewhere
4061             // No MSAWS used any more:
4062             // Vector msaws = null; // (Vector)
4063             // Discoverer.services.get("MsaWS");
4064             Vector secstrpr = (Vector) Discoverer.services
4065                     .get("SecStrPred");
4066             if (secstrpr != null)
4067             {
4068               // Add any secondary structure prediction services
4069               for (int i = 0, j = secstrpr.size(); i < j; i++)
4070               {
4071                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4072                         .get(i);
4073                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4074                         .getServiceClient(sh);
4075                 int p = secstrmenu.getItemCount();
4076                 impl.attachWSMenuEntry(secstrmenu, me);
4077                 int q = secstrmenu.getItemCount();
4078                 for (int litm = p; litm < q; litm++)
4079                 {
4080                   legacyItems.add(secstrmenu.getItem(litm));
4081                 }
4082               }
4083             }
4084           }
4085
4086           // Add all submenus in the order they should appear on the web
4087           // services menu
4088           wsmenu.add(msawsmenu);
4089           wsmenu.add(secstrmenu);
4090           wsmenu.add(dismenu);
4091           wsmenu.add(analymenu);
4092           // No search services yet
4093           // wsmenu.add(seqsrchmenu);
4094
4095           javax.swing.SwingUtilities.invokeLater(new Runnable()
4096           {
4097             @Override
4098             public void run()
4099             {
4100               try
4101               {
4102                 webService.removeAll();
4103                 // first, add discovered services onto the webservices menu
4104                 if (wsmenu.size() > 0)
4105                 {
4106                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4107                   {
4108                     webService.add(wsmenu.get(i));
4109                   }
4110                 }
4111                 else
4112                 {
4113                   webService.add(me.webServiceNoServices);
4114                 }
4115                 // TODO: move into separate menu builder class.
4116                 boolean new_sspred = false;
4117                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4118                 {
4119                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4120                   if (jws2servs != null)
4121                   {
4122                     if (jws2servs.hasServices())
4123                     {
4124                       jws2servs.attachWSMenuEntry(webService, me);
4125                       for (Jws2Instance sv : jws2servs.getServices())
4126                       {
4127                         if (sv.description.toLowerCase().contains("jpred"))
4128                         {
4129                           for (JMenuItem jmi : legacyItems)
4130                           {
4131                             jmi.setVisible(false);
4132                           }
4133                         }
4134                       }
4135
4136                     }
4137                     if (jws2servs.isRunning())
4138                     {
4139                       JMenuItem tm = new JMenuItem(
4140                               "Still discovering JABA Services");
4141                       tm.setEnabled(false);
4142                       webService.add(tm);
4143                     }
4144                   }
4145                 }
4146                 build_urlServiceMenu(me.webService);
4147                 build_fetchdbmenu(webService);
4148                 for (JMenu item : wsmenu)
4149                 {
4150                   if (item.getItemCount() == 0)
4151                   {
4152                     item.setEnabled(false);
4153                   }
4154                   else
4155                   {
4156                     item.setEnabled(true);
4157                   }
4158                 }
4159               } catch (Exception e)
4160               {
4161                 Cache.log.debug(
4162                         "Exception during web service menu building process.",
4163                         e);
4164               }
4165             }
4166           });
4167         } catch (Exception e)
4168         {
4169         }
4170         buildingMenu = false;
4171       }
4172     }).start();
4173
4174   }
4175
4176   /**
4177    * construct any groupURL type service menu entries.
4178    *
4179    * @param webService
4180    */
4181   private void build_urlServiceMenu(JMenu webService)
4182   {
4183     // TODO: remove this code when 2.7 is released
4184     // DEBUG - alignmentView
4185     /*
4186      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4187      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4188      *
4189      * @Override public void actionPerformed(ActionEvent e) {
4190      * jalview.datamodel.AlignmentView
4191      * .testSelectionViews(af.viewport.getAlignment(),
4192      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4193      *
4194      * }); webService.add(testAlView);
4195      */
4196     // TODO: refactor to RestClient discoverer and merge menu entries for
4197     // rest-style services with other types of analysis/calculation service
4198     // SHmmr test client - still being implemented.
4199     // DEBUG - alignmentView
4200
4201     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4202             .getRestClients())
4203     {
4204       client.attachWSMenuEntry(
4205               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4206               this);
4207     }
4208   }
4209
4210   /**
4211    * Searches the alignment sequences for xRefs and builds the Show
4212    * Cross-References menu (formerly called Show Products), with database
4213    * sources for which cross-references are found (protein sources for a
4214    * nucleotide alignment and vice versa)
4215    *
4216    * @return true if Show Cross-references menu should be enabled
4217    */
4218   public boolean canShowProducts()
4219   {
4220     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4221     AlignmentI dataset = viewport.getAlignment().getDataset();
4222
4223     showProducts.removeAll();
4224     final boolean dna = viewport.getAlignment().isNucleotide();
4225
4226     if (seqs == null || seqs.length == 0)
4227     {
4228       // nothing to see here.
4229       return false;
4230     }
4231
4232     boolean showp = false;
4233     try
4234     {
4235       List<String> ptypes = new CrossRef(seqs, dataset)
4236               .findXrefSourcesForSequences(dna);
4237
4238       for (final String source : ptypes)
4239       {
4240         showp = true;
4241         final AlignFrame af = this;
4242         JMenuItem xtype = new JMenuItem(source);
4243         xtype.addActionListener(new ActionListener()
4244         {
4245           @Override
4246           public void actionPerformed(ActionEvent e)
4247           {
4248             showProductsFor(af.viewport.getSequenceSelection(), dna,
4249                     source);
4250           }
4251         });
4252         showProducts.add(xtype);
4253       }
4254       showProducts.setVisible(showp);
4255       showProducts.setEnabled(showp);
4256     } catch (Exception e)
4257     {
4258       Cache.log.warn(
4259               "canShowProducts threw an exception - please report to help@jalview.org",
4260               e);
4261       return false;
4262     }
4263     return showp;
4264   }
4265
4266   /**
4267    * Finds and displays cross-references for the selected sequences (protein
4268    * products for nucleotide sequences, dna coding sequences for peptides).
4269    *
4270    * @param sel
4271    *          the sequences to show cross-references for
4272    * @param dna
4273    *          true if from a nucleotide alignment (so showing proteins)
4274    * @param source
4275    *          the database to show cross-references for
4276    */
4277   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4278           final String source)
4279   {
4280     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4281             .start();
4282   }
4283
4284   /**
4285    * Construct and display a new frame containing the translation of this
4286    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4287    */
4288   @Override
4289   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4290   {
4291     AlignmentI al = null;
4292     try
4293     {
4294       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4295
4296       al = dna.translateCdna(codeTable);
4297     } catch (Exception ex)
4298     {
4299       jalview.bin.Cache.log.error(
4300               "Exception during translation. Please report this !", ex);
4301       final String msg = MessageManager.getString(
4302               "label.error_when_translating_sequences_submit_bug_report");
4303       final String errorTitle = MessageManager
4304               .getString("label.implementation_error")
4305               + MessageManager.getString("label.translation_failed");
4306       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4307               JvOptionPane.ERROR_MESSAGE);
4308       return;
4309     }
4310     if (al == null || al.getHeight() == 0)
4311     {
4312       final String msg = MessageManager.getString(
4313               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4314       final String errorTitle = MessageManager
4315               .getString("label.translation_failed");
4316       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4317               JvOptionPane.WARNING_MESSAGE);
4318     }
4319     else
4320     {
4321       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4322       af.setFileFormat(this.currentFileFormat);
4323       final String newTitle = MessageManager
4324               .formatMessage("label.translation_of_params", new Object[]
4325               { this.getTitle(), codeTable.getId() });
4326       af.setTitle(newTitle);
4327       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4328       {
4329         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4330         viewport.openSplitFrame(af, new Alignment(seqs));
4331       }
4332       else
4333       {
4334         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4335                 DEFAULT_HEIGHT);
4336       }
4337     }
4338   }
4339
4340   /**
4341    * Set the file format
4342    *
4343    * @param format
4344    */
4345   public void setFileFormat(FileFormatI format)
4346   {
4347     this.currentFileFormat = format;
4348   }
4349
4350   /**
4351    * Try to load a features file onto the alignment.
4352    *
4353    * @param file
4354    *          contents or path to retrieve file
4355    * @param sourceType
4356    *          access mode of file (see jalview.io.AlignFile)
4357    * @return true if features file was parsed correctly.
4358    */
4359   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4360   {
4361     return avc.parseFeaturesFile(file, sourceType,
4362             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4363
4364   }
4365
4366   @Override
4367   public void refreshFeatureUI(boolean enableIfNecessary)
4368   {
4369     // note - currently this is only still here rather than in the controller
4370     // because of the featureSettings hard reference that is yet to be
4371     // abstracted
4372     if (enableIfNecessary)
4373     {
4374       viewport.setShowSequenceFeatures(true);
4375       showSeqFeatures.setSelected(true);
4376     }
4377
4378   }
4379
4380   @Override
4381   public void dragEnter(DropTargetDragEvent evt)
4382   {
4383   }
4384
4385   @Override
4386   public void dragExit(DropTargetEvent evt)
4387   {
4388   }
4389
4390   @Override
4391   public void dragOver(DropTargetDragEvent evt)
4392   {
4393   }
4394
4395   @Override
4396   public void dropActionChanged(DropTargetDragEvent evt)
4397   {
4398   }
4399
4400   @Override
4401   public void drop(DropTargetDropEvent evt)
4402   {
4403     // JAL-1552 - acceptDrop required before getTransferable call for
4404     // Java's Transferable for native dnd
4405     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4406     Transferable t = evt.getTransferable();
4407     final AlignFrame thisaf = this;
4408     final List<String> files = new ArrayList<>();
4409     List<DataSourceType> protocols = new ArrayList<>();
4410
4411     try
4412     {
4413       Desktop.transferFromDropTarget(files, protocols, evt, t);
4414     } catch (Exception e)
4415     {
4416       e.printStackTrace();
4417     }
4418     if (files != null)
4419     {
4420       new Thread(new Runnable()
4421       {
4422         @Override
4423         public void run()
4424         {
4425           try
4426           {
4427             // check to see if any of these files have names matching sequences
4428             // in
4429             // the alignment
4430             SequenceIdMatcher idm = new SequenceIdMatcher(
4431                     viewport.getAlignment().getSequencesArray());
4432             /**
4433              * Object[] { String,SequenceI}
4434              */
4435             ArrayList<Object[]> filesmatched = new ArrayList<>();
4436             ArrayList<String> filesnotmatched = new ArrayList<>();
4437             for (int i = 0; i < files.size(); i++)
4438             {
4439               String file = files.get(i).toString();
4440               String pdbfn = "";
4441               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4442               if (protocol == DataSourceType.FILE)
4443               {
4444                 File fl = new File(file);
4445                 pdbfn = fl.getName();
4446               }
4447               else if (protocol == DataSourceType.URL)
4448               {
4449                 URL url = new URL(file);
4450                 pdbfn = url.getFile();
4451               }
4452               if (pdbfn.length() > 0)
4453               {
4454                 // attempt to find a match in the alignment
4455                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4456                 int l = 0, c = pdbfn.indexOf(".");
4457                 while (mtch == null && c != -1)
4458                 {
4459                   do
4460                   {
4461                     l = c;
4462                   } while ((c = pdbfn.indexOf(".", l)) > l);
4463                   if (l > -1)
4464                   {
4465                     pdbfn = pdbfn.substring(0, l);
4466                   }
4467                   mtch = idm.findAllIdMatches(pdbfn);
4468                 }
4469                 if (mtch != null)
4470                 {
4471                   FileFormatI type = null;
4472                   try
4473                   {
4474                     type = new IdentifyFile().identify(file, protocol);
4475                   } catch (Exception ex)
4476                   {
4477                     type = null;
4478                   }
4479                   if (type != null && type.isStructureFile())
4480                   {
4481                     filesmatched.add(new Object[] { file, protocol, mtch });
4482                     continue;
4483                   }
4484                 }
4485                 // File wasn't named like one of the sequences or wasn't a PDB
4486                 // file.
4487                 filesnotmatched.add(file);
4488               }
4489             }
4490             int assocfiles = 0;
4491             if (filesmatched.size() > 0)
4492             {
4493               boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4494               if (!autoAssociate)
4495               {
4496                 String msg = MessageManager.formatMessage(
4497                         "label.automatically_associate_structure_files_with_sequences_same_name",
4498                         new Object[]
4499                         { Integer.valueOf(filesmatched.size())
4500                                 .toString() });
4501                 String ttl = MessageManager.getString(
4502                         "label.automatically_associate_structure_files_by_name");
4503                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4504                         ttl, JvOptionPane.YES_NO_OPTION);
4505                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4506               }
4507               if (autoAssociate)
4508               {
4509                 for (Object[] fm : filesmatched)
4510                 {
4511                   // try and associate
4512                   // TODO: may want to set a standard ID naming formalism for
4513                   // associating PDB files which have no IDs.
4514                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4515                   {
4516                     PDBEntry pe = new AssociatePdbFileWithSeq()
4517                             .associatePdbWithSeq((String) fm[0],
4518                                     (DataSourceType) fm[1], toassoc, false,
4519                                     Desktop.instance);
4520                     if (pe != null)
4521                     {
4522                       System.err.println("Associated file : "
4523                               + ((String) fm[0]) + " with "
4524                               + toassoc.getDisplayId(true));
4525                       assocfiles++;
4526                     }
4527                   }
4528                   // TODO: do we need to update overview ? only if features are
4529                   // shown I guess
4530                   alignPanel.paintAlignment(true, false);
4531                 }
4532               }
4533               else
4534               {
4535                 /*
4536                  * add declined structures as sequences
4537                  */
4538                 for (Object[] o : filesmatched)
4539                 {
4540                   filesnotmatched.add((String) o[0]);
4541                 }
4542               }
4543             }
4544             if (filesnotmatched.size() > 0)
4545             {
4546               if (assocfiles > 0 && (Cache.getDefault(
4547                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4548                       || JvOptionPane.showConfirmDialog(thisaf,
4549                               "<html>" + MessageManager.formatMessage(
4550                                       "label.ignore_unmatched_dropped_files_info",
4551                                       new Object[]
4552                                       { Integer.valueOf(
4553                                               filesnotmatched.size())
4554                                               .toString() })
4555                                       + "</html>",
4556                               MessageManager.getString(
4557                                       "label.ignore_unmatched_dropped_files"),
4558                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4559               {
4560                 return;
4561               }
4562               for (String fn : filesnotmatched)
4563               {
4564                 loadJalviewDataFile(fn, null, null, null);
4565               }
4566
4567             }
4568           } catch (Exception ex)
4569           {
4570             ex.printStackTrace();
4571           }
4572         }
4573       }).start();
4574     }
4575   }
4576
4577   /**
4578    * Attempt to load a "dropped" file or URL string, by testing in turn for
4579    * <ul>
4580    * <li>an Annotation file</li>
4581    * <li>a JNet file</li>
4582    * <li>a features file</li>
4583    * <li>else try to interpret as an alignment file</li>
4584    * </ul>
4585    *
4586    * @param file
4587    *          either a filename or a URL string.
4588    */
4589   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4590           FileFormatI format, SequenceI assocSeq)
4591   {
4592     try
4593     {
4594       if (sourceType == null)
4595       {
4596         sourceType = FormatAdapter.checkProtocol(file);
4597       }
4598       // if the file isn't identified, or not positively identified as some
4599       // other filetype (PFAM is default unidentified alignment file type) then
4600       // try to parse as annotation.
4601       boolean isAnnotation = (format == null
4602               || FileFormat.Pfam.equals(format))
4603                       ? new AnnotationFile().annotateAlignmentView(viewport,
4604                               file, sourceType)
4605                       : false;
4606
4607       if (!isAnnotation)
4608       {
4609         // first see if its a T-COFFEE score file
4610         TCoffeeScoreFile tcf = null;
4611         try
4612         {
4613           tcf = new TCoffeeScoreFile(file, sourceType);
4614           if (tcf.isValid())
4615           {
4616             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4617             {
4618               buildColourMenu();
4619               changeColour(
4620                       new TCoffeeColourScheme(viewport.getAlignment()));
4621               isAnnotation = true;
4622               statusBar.setText(MessageManager.getString(
4623                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4624             }
4625             else
4626             {
4627               // some problem - if no warning its probable that the ID matching
4628               // process didn't work
4629               JvOptionPane.showMessageDialog(Desktop.desktop,
4630                       tcf.getWarningMessage() == null
4631                               ? MessageManager.getString(
4632                                       "label.check_file_matches_sequence_ids_alignment")
4633                               : tcf.getWarningMessage(),
4634                       MessageManager.getString(
4635                               "label.problem_reading_tcoffee_score_file"),
4636                       JvOptionPane.WARNING_MESSAGE);
4637             }
4638           }
4639           else
4640           {
4641             tcf = null;
4642           }
4643         } catch (Exception x)
4644         {
4645           Cache.log.debug(
4646                   "Exception when processing data source as T-COFFEE score file",
4647                   x);
4648           tcf = null;
4649         }
4650         if (tcf == null)
4651         {
4652           // try to see if its a JNet 'concise' style annotation file *before*
4653           // we
4654           // try to parse it as a features file
4655           if (format == null)
4656           {
4657             format = new IdentifyFile().identify(file, sourceType);
4658           }
4659           if (FileFormat.ScoreMatrix == format)
4660           {
4661             ScoreMatrixFile sm = new ScoreMatrixFile(
4662                     new FileParse(file, sourceType));
4663             sm.parse();
4664             // todo: i18n this message
4665             statusBar.setText(MessageManager.formatMessage(
4666                     "label.successfully_loaded_matrix",
4667                     sm.getMatrixName()));
4668           }
4669           else if (FileFormat.Jnet.equals(format))
4670           {
4671             JPredFile predictions = new JPredFile(file, sourceType);
4672             new JnetAnnotationMaker();
4673             JnetAnnotationMaker.add_annotation(predictions,
4674                     viewport.getAlignment(), 0, false);
4675             viewport.getAlignment().setupJPredAlignment();
4676             isAnnotation = true;
4677           }
4678           // else if (IdentifyFile.FeaturesFile.equals(format))
4679           else if (FileFormat.Features.equals(format))
4680           {
4681             if (parseFeaturesFile(file, sourceType))
4682             {
4683               alignPanel.paintAlignment(true, true);
4684             }
4685           }
4686           else
4687           {
4688             new FileLoader().LoadFile(viewport, file, sourceType, format);
4689           }
4690         }
4691       }
4692       if (isAnnotation)
4693       {
4694         alignPanel.sortAnnotations(false);
4695         alignPanel.adjustAnnotationHeight();
4696         viewport.updateSequenceIdColours();
4697         buildSortByAnnotationScoresMenu();
4698         alignPanel.paintAlignment(true, true);
4699       }
4700     } catch (Exception ex)
4701     {
4702       ex.printStackTrace();
4703     } catch (OutOfMemoryError oom)
4704     {
4705       try
4706       {
4707         System.gc();
4708       } catch (Exception x)
4709       {
4710       }
4711       new OOMWarning(
4712               "loading data "
4713                       + (sourceType != null
4714                               ? (sourceType == DataSourceType.PASTE
4715                                       ? "from clipboard."
4716                                       : "using " + sourceType + " from "
4717                                               + file)
4718                               : ".")
4719                       + (format != null
4720                               ? "(parsing as '" + format + "' file)"
4721                               : ""),
4722               oom, Desktop.desktop);
4723     }
4724   }
4725
4726   /**
4727    * Method invoked by the ChangeListener on the tabbed pane, in other words
4728    * when a different tabbed pane is selected by the user or programmatically.
4729    */
4730   @Override
4731   public void tabSelectionChanged(int index)
4732   {
4733     if (index > -1)
4734     {
4735       alignPanel = alignPanels.get(index);
4736       viewport = alignPanel.av;
4737       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4738       setMenusFromViewport(viewport);
4739     }
4740
4741     /*
4742      * 'focus' any colour slider that is open to the selected viewport
4743      */
4744     if (viewport.getConservationSelected())
4745     {
4746       SliderPanel.setConservationSlider(alignPanel,
4747               viewport.getResidueShading(), alignPanel.getViewName());
4748     }
4749     else
4750     {
4751       SliderPanel.hideConservationSlider();
4752     }
4753     if (viewport.getAbovePIDThreshold())
4754     {
4755       SliderPanel.setPIDSliderSource(alignPanel,
4756               viewport.getResidueShading(), alignPanel.getViewName());
4757     }
4758     else
4759     {
4760       SliderPanel.hidePIDSlider();
4761     }
4762
4763     /*
4764      * If there is a frame linked to this one in a SplitPane, switch it to the
4765      * same view tab index. No infinite recursion of calls should happen, since
4766      * tabSelectionChanged() should not get invoked on setting the selected
4767      * index to an unchanged value. Guard against setting an invalid index
4768      * before the new view peer tab has been created.
4769      */
4770     final AlignViewportI peer = viewport.getCodingComplement();
4771     if (peer != null)
4772     {
4773       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4774               .getAlignPanel().alignFrame;
4775       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4776       {
4777         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4778       }
4779     }
4780   }
4781
4782   /**
4783    * On right mouse click on view tab, prompt for and set new view name.
4784    */
4785   @Override
4786   public void tabbedPane_mousePressed(MouseEvent e)
4787   {
4788     if (e.isPopupTrigger())
4789     {
4790       String msg = MessageManager.getString("label.enter_view_name");
4791       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4792               JvOptionPane.QUESTION_MESSAGE);
4793
4794       if (reply != null)
4795       {
4796         viewport.setViewName(reply);
4797         // TODO warn if reply is in getExistingViewNames()?
4798         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4799       }
4800     }
4801   }
4802
4803   public AlignViewport getCurrentView()
4804   {
4805     return viewport;
4806   }
4807
4808   /**
4809    * Open the dialog for regex description parsing.
4810    */
4811   @Override
4812   protected void extractScores_actionPerformed(ActionEvent e)
4813   {
4814     ParseProperties pp = new jalview.analysis.ParseProperties(
4815             viewport.getAlignment());
4816     // TODO: verify regex and introduce GUI dialog for version 2.5
4817     // if (pp.getScoresFromDescription("col", "score column ",
4818     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4819     // true)>0)
4820     if (pp.getScoresFromDescription("description column",
4821             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4822     {
4823       buildSortByAnnotationScoresMenu();
4824     }
4825   }
4826
4827   /*
4828    * (non-Javadoc)
4829    *
4830    * @see
4831    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4832    * )
4833    */
4834   @Override
4835   protected void showDbRefs_actionPerformed(ActionEvent e)
4836   {
4837     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4838   }
4839
4840   /*
4841    * (non-Javadoc)
4842    *
4843    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4844    * ActionEvent)
4845    */
4846   @Override
4847   protected void showNpFeats_actionPerformed(ActionEvent e)
4848   {
4849     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4850   }
4851
4852   /**
4853    * find the viewport amongst the tabs in this alignment frame and close that
4854    * tab
4855    *
4856    * @param av
4857    */
4858   public boolean closeView(AlignViewportI av)
4859   {
4860     if (viewport == av)
4861     {
4862       this.closeMenuItem_actionPerformed(false);
4863       return true;
4864     }
4865     Component[] comp = tabbedPane.getComponents();
4866     for (int i = 0; comp != null && i < comp.length; i++)
4867     {
4868       if (comp[i] instanceof AlignmentPanel)
4869       {
4870         if (((AlignmentPanel) comp[i]).av == av)
4871         {
4872           // close the view.
4873           closeView((AlignmentPanel) comp[i]);
4874           return true;
4875         }
4876       }
4877     }
4878     return false;
4879   }
4880
4881   protected void build_fetchdbmenu(JMenu webService)
4882   {
4883     // Temporary hack - DBRef Fetcher always top level ws entry.
4884     // TODO We probably want to store a sequence database checklist in
4885     // preferences and have checkboxes.. rather than individual sources selected
4886     // here
4887     final JMenu rfetch = new JMenu(
4888             MessageManager.getString("action.fetch_db_references"));
4889     rfetch.setToolTipText(MessageManager.getString(
4890             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4891     webService.add(rfetch);
4892
4893     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4894             MessageManager.getString("option.trim_retrieved_seqs"));
4895     trimrs.setToolTipText(
4896             MessageManager.getString("label.trim_retrieved_sequences"));
4897     trimrs.setSelected(
4898             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4899     trimrs.addActionListener(new ActionListener()
4900     {
4901       @Override
4902       public void actionPerformed(ActionEvent e)
4903       {
4904         trimrs.setSelected(trimrs.isSelected());
4905         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4906                 Boolean.valueOf(trimrs.isSelected()).toString());
4907       };
4908     });
4909     rfetch.add(trimrs);
4910     JMenuItem fetchr = new JMenuItem(
4911             MessageManager.getString("label.standard_databases"));
4912     fetchr.setToolTipText(
4913             MessageManager.getString("label.fetch_embl_uniprot"));
4914     fetchr.addActionListener(new ActionListener()
4915     {
4916
4917       @Override
4918       public void actionPerformed(ActionEvent e)
4919       {
4920         new Thread(new Runnable()
4921         {
4922           @Override
4923           public void run()
4924           {
4925             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4926                     .getAlignment().isNucleotide();
4927             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4928                     alignPanel.av.getSequenceSelection(),
4929                     alignPanel.alignFrame, null,
4930                     alignPanel.alignFrame.featureSettings, isNucleotide);
4931             dbRefFetcher.addListener(new FetchFinishedListenerI()
4932             {
4933               @Override
4934               public void finished()
4935               {
4936                 AlignFrame.this.setMenusForViewport();
4937               }
4938             });
4939             dbRefFetcher.fetchDBRefs(false);
4940           }
4941         }).start();
4942
4943       }
4944
4945     });
4946     rfetch.add(fetchr);
4947     final AlignFrame me = this;
4948     new Thread(new Runnable()
4949     {
4950       @Override
4951       public void run()
4952       {
4953         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4954                 .getSequenceFetcherSingleton(me);
4955         javax.swing.SwingUtilities.invokeLater(new Runnable()
4956         {
4957           @Override
4958           public void run()
4959           {
4960             String[] dbclasses = sf.getOrderedSupportedSources();
4961             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4962             // jalview.util.QuickSort.sort(otherdb, otherdb);
4963             List<DbSourceProxy> otherdb;
4964             JMenu dfetch = new JMenu();
4965             JMenu ifetch = new JMenu();
4966             JMenuItem fetchr = null;
4967             int comp = 0, icomp = 0, mcomp = 15;
4968             String mname = null;
4969             int dbi = 0;
4970             for (String dbclass : dbclasses)
4971             {
4972               otherdb = sf.getSourceProxy(dbclass);
4973               // add a single entry for this class, or submenu allowing 'fetch
4974               // all' or pick one
4975               if (otherdb == null || otherdb.size() < 1)
4976               {
4977                 continue;
4978               }
4979               // List<DbSourceProxy> dbs=otherdb;
4980               // otherdb=new ArrayList<DbSourceProxy>();
4981               // for (DbSourceProxy db:dbs)
4982               // {
4983               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4984               // }
4985               if (mname == null)
4986               {
4987                 mname = "From " + dbclass;
4988               }
4989               if (otherdb.size() == 1)
4990               {
4991                 final DbSourceProxy[] dassource = otherdb
4992                         .toArray(new DbSourceProxy[0]);
4993                 DbSourceProxy src = otherdb.get(0);
4994                 fetchr = new JMenuItem(src.getDbSource());
4995                 fetchr.addActionListener(new ActionListener()
4996                 {
4997
4998                   @Override
4999                   public void actionPerformed(ActionEvent e)
5000                   {
5001                     new Thread(new Runnable()
5002                     {
5003
5004                       @Override
5005                       public void run()
5006                       {
5007                         boolean isNucleotide = alignPanel.alignFrame
5008                                 .getViewport().getAlignment()
5009                                 .isNucleotide();
5010                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5011                                 alignPanel.av.getSequenceSelection(),
5012                                 alignPanel.alignFrame, dassource,
5013                                 alignPanel.alignFrame.featureSettings,
5014                                 isNucleotide);
5015                         dbRefFetcher
5016                                 .addListener(new FetchFinishedListenerI()
5017                                 {
5018                                   @Override
5019                                   public void finished()
5020                                   {
5021                                     AlignFrame.this.setMenusForViewport();
5022                                   }
5023                                 });
5024                         dbRefFetcher.fetchDBRefs(false);
5025                       }
5026                     }).start();
5027                   }
5028
5029                 });
5030                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5031                         MessageManager.formatMessage(
5032                                 "label.fetch_retrieve_from", new Object[]
5033                                 { src.getDbName() })));
5034                 dfetch.add(fetchr);
5035                 comp++;
5036               }
5037               else
5038               {
5039                 final DbSourceProxy[] dassource = otherdb
5040                         .toArray(new DbSourceProxy[0]);
5041                 // fetch all entry
5042                 DbSourceProxy src = otherdb.get(0);
5043                 fetchr = new JMenuItem(MessageManager
5044                         .formatMessage("label.fetch_all_param", new Object[]
5045                         { src.getDbSource() }));
5046                 fetchr.addActionListener(new ActionListener()
5047                 {
5048                   @Override
5049                   public void actionPerformed(ActionEvent e)
5050                   {
5051                     new Thread(new Runnable()
5052                     {
5053
5054                       @Override
5055                       public void run()
5056                       {
5057                         boolean isNucleotide = alignPanel.alignFrame
5058                                 .getViewport().getAlignment()
5059                                 .isNucleotide();
5060                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5061                                 alignPanel.av.getSequenceSelection(),
5062                                 alignPanel.alignFrame, dassource,
5063                                 alignPanel.alignFrame.featureSettings,
5064                                 isNucleotide);
5065                         dbRefFetcher
5066                                 .addListener(new FetchFinishedListenerI()
5067                                 {
5068                                   @Override
5069                                   public void finished()
5070                                   {
5071                                     AlignFrame.this.setMenusForViewport();
5072                                   }
5073                                 });
5074                         dbRefFetcher.fetchDBRefs(false);
5075                       }
5076                     }).start();
5077                   }
5078                 });
5079
5080                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5081                         MessageManager.formatMessage(
5082                                 "label.fetch_retrieve_from_all_sources",
5083                                 new Object[]
5084                                 { Integer.valueOf(otherdb.size())
5085                                         .toString(),
5086                                     src.getDbSource(), src.getDbName() })));
5087                 dfetch.add(fetchr);
5088                 comp++;
5089                 // and then build the rest of the individual menus
5090                 ifetch = new JMenu(MessageManager.formatMessage(
5091                         "label.source_from_db_source", new Object[]
5092                         { src.getDbSource() }));
5093                 icomp = 0;
5094                 String imname = null;
5095                 int i = 0;
5096                 for (DbSourceProxy sproxy : otherdb)
5097                 {
5098                   String dbname = sproxy.getDbName();
5099                   String sname = dbname.length() > 5
5100                           ? dbname.substring(0, 5) + "..."
5101                           : dbname;
5102                   String msname = dbname.length() > 10
5103                           ? dbname.substring(0, 10) + "..."
5104                           : dbname;
5105                   if (imname == null)
5106                   {
5107                     imname = MessageManager
5108                             .formatMessage("label.from_msname", new Object[]
5109                             { sname });
5110                   }
5111                   fetchr = new JMenuItem(msname);
5112                   final DbSourceProxy[] dassrc = { sproxy };
5113                   fetchr.addActionListener(new ActionListener()
5114                   {
5115
5116                     @Override
5117                     public void actionPerformed(ActionEvent e)
5118                     {
5119                       new Thread(new Runnable()
5120                       {
5121
5122                         @Override
5123                         public void run()
5124                         {
5125                           boolean isNucleotide = alignPanel.alignFrame
5126                                   .getViewport().getAlignment()
5127                                   .isNucleotide();
5128                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5129                                   alignPanel.av.getSequenceSelection(),
5130                                   alignPanel.alignFrame, dassrc,
5131                                   alignPanel.alignFrame.featureSettings,
5132                                   isNucleotide);
5133                           dbRefFetcher
5134                                   .addListener(new FetchFinishedListenerI()
5135                                   {
5136                                     @Override
5137                                     public void finished()
5138                                     {
5139                                       AlignFrame.this.setMenusForViewport();
5140                                     }
5141                                   });
5142                           dbRefFetcher.fetchDBRefs(false);
5143                         }
5144                       }).start();
5145                     }
5146
5147                   });
5148                   fetchr.setToolTipText(
5149                           "<html>" + MessageManager.formatMessage(
5150                                   "label.fetch_retrieve_from", new Object[]
5151                                   { dbname }));
5152                   ifetch.add(fetchr);
5153                   ++i;
5154                   if (++icomp >= mcomp || i == (otherdb.size()))
5155                   {
5156                     ifetch.setText(MessageManager.formatMessage(
5157                             "label.source_to_target", imname, sname));
5158                     dfetch.add(ifetch);
5159                     ifetch = new JMenu();
5160                     imname = null;
5161                     icomp = 0;
5162                     comp++;
5163                   }
5164                 }
5165               }
5166               ++dbi;
5167               if (comp >= mcomp || dbi >= (dbclasses.length))
5168               {
5169                 dfetch.setText(MessageManager.formatMessage(
5170                         "label.source_to_target", mname, dbclass));
5171                 rfetch.add(dfetch);
5172                 dfetch = new JMenu();
5173                 mname = null;
5174                 comp = 0;
5175               }
5176             }
5177           }
5178         });
5179       }
5180     }).start();
5181
5182   }
5183
5184   /**
5185    * Left justify the whole alignment.
5186    */
5187   @Override
5188   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5189   {
5190     AlignmentI al = viewport.getAlignment();
5191     al.justify(false);
5192     viewport.firePropertyChange("alignment", null, al);
5193   }
5194
5195   /**
5196    * Right justify the whole alignment.
5197    */
5198   @Override
5199   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5200   {
5201     AlignmentI al = viewport.getAlignment();
5202     al.justify(true);
5203     viewport.firePropertyChange("alignment", null, al);
5204   }
5205
5206   @Override
5207   public void setShowSeqFeatures(boolean b)
5208   {
5209     showSeqFeatures.setSelected(b);
5210     viewport.setShowSequenceFeatures(b);
5211   }
5212
5213   /*
5214    * (non-Javadoc)
5215    *
5216    * @see
5217    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5218    * awt.event.ActionEvent)
5219    */
5220   @Override
5221   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5222   {
5223     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5224     alignPanel.paintAlignment(false, false);
5225   }
5226
5227   /*
5228    * (non-Javadoc)
5229    *
5230    * @see
5231    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5232    * .ActionEvent)
5233    */
5234   @Override
5235   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5236   {
5237     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5238     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5239
5240   }
5241
5242   /*
5243    * (non-Javadoc)
5244    *
5245    * @see
5246    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5247    * .event.ActionEvent)
5248    */
5249   @Override
5250   protected void showGroupConservation_actionPerformed(ActionEvent e)
5251   {
5252     viewport.setShowGroupConservation(showGroupConservation.getState());
5253     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5254   }
5255
5256   /*
5257    * (non-Javadoc)
5258    *
5259    * @see
5260    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5261    * .event.ActionEvent)
5262    */
5263   @Override
5264   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5265   {
5266     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5267     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5268   }
5269
5270   /*
5271    * (non-Javadoc)
5272    *
5273    * @see
5274    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5275    * .event.ActionEvent)
5276    */
5277   @Override
5278   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5279   {
5280     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5281     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5282   }
5283
5284   @Override
5285   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5286   {
5287     showSequenceLogo.setState(true);
5288     viewport.setShowSequenceLogo(true);
5289     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5290     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5291   }
5292
5293   @Override
5294   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5295   {
5296     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5297   }
5298
5299   /*
5300    * (non-Javadoc)
5301    *
5302    * @see
5303    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5304    * .event.ActionEvent)
5305    */
5306   @Override
5307   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5308   {
5309     if (avc.makeGroupsFromSelection())
5310     {
5311       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5312       alignPanel.updateAnnotation();
5313       alignPanel.paintAlignment(true,
5314               viewport.needToUpdateStructureViews());
5315     }
5316   }
5317
5318   public void clearAlignmentSeqRep()
5319   {
5320     // TODO refactor alignmentseqrep to controller
5321     if (viewport.getAlignment().hasSeqrep())
5322     {
5323       viewport.getAlignment().setSeqrep(null);
5324       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5325       alignPanel.updateAnnotation();
5326       alignPanel.paintAlignment(true, true);
5327     }
5328   }
5329
5330   @Override
5331   protected void createGroup_actionPerformed(ActionEvent e)
5332   {
5333     if (avc.createGroup())
5334     {
5335       if (applyAutoAnnotationSettings.isSelected())
5336       {
5337         alignPanel.updateAnnotation(true, false);
5338       }
5339       alignPanel.alignmentChanged();
5340     }
5341   }
5342
5343   @Override
5344   protected void unGroup_actionPerformed(ActionEvent e)
5345   {
5346     if (avc.unGroup())
5347     {
5348       alignPanel.alignmentChanged();
5349     }
5350   }
5351
5352   /**
5353    * make the given alignmentPanel the currently selected tab
5354    *
5355    * @param alignmentPanel
5356    */
5357   public void setDisplayedView(AlignmentPanel alignmentPanel)
5358   {
5359     if (!viewport.getSequenceSetId()
5360             .equals(alignmentPanel.av.getSequenceSetId()))
5361     {
5362       throw new Error(MessageManager.getString(
5363               "error.implementation_error_cannot_show_view_alignment_frame"));
5364     }
5365     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5366             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5367     {
5368       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5369     }
5370   }
5371
5372   /**
5373    * Action on selection of menu options to Show or Hide annotations.
5374    *
5375    * @param visible
5376    * @param forSequences
5377    *          update sequence-related annotations
5378    * @param forAlignment
5379    *          update non-sequence-related annotations
5380    */
5381   @Override
5382   protected void setAnnotationsVisibility(boolean visible,
5383           boolean forSequences, boolean forAlignment)
5384   {
5385     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5386             .getAlignmentAnnotation();
5387     if (anns == null)
5388     {
5389       return;
5390     }
5391     for (AlignmentAnnotation aa : anns)
5392     {
5393       /*
5394        * don't display non-positional annotations on an alignment
5395        */
5396       if (aa.annotations == null)
5397       {
5398         continue;
5399       }
5400       boolean apply = (aa.sequenceRef == null && forAlignment)
5401               || (aa.sequenceRef != null && forSequences);
5402       if (apply)
5403       {
5404         aa.visible = visible;
5405       }
5406     }
5407     alignPanel.validateAnnotationDimensions(true);
5408     alignPanel.alignmentChanged();
5409   }
5410
5411   /**
5412    * Sorts annotations and repaints the alignment
5413    */
5414   @Override
5415   public void sortAnnotations(boolean autoCalcOnly)
5416   {
5417     alignPanel.sortAnnotations(autoCalcOnly);
5418     alignPanel.paintAlignment(false, false);
5419   }
5420
5421   /**
5422    *
5423    * @return alignment panels in this alignment frame
5424    */
5425   public List<? extends AlignmentViewPanel> getAlignPanels()
5426   {
5427     // alignPanels is never null
5428     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5429     return alignPanels;
5430   }
5431
5432   /**
5433    * Open a new alignment window, with the cDNA associated with this (protein)
5434    * alignment, aligned as is the protein.
5435    */
5436   protected void viewAsCdna_actionPerformed()
5437   {
5438     // TODO no longer a menu action - refactor as required
5439     final AlignmentI alignment = getViewport().getAlignment();
5440     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5441     if (mappings == null)
5442     {
5443       return;
5444     }
5445     List<SequenceI> cdnaSeqs = new ArrayList<>();
5446     for (SequenceI aaSeq : alignment.getSequences())
5447     {
5448       for (AlignedCodonFrame acf : mappings)
5449       {
5450         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5451         if (dnaSeq != null)
5452         {
5453           /*
5454            * There is a cDNA mapping for this protein sequence - add to new
5455            * alignment. It will share the same dataset sequence as other mapped
5456            * cDNA (no new mappings need to be created).
5457            */
5458           final Sequence newSeq = new Sequence(dnaSeq);
5459           newSeq.setDatasetSequence(dnaSeq);
5460           cdnaSeqs.add(newSeq);
5461         }
5462       }
5463     }
5464     if (cdnaSeqs.size() == 0)
5465     {
5466       // show a warning dialog no mapped cDNA
5467       return;
5468     }
5469     AlignmentI cdna = new Alignment(
5470             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5471     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5472             AlignFrame.DEFAULT_HEIGHT);
5473     cdna.alignAs(alignment);
5474     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5475             + this.title;
5476     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5477             AlignFrame.DEFAULT_HEIGHT);
5478   }
5479
5480   /**
5481    * Set visibility of dna/protein complement view (available when shown in a
5482    * split frame).
5483    *
5484    * @param show
5485    */
5486   @Override
5487   protected void showComplement_actionPerformed(boolean show)
5488   {
5489     SplitContainerI sf = getSplitViewContainer();
5490     if (sf != null)
5491     {
5492       sf.setComplementVisible(this, show);
5493     }
5494   }
5495
5496   /**
5497    * Generate the reverse (optionally complemented) of the selected sequences,
5498    * and add them to the alignment
5499    */
5500   @Override
5501   protected void showReverse_actionPerformed(boolean complement)
5502   {
5503     AlignmentI al = null;
5504     try
5505     {
5506       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5507       al = dna.reverseCdna(complement);
5508       viewport.addAlignment(al, "");
5509       addHistoryItem(new EditCommand(
5510               MessageManager.getString("label.add_sequences"), Action.PASTE,
5511               al.getSequencesArray(), 0, al.getWidth(),
5512               viewport.getAlignment()));
5513     } catch (Exception ex)
5514     {
5515       System.err.println(ex.getMessage());
5516       return;
5517     }
5518   }
5519
5520   /**
5521    * Try to run a script in the Groovy console, having first ensured that this
5522    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5523    * be targeted at this alignment.
5524    */
5525   @Override
5526   protected void runGroovy_actionPerformed()
5527   {
5528     Jalview.setCurrentAlignFrame(this);
5529     groovy.ui.Console console = Desktop.getGroovyConsole();
5530     if (console != null)
5531     {
5532       try
5533       {
5534         console.runScript();
5535       } catch (Exception ex)
5536       {
5537         System.err.println((ex.toString()));
5538         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5539                 MessageManager.getString("label.couldnt_run_groovy_script"),
5540                 MessageManager.getString("label.groovy_support_failed"),
5541                 JvOptionPane.ERROR_MESSAGE);
5542       }
5543     }
5544     else
5545     {
5546       System.err.println("Can't run Groovy script as console not found");
5547     }
5548   }
5549
5550   /**
5551    * Hides columns containing (or not containing) a specified feature, provided
5552    * that would not leave all columns hidden
5553    *
5554    * @param featureType
5555    * @param columnsContaining
5556    * @return
5557    */
5558   public boolean hideFeatureColumns(String featureType,
5559           boolean columnsContaining)
5560   {
5561     boolean notForHiding = avc.markColumnsContainingFeatures(
5562             columnsContaining, false, false, featureType);
5563     if (notForHiding)
5564     {
5565       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5566               false, featureType))
5567       {
5568         getViewport().hideSelectedColumns();
5569         return true;
5570       }
5571     }
5572     return false;
5573   }
5574
5575   @Override
5576   protected void selectHighlightedColumns_actionPerformed(
5577           ActionEvent actionEvent)
5578   {
5579     // include key modifier check in case user selects from menu
5580     avc.markHighlightedColumns(
5581             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5582             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5583                     | ActionEvent.CTRL_MASK)) != 0);
5584   }
5585
5586   /**
5587    * Rebuilds the Colour menu, including any user-defined colours which have
5588    * been loaded either on startup or during the session
5589    */
5590   public void buildColourMenu()
5591   {
5592     colourMenu.removeAll();
5593
5594     colourMenu.add(applyToAllGroups);
5595     colourMenu.add(textColour);
5596     colourMenu.addSeparator();
5597
5598     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5599             viewport.getAlignment(), false);
5600
5601     colourMenu.add(annotationColour);
5602     bg.add(annotationColour);
5603     colourMenu.addSeparator();
5604     colourMenu.add(conservationMenuItem);
5605     colourMenu.add(modifyConservation);
5606     colourMenu.add(abovePIDThreshold);
5607     colourMenu.add(modifyPID);
5608
5609     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5610     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5611   }
5612
5613   /**
5614    * Open a dialog (if not already open) that allows the user to select and
5615    * calculate PCA or Tree analysis
5616    */
5617   protected void openTreePcaDialog()
5618   {
5619     if (alignPanel.getCalculationDialog() == null)
5620     {
5621       new CalculationChooser(AlignFrame.this);
5622     }
5623   }
5624
5625   @Override
5626   protected void loadVcf_actionPerformed()
5627   {
5628     JalviewFileChooser chooser = new JalviewFileChooser(
5629             Cache.getProperty("LAST_DIRECTORY"));
5630     chooser.setFileView(new JalviewFileView());
5631     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5632     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5633
5634     int value = chooser.showOpenDialog(null);
5635
5636     if (value == JalviewFileChooser.APPROVE_OPTION)
5637     {
5638       String choice = chooser.getSelectedFile().getPath();
5639       Cache.setProperty("LAST_DIRECTORY", choice);
5640       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5641       new VCFLoader(choice).loadVCF(seqs, this);
5642     }
5643
5644   }
5645
5646   /**
5647    * Sets the flag for whether auto-calculated annotations should be shown above
5648    * other annotations. If the given value is the same as the current setting,
5649    * simply returns false. Otherwise updates the setting, and returns true. If
5650    * annotation sort order is currently set to 'Custom', this is changed to
5651    * 'None', because 'Custom' ordering ignores all sort options.
5652    */
5653   @Override
5654   public boolean setShowAutoCalculatedAbove(boolean b)
5655   {
5656     if (viewport.isShowAutocalculatedAbove() != b)
5657     {
5658       viewport.setShowAutocalculatedAbove(b);
5659
5660       /*
5661        * change CUSTOM annotation ordering to NONE
5662        * so that sorting actually does something
5663        */
5664       if (viewport.getSortAnnotationsBy() == SequenceAnnotationOrder.CUSTOM)
5665       {
5666         viewport.setSortAnnotationsBy(SequenceAnnotationOrder.NONE);
5667       }
5668       return true;
5669     }
5670     return false;
5671   }
5672
5673   @Override
5674   public void setAnnotationSortOrder(
5675           SequenceAnnotationOrder annotationSortOrder)
5676   {
5677     viewport.setSortAnnotationsBy(annotationSortOrder);
5678   }
5679 }
5680
5681 class PrintThread extends Thread
5682 {
5683   AlignmentPanel ap;
5684
5685   public PrintThread(AlignmentPanel ap)
5686   {
5687     this.ap = ap;
5688   }
5689
5690   static PageFormat pf;
5691
5692   @Override
5693   public void run()
5694   {
5695     PrinterJob printJob = PrinterJob.getPrinterJob();
5696
5697     if (pf != null)
5698     {
5699       printJob.setPrintable(ap, pf);
5700     }
5701     else
5702     {
5703       printJob.setPrintable(ap);
5704     }
5705
5706     if (printJob.printDialog())
5707     {
5708       try
5709       {
5710         printJob.print();
5711       } catch (Exception PrintException)
5712       {
5713         PrintException.printStackTrace();
5714       }
5715     }
5716   }
5717 }